Starting phenix.real_space_refine on Sun Feb 8 07:51:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srd_40727/02_2026/8srd_40727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srd_40727/02_2026/8srd_40727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8srd_40727/02_2026/8srd_40727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srd_40727/02_2026/8srd_40727.map" model { file = "/net/cci-nas-00/data/ceres_data/8srd_40727/02_2026/8srd_40727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srd_40727/02_2026/8srd_40727.cif" } resolution = 2.91 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= 0.076 sd= 1.011 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 16 5.49 5 Mg 21 5.21 5 S 248 5.16 5 C 27404 2.51 5 N 7344 2.21 5 O 7653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42686 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 10508 Classifications: {'peptide': 1368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 55, 'TRANS': 1312} Chain breaks: 4 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 22, 'HIS:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 251 Chain: "B" Number of atoms: 10508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 10508 Classifications: {'peptide': 1368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 55, 'TRANS': 1312} Chain breaks: 4 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 22, 'HIS:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 251 Chain: "C" Number of atoms: 10508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 10508 Classifications: {'peptide': 1368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 55, 'TRANS': 1312} Chain breaks: 4 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 22, 'HIS:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 251 Chain: "D" Number of atoms: 10508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 10508 Classifications: {'peptide': 1368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 55, 'TRANS': 1312} Chain breaks: 4 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 22, 'HIS:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 251 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {' MG': 6, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 161 Unusual residues: {' MG': 5, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 161 Unusual residues: {' MG': 5, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 161 Unusual residues: {' MG': 5, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 9.72, per 1000 atoms: 0.23 Number of scatterers: 42686 At special positions: 0 Unit cell: (146.202, 146.202, 182.546, 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 248 16.00 P 16 15.00 Mg 21 11.99 O 7653 8.00 N 7344 7.00 C 27404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.02 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.02 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.02 Simple disulfide: pdb=" SG CYS D 997 " - pdb=" SG CYS D1006 " distance=2.02 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: 3.65 Conformation dependent library (CDL) restraints added in 1.9 seconds 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10304 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 36 sheets defined 57.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.772A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 221 through 227 removed outlier: 3.501A pdb=" N MET A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.735A pdb=" N PHE A 342 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.684A pdb=" N ASN A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.653A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 406 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.641A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 457 removed outlier: 4.878A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.965A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.666A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.738A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.621A pdb=" N ARG A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.629A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.570A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.661A pdb=" N ARG A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 641 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 651 through 678 removed outlier: 3.959A pdb=" N LEU A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 728 Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 788 through 799 removed outlier: 4.100A pdb=" N ARG A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 Processing helix chain 'A' and resid 833 through 856 Processing helix chain 'A' and resid 859 through 866 removed outlier: 4.098A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 4.405A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 3.940A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 921 removed outlier: 3.529A pdb=" N ALA A 919 " --> pdb=" O ARG A 916 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 4.200A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 929 " --> pdb=" O GLY A 925 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 940 " --> pdb=" O LYS A 936 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.603A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 975 " --> pdb=" O PHE A 971 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1009 through 1012 removed outlier: 3.571A pdb=" N ARG A1012 " --> pdb=" O GLU A1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1009 through 1012' Processing helix chain 'A' and resid 1013 through 1026 removed outlier: 3.931A pdb=" N LEU A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1047 removed outlier: 4.011A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1066 removed outlier: 4.348A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1088 removed outlier: 4.211A pdb=" N ALA A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1129 Processing helix chain 'A' and resid 1131 through 1169 Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1378 through 1392 Processing helix chain 'A' and resid 1403 through 1413 Processing helix chain 'A' and resid 1449 through 1453 Processing helix chain 'A' and resid 1478 through 1491 removed outlier: 3.502A pdb=" N LEU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.772A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.502A pdb=" N MET B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.735A pdb=" N PHE B 342 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.683A pdb=" N ASN B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.654A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 406 Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.641A pdb=" N ALA B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 457 removed outlier: 4.878A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.965A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.665A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 503 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 504 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.738A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 removed outlier: 3.621A pdb=" N ARG B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.629A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 removed outlier: 3.570A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.661A pdb=" N ARG B 594 " --> pdb=" O GLY B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 641 Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 651 through 678 removed outlier: 3.959A pdb=" N LEU B 673 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 715 through 728 Processing helix chain 'B' and resid 735 through 745 Processing helix chain 'B' and resid 788 through 799 removed outlier: 4.101A pdb=" N ARG B 793 " --> pdb=" O HIS B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 Processing helix chain 'B' and resid 833 through 856 Processing helix chain 'B' and resid 859 through 866 removed outlier: 4.098A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 4.405A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 3.940A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 3.529A pdb=" N ALA B 919 " --> pdb=" O ARG B 916 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 4.200A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 928 " --> pdb=" O LEU B 924 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 929 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.603A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 975 " --> pdb=" O PHE B 971 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 982 through 984 No H-bonds generated for 'chain 'B' and resid 982 through 984' Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1009 through 1012 removed outlier: 3.570A pdb=" N ARG B1012 " --> pdb=" O GLU B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1009 through 1012' Processing helix chain 'B' and resid 1013 through 1026 removed outlier: 3.931A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1047 removed outlier: 4.010A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1066 removed outlier: 4.348A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1088 removed outlier: 4.211A pdb=" N ALA B1077 " --> pdb=" O PHE B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1129 Processing helix chain 'B' and resid 1131 through 1169 Processing helix chain 'B' and resid 1202 through 1206 Processing helix chain 'B' and resid 1378 through 1392 Processing helix chain 'B' and resid 1403 through 1413 Processing helix chain 'B' and resid 1449 through 1453 Processing helix chain 'B' and resid 1478 through 1491 removed outlier: 3.503A pdb=" N LEU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.772A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 Processing helix chain 'C' and resid 187 through 201 Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.501A pdb=" N MET C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.736A pdb=" N PHE C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 359 removed outlier: 3.684A pdb=" N ASN C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.654A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 406 Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.641A pdb=" N ALA C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 457 removed outlier: 4.878A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.965A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.665A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 500 " --> pdb=" O PHE C 496 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 503 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.738A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 553 removed outlier: 3.621A pdb=" N ARG C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.629A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 582 removed outlier: 3.570A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.662A pdb=" N ARG C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 641 Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 651 through 678 removed outlier: 3.960A pdb=" N LEU C 673 " --> pdb=" O ALA C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 715 through 728 Processing helix chain 'C' and resid 735 through 745 Processing helix chain 'C' and resid 788 through 799 removed outlier: 4.101A pdb=" N ARG C 793 " --> pdb=" O HIS C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 826 Processing helix chain 'C' and resid 833 through 856 Processing helix chain 'C' and resid 859 through 866 removed outlier: 4.098A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 4.405A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 3.940A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 921 removed outlier: 3.529A pdb=" N ALA C 919 " --> pdb=" O ARG C 916 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 4.201A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 928 " --> pdb=" O LEU C 924 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 929 " --> pdb=" O GLY C 925 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 940 " --> pdb=" O LYS C 936 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.603A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 975 " --> pdb=" O PHE C 971 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 982 through 984 No H-bonds generated for 'chain 'C' and resid 982 through 984' Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1009 through 1012 removed outlier: 3.570A pdb=" N ARG C1012 " --> pdb=" O GLU C1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1009 through 1012' Processing helix chain 'C' and resid 1013 through 1026 removed outlier: 3.931A pdb=" N LEU C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1047 removed outlier: 4.012A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1066 removed outlier: 4.348A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C1066 " --> pdb=" O GLU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1088 removed outlier: 4.210A pdb=" N ALA C1077 " --> pdb=" O PHE C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1129 Processing helix chain 'C' and resid 1131 through 1169 Processing helix chain 'C' and resid 1202 through 1206 Processing helix chain 'C' and resid 1378 through 1392 Processing helix chain 'C' and resid 1403 through 1413 Processing helix chain 'C' and resid 1449 through 1453 Processing helix chain 'C' and resid 1478 through 1491 removed outlier: 3.503A pdb=" N LEU C1482 " --> pdb=" O SER C1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.772A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 221 through 227 removed outlier: 3.501A pdb=" N MET D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 286 Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.736A pdb=" N PHE D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 359 removed outlier: 3.683A pdb=" N ASN D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.654A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 406 Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.641A pdb=" N ALA D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 457 removed outlier: 4.878A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.965A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.665A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 500 " --> pdb=" O PHE D 496 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 503 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.738A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 553 removed outlier: 3.622A pdb=" N ARG D 553 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.630A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 582 removed outlier: 3.570A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.662A pdb=" N ARG D 594 " --> pdb=" O GLY D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 641 Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 651 through 678 removed outlier: 3.959A pdb=" N LEU D 673 " --> pdb=" O ALA D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 715 through 728 Processing helix chain 'D' and resid 735 through 745 Processing helix chain 'D' and resid 788 through 799 removed outlier: 4.100A pdb=" N ARG D 793 " --> pdb=" O HIS D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 826 Processing helix chain 'D' and resid 833 through 856 Processing helix chain 'D' and resid 859 through 866 removed outlier: 4.098A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 4.405A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 3.940A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 921 removed outlier: 3.529A pdb=" N ALA D 919 " --> pdb=" O ARG D 916 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 4.201A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 928 " --> pdb=" O LEU D 924 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE D 929 " --> pdb=" O GLY D 925 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 940 " --> pdb=" O LYS D 936 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.602A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 975 " --> pdb=" O PHE D 971 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 978 - end of helix Processing helix chain 'D' and resid 982 through 984 No H-bonds generated for 'chain 'D' and resid 982 through 984' Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1009 through 1012 removed outlier: 3.571A pdb=" N ARG D1012 " --> pdb=" O GLU D1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1009 through 1012' Processing helix chain 'D' and resid 1013 through 1026 removed outlier: 3.931A pdb=" N LEU D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1047 removed outlier: 4.011A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1066 removed outlier: 4.348A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D1066 " --> pdb=" O GLU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1088 removed outlier: 4.211A pdb=" N ALA D1077 " --> pdb=" O PHE D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1129 Processing helix chain 'D' and resid 1131 through 1169 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1378 through 1391 Processing helix chain 'D' and resid 1403 through 1413 Processing helix chain 'D' and resid 1449 through 1453 Processing helix chain 'D' and resid 1478 through 1491 removed outlier: 3.501A pdb=" N LEU D1482 " --> pdb=" O SER D1478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 236 removed outlier: 7.549A pdb=" N TRP A 96 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY A 182 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N GLY A 149 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL A 295 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 148 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1199 through 1200 removed outlier: 7.208A pdb=" N GLY B1416 " --> pdb=" O HIS B1443 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N HIS B1443 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TRP B1336 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 17.489A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.565A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.489A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1251 through 1254 removed outlier: 6.146A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG A1317 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N TYR A1253 " --> pdb=" O ARG A1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1279 through 1281 Processing sheet with id=AA8, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 4.545A pdb=" N SER A1297 " --> pdb=" O ILE A1306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1366 through 1367 removed outlier: 5.565A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.488A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 17.488A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1353 through 1360 current: chain 'A' and resid 1416 through 1423 Processing sheet with id=AB2, first strand: chain 'A' and resid 1346 through 1347 Processing sheet with id=AB3, first strand: chain 'B' and resid 56 through 58 Processing sheet with id=AB4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB5, first strand: chain 'B' and resid 231 through 236 removed outlier: 7.550A pdb=" N TRP B 96 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY B 182 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N GLY B 149 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL B 295 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR B 148 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1199 through 1200 removed outlier: 7.208A pdb=" N GLY C1416 " --> pdb=" O HIS C1443 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N HIS C1443 " --> pdb=" O GLY C1416 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TRP C1336 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 17.488A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.741A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.469A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.565A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.469A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.741A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.488A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1251 through 1254 removed outlier: 6.146A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG B1317 " --> pdb=" O VAL B1251 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N TYR B1253 " --> pdb=" O ARG B1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 1279 through 1281 Processing sheet with id=AC1, first strand: chain 'B' and resid 1297 through 1298 removed outlier: 4.545A pdb=" N SER B1297 " --> pdb=" O ILE B1306 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1346 through 1347 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 80 through 81 Processing sheet with id=AC5, first strand: chain 'C' and resid 231 through 236 removed outlier: 7.549A pdb=" N TRP C 96 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY C 182 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N GLY C 149 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL C 295 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR C 148 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1199 through 1200 removed outlier: 7.208A pdb=" N GLY D1416 " --> pdb=" O HIS D1443 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N HIS D1443 " --> pdb=" O GLY D1416 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TRP D1336 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 17.489A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.564A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.740A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.489A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1251 through 1254 removed outlier: 6.146A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG C1317 " --> pdb=" O VAL C1251 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TYR C1253 " --> pdb=" O ARG C1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 1279 through 1281 Processing sheet with id=AD1, first strand: chain 'C' and resid 1297 through 1298 removed outlier: 4.545A pdb=" N SER C1297 " --> pdb=" O ILE C1306 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1346 through 1347 Processing sheet with id=AD3, first strand: chain 'D' and resid 56 through 58 Processing sheet with id=AD4, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AD5, first strand: chain 'D' and resid 231 through 236 removed outlier: 7.549A pdb=" N TRP D 96 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY D 182 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N GLY D 149 " --> pdb=" O GLY D 182 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL D 295 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR D 148 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1251 through 1254 removed outlier: 6.146A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ARG D1317 " --> pdb=" O VAL D1251 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N TYR D1253 " --> pdb=" O ARG D1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AD8, first strand: chain 'D' and resid 1297 through 1298 removed outlier: 4.545A pdb=" N SER D1297 " --> pdb=" O ILE D1306 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1346 through 1347 2311 hydrogen bonds defined for protein. 6741 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: 10.92 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6875 1.31 - 1.44: 11697 1.44 - 1.56: 24604 1.56 - 1.69: 56 1.69 - 1.82: 436 Bond restraints: 43668 Sorted by residual: bond pdb=" C PRO C 978 " pdb=" O PRO C 978 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C PRO A 978 " pdb=" O PRO A 978 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C PRO B 978 " pdb=" O PRO B 978 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" C PRO D 978 " pdb=" O PRO D 978 " ideal model delta sigma weight residual 1.235 1.187 0.049 1.30e-02 5.92e+03 1.40e+01 bond pdb=" N THR B 357 " pdb=" CA THR B 357 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.27e-02 6.20e+03 1.39e+01 ... (remaining 43663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 50629 2.35 - 4.70: 7154 4.70 - 7.05: 1334 7.05 - 9.40: 219 9.40 - 11.75: 36 Bond angle restraints: 59372 Sorted by residual: angle pdb=" N PRO C 244 " pdb=" CA PRO C 244 " pdb=" C PRO C 244 " ideal model delta sigma weight residual 110.70 121.76 -11.06 1.22e+00 6.72e-01 8.21e+01 angle pdb=" N PRO B 244 " pdb=" CA PRO B 244 " pdb=" C PRO B 244 " ideal model delta sigma weight residual 110.70 121.76 -11.06 1.22e+00 6.72e-01 8.21e+01 angle pdb=" N PRO D 244 " pdb=" CA PRO D 244 " pdb=" C PRO D 244 " ideal model delta sigma weight residual 110.70 121.73 -11.03 1.22e+00 6.72e-01 8.17e+01 angle pdb=" N PRO A 244 " pdb=" CA PRO A 244 " pdb=" C PRO A 244 " ideal model delta sigma weight residual 110.70 121.73 -11.03 1.22e+00 6.72e-01 8.17e+01 angle pdb=" N VAL D 844 " pdb=" CA VAL D 844 " pdb=" C VAL D 844 " ideal model delta sigma weight residual 110.53 103.33 7.20 9.40e-01 1.13e+00 5.87e+01 ... (remaining 59367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 24312 17.80 - 35.61: 1943 35.61 - 53.41: 381 53.41 - 71.21: 96 71.21 - 89.02: 60 Dihedral angle restraints: 26792 sinusoidal: 10884 harmonic: 15908 Sorted by residual: dihedral pdb=" C ASP B 611 " pdb=" N ASP B 611 " pdb=" CA ASP B 611 " pdb=" CB ASP B 611 " ideal model delta harmonic sigma weight residual -122.60 -139.61 17.01 0 2.50e+00 1.60e-01 4.63e+01 dihedral pdb=" C ASP D 611 " pdb=" N ASP D 611 " pdb=" CA ASP D 611 " pdb=" CB ASP D 611 " ideal model delta harmonic sigma weight residual -122.60 -139.58 16.98 0 2.50e+00 1.60e-01 4.61e+01 dihedral pdb=" C ASP A 611 " pdb=" N ASP A 611 " pdb=" CA ASP A 611 " pdb=" CB ASP A 611 " ideal model delta harmonic sigma weight residual -122.60 -139.54 16.94 0 2.50e+00 1.60e-01 4.59e+01 ... (remaining 26789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 5528 0.121 - 0.241: 1016 0.241 - 0.362: 160 0.362 - 0.482: 32 0.482 - 0.603: 4 Chirality restraints: 6740 Sorted by residual: chirality pdb=" CA ASP B 611 " pdb=" N ASP B 611 " pdb=" C ASP B 611 " pdb=" CB ASP B 611 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.09e+00 chirality pdb=" CA ASP D 611 " pdb=" N ASP D 611 " pdb=" C ASP D 611 " pdb=" CB ASP D 611 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.04e+00 chirality pdb=" CA ASP A 611 " pdb=" N ASP A 611 " pdb=" C ASP A 611 " pdb=" CB ASP A 611 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.97e+00 ... (remaining 6737 not shown) Planarity restraints: 7504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 649 " -0.025 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C PRO A 649 " 0.088 2.00e-02 2.50e+03 pdb=" O PRO A 649 " -0.033 2.00e-02 2.50e+03 pdb=" N HIS A 650 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 649 " 0.025 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C PRO C 649 " -0.088 2.00e-02 2.50e+03 pdb=" O PRO C 649 " 0.033 2.00e-02 2.50e+03 pdb=" N HIS C 650 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 649 " -0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C PRO D 649 " 0.087 2.00e-02 2.50e+03 pdb=" O PRO D 649 " -0.033 2.00e-02 2.50e+03 pdb=" N HIS D 650 " -0.029 2.00e-02 2.50e+03 ... (remaining 7501 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 467 2.62 - 3.19: 34786 3.19 - 3.76: 65688 3.76 - 4.33: 91405 4.33 - 4.90: 152489 Nonbonded interactions: 344835 Sorted by model distance: nonbonded pdb="MG MG C1704 " pdb=" O2B APR C1708 " model vdw 2.051 2.170 nonbonded pdb="MG MG B1704 " pdb=" O2B APR B1708 " model vdw 2.051 2.170 nonbonded pdb="MG MG A1704 " pdb=" O2B APR A1708 " model vdw 2.051 2.170 nonbonded pdb="MG MG D6006 " pdb=" O2B APR D6010 " model vdw 2.052 2.170 nonbonded pdb="MG MG A1711 " pdb=" O HOH C4003 " model vdw 2.165 2.170 ... (remaining 344830 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 51 through 1494 or resid 1704 through 1706 or resid 1709)) \ selection = (chain 'B' and (resid 51 through 1494 or resid 1704 through 1706 or resid 1709)) \ selection = (chain 'C' and (resid 51 through 1494 or resid 1704 through 1706 or resid 1709)) \ selection = (chain 'D' and (resid 51 through 1494 or resid 6004 through 6006 or resid 6009)) \ } 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: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 40.950 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 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 : 0.011 0.090 43672 Z= 0.697 Angle : 1.759 11.751 59380 Z= 1.160 Chirality : 0.098 0.603 6740 Planarity : 0.011 0.055 7504 Dihedral : 14.224 89.018 16476 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.94 % Allowed : 3.29 % Favored : 95.77 % Cbeta Deviations : 0.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.11), residues: 5432 helix: 0.61 (0.09), residues: 2916 sheet: -0.87 (0.23), residues: 408 loop : -1.21 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C1452 TYR 0.055 0.004 TYR B 504 PHE 0.070 0.005 PHE D 941 TRP 0.022 0.003 TRP B1052 HIS 0.035 0.002 HIS D 903 Details of bonding type rmsd covalent geometry : bond 0.01139 (43668) covalent geometry : angle 1.75867 (59372) SS BOND : bond 0.00667 ( 4) SS BOND : angle 0.73916 ( 8) hydrogen bonds : bond 0.17925 ( 2299) hydrogen bonds : angle 7.48092 ( 6741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 1064 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.6967 (m-30) cc_final: 0.6572 (t0) REVERT: A 81 MET cc_start: 0.7325 (ptm) cc_final: 0.7064 (ptm) REVERT: A 156 LEU cc_start: 0.6909 (tp) cc_final: 0.6681 (OUTLIER) REVERT: A 166 LYS cc_start: 0.6819 (ttpt) cc_final: 0.6469 (ptmm) REVERT: A 174 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.6810 (ptp-170) REVERT: A 225 MET cc_start: 0.7325 (mtp) cc_final: 0.7072 (mtp) REVERT: A 251 ASP cc_start: 0.7589 (t0) cc_final: 0.7215 (t0) REVERT: A 284 GLN cc_start: 0.7079 (mt0) cc_final: 0.6723 (mt0) REVERT: A 306 LEU cc_start: 0.7478 (tp) cc_final: 0.7191 (tm) REVERT: A 356 GLN cc_start: 0.6737 (mt0) cc_final: 0.6018 (mm-40) REVERT: A 440 HIS cc_start: 0.4767 (p90) cc_final: 0.4541 (p-80) REVERT: A 456 MET cc_start: 0.5947 (mtt) cc_final: 0.5698 (mtt) REVERT: A 477 LYS cc_start: 0.6110 (mttm) cc_final: 0.5881 (mppt) REVERT: A 560 MET cc_start: 0.6744 (mmm) cc_final: 0.6498 (mmm) REVERT: A 592 GLN cc_start: 0.5410 (tt0) cc_final: 0.4921 (pt0) REVERT: A 594 ARG cc_start: 0.5745 (mtp180) cc_final: 0.5534 (mtp85) REVERT: A 638 GLU cc_start: 0.5824 (mt-10) cc_final: 0.5200 (pt0) REVERT: A 654 GLU cc_start: 0.6119 (tp30) cc_final: 0.5850 (tp30) REVERT: A 663 LYS cc_start: 0.6115 (mmmt) cc_final: 0.5246 (mttm) REVERT: A 694 MET cc_start: 0.6631 (mtm) cc_final: 0.6417 (mtp) REVERT: A 725 ASP cc_start: 0.7345 (m-30) cc_final: 0.6852 (m-30) REVERT: A 731 LYS cc_start: 0.6692 (ttpt) cc_final: 0.6294 (mmpt) REVERT: A 829 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6010 (mm-30) REVERT: A 833 SER cc_start: 0.6288 (t) cc_final: 0.5882 (p) REVERT: A 854 MET cc_start: 0.6462 (mtm) cc_final: 0.6231 (mtt) REVERT: A 870 ARG cc_start: 0.6665 (mtt180) cc_final: 0.6372 (mtt180) REVERT: A 875 MET cc_start: 0.6744 (ptt) cc_final: 0.6469 (ptt) REVERT: A 932 MET cc_start: 0.6612 (mmt) cc_final: 0.6223 (mmt) REVERT: A 969 ARG cc_start: 0.6482 (mtm110) cc_final: 0.6101 (mtm-85) REVERT: A 972 ILE cc_start: 0.7306 (mt) cc_final: 0.6869 (mm) REVERT: A 998 LEU cc_start: 0.6660 (mt) cc_final: 0.6299 (mm) REVERT: A 1005 GLU cc_start: 0.6061 (mt-10) cc_final: 0.5026 (tt0) REVERT: A 1043 LYS cc_start: 0.6901 (mttp) cc_final: 0.6585 (mttp) REVERT: A 1046 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6524 (pt0) REVERT: A 1049 GLU cc_start: 0.5823 (mm-30) cc_final: 0.5604 (mm-30) REVERT: A 1050 ASP cc_start: 0.6515 (m-30) cc_final: 0.5973 (m-30) REVERT: A 1062 GLU cc_start: 0.6707 (tt0) cc_final: 0.6242 (tt0) REVERT: A 1068 PHE cc_start: 0.6109 (t80) cc_final: 0.5869 (t80) REVERT: A 1081 MET cc_start: 0.5662 (mtm) cc_final: 0.5271 (mtp) REVERT: A 1122 ARG cc_start: 0.5843 (mtm-85) cc_final: 0.4829 (mtm-85) REVERT: A 1125 GLU cc_start: 0.5812 (mt-10) cc_final: 0.4656 (pp20) REVERT: A 1128 ARG cc_start: 0.6304 (tmm160) cc_final: 0.5892 (tmm160) REVERT: A 1149 MET cc_start: 0.7643 (mtp) cc_final: 0.7378 (mtm) REVERT: A 1150 MET cc_start: 0.7560 (tpp) cc_final: 0.7349 (mtp) REVERT: A 1152 GLN cc_start: 0.7387 (mt0) cc_final: 0.7046 (mt0) REVERT: A 1160 PHE cc_start: 0.7390 (m-10) cc_final: 0.7104 (m-10) REVERT: A 1248 TYR cc_start: 0.6876 (t80) cc_final: 0.6659 (t80) REVERT: A 1304 ARG cc_start: 0.7714 (ptp-170) cc_final: 0.7084 (mtp180) REVERT: A 1377 GLU cc_start: 0.6632 (pt0) cc_final: 0.6247 (pt0) REVERT: A 1389 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 1445 GLU cc_start: 0.6987 (pm20) cc_final: 0.6772 (mp0) REVERT: A 1456 GLN cc_start: 0.7333 (tm-30) cc_final: 0.7043 (pt0) REVERT: A 1463 HIS cc_start: 0.6939 (m90) cc_final: 0.6228 (t-170) REVERT: A 1491 ASN cc_start: 0.8134 (t0) cc_final: 0.7852 (t0) REVERT: B 74 ASP cc_start: 0.6947 (m-30) cc_final: 0.6554 (t0) REVERT: B 81 MET cc_start: 0.7347 (ptm) cc_final: 0.7088 (ptm) REVERT: B 156 LEU cc_start: 0.6881 (tp) cc_final: 0.6667 (mt) REVERT: B 166 LYS cc_start: 0.6790 (ttpt) cc_final: 0.6412 (ptmm) REVERT: B 174 ARG cc_start: 0.7461 (mtm-85) cc_final: 0.6825 (ptp-170) REVERT: B 225 MET cc_start: 0.7339 (mtp) cc_final: 0.7084 (mtp) REVERT: B 251 ASP cc_start: 0.7585 (t0) cc_final: 0.7213 (t0) REVERT: B 284 GLN cc_start: 0.7073 (mt0) cc_final: 0.6714 (mt0) REVERT: B 306 LEU cc_start: 0.7474 (tp) cc_final: 0.7188 (tm) REVERT: B 356 GLN cc_start: 0.6735 (mt0) cc_final: 0.6026 (mm-40) REVERT: B 440 HIS cc_start: 0.4764 (p90) cc_final: 0.4541 (p-80) REVERT: B 456 MET cc_start: 0.5950 (mtt) cc_final: 0.5698 (mtt) REVERT: B 477 LYS cc_start: 0.6108 (mttm) cc_final: 0.5880 (mppt) REVERT: B 560 MET cc_start: 0.6731 (mmm) cc_final: 0.6486 (mmm) REVERT: B 577 ASP cc_start: 0.6231 (t0) cc_final: 0.5838 (t70) REVERT: B 592 GLN cc_start: 0.5461 (tt0) cc_final: 0.4957 (pt0) REVERT: B 594 ARG cc_start: 0.5743 (mtp180) cc_final: 0.5535 (mtp85) REVERT: B 638 GLU cc_start: 0.5820 (mt-10) cc_final: 0.5192 (pt0) REVERT: B 654 GLU cc_start: 0.6112 (tp30) cc_final: 0.5837 (tp30) REVERT: B 663 LYS cc_start: 0.6310 (mmmt) cc_final: 0.5390 (mttm) REVERT: B 694 MET cc_start: 0.6596 (mtm) cc_final: 0.6384 (mtp) REVERT: B 725 ASP cc_start: 0.7360 (m-30) cc_final: 0.6879 (m-30) REVERT: B 731 LYS cc_start: 0.6685 (ttpt) cc_final: 0.6298 (mmpt) REVERT: B 829 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6027 (mm-30) REVERT: B 833 SER cc_start: 0.6256 (t) cc_final: 0.5877 (p) REVERT: B 854 MET cc_start: 0.6443 (mtm) cc_final: 0.6219 (mtt) REVERT: B 870 ARG cc_start: 0.6673 (mtt180) cc_final: 0.6408 (mtt180) REVERT: B 875 MET cc_start: 0.6760 (ptt) cc_final: 0.6441 (ptp) REVERT: B 932 MET cc_start: 0.6540 (mmt) cc_final: 0.6155 (mmt) REVERT: B 969 ARG cc_start: 0.6478 (mtm110) cc_final: 0.6069 (mtm-85) REVERT: B 972 ILE cc_start: 0.7309 (mt) cc_final: 0.6873 (mm) REVERT: B 998 LEU cc_start: 0.6669 (mt) cc_final: 0.6334 (mm) REVERT: B 1005 GLU cc_start: 0.6049 (mt-10) cc_final: 0.5055 (tt0) REVERT: B 1043 LYS cc_start: 0.6923 (mttp) cc_final: 0.6588 (mttp) REVERT: B 1046 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6487 (pt0) REVERT: B 1049 GLU cc_start: 0.5889 (mm-30) cc_final: 0.5683 (mm-30) REVERT: B 1050 ASP cc_start: 0.6474 (m-30) cc_final: 0.5925 (m-30) REVERT: B 1062 GLU cc_start: 0.6679 (tt0) cc_final: 0.6198 (tt0) REVERT: B 1068 PHE cc_start: 0.6136 (t80) cc_final: 0.5884 (t80) REVERT: B 1081 MET cc_start: 0.5665 (mtm) cc_final: 0.5224 (mtp) REVERT: B 1122 ARG cc_start: 0.5852 (mtm-85) cc_final: 0.4841 (mtm-85) REVERT: B 1125 GLU cc_start: 0.5762 (mt-10) cc_final: 0.4634 (pp20) REVERT: B 1128 ARG cc_start: 0.6262 (tmm160) cc_final: 0.5827 (tmm160) REVERT: B 1149 MET cc_start: 0.7671 (mtp) cc_final: 0.7447 (mtm) REVERT: B 1150 MET cc_start: 0.7546 (tpp) cc_final: 0.7269 (mtp) REVERT: B 1152 GLN cc_start: 0.7372 (mt0) cc_final: 0.7022 (mt0) REVERT: B 1160 PHE cc_start: 0.7341 (m-10) cc_final: 0.7124 (m-10) REVERT: B 1248 TYR cc_start: 0.6889 (t80) cc_final: 0.6652 (t80) REVERT: B 1272 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6389 (pttt) REVERT: B 1304 ARG cc_start: 0.7724 (ptp-170) cc_final: 0.7101 (mtp180) REVERT: B 1377 GLU cc_start: 0.6640 (pt0) cc_final: 0.6252 (pt0) REVERT: B 1389 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7476 (mt-10) REVERT: B 1445 GLU cc_start: 0.6986 (pm20) cc_final: 0.6752 (mp0) REVERT: B 1456 GLN cc_start: 0.7336 (tm-30) cc_final: 0.7047 (pt0) REVERT: B 1463 HIS cc_start: 0.6931 (m90) cc_final: 0.6238 (t-170) REVERT: B 1491 ASN cc_start: 0.8145 (t0) cc_final: 0.7863 (t0) REVERT: C 74 ASP cc_start: 0.6973 (m-30) cc_final: 0.6584 (t0) REVERT: C 81 MET cc_start: 0.7362 (ptm) cc_final: 0.7099 (ptm) REVERT: C 156 LEU cc_start: 0.6880 (tp) cc_final: 0.6669 (mt) REVERT: C 166 LYS cc_start: 0.6789 (ttpt) cc_final: 0.6413 (ptmm) REVERT: C 174 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.6825 (ptp-170) REVERT: C 225 MET cc_start: 0.7355 (mtp) cc_final: 0.7103 (mtp) REVERT: C 251 ASP cc_start: 0.7582 (t0) cc_final: 0.7268 (t0) REVERT: C 284 GLN cc_start: 0.7074 (mt0) cc_final: 0.6417 (mp10) REVERT: C 306 LEU cc_start: 0.7474 (tp) cc_final: 0.7191 (tm) REVERT: C 356 GLN cc_start: 0.6778 (mt0) cc_final: 0.6073 (mm-40) REVERT: C 440 HIS cc_start: 0.4769 (p90) cc_final: 0.4543 (p-80) REVERT: C 456 MET cc_start: 0.5950 (mtt) cc_final: 0.5699 (mtt) REVERT: C 477 LYS cc_start: 0.6116 (mttm) cc_final: 0.5889 (mppt) REVERT: C 560 MET cc_start: 0.6743 (mmm) cc_final: 0.6498 (mmm) REVERT: C 592 GLN cc_start: 0.5412 (tt0) cc_final: 0.4916 (pt0) REVERT: C 594 ARG cc_start: 0.5736 (mtp180) cc_final: 0.5535 (mtp85) REVERT: C 638 GLU cc_start: 0.5819 (mt-10) cc_final: 0.5189 (pt0) REVERT: C 654 GLU cc_start: 0.6098 (tp30) cc_final: 0.5824 (tp30) REVERT: C 663 LYS cc_start: 0.6300 (mmmt) cc_final: 0.5386 (mttm) REVERT: C 694 MET cc_start: 0.6620 (mtm) cc_final: 0.6408 (mtp) REVERT: C 725 ASP cc_start: 0.7362 (m-30) cc_final: 0.6882 (m-30) REVERT: C 731 LYS cc_start: 0.6671 (ttpt) cc_final: 0.6274 (mmpt) REVERT: C 829 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6024 (mm-30) REVERT: C 833 SER cc_start: 0.6268 (t) cc_final: 0.5889 (p) REVERT: C 854 MET cc_start: 0.6445 (mtm) cc_final: 0.6221 (mtt) REVERT: C 870 ARG cc_start: 0.6672 (mtt180) cc_final: 0.6409 (mtt180) REVERT: C 875 MET cc_start: 0.6737 (ptt) cc_final: 0.6413 (ptp) REVERT: C 932 MET cc_start: 0.6537 (mmt) cc_final: 0.6161 (mmt) REVERT: C 969 ARG cc_start: 0.6486 (mtm110) cc_final: 0.6079 (mtm-85) REVERT: C 972 ILE cc_start: 0.7309 (mt) cc_final: 0.6885 (mm) REVERT: C 998 LEU cc_start: 0.6663 (mt) cc_final: 0.6335 (mm) REVERT: C 1005 GLU cc_start: 0.6042 (mt-10) cc_final: 0.5044 (tt0) REVERT: C 1043 LYS cc_start: 0.6927 (mttp) cc_final: 0.6590 (mttp) REVERT: C 1046 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6545 (pt0) REVERT: C 1049 GLU cc_start: 0.5885 (mm-30) cc_final: 0.5676 (mm-30) REVERT: C 1050 ASP cc_start: 0.6463 (m-30) cc_final: 0.5918 (m-30) REVERT: C 1062 GLU cc_start: 0.6708 (tt0) cc_final: 0.6232 (tt0) REVERT: C 1068 PHE cc_start: 0.6136 (t80) cc_final: 0.5890 (t80) REVERT: C 1081 MET cc_start: 0.5666 (mtm) cc_final: 0.5222 (mtp) REVERT: C 1122 ARG cc_start: 0.5852 (mtm-85) cc_final: 0.4838 (mtm-85) REVERT: C 1125 GLU cc_start: 0.5790 (mt-10) cc_final: 0.4663 (pp20) REVERT: C 1128 ARG cc_start: 0.6271 (tmm160) cc_final: 0.5858 (tmm160) REVERT: C 1149 MET cc_start: 0.7630 (mtp) cc_final: 0.7404 (mtm) REVERT: C 1150 MET cc_start: 0.7548 (tpp) cc_final: 0.7264 (mtp) REVERT: C 1152 GLN cc_start: 0.7356 (mt0) cc_final: 0.6992 (mt0) REVERT: C 1160 PHE cc_start: 0.7343 (m-10) cc_final: 0.7131 (m-10) REVERT: C 1248 TYR cc_start: 0.6895 (t80) cc_final: 0.6647 (t80) REVERT: C 1272 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6393 (pttt) REVERT: C 1304 ARG cc_start: 0.7737 (ptp-170) cc_final: 0.7104 (mtp180) REVERT: C 1377 GLU cc_start: 0.6635 (pt0) cc_final: 0.6247 (pt0) REVERT: C 1389 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7475 (mt-10) REVERT: C 1445 GLU cc_start: 0.7040 (pm20) cc_final: 0.6766 (mp0) REVERT: C 1456 GLN cc_start: 0.7338 (tm-30) cc_final: 0.7056 (pt0) REVERT: C 1463 HIS cc_start: 0.6928 (m90) cc_final: 0.6232 (t-170) REVERT: C 1491 ASN cc_start: 0.8147 (t0) cc_final: 0.7859 (t0) REVERT: D 74 ASP cc_start: 0.6945 (m-30) cc_final: 0.6554 (t0) REVERT: D 81 MET cc_start: 0.7352 (ptm) cc_final: 0.7093 (ptm) REVERT: D 156 LEU cc_start: 0.6881 (tp) cc_final: 0.6667 (mt) REVERT: D 166 LYS cc_start: 0.6788 (ttpt) cc_final: 0.6410 (ptmm) REVERT: D 174 ARG cc_start: 0.7460 (mtm-85) cc_final: 0.6822 (ptp-170) REVERT: D 225 MET cc_start: 0.7339 (mtp) cc_final: 0.7086 (mtp) REVERT: D 251 ASP cc_start: 0.7584 (t0) cc_final: 0.7213 (t0) REVERT: D 284 GLN cc_start: 0.7072 (mt0) cc_final: 0.6713 (mt0) REVERT: D 306 LEU cc_start: 0.7473 (tp) cc_final: 0.7190 (tm) REVERT: D 356 GLN cc_start: 0.6736 (mt0) cc_final: 0.6028 (mm-40) REVERT: D 440 HIS cc_start: 0.4767 (p90) cc_final: 0.4540 (p-80) REVERT: D 456 MET cc_start: 0.5948 (mtt) cc_final: 0.5697 (mtt) REVERT: D 477 LYS cc_start: 0.6108 (mttm) cc_final: 0.5880 (mppt) REVERT: D 560 MET cc_start: 0.6734 (mmm) cc_final: 0.6489 (mmm) REVERT: D 577 ASP cc_start: 0.6230 (t0) cc_final: 0.5835 (t70) REVERT: D 592 GLN cc_start: 0.5454 (tt0) cc_final: 0.4953 (pt0) REVERT: D 594 ARG cc_start: 0.5744 (mtp180) cc_final: 0.5535 (mtp85) REVERT: D 638 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5192 (pt0) REVERT: D 654 GLU cc_start: 0.6110 (tp30) cc_final: 0.5835 (tp30) REVERT: D 663 LYS cc_start: 0.6302 (mmmt) cc_final: 0.5387 (mttm) REVERT: D 694 MET cc_start: 0.6598 (mtm) cc_final: 0.6386 (mtp) REVERT: D 725 ASP cc_start: 0.7360 (m-30) cc_final: 0.6880 (m-30) REVERT: D 731 LYS cc_start: 0.6681 (ttpt) cc_final: 0.6294 (mmpt) REVERT: D 829 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6025 (mm-30) REVERT: D 833 SER cc_start: 0.6257 (t) cc_final: 0.5876 (p) REVERT: D 854 MET cc_start: 0.6445 (mtm) cc_final: 0.6220 (mtt) REVERT: D 870 ARG cc_start: 0.6675 (mtt180) cc_final: 0.6407 (mtt180) REVERT: D 875 MET cc_start: 0.6737 (ptt) cc_final: 0.6416 (ptp) REVERT: D 932 MET cc_start: 0.6543 (mmt) cc_final: 0.6157 (mmt) REVERT: D 969 ARG cc_start: 0.6484 (mtm110) cc_final: 0.6077 (mtm-85) REVERT: D 972 ILE cc_start: 0.7307 (mt) cc_final: 0.6873 (mm) REVERT: D 998 LEU cc_start: 0.6667 (mt) cc_final: 0.6333 (mm) REVERT: D 1005 GLU cc_start: 0.6048 (mt-10) cc_final: 0.5054 (tt0) REVERT: D 1043 LYS cc_start: 0.6922 (mttp) cc_final: 0.6587 (mttp) REVERT: D 1046 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6558 (pt0) REVERT: D 1049 GLU cc_start: 0.5888 (mm-30) cc_final: 0.5681 (mm-30) REVERT: D 1050 ASP cc_start: 0.6472 (m-30) cc_final: 0.5927 (m-30) REVERT: D 1062 GLU cc_start: 0.6678 (tt0) cc_final: 0.6201 (tt0) REVERT: D 1068 PHE cc_start: 0.6145 (t80) cc_final: 0.5902 (t80) REVERT: D 1081 MET cc_start: 0.5663 (mtm) cc_final: 0.5223 (mtp) REVERT: D 1122 ARG cc_start: 0.5851 (mtm-85) cc_final: 0.4838 (mtm-85) REVERT: D 1125 GLU cc_start: 0.5761 (mt-10) cc_final: 0.4634 (pp20) REVERT: D 1128 ARG cc_start: 0.6262 (tmm160) cc_final: 0.5827 (tmm160) REVERT: D 1149 MET cc_start: 0.7668 (mtp) cc_final: 0.7415 (mtm) REVERT: D 1150 MET cc_start: 0.7544 (tpp) cc_final: 0.7261 (mtp) REVERT: D 1152 GLN cc_start: 0.7373 (mt0) cc_final: 0.7026 (mt0) REVERT: D 1248 TYR cc_start: 0.6887 (t80) cc_final: 0.6647 (t80) REVERT: D 1272 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6391 (pttt) REVERT: D 1304 ARG cc_start: 0.7720 (ptp-170) cc_final: 0.7100 (mtp180) REVERT: D 1377 GLU cc_start: 0.6638 (pt0) cc_final: 0.6250 (pt0) REVERT: D 1389 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7475 (mt-10) REVERT: D 1445 GLU cc_start: 0.6987 (pm20) cc_final: 0.6751 (mp0) REVERT: D 1456 GLN cc_start: 0.7338 (tm-30) cc_final: 0.7050 (pt0) REVERT: D 1463 HIS cc_start: 0.6931 (m90) cc_final: 0.6236 (t-170) REVERT: D 1491 ASN cc_start: 0.8144 (t0) cc_final: 0.7861 (t0) outliers start: 40 outliers final: 5 residues processed: 1092 average time/residue: 0.8910 time to fit residues: 1161.1095 Evaluate side-chains 628 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 621 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 1272 LYS Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 1272 LYS Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 1272 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 0.7980 chunk 497 optimal weight: 0.6980 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 368 ASN A 450 ASN A 457 HIS A 514 HIS A 893 GLN A1056 ASN A1129 GLN B 73 GLN B 368 ASN B 450 ASN B 457 HIS B 514 HIS B 893 GLN B1045 GLN B1056 ASN B1129 GLN C 73 GLN C 368 ASN C 450 ASN C 457 HIS C 514 HIS C 893 GLN C1045 GLN C1056 ASN C1129 GLN D 73 GLN D 368 ASN D 450 ASN D 457 HIS D 514 HIS D 893 GLN D 957 GLN D1045 GLN D1056 ASN D1129 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121047 restraints weight = 58575.709| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.67 r_work: 0.3353 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43672 Z= 0.150 Angle : 0.592 7.770 59380 Z= 0.316 Chirality : 0.041 0.195 6740 Planarity : 0.004 0.043 7504 Dihedral : 9.046 88.954 7068 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.45 % Allowed : 9.69 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.11), residues: 5432 helix: 1.68 (0.09), residues: 3000 sheet: -0.62 (0.23), residues: 416 loop : -1.06 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 159 TYR 0.018 0.002 TYR C 979 PHE 0.021 0.002 PHE A1083 TRP 0.011 0.001 TRP B 726 HIS 0.008 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00317 (43668) covalent geometry : angle 0.59237 (59372) SS BOND : bond 0.00013 ( 4) SS BOND : angle 0.67983 ( 8) hydrogen bonds : bond 0.05149 ( 2299) hydrogen bonds : angle 4.40159 ( 6741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 686 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7697 (mtp85) REVERT: A 174 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7600 (mtm180) REVERT: A 352 GLN cc_start: 0.7848 (tt0) cc_final: 0.7334 (mt0) REVERT: A 365 GLN cc_start: 0.6755 (mt0) cc_final: 0.5827 (mp10) REVERT: A 456 MET cc_start: 0.7237 (mtt) cc_final: 0.6976 (mtp) REVERT: A 473 ILE cc_start: 0.7925 (mt) cc_final: 0.7716 (mp) REVERT: A 560 MET cc_start: 0.8281 (mmm) cc_final: 0.7968 (mmm) REVERT: A 594 ARG cc_start: 0.6801 (mtp180) cc_final: 0.6510 (mtp85) REVERT: A 618 HIS cc_start: 0.6736 (t70) cc_final: 0.6050 (m170) REVERT: A 663 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7290 (mttm) REVERT: A 666 GLU cc_start: 0.7517 (pt0) cc_final: 0.7301 (tt0) REVERT: A 731 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7594 (mmmt) REVERT: A 829 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6971 (mm-30) REVERT: A 833 SER cc_start: 0.7672 (t) cc_final: 0.7418 (p) REVERT: A 870 ARG cc_start: 0.8106 (mtt180) cc_final: 0.7763 (mtp85) REVERT: A 875 MET cc_start: 0.8332 (ptt) cc_final: 0.7939 (ptp) REVERT: A 1005 GLU cc_start: 0.6512 (mt-10) cc_final: 0.5904 (tt0) REVERT: A 1050 ASP cc_start: 0.7854 (m-30) cc_final: 0.7591 (m-30) REVERT: A 1062 GLU cc_start: 0.7966 (tt0) cc_final: 0.7591 (tt0) REVERT: A 1064 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7846 (mttt) REVERT: A 1085 ARG cc_start: 0.5564 (ttt90) cc_final: 0.5145 (tpt170) REVERT: A 1105 THR cc_start: 0.6984 (m) cc_final: 0.6596 (p) REVERT: A 1145 GLN cc_start: 0.8427 (tt0) cc_final: 0.7834 (mt0) REVERT: A 1244 MET cc_start: 0.5995 (ptp) cc_final: 0.5755 (ptp) REVERT: A 1453 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8387 (mp) REVERT: B 78 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7713 (mtp85) REVERT: B 174 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7626 (mtm180) REVERT: B 352 GLN cc_start: 0.7840 (tt0) cc_final: 0.7321 (mt0) REVERT: B 365 GLN cc_start: 0.6799 (mt0) cc_final: 0.5889 (mp10) REVERT: B 456 MET cc_start: 0.7249 (mtt) cc_final: 0.6982 (mtp) REVERT: B 473 ILE cc_start: 0.7917 (mt) cc_final: 0.7700 (mp) REVERT: B 560 MET cc_start: 0.8268 (mmm) cc_final: 0.7954 (mmm) REVERT: B 594 ARG cc_start: 0.6792 (mtp180) cc_final: 0.6501 (mtp85) REVERT: B 618 HIS cc_start: 0.6718 (t70) cc_final: 0.6021 (m170) REVERT: B 663 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7272 (mttm) REVERT: B 666 GLU cc_start: 0.7563 (pt0) cc_final: 0.7361 (tt0) REVERT: B 731 LYS cc_start: 0.7833 (ttpt) cc_final: 0.7553 (mmmt) REVERT: B 829 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6979 (mm-30) REVERT: B 833 SER cc_start: 0.7641 (t) cc_final: 0.7403 (p) REVERT: B 849 GLU cc_start: 0.8220 (tp30) cc_final: 0.8018 (tp30) REVERT: B 870 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7772 (mtp85) REVERT: B 875 MET cc_start: 0.8343 (ptt) cc_final: 0.7963 (ptp) REVERT: B 1005 GLU cc_start: 0.6565 (mt-10) cc_final: 0.5926 (tt0) REVERT: B 1050 ASP cc_start: 0.7866 (m-30) cc_final: 0.7587 (m-30) REVERT: B 1062 GLU cc_start: 0.7940 (tt0) cc_final: 0.7579 (tt0) REVERT: B 1064 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7856 (mttt) REVERT: B 1085 ARG cc_start: 0.5587 (ttt90) cc_final: 0.5165 (tpt170) REVERT: B 1105 THR cc_start: 0.6984 (m) cc_final: 0.6589 (p) REVERT: B 1145 GLN cc_start: 0.8425 (tt0) cc_final: 0.7847 (mt0) REVERT: B 1244 MET cc_start: 0.6005 (ptp) cc_final: 0.5774 (ptp) REVERT: B 1453 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8381 (mp) REVERT: C 78 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7710 (mtp85) REVERT: C 174 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7618 (mtm180) REVERT: C 352 GLN cc_start: 0.7842 (tt0) cc_final: 0.7332 (mt0) REVERT: C 365 GLN cc_start: 0.6785 (mt0) cc_final: 0.5875 (mp10) REVERT: C 456 MET cc_start: 0.7260 (mtt) cc_final: 0.6983 (mtp) REVERT: C 473 ILE cc_start: 0.7927 (mt) cc_final: 0.7712 (mp) REVERT: C 560 MET cc_start: 0.8268 (mmm) cc_final: 0.7955 (mmm) REVERT: C 594 ARG cc_start: 0.6763 (mtp180) cc_final: 0.6470 (mtp85) REVERT: C 618 HIS cc_start: 0.6770 (t70) cc_final: 0.6054 (m170) REVERT: C 663 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7276 (mttm) REVERT: C 666 GLU cc_start: 0.7503 (pt0) cc_final: 0.7287 (tt0) REVERT: C 731 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7514 (mmmt) REVERT: C 829 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6985 (mm-30) REVERT: C 833 SER cc_start: 0.7642 (t) cc_final: 0.7411 (p) REVERT: C 870 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7763 (mtp85) REVERT: C 875 MET cc_start: 0.8342 (ptt) cc_final: 0.7957 (ptp) REVERT: C 1005 GLU cc_start: 0.6560 (mt-10) cc_final: 0.5911 (tt0) REVERT: C 1050 ASP cc_start: 0.7871 (m-30) cc_final: 0.7592 (m-30) REVERT: C 1062 GLU cc_start: 0.7934 (tt0) cc_final: 0.7565 (tt0) REVERT: C 1064 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7854 (mttt) REVERT: C 1085 ARG cc_start: 0.5560 (ttt90) cc_final: 0.5142 (tpt170) REVERT: C 1105 THR cc_start: 0.6987 (m) cc_final: 0.6594 (p) REVERT: C 1145 GLN cc_start: 0.8422 (tt0) cc_final: 0.7834 (mt0) REVERT: C 1244 MET cc_start: 0.5986 (ptp) cc_final: 0.5755 (ptp) REVERT: C 1389 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8008 (mt-10) REVERT: C 1453 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8376 (mp) REVERT: D 78 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7713 (mtp85) REVERT: D 174 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7626 (mtm180) REVERT: D 352 GLN cc_start: 0.7842 (tt0) cc_final: 0.7323 (mt0) REVERT: D 365 GLN cc_start: 0.6788 (mt0) cc_final: 0.5883 (mp10) REVERT: D 456 MET cc_start: 0.7255 (mtt) cc_final: 0.6992 (mtp) REVERT: D 473 ILE cc_start: 0.7918 (mt) cc_final: 0.7704 (mp) REVERT: D 560 MET cc_start: 0.8264 (mmm) cc_final: 0.7954 (mmm) REVERT: D 594 ARG cc_start: 0.6800 (mtp180) cc_final: 0.6514 (mtp85) REVERT: D 618 HIS cc_start: 0.6734 (t70) cc_final: 0.6033 (m170) REVERT: D 663 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7273 (mttm) REVERT: D 666 GLU cc_start: 0.7556 (pt0) cc_final: 0.7354 (tt0) REVERT: D 731 LYS cc_start: 0.7839 (ttpt) cc_final: 0.7556 (mmmt) REVERT: D 829 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6988 (mm-30) REVERT: D 833 SER cc_start: 0.7653 (t) cc_final: 0.7414 (p) REVERT: D 870 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7766 (mtp85) REVERT: D 875 MET cc_start: 0.8344 (ptt) cc_final: 0.7962 (ptp) REVERT: D 1005 GLU cc_start: 0.6546 (mt-10) cc_final: 0.5917 (tt0) REVERT: D 1050 ASP cc_start: 0.7867 (m-30) cc_final: 0.7586 (m-30) REVERT: D 1062 GLU cc_start: 0.7949 (tt0) cc_final: 0.7585 (tt0) REVERT: D 1064 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7868 (mttt) REVERT: D 1085 ARG cc_start: 0.5569 (ttt90) cc_final: 0.5144 (tpt170) REVERT: D 1105 THR cc_start: 0.6980 (m) cc_final: 0.6583 (p) REVERT: D 1145 GLN cc_start: 0.8428 (tt0) cc_final: 0.7850 (mt0) REVERT: D 1244 MET cc_start: 0.6021 (ptp) cc_final: 0.5791 (ptp) REVERT: D 1453 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8392 (mp) outliers start: 104 outliers final: 24 residues processed: 762 average time/residue: 0.8413 time to fit residues: 765.7646 Evaluate side-chains 540 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 504 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain B residue 1453 LEU Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain C residue 1453 LEU Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain D residue 1453 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 19 optimal weight: 0.0970 chunk 161 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 399 optimal weight: 0.7980 chunk 494 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 522 optimal weight: 0.0170 chunk 355 optimal weight: 0.9980 chunk 417 optimal weight: 8.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN A 417 GLN A 514 HIS A 893 GLN A 957 GLN A 992 ASN A1282 ASN A1456 GLN A1463 HIS B 284 GLN B 417 GLN B 514 HIS B 893 GLN B 957 GLN B 992 ASN B1282 ASN B1456 GLN B1463 HIS C 284 GLN C 514 HIS C 893 GLN C 957 GLN C1282 ASN C1456 GLN C1463 HIS D 284 GLN D 514 HIS D 893 GLN D 992 ASN D1282 ASN D1456 GLN D1463 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.142567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119300 restraints weight = 58328.967| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.52 r_work: 0.3290 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 43672 Z= 0.113 Angle : 0.511 9.050 59380 Z= 0.270 Chirality : 0.039 0.169 6740 Planarity : 0.004 0.042 7504 Dihedral : 8.376 88.239 7056 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.87 % Allowed : 12.23 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.11), residues: 5432 helix: 2.04 (0.09), residues: 2992 sheet: -0.58 (0.23), residues: 412 loop : -0.82 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 159 TYR 0.016 0.001 TYR C 216 PHE 0.016 0.001 PHE A1068 TRP 0.011 0.001 TRP A 726 HIS 0.011 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00235 (43668) covalent geometry : angle 0.51075 (59372) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.42181 ( 8) hydrogen bonds : bond 0.04158 ( 2299) hydrogen bonds : angle 3.99309 ( 6741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 556 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5946 (ppp) cc_final: 0.5659 (ppp) REVERT: A 174 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7487 (mtm180) REVERT: A 352 GLN cc_start: 0.7859 (tt0) cc_final: 0.7381 (mt0) REVERT: A 365 GLN cc_start: 0.6954 (mt0) cc_final: 0.6082 (mp10) REVERT: A 473 ILE cc_start: 0.7938 (mt) cc_final: 0.7731 (mp) REVERT: A 560 MET cc_start: 0.8480 (mmm) cc_final: 0.8216 (mmm) REVERT: A 566 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.7188 (mtt-85) REVERT: A 592 GLN cc_start: 0.6615 (OUTLIER) cc_final: 0.6200 (tp-100) REVERT: A 594 ARG cc_start: 0.6808 (mtp180) cc_final: 0.6556 (mtp85) REVERT: A 596 THR cc_start: 0.7737 (m) cc_final: 0.7455 (t) REVERT: A 618 HIS cc_start: 0.6732 (t70) cc_final: 0.6202 (m170) REVERT: A 663 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7295 (mttm) REVERT: A 731 LYS cc_start: 0.7864 (ttpt) cc_final: 0.7590 (mttp) REVERT: A 829 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6996 (mm-30) REVERT: A 833 SER cc_start: 0.7772 (t) cc_final: 0.7470 (p) REVERT: A 870 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7899 (mtt90) REVERT: A 875 MET cc_start: 0.8353 (ptt) cc_final: 0.7850 (ptp) REVERT: A 1046 GLU cc_start: 0.7828 (pt0) cc_final: 0.7391 (mt-10) REVERT: A 1050 ASP cc_start: 0.7966 (m-30) cc_final: 0.7680 (m-30) REVERT: A 1062 GLU cc_start: 0.7922 (tt0) cc_final: 0.7620 (tt0) REVERT: A 1064 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7770 (mttt) REVERT: A 1085 ARG cc_start: 0.5574 (ttt90) cc_final: 0.5066 (tpt170) REVERT: A 1105 THR cc_start: 0.6922 (m) cc_final: 0.6531 (p) REVERT: A 1145 GLN cc_start: 0.8478 (tt0) cc_final: 0.7916 (mt0) REVERT: A 1164 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8444 (mt) REVERT: B 70 MET cc_start: 0.5926 (ppp) cc_final: 0.5647 (ppp) REVERT: B 174 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7498 (mtm180) REVERT: B 352 GLN cc_start: 0.7864 (tt0) cc_final: 0.7382 (mt0) REVERT: B 365 GLN cc_start: 0.6960 (mt0) cc_final: 0.6074 (mp10) REVERT: B 560 MET cc_start: 0.8466 (mmm) cc_final: 0.8201 (mmm) REVERT: B 566 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7169 (mtt-85) REVERT: B 592 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6049 (tp-100) REVERT: B 594 ARG cc_start: 0.6811 (mtp180) cc_final: 0.6560 (mtp85) REVERT: B 618 HIS cc_start: 0.6832 (t70) cc_final: 0.6325 (m170) REVERT: B 663 LYS cc_start: 0.7961 (mmmt) cc_final: 0.7388 (mmtp) REVERT: B 731 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7503 (mmmt) REVERT: B 829 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7040 (mm-30) REVERT: B 870 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7910 (mtt90) REVERT: B 875 MET cc_start: 0.8362 (ptt) cc_final: 0.7870 (ptp) REVERT: B 937 ASP cc_start: 0.8374 (m-30) cc_final: 0.8079 (m-30) REVERT: B 1046 GLU cc_start: 0.7838 (pt0) cc_final: 0.7409 (mt-10) REVERT: B 1050 ASP cc_start: 0.7965 (m-30) cc_final: 0.7668 (m-30) REVERT: B 1062 GLU cc_start: 0.7938 (tt0) cc_final: 0.7649 (tt0) REVERT: B 1064 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7784 (mttt) REVERT: B 1085 ARG cc_start: 0.5572 (ttt90) cc_final: 0.5080 (tpt170) REVERT: B 1105 THR cc_start: 0.6930 (m) cc_final: 0.6521 (p) REVERT: B 1145 GLN cc_start: 0.8479 (tt0) cc_final: 0.7909 (mt0) REVERT: B 1164 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (mt) REVERT: C 70 MET cc_start: 0.5923 (ppp) cc_final: 0.5634 (ppp) REVERT: C 174 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7500 (mtm180) REVERT: C 352 GLN cc_start: 0.7832 (tt0) cc_final: 0.7353 (mt0) REVERT: C 365 GLN cc_start: 0.6945 (mt0) cc_final: 0.6061 (mp10) REVERT: C 560 MET cc_start: 0.8470 (mmm) cc_final: 0.8206 (mmm) REVERT: C 566 ARG cc_start: 0.7448 (mtm-85) cc_final: 0.7171 (mtt-85) REVERT: C 592 GLN cc_start: 0.6603 (OUTLIER) cc_final: 0.6187 (tp-100) REVERT: C 594 ARG cc_start: 0.6799 (mtp180) cc_final: 0.6546 (mtp85) REVERT: C 596 THR cc_start: 0.7736 (m) cc_final: 0.7457 (t) REVERT: C 618 HIS cc_start: 0.6684 (t70) cc_final: 0.6159 (m170) REVERT: C 663 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7297 (mttm) REVERT: C 731 LYS cc_start: 0.7837 (ttpt) cc_final: 0.7523 (mmmt) REVERT: C 829 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7025 (mm-30) REVERT: C 833 SER cc_start: 0.7757 (t) cc_final: 0.7487 (p) REVERT: C 870 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7897 (mtt90) REVERT: C 875 MET cc_start: 0.8344 (ptt) cc_final: 0.7845 (ptp) REVERT: C 1046 GLU cc_start: 0.7839 (pt0) cc_final: 0.7419 (mt-10) REVERT: C 1050 ASP cc_start: 0.7943 (m-30) cc_final: 0.7680 (m-30) REVERT: C 1062 GLU cc_start: 0.7911 (tt0) cc_final: 0.7610 (tt0) REVERT: C 1064 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7786 (mttt) REVERT: C 1085 ARG cc_start: 0.5593 (ttt90) cc_final: 0.5087 (tpt170) REVERT: C 1105 THR cc_start: 0.6917 (m) cc_final: 0.6502 (p) REVERT: C 1145 GLN cc_start: 0.8473 (tt0) cc_final: 0.7909 (mt0) REVERT: C 1164 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8438 (mt) REVERT: C 1389 GLU cc_start: 0.8221 (mt-10) cc_final: 0.8019 (mt-10) REVERT: D 70 MET cc_start: 0.5923 (ppp) cc_final: 0.5631 (ppp) REVERT: D 174 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7503 (mtm180) REVERT: D 352 GLN cc_start: 0.7876 (tt0) cc_final: 0.7378 (mt0) REVERT: D 365 GLN cc_start: 0.6956 (mt0) cc_final: 0.6067 (mp10) REVERT: D 560 MET cc_start: 0.8472 (mmm) cc_final: 0.8214 (mmm) REVERT: D 566 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7180 (mtt-85) REVERT: D 592 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6192 (tp-100) REVERT: D 594 ARG cc_start: 0.6815 (mtp180) cc_final: 0.6560 (mtp85) REVERT: D 596 THR cc_start: 0.7740 (m) cc_final: 0.7471 (t) REVERT: D 618 HIS cc_start: 0.6727 (t70) cc_final: 0.6191 (m170) REVERT: D 663 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7385 (mmtp) REVERT: D 731 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7504 (mmmt) REVERT: D 829 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7045 (mm-30) REVERT: D 870 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7899 (mtt90) REVERT: D 875 MET cc_start: 0.8350 (ptt) cc_final: 0.7857 (ptp) REVERT: D 937 ASP cc_start: 0.8370 (m-30) cc_final: 0.8078 (m-30) REVERT: D 1046 GLU cc_start: 0.7838 (pt0) cc_final: 0.7416 (mt-10) REVERT: D 1050 ASP cc_start: 0.7971 (m-30) cc_final: 0.7674 (m-30) REVERT: D 1062 GLU cc_start: 0.7920 (tt0) cc_final: 0.7631 (tt0) REVERT: D 1064 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7801 (mttt) REVERT: D 1085 ARG cc_start: 0.5571 (ttt90) cc_final: 0.5075 (tpt170) REVERT: D 1105 THR cc_start: 0.6921 (m) cc_final: 0.6501 (p) REVERT: D 1145 GLN cc_start: 0.8479 (tt0) cc_final: 0.7927 (mt0) REVERT: D 1164 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8444 (mt) outliers start: 122 outliers final: 38 residues processed: 646 average time/residue: 0.8904 time to fit residues: 684.3547 Evaluate side-chains 520 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 470 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 733 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1159 SER Chi-restraints excluded: chain D residue 1164 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 178 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 326 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 395 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 813 HIS A 893 GLN A1255 HIS A1463 HIS B 514 HIS B 813 HIS B 893 GLN B1255 HIS B1282 ASN B1463 HIS C 514 HIS C 813 HIS C 893 GLN C 992 ASN C1255 HIS C1463 HIS D 514 HIS D 813 HIS D 893 GLN D1255 HIS D1282 ASN D1463 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.134769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.111584 restraints weight = 58720.354| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.50 r_work: 0.3186 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 43672 Z= 0.221 Angle : 0.635 8.724 59380 Z= 0.330 Chirality : 0.043 0.193 6740 Planarity : 0.005 0.046 7504 Dihedral : 8.865 88.104 7056 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.65 % Allowed : 12.49 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.11), residues: 5432 helix: 1.76 (0.09), residues: 2992 sheet: -0.65 (0.23), residues: 384 loop : -0.77 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1008 TYR 0.021 0.002 TYR A 917 PHE 0.027 0.002 PHE A1068 TRP 0.019 0.002 TRP B1216 HIS 0.009 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00517 (43668) covalent geometry : angle 0.63462 (59372) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.26970 ( 8) hydrogen bonds : bond 0.04989 ( 2299) hydrogen bonds : angle 4.17744 ( 6741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 521 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6114 (ppp) cc_final: 0.5643 (ppp) REVERT: A 139 ASP cc_start: 0.7654 (m-30) cc_final: 0.7362 (m-30) REVERT: A 174 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7706 (mtp180) REVERT: A 240 HIS cc_start: 0.6761 (m-70) cc_final: 0.6462 (m170) REVERT: A 352 GLN cc_start: 0.7874 (tt0) cc_final: 0.7536 (mt0) REVERT: A 365 GLN cc_start: 0.7130 (mt0) cc_final: 0.6195 (mp10) REVERT: A 410 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7586 (mtpt) REVERT: A 577 ASP cc_start: 0.7246 (t0) cc_final: 0.6874 (t70) REVERT: A 592 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6326 (tp-100) REVERT: A 594 ARG cc_start: 0.7000 (mtp180) cc_final: 0.6578 (mtp85) REVERT: A 596 THR cc_start: 0.7850 (m) cc_final: 0.7612 (t) REVERT: A 618 HIS cc_start: 0.7153 (t70) cc_final: 0.6478 (m170) REVERT: A 663 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7494 (mttt) REVERT: A 731 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7650 (mptt) REVERT: A 829 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7124 (mm-30) REVERT: A 870 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7926 (mtt90) REVERT: A 875 MET cc_start: 0.8582 (ptt) cc_final: 0.8127 (ptt) REVERT: A 1062 GLU cc_start: 0.8042 (tt0) cc_final: 0.7692 (tt0) REVERT: A 1064 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7790 (mttt) REVERT: A 1085 ARG cc_start: 0.5697 (ttt90) cc_final: 0.5221 (tpt90) REVERT: A 1105 THR cc_start: 0.6884 (m) cc_final: 0.6376 (p) REVERT: A 1126 ARG cc_start: 0.7249 (ttp-110) cc_final: 0.6984 (ttp-110) REVERT: A 1130 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7425 (mm-30) REVERT: A 1145 GLN cc_start: 0.8457 (tt0) cc_final: 0.7940 (mt0) REVERT: A 1150 MET cc_start: 0.8477 (mmt) cc_final: 0.8225 (mtp) REVERT: A 1204 VAL cc_start: 0.8336 (t) cc_final: 0.8088 (p) REVERT: B 70 MET cc_start: 0.6122 (ppp) cc_final: 0.5649 (ppp) REVERT: B 139 ASP cc_start: 0.7662 (m-30) cc_final: 0.7373 (m-30) REVERT: B 174 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7729 (mtp180) REVERT: B 240 HIS cc_start: 0.6749 (m-70) cc_final: 0.6458 (m170) REVERT: B 352 GLN cc_start: 0.7870 (tt0) cc_final: 0.7540 (mt0) REVERT: B 365 GLN cc_start: 0.7135 (mt0) cc_final: 0.6193 (mp10) REVERT: B 410 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7644 (mtpt) REVERT: B 577 ASP cc_start: 0.7256 (t0) cc_final: 0.6878 (t70) REVERT: B 592 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6155 (tp-100) REVERT: B 594 ARG cc_start: 0.7023 (mtp180) cc_final: 0.6604 (mtp85) REVERT: B 618 HIS cc_start: 0.7146 (t70) cc_final: 0.6480 (m170) REVERT: B 663 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7525 (mttt) REVERT: B 731 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7614 (mttp) REVERT: B 829 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7183 (mm-30) REVERT: B 875 MET cc_start: 0.8590 (ptt) cc_final: 0.8131 (ptt) REVERT: B 1062 GLU cc_start: 0.8094 (tt0) cc_final: 0.7748 (tt0) REVERT: B 1064 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7817 (mttt) REVERT: B 1065 ASP cc_start: 0.7651 (p0) cc_final: 0.7416 (p0) REVERT: B 1085 ARG cc_start: 0.5710 (ttt90) cc_final: 0.5173 (tpt170) REVERT: B 1105 THR cc_start: 0.6887 (m) cc_final: 0.6379 (p) REVERT: B 1115 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7774 (tp) REVERT: B 1126 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.7005 (mtp-110) REVERT: B 1145 GLN cc_start: 0.8506 (tt0) cc_final: 0.7943 (mt0) REVERT: B 1204 VAL cc_start: 0.8333 (t) cc_final: 0.8092 (p) REVERT: C 70 MET cc_start: 0.6102 (ppp) cc_final: 0.5633 (ppp) REVERT: C 139 ASP cc_start: 0.7658 (m-30) cc_final: 0.7372 (m-30) REVERT: C 174 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7716 (mtp180) REVERT: C 240 HIS cc_start: 0.6761 (m-70) cc_final: 0.6472 (m170) REVERT: C 352 GLN cc_start: 0.7897 (tt0) cc_final: 0.7551 (mt0) REVERT: C 365 GLN cc_start: 0.7114 (mt0) cc_final: 0.6176 (mp10) REVERT: C 410 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7638 (mtpt) REVERT: C 577 ASP cc_start: 0.7251 (t0) cc_final: 0.6869 (t70) REVERT: C 592 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6245 (tp40) REVERT: C 594 ARG cc_start: 0.7016 (mtp180) cc_final: 0.6596 (mtp85) REVERT: C 618 HIS cc_start: 0.7164 (t70) cc_final: 0.6489 (m170) REVERT: C 663 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7497 (mttt) REVERT: C 731 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7619 (mttp) REVERT: C 829 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7177 (mm-30) REVERT: C 870 ARG cc_start: 0.8221 (mtt180) cc_final: 0.7947 (mtt90) REVERT: C 875 MET cc_start: 0.8592 (ptt) cc_final: 0.8136 (ptt) REVERT: C 1062 GLU cc_start: 0.8020 (tt0) cc_final: 0.7726 (tt0) REVERT: C 1064 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7787 (mttt) REVERT: C 1085 ARG cc_start: 0.5723 (ttt90) cc_final: 0.5177 (tpt170) REVERT: C 1105 THR cc_start: 0.6880 (m) cc_final: 0.6363 (p) REVERT: C 1145 GLN cc_start: 0.8445 (tt0) cc_final: 0.7925 (mt0) REVERT: C 1204 VAL cc_start: 0.8336 (t) cc_final: 0.8088 (p) REVERT: D 70 MET cc_start: 0.6130 (ppp) cc_final: 0.5641 (ppp) REVERT: D 139 ASP cc_start: 0.7648 (m-30) cc_final: 0.7360 (m-30) REVERT: D 174 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7719 (mtp180) REVERT: D 240 HIS cc_start: 0.6717 (m-70) cc_final: 0.6431 (m170) REVERT: D 352 GLN cc_start: 0.7888 (tt0) cc_final: 0.7543 (mt0) REVERT: D 365 GLN cc_start: 0.7131 (mt0) cc_final: 0.6192 (mp10) REVERT: D 410 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7631 (mtpt) REVERT: D 577 ASP cc_start: 0.7260 (t0) cc_final: 0.6884 (t70) REVERT: D 592 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6203 (tp40) REVERT: D 594 ARG cc_start: 0.7013 (mtp180) cc_final: 0.6589 (mtp85) REVERT: D 618 HIS cc_start: 0.7163 (t70) cc_final: 0.6487 (m170) REVERT: D 663 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7520 (mttt) REVERT: D 731 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7626 (mttp) REVERT: D 829 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7170 (mm-30) REVERT: D 870 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7942 (mtt90) REVERT: D 875 MET cc_start: 0.8589 (ptt) cc_final: 0.8129 (ptt) REVERT: D 1062 GLU cc_start: 0.8033 (tt0) cc_final: 0.7699 (tt0) REVERT: D 1064 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7824 (mttt) REVERT: D 1065 ASP cc_start: 0.7635 (p0) cc_final: 0.7400 (p0) REVERT: D 1085 ARG cc_start: 0.5678 (ttt90) cc_final: 0.5148 (tpt170) REVERT: D 1105 THR cc_start: 0.6870 (m) cc_final: 0.6352 (p) REVERT: D 1145 GLN cc_start: 0.8467 (tt0) cc_final: 0.7934 (mt0) REVERT: D 1150 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8261 (mtp) REVERT: D 1204 VAL cc_start: 0.8320 (t) cc_final: 0.8072 (p) outliers start: 155 outliers final: 60 residues processed: 646 average time/residue: 0.8024 time to fit residues: 621.8914 Evaluate side-chains 539 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 465 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1274 LYS Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1274 LYS Chi-restraints excluded: chain B residue 1277 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain B residue 1453 LEU Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1274 LYS Chi-restraints excluded: chain C residue 1277 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain C residue 1453 LEU Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 733 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1150 MET Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1274 LYS Chi-restraints excluded: chain D residue 1277 VAL Chi-restraints excluded: chain D residue 1281 VAL Chi-restraints excluded: chain D residue 1453 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 516 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 505 optimal weight: 3.9990 chunk 394 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 477 optimal weight: 10.0000 chunk 403 optimal weight: 0.6980 chunk 231 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 893 GLN A1463 HIS B 514 HIS B 893 GLN B1463 HIS C 514 HIS C 893 GLN C1463 HIS D 514 HIS D 893 GLN D1463 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112395 restraints weight = 58372.879| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.53 r_work: 0.3193 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 43672 Z= 0.155 Angle : 0.546 8.203 59380 Z= 0.286 Chirality : 0.041 0.177 6740 Planarity : 0.004 0.048 7504 Dihedral : 8.523 85.980 7056 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 3.13 % Allowed : 14.49 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.11), residues: 5432 helix: 1.86 (0.09), residues: 3000 sheet: -0.86 (0.24), residues: 388 loop : -0.66 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 159 TYR 0.016 0.002 TYR D 917 PHE 0.022 0.002 PHE D1068 TRP 0.010 0.001 TRP A 726 HIS 0.010 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00351 (43668) covalent geometry : angle 0.54643 (59372) SS BOND : bond 0.00023 ( 4) SS BOND : angle 0.54602 ( 8) hydrogen bonds : bond 0.04349 ( 2299) hydrogen bonds : angle 4.03548 ( 6741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 471 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6092 (ppp) cc_final: 0.5631 (ppp) REVERT: A 139 ASP cc_start: 0.7606 (m-30) cc_final: 0.7357 (m-30) REVERT: A 240 HIS cc_start: 0.6848 (m-70) cc_final: 0.6556 (m170) REVERT: A 352 GLN cc_start: 0.7932 (tt0) cc_final: 0.7588 (mt0) REVERT: A 365 GLN cc_start: 0.7146 (mt0) cc_final: 0.6238 (mp10) REVERT: A 594 ARG cc_start: 0.7019 (mtp180) cc_final: 0.6685 (mtp85) REVERT: A 618 HIS cc_start: 0.7173 (t70) cc_final: 0.6587 (m170) REVERT: A 663 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7618 (mttt) REVERT: A 731 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7715 (mttp) REVERT: A 829 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7213 (mm-30) REVERT: A 870 ARG cc_start: 0.8299 (mtt180) cc_final: 0.8021 (mtt90) REVERT: A 875 MET cc_start: 0.8571 (ptt) cc_final: 0.8066 (ptp) REVERT: A 996 ASN cc_start: 0.8273 (m-40) cc_final: 0.7913 (m-40) REVERT: A 1062 GLU cc_start: 0.8096 (tt0) cc_final: 0.7751 (tt0) REVERT: A 1064 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7673 (mttt) REVERT: A 1085 ARG cc_start: 0.5754 (ttt90) cc_final: 0.5197 (tpt170) REVERT: A 1105 THR cc_start: 0.6898 (m) cc_final: 0.6421 (p) REVERT: A 1126 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.7001 (ttp-110) REVERT: A 1130 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7483 (mm-30) REVERT: A 1145 GLN cc_start: 0.8466 (tt0) cc_final: 0.8013 (mt0) REVERT: A 1150 MET cc_start: 0.8509 (mmt) cc_final: 0.8179 (mtp) REVERT: A 1164 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8551 (mt) REVERT: A 1204 VAL cc_start: 0.8280 (t) cc_final: 0.8056 (p) REVERT: A 1467 MET cc_start: 0.8605 (mtm) cc_final: 0.8311 (mtm) REVERT: B 70 MET cc_start: 0.6112 (ppp) cc_final: 0.5628 (ppp) REVERT: B 77 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7469 (mmtt) REVERT: B 139 ASP cc_start: 0.7631 (m-30) cc_final: 0.7388 (m-30) REVERT: B 240 HIS cc_start: 0.6853 (m-70) cc_final: 0.6564 (m170) REVERT: B 272 ILE cc_start: 0.8312 (mm) cc_final: 0.8036 (mt) REVERT: B 352 GLN cc_start: 0.7929 (tt0) cc_final: 0.7594 (mt0) REVERT: B 365 GLN cc_start: 0.7148 (mt0) cc_final: 0.6237 (mp10) REVERT: B 594 ARG cc_start: 0.7014 (mtp180) cc_final: 0.6615 (mtp85) REVERT: B 618 HIS cc_start: 0.7175 (t70) cc_final: 0.6572 (m170) REVERT: B 663 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7617 (mttt) REVERT: B 731 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7639 (mttp) REVERT: B 829 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7229 (mm-30) REVERT: B 870 ARG cc_start: 0.8305 (mtt180) cc_final: 0.8028 (mtt90) REVERT: B 875 MET cc_start: 0.8575 (ptt) cc_final: 0.8066 (ptp) REVERT: B 996 ASN cc_start: 0.8290 (m-40) cc_final: 0.7920 (m-40) REVERT: B 1062 GLU cc_start: 0.8068 (tt0) cc_final: 0.7748 (tt0) REVERT: B 1064 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7693 (mttt) REVERT: B 1085 ARG cc_start: 0.5784 (ttt90) cc_final: 0.5219 (tpt170) REVERT: B 1105 THR cc_start: 0.6882 (m) cc_final: 0.6405 (p) REVERT: B 1115 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7846 (tp) REVERT: B 1145 GLN cc_start: 0.8507 (tt0) cc_final: 0.8019 (mt0) REVERT: B 1164 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8560 (mt) REVERT: B 1204 VAL cc_start: 0.8266 (t) cc_final: 0.8048 (p) REVERT: B 1467 MET cc_start: 0.8597 (mtm) cc_final: 0.8301 (mtm) REVERT: C 70 MET cc_start: 0.6091 (ppp) cc_final: 0.5617 (ppp) REVERT: C 139 ASP cc_start: 0.7612 (m-30) cc_final: 0.7373 (m-30) REVERT: C 240 HIS cc_start: 0.6858 (m-70) cc_final: 0.6569 (m170) REVERT: C 272 ILE cc_start: 0.8310 (mm) cc_final: 0.8045 (mt) REVERT: C 352 GLN cc_start: 0.7951 (tt0) cc_final: 0.7602 (mt0) REVERT: C 365 GLN cc_start: 0.7132 (mt0) cc_final: 0.6228 (mp10) REVERT: C 594 ARG cc_start: 0.7009 (mtp180) cc_final: 0.6614 (mtp85) REVERT: C 618 HIS cc_start: 0.7176 (t70) cc_final: 0.6557 (m170) REVERT: C 663 LYS cc_start: 0.8278 (mmmt) cc_final: 0.7622 (mttt) REVERT: C 731 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7630 (mttp) REVERT: C 829 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7217 (mm-30) REVERT: C 870 ARG cc_start: 0.8313 (mtt180) cc_final: 0.8036 (mtt90) REVERT: C 875 MET cc_start: 0.8575 (ptt) cc_final: 0.8064 (ptp) REVERT: C 996 ASN cc_start: 0.8292 (m-40) cc_final: 0.7922 (m-40) REVERT: C 1062 GLU cc_start: 0.8086 (tt0) cc_final: 0.7742 (tt0) REVERT: C 1064 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7672 (mttt) REVERT: C 1085 ARG cc_start: 0.5813 (ttt90) cc_final: 0.5240 (tpt170) REVERT: C 1105 THR cc_start: 0.6901 (m) cc_final: 0.6423 (p) REVERT: C 1115 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7826 (tp) REVERT: C 1145 GLN cc_start: 0.8420 (tt0) cc_final: 0.7972 (mt0) REVERT: C 1164 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8570 (mt) REVERT: C 1204 VAL cc_start: 0.8277 (t) cc_final: 0.8051 (p) REVERT: C 1467 MET cc_start: 0.8595 (mtm) cc_final: 0.8291 (mtm) REVERT: D 70 MET cc_start: 0.6103 (ppp) cc_final: 0.5625 (ppp) REVERT: D 77 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7465 (mmtt) REVERT: D 139 ASP cc_start: 0.7662 (m-30) cc_final: 0.7421 (m-30) REVERT: D 240 HIS cc_start: 0.6854 (m-70) cc_final: 0.6568 (m170) REVERT: D 272 ILE cc_start: 0.8314 (mm) cc_final: 0.8036 (mt) REVERT: D 352 GLN cc_start: 0.7954 (tt0) cc_final: 0.7595 (mt0) REVERT: D 365 GLN cc_start: 0.7139 (mt0) cc_final: 0.6234 (mp10) REVERT: D 594 ARG cc_start: 0.7008 (mtp180) cc_final: 0.6611 (mtp85) REVERT: D 618 HIS cc_start: 0.7170 (t70) cc_final: 0.6568 (m170) REVERT: D 663 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7607 (mttt) REVERT: D 731 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7660 (mttp) REVERT: D 829 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7214 (mm-30) REVERT: D 870 ARG cc_start: 0.8304 (mtt180) cc_final: 0.8027 (mtt90) REVERT: D 875 MET cc_start: 0.8574 (ptt) cc_final: 0.8061 (ptp) REVERT: D 996 ASN cc_start: 0.8284 (m-40) cc_final: 0.7921 (m-40) REVERT: D 1062 GLU cc_start: 0.8085 (tt0) cc_final: 0.7759 (tt0) REVERT: D 1064 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7723 (mttt) REVERT: D 1065 ASP cc_start: 0.7738 (p0) cc_final: 0.7491 (p0) REVERT: D 1085 ARG cc_start: 0.5737 (ttt90) cc_final: 0.5186 (tpt170) REVERT: D 1105 THR cc_start: 0.6875 (m) cc_final: 0.6381 (p) REVERT: D 1145 GLN cc_start: 0.8451 (tt0) cc_final: 0.7990 (mt0) REVERT: D 1150 MET cc_start: 0.8797 (tpp) cc_final: 0.8238 (mtp) REVERT: D 1164 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8556 (mt) REVERT: D 1204 VAL cc_start: 0.8258 (t) cc_final: 0.8040 (p) REVERT: D 1467 MET cc_start: 0.8596 (mtm) cc_final: 0.8297 (mtm) outliers start: 133 outliers final: 62 residues processed: 573 average time/residue: 0.8827 time to fit residues: 604.1444 Evaluate side-chains 517 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 445 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1274 LYS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1274 LYS Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1274 LYS Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1164 LEU Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1274 LYS Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 219 optimal weight: 0.5980 chunk 141 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 427 optimal weight: 0.3980 chunk 258 optimal weight: 0.7980 chunk 538 optimal weight: 0.4980 chunk 114 optimal weight: 0.0670 chunk 333 optimal weight: 0.0870 chunk 403 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 893 GLN A1463 HIS B 514 HIS B 893 GLN B1080 HIS B1463 HIS C 514 HIS C 893 GLN C1080 HIS C1463 HIS D 514 HIS D 893 GLN D1080 HIS D1463 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114614 restraints weight = 58978.072| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.48 r_work: 0.3232 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 43672 Z= 0.102 Angle : 0.481 7.525 59380 Z= 0.252 Chirality : 0.038 0.165 6740 Planarity : 0.004 0.046 7504 Dihedral : 7.967 83.885 7056 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.88 % Rotamer: Outliers : 2.09 % Allowed : 15.50 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.12), residues: 5432 helix: 2.16 (0.09), residues: 3000 sheet: -1.05 (0.24), residues: 380 loop : -0.48 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 159 TYR 0.012 0.001 TYR D 799 PHE 0.015 0.001 PHE D1068 TRP 0.011 0.001 TRP B 726 HIS 0.008 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00216 (43668) covalent geometry : angle 0.48069 (59372) SS BOND : bond 0.00066 ( 4) SS BOND : angle 0.48380 ( 8) hydrogen bonds : bond 0.03649 ( 2299) hydrogen bonds : angle 3.78768 ( 6741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 488 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5957 (ppp) cc_final: 0.5598 (ppp) REVERT: A 77 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7485 (mptt) REVERT: A 139 ASP cc_start: 0.7553 (m-30) cc_final: 0.7313 (m-30) REVERT: A 240 HIS cc_start: 0.6809 (m-70) cc_final: 0.6505 (m170) REVERT: A 352 GLN cc_start: 0.7840 (tt0) cc_final: 0.7533 (mt0) REVERT: A 506 ARG cc_start: 0.7053 (ttt-90) cc_final: 0.6793 (ttt-90) REVERT: A 594 ARG cc_start: 0.6863 (mtp180) cc_final: 0.6511 (mtp85) REVERT: A 618 HIS cc_start: 0.7156 (t70) cc_final: 0.6616 (m170) REVERT: A 663 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7612 (mttt) REVERT: A 731 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7816 (tttp) REVERT: A 829 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7116 (mm-30) REVERT: A 870 ARG cc_start: 0.8353 (mtt180) cc_final: 0.8080 (mtt90) REVERT: A 875 MET cc_start: 0.8566 (ptt) cc_final: 0.8094 (ptp) REVERT: A 1085 ARG cc_start: 0.5814 (ttt90) cc_final: 0.5137 (tpt170) REVERT: A 1105 THR cc_start: 0.6872 (m) cc_final: 0.6402 (p) REVERT: A 1145 GLN cc_start: 0.8397 (tt0) cc_final: 0.8011 (mt0) REVERT: A 1467 MET cc_start: 0.8628 (mtm) cc_final: 0.8313 (mtm) REVERT: B 139 ASP cc_start: 0.7594 (m-30) cc_final: 0.7363 (m-30) REVERT: B 240 HIS cc_start: 0.6806 (m-70) cc_final: 0.6505 (m170) REVERT: B 352 GLN cc_start: 0.7819 (tt0) cc_final: 0.7516 (mt0) REVERT: B 506 ARG cc_start: 0.7055 (ttt-90) cc_final: 0.6798 (ttt-90) REVERT: B 594 ARG cc_start: 0.6886 (mtp180) cc_final: 0.6578 (mtp85) REVERT: B 618 HIS cc_start: 0.7090 (t70) cc_final: 0.6590 (m170) REVERT: B 663 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7659 (mmtp) REVERT: B 731 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7706 (mptt) REVERT: B 829 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7118 (mm-30) REVERT: B 870 ARG cc_start: 0.8350 (mtt180) cc_final: 0.8074 (mtt90) REVERT: B 875 MET cc_start: 0.8556 (ptt) cc_final: 0.8092 (ptp) REVERT: B 1062 GLU cc_start: 0.8144 (tt0) cc_final: 0.7785 (tt0) REVERT: B 1064 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7676 (mttt) REVERT: B 1085 ARG cc_start: 0.5795 (ttt90) cc_final: 0.5118 (tpt170) REVERT: B 1105 THR cc_start: 0.6870 (m) cc_final: 0.6393 (p) REVERT: B 1145 GLN cc_start: 0.8417 (tt0) cc_final: 0.8001 (mt0) REVERT: B 1467 MET cc_start: 0.8630 (mtm) cc_final: 0.8377 (mtm) REVERT: C 77 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7539 (mptt) REVERT: C 139 ASP cc_start: 0.7556 (m-30) cc_final: 0.7323 (m-30) REVERT: C 240 HIS cc_start: 0.6799 (m-70) cc_final: 0.6502 (m170) REVERT: C 352 GLN cc_start: 0.7856 (tt0) cc_final: 0.7546 (mt0) REVERT: C 502 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6916 (pt0) REVERT: C 594 ARG cc_start: 0.6857 (mtp180) cc_final: 0.6545 (mtp85) REVERT: C 618 HIS cc_start: 0.7160 (t70) cc_final: 0.6588 (m170) REVERT: C 663 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7613 (mttt) REVERT: C 731 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7694 (mptt) REVERT: C 829 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7113 (mm-30) REVERT: C 870 ARG cc_start: 0.8357 (mtt180) cc_final: 0.8080 (mtt90) REVERT: C 875 MET cc_start: 0.8564 (ptt) cc_final: 0.8091 (ptp) REVERT: C 1085 ARG cc_start: 0.5837 (ttt90) cc_final: 0.5179 (tpt170) REVERT: C 1105 THR cc_start: 0.6864 (m) cc_final: 0.6391 (p) REVERT: C 1115 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7697 (tp) REVERT: C 1145 GLN cc_start: 0.8334 (tt0) cc_final: 0.8015 (mt0) REVERT: C 1467 MET cc_start: 0.8612 (mtm) cc_final: 0.8352 (mtm) REVERT: D 139 ASP cc_start: 0.7566 (m-30) cc_final: 0.7336 (m-30) REVERT: D 240 HIS cc_start: 0.6806 (m-70) cc_final: 0.6513 (m170) REVERT: D 352 GLN cc_start: 0.7828 (tt0) cc_final: 0.7529 (mt0) REVERT: D 506 ARG cc_start: 0.7041 (ttt-90) cc_final: 0.6786 (ttt-90) REVERT: D 594 ARG cc_start: 0.6862 (mtp180) cc_final: 0.6554 (mtp85) REVERT: D 618 HIS cc_start: 0.7147 (t70) cc_final: 0.6620 (m170) REVERT: D 663 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7667 (mmtp) REVERT: D 731 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7697 (mptt) REVERT: D 829 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7134 (mm-30) REVERT: D 870 ARG cc_start: 0.8321 (mtt180) cc_final: 0.8043 (mtt90) REVERT: D 875 MET cc_start: 0.8560 (ptt) cc_final: 0.8090 (ptp) REVERT: D 1062 GLU cc_start: 0.8155 (tt0) cc_final: 0.7798 (tt0) REVERT: D 1064 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7685 (mttt) REVERT: D 1085 ARG cc_start: 0.5817 (ttt90) cc_final: 0.5127 (tpt170) REVERT: D 1105 THR cc_start: 0.6869 (m) cc_final: 0.6383 (p) REVERT: D 1145 GLN cc_start: 0.8369 (tt0) cc_final: 0.8018 (mt0) REVERT: D 1150 MET cc_start: 0.8658 (tpp) cc_final: 0.8253 (mtp) REVERT: D 1467 MET cc_start: 0.8635 (mtm) cc_final: 0.8387 (mtm) outliers start: 89 outliers final: 35 residues processed: 552 average time/residue: 0.9050 time to fit residues: 594.2813 Evaluate side-chains 481 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 440 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 498 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 472 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 405 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 381 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 336 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 514 HIS A 893 GLN A1463 HIS B 255 ASN B 514 HIS B 893 GLN B1463 HIS C 255 ASN C 514 HIS C 893 GLN C1463 HIS D 255 ASN D 514 HIS D 893 GLN D1463 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112942 restraints weight = 58803.083| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.52 r_work: 0.3221 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43672 Z= 0.119 Angle : 0.503 7.312 59380 Z= 0.264 Chirality : 0.039 0.168 6740 Planarity : 0.004 0.046 7504 Dihedral : 7.956 84.357 7056 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.06 % Rotamer: Outliers : 2.00 % Allowed : 16.09 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.12), residues: 5432 helix: 2.19 (0.09), residues: 2972 sheet: -0.92 (0.24), residues: 372 loop : -0.48 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 159 TYR 0.014 0.001 TYR A 917 PHE 0.017 0.001 PHE D1068 TRP 0.008 0.001 TRP C 726 HIS 0.009 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00267 (43668) covalent geometry : angle 0.50350 (59372) SS BOND : bond 0.00019 ( 4) SS BOND : angle 0.31489 ( 8) hydrogen bonds : bond 0.03850 ( 2299) hydrogen bonds : angle 3.79540 ( 6741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 447 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7563 (m-30) cc_final: 0.7335 (m-30) REVERT: A 174 ARG cc_start: 0.7890 (mtm180) cc_final: 0.7531 (mtm180) REVERT: A 240 HIS cc_start: 0.6854 (m-70) cc_final: 0.6545 (m170) REVERT: A 352 GLN cc_start: 0.7788 (tt0) cc_final: 0.7488 (mt0) REVERT: A 594 ARG cc_start: 0.6916 (mtp180) cc_final: 0.6621 (mtp85) REVERT: A 663 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7589 (mttp) REVERT: A 731 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7802 (mttp) REVERT: A 829 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7125 (mm-30) REVERT: A 870 ARG cc_start: 0.8352 (mtt180) cc_final: 0.7993 (mtt180) REVERT: A 875 MET cc_start: 0.8613 (ptt) cc_final: 0.8104 (ptp) REVERT: A 1085 ARG cc_start: 0.5831 (ttt90) cc_final: 0.5125 (tpt170) REVERT: A 1105 THR cc_start: 0.6908 (m) cc_final: 0.6424 (p) REVERT: A 1145 GLN cc_start: 0.8378 (tt0) cc_final: 0.7993 (mt0) REVERT: A 1467 MET cc_start: 0.8619 (mtm) cc_final: 0.8352 (mtm) REVERT: B 70 MET cc_start: 0.5976 (ppp) cc_final: 0.5566 (ppp) REVERT: B 139 ASP cc_start: 0.7599 (m-30) cc_final: 0.7375 (m-30) REVERT: B 240 HIS cc_start: 0.6851 (m-70) cc_final: 0.6546 (m170) REVERT: B 352 GLN cc_start: 0.7820 (tt0) cc_final: 0.7506 (mt0) REVERT: B 594 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6626 (mtp85) REVERT: B 663 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7665 (mmtp) REVERT: B 731 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7703 (mptt) REVERT: B 829 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7121 (mm-30) REVERT: B 870 ARG cc_start: 0.8353 (mtt180) cc_final: 0.7997 (mtt180) REVERT: B 875 MET cc_start: 0.8610 (ptt) cc_final: 0.8099 (ptp) REVERT: B 1062 GLU cc_start: 0.8173 (tt0) cc_final: 0.7880 (tt0) REVERT: B 1064 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7662 (mttt) REVERT: B 1085 ARG cc_start: 0.5809 (ttt90) cc_final: 0.5138 (tpt170) REVERT: B 1105 THR cc_start: 0.6869 (m) cc_final: 0.6381 (p) REVERT: B 1145 GLN cc_start: 0.8437 (tt0) cc_final: 0.8021 (mt0) REVERT: B 1467 MET cc_start: 0.8616 (mtm) cc_final: 0.8348 (mtm) REVERT: C 70 MET cc_start: 0.6001 (ppp) cc_final: 0.5585 (ppp) REVERT: C 77 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7472 (mptt) REVERT: C 139 ASP cc_start: 0.7593 (m-30) cc_final: 0.7368 (m-30) REVERT: C 240 HIS cc_start: 0.6851 (m-70) cc_final: 0.6547 (m170) REVERT: C 352 GLN cc_start: 0.7843 (tt0) cc_final: 0.7521 (mt0) REVERT: C 594 ARG cc_start: 0.6914 (mtp180) cc_final: 0.6621 (mtp85) REVERT: C 663 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7581 (mttp) REVERT: C 731 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7684 (mptt) REVERT: C 829 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7132 (mm-30) REVERT: C 870 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7988 (mtt180) REVERT: C 875 MET cc_start: 0.8612 (ptt) cc_final: 0.8104 (ptp) REVERT: C 1085 ARG cc_start: 0.5851 (ttt90) cc_final: 0.5172 (tpt170) REVERT: C 1105 THR cc_start: 0.6902 (m) cc_final: 0.6418 (p) REVERT: C 1145 GLN cc_start: 0.8300 (tt0) cc_final: 0.7984 (mt0) REVERT: C 1467 MET cc_start: 0.8621 (mtm) cc_final: 0.8347 (mtm) REVERT: D 70 MET cc_start: 0.5991 (ppp) cc_final: 0.5566 (ppp) REVERT: D 139 ASP cc_start: 0.7578 (m-30) cc_final: 0.7355 (m-30) REVERT: D 240 HIS cc_start: 0.6866 (m-70) cc_final: 0.6562 (m170) REVERT: D 352 GLN cc_start: 0.7853 (tt0) cc_final: 0.7519 (mt0) REVERT: D 594 ARG cc_start: 0.6909 (mtp180) cc_final: 0.6612 (mtp85) REVERT: D 663 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7673 (mmtp) REVERT: D 731 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7679 (mptt) REVERT: D 829 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7139 (mm-30) REVERT: D 870 ARG cc_start: 0.8346 (mtt180) cc_final: 0.7986 (mtt180) REVERT: D 875 MET cc_start: 0.8612 (ptt) cc_final: 0.8100 (ptp) REVERT: D 1062 GLU cc_start: 0.8171 (tt0) cc_final: 0.7876 (tt0) REVERT: D 1064 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7684 (mttt) REVERT: D 1085 ARG cc_start: 0.5833 (ttt90) cc_final: 0.5150 (tpt170) REVERT: D 1105 THR cc_start: 0.6863 (m) cc_final: 0.6375 (p) REVERT: D 1145 GLN cc_start: 0.8368 (tt0) cc_final: 0.8015 (mt0) REVERT: D 1150 MET cc_start: 0.8641 (tpp) cc_final: 0.8305 (mtp) REVERT: D 1467 MET cc_start: 0.8627 (mtm) cc_final: 0.8362 (mtm) outliers start: 85 outliers final: 51 residues processed: 513 average time/residue: 0.9400 time to fit residues: 571.6232 Evaluate side-chains 482 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 428 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 527 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 252 optimal weight: 0.0870 chunk 284 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 357 optimal weight: 3.9990 chunk 447 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 893 GLN A1463 HIS B 514 HIS B 893 GLN B1463 HIS C 514 HIS C 893 GLN C1463 HIS D 514 HIS D 893 GLN D1463 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.137417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114709 restraints weight = 59061.765| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.54 r_work: 0.3231 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43672 Z= 0.120 Angle : 0.500 7.349 59380 Z= 0.263 Chirality : 0.039 0.167 6740 Planarity : 0.004 0.046 7504 Dihedral : 7.941 84.155 7056 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 1.83 % Allowed : 16.39 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.12), residues: 5432 helix: 2.17 (0.09), residues: 2984 sheet: -0.93 (0.24), residues: 372 loop : -0.44 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 159 TYR 0.013 0.001 TYR A 917 PHE 0.016 0.001 PHE D1068 TRP 0.008 0.001 TRP C 96 HIS 0.009 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00269 (43668) covalent geometry : angle 0.50014 (59372) SS BOND : bond 0.00016 ( 4) SS BOND : angle 0.37390 ( 8) hydrogen bonds : bond 0.03846 ( 2299) hydrogen bonds : angle 3.79785 ( 6741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 445 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6024 (ppp) cc_final: 0.5486 (ppp) REVERT: A 77 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7438 (mmtt) REVERT: A 139 ASP cc_start: 0.7701 (m-30) cc_final: 0.7485 (m-30) REVERT: A 240 HIS cc_start: 0.6872 (m-70) cc_final: 0.6565 (m170) REVERT: A 352 GLN cc_start: 0.8000 (tt0) cc_final: 0.7600 (mt0) REVERT: A 594 ARG cc_start: 0.6955 (mtp180) cc_final: 0.6667 (mtp85) REVERT: A 663 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7576 (mttt) REVERT: A 731 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7865 (mttp) REVERT: A 829 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7136 (mm-30) REVERT: A 870 ARG cc_start: 0.8350 (mtt180) cc_final: 0.8018 (mtt180) REVERT: A 875 MET cc_start: 0.8606 (ptt) cc_final: 0.8042 (ptp) REVERT: A 1062 GLU cc_start: 0.8118 (tt0) cc_final: 0.7833 (tt0) REVERT: A 1085 ARG cc_start: 0.5903 (ttt90) cc_final: 0.5233 (tpt170) REVERT: A 1105 THR cc_start: 0.6859 (m) cc_final: 0.6355 (p) REVERT: A 1145 GLN cc_start: 0.8323 (tt0) cc_final: 0.7945 (mt0) REVERT: A 1244 MET cc_start: 0.5739 (ptp) cc_final: 0.5157 (mmt) REVERT: A 1467 MET cc_start: 0.8664 (mtm) cc_final: 0.8398 (mtm) REVERT: B 70 MET cc_start: 0.6032 (ppp) cc_final: 0.5504 (ppp) REVERT: B 139 ASP cc_start: 0.7663 (m-30) cc_final: 0.7444 (m-30) REVERT: B 240 HIS cc_start: 0.6901 (m-70) cc_final: 0.6598 (m170) REVERT: B 352 GLN cc_start: 0.7984 (tt0) cc_final: 0.7595 (mt0) REVERT: B 594 ARG cc_start: 0.6951 (mtp180) cc_final: 0.6669 (mtp85) REVERT: B 663 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7675 (mmtp) REVERT: B 731 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7815 (mptt) REVERT: B 829 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7221 (mm-30) REVERT: B 870 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7987 (mtt180) REVERT: B 875 MET cc_start: 0.8620 (ptt) cc_final: 0.8066 (ptp) REVERT: B 1062 GLU cc_start: 0.8202 (tt0) cc_final: 0.7912 (tt0) REVERT: B 1064 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7697 (mttt) REVERT: B 1085 ARG cc_start: 0.5919 (ttt90) cc_final: 0.5245 (tpt170) REVERT: B 1105 THR cc_start: 0.6880 (m) cc_final: 0.6380 (p) REVERT: B 1145 GLN cc_start: 0.8408 (tt0) cc_final: 0.8001 (mt0) REVERT: B 1244 MET cc_start: 0.5757 (ptp) cc_final: 0.5174 (mmt) REVERT: B 1467 MET cc_start: 0.8663 (mtm) cc_final: 0.8398 (mtm) REVERT: C 70 MET cc_start: 0.6015 (ppp) cc_final: 0.5483 (ppp) REVERT: C 77 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7490 (mptt) REVERT: C 139 ASP cc_start: 0.7643 (m-30) cc_final: 0.7425 (m-30) REVERT: C 240 HIS cc_start: 0.6878 (m-70) cc_final: 0.6574 (m170) REVERT: C 352 GLN cc_start: 0.7999 (tt0) cc_final: 0.7602 (mt0) REVERT: C 594 ARG cc_start: 0.6933 (mtp180) cc_final: 0.6645 (mtp85) REVERT: C 663 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7582 (mttt) REVERT: C 731 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7809 (mptt) REVERT: C 829 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7206 (mm-30) REVERT: C 870 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7999 (mtt180) REVERT: C 875 MET cc_start: 0.8618 (ptt) cc_final: 0.8059 (ptp) REVERT: C 1062 GLU cc_start: 0.8115 (tt0) cc_final: 0.7767 (tt0) REVERT: C 1085 ARG cc_start: 0.5941 (ttt90) cc_final: 0.5268 (tpt170) REVERT: C 1105 THR cc_start: 0.6833 (m) cc_final: 0.6320 (p) REVERT: C 1145 GLN cc_start: 0.8356 (tt0) cc_final: 0.7988 (mt0) REVERT: C 1244 MET cc_start: 0.5789 (ptp) cc_final: 0.5179 (mmt) REVERT: C 1467 MET cc_start: 0.8655 (mtm) cc_final: 0.8382 (mtm) REVERT: D 70 MET cc_start: 0.6037 (ppp) cc_final: 0.5494 (ppp) REVERT: D 139 ASP cc_start: 0.7683 (m-30) cc_final: 0.7470 (m-30) REVERT: D 240 HIS cc_start: 0.6887 (m-70) cc_final: 0.6582 (m170) REVERT: D 352 GLN cc_start: 0.8025 (tt0) cc_final: 0.7612 (mt0) REVERT: D 594 ARG cc_start: 0.6947 (mtp180) cc_final: 0.6660 (mtp85) REVERT: D 663 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7661 (mmtp) REVERT: D 731 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7811 (mptt) REVERT: D 829 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7194 (mm-30) REVERT: D 870 ARG cc_start: 0.8369 (mtt180) cc_final: 0.8039 (mtt180) REVERT: D 875 MET cc_start: 0.8613 (ptt) cc_final: 0.8053 (ptp) REVERT: D 1062 GLU cc_start: 0.8191 (tt0) cc_final: 0.7900 (tt0) REVERT: D 1064 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7681 (mttt) REVERT: D 1085 ARG cc_start: 0.5942 (ttt90) cc_final: 0.5262 (tpt170) REVERT: D 1105 THR cc_start: 0.6870 (m) cc_final: 0.6366 (p) REVERT: D 1145 GLN cc_start: 0.8352 (tt0) cc_final: 0.7988 (mt0) REVERT: D 1150 MET cc_start: 0.8604 (tpp) cc_final: 0.8378 (mtp) REVERT: D 1244 MET cc_start: 0.5780 (ptp) cc_final: 0.5176 (mmt) REVERT: D 1467 MET cc_start: 0.8657 (mtm) cc_final: 0.8383 (mtm) outliers start: 78 outliers final: 53 residues processed: 503 average time/residue: 0.9345 time to fit residues: 557.6012 Evaluate side-chains 490 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 433 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1238 MET Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1238 MET Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 29 optimal weight: 0.9990 chunk 457 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 404 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 197 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 893 GLN A1463 HIS B 514 HIS B 893 GLN B1463 HIS C 514 HIS C 893 GLN C1463 HIS D 514 HIS D 893 GLN D1463 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114376 restraints weight = 58495.124| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.54 r_work: 0.3225 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 43672 Z= 0.122 Angle : 0.510 7.437 59380 Z= 0.268 Chirality : 0.039 0.167 6740 Planarity : 0.004 0.047 7504 Dihedral : 7.926 83.893 7056 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 1.67 % Allowed : 16.82 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.12), residues: 5432 helix: 2.10 (0.09), residues: 3012 sheet: -1.01 (0.24), residues: 380 loop : -0.44 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 159 TYR 0.014 0.001 TYR C 917 PHE 0.015 0.001 PHE D1068 TRP 0.008 0.001 TRP B 726 HIS 0.007 0.001 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.00276 (43668) covalent geometry : angle 0.51013 (59372) SS BOND : bond 0.00016 ( 4) SS BOND : angle 0.36645 ( 8) hydrogen bonds : bond 0.03878 ( 2299) hydrogen bonds : angle 3.81006 ( 6741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 435 time to evaluate : 1.808 Fit side-chains REVERT: A 70 MET cc_start: 0.6041 (ppp) cc_final: 0.5506 (ppp) REVERT: A 77 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7405 (mmtt) REVERT: A 139 ASP cc_start: 0.7691 (m-30) cc_final: 0.7476 (m-30) REVERT: A 240 HIS cc_start: 0.6929 (m-70) cc_final: 0.6608 (m170) REVERT: A 352 GLN cc_start: 0.8019 (tt0) cc_final: 0.7627 (mt0) REVERT: A 388 LEU cc_start: 0.8024 (tp) cc_final: 0.7818 (tp) REVERT: A 464 GLU cc_start: 0.7296 (tp30) cc_final: 0.6819 (mm-30) REVERT: A 594 ARG cc_start: 0.6951 (mtp180) cc_final: 0.6662 (mtp85) REVERT: A 663 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7596 (mttt) REVERT: A 731 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7849 (mttp) REVERT: A 829 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7218 (mm-30) REVERT: A 870 ARG cc_start: 0.8325 (mtt180) cc_final: 0.7982 (mtt180) REVERT: A 875 MET cc_start: 0.8602 (ptt) cc_final: 0.8023 (ptp) REVERT: A 1062 GLU cc_start: 0.8118 (tt0) cc_final: 0.7759 (tt0) REVERT: A 1085 ARG cc_start: 0.5861 (ttt90) cc_final: 0.5190 (tpt170) REVERT: A 1105 THR cc_start: 0.6854 (m) cc_final: 0.6335 (p) REVERT: A 1145 GLN cc_start: 0.8330 (tt0) cc_final: 0.7951 (mt0) REVERT: A 1244 MET cc_start: 0.5583 (ptp) cc_final: 0.5016 (mmt) REVERT: A 1467 MET cc_start: 0.8666 (mtm) cc_final: 0.8391 (mtm) REVERT: B 139 ASP cc_start: 0.7708 (m-30) cc_final: 0.7500 (m-30) REVERT: B 240 HIS cc_start: 0.6932 (m-70) cc_final: 0.6615 (m170) REVERT: B 352 GLN cc_start: 0.7977 (tt0) cc_final: 0.7603 (mt0) REVERT: B 388 LEU cc_start: 0.8022 (tp) cc_final: 0.7805 (tp) REVERT: B 464 GLU cc_start: 0.7283 (tp30) cc_final: 0.6849 (mm-30) REVERT: B 594 ARG cc_start: 0.6953 (mtp180) cc_final: 0.6676 (mtp85) REVERT: B 663 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7675 (mmtp) REVERT: B 731 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7793 (mptt) REVERT: B 829 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7224 (mm-30) REVERT: B 870 ARG cc_start: 0.8340 (mtt180) cc_final: 0.8005 (mtt180) REVERT: B 875 MET cc_start: 0.8614 (ptt) cc_final: 0.8049 (ptp) REVERT: B 1062 GLU cc_start: 0.8234 (tt0) cc_final: 0.7944 (tt0) REVERT: B 1064 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7680 (mttt) REVERT: B 1085 ARG cc_start: 0.5860 (ttt90) cc_final: 0.5189 (tpt170) REVERT: B 1105 THR cc_start: 0.6859 (m) cc_final: 0.6346 (p) REVERT: B 1145 GLN cc_start: 0.8366 (tt0) cc_final: 0.8001 (mt0) REVERT: B 1244 MET cc_start: 0.5594 (ptp) cc_final: 0.5035 (mmt) REVERT: B 1467 MET cc_start: 0.8656 (mtm) cc_final: 0.8378 (mtm) REVERT: C 77 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7478 (mptt) REVERT: C 240 HIS cc_start: 0.6912 (m-70) cc_final: 0.6595 (m170) REVERT: C 352 GLN cc_start: 0.8000 (tt0) cc_final: 0.7608 (mt0) REVERT: C 594 ARG cc_start: 0.6922 (mtp180) cc_final: 0.6635 (mtp85) REVERT: C 663 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7597 (mttt) REVERT: C 731 LYS cc_start: 0.8032 (ttpt) cc_final: 0.7807 (mptt) REVERT: C 829 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7209 (mm-30) REVERT: C 870 ARG cc_start: 0.8345 (mtt180) cc_final: 0.8011 (mtt180) REVERT: C 875 MET cc_start: 0.8610 (ptt) cc_final: 0.8036 (ptp) REVERT: C 1062 GLU cc_start: 0.8115 (tt0) cc_final: 0.7762 (tt0) REVERT: C 1085 ARG cc_start: 0.5866 (ttt90) cc_final: 0.5195 (tpt170) REVERT: C 1105 THR cc_start: 0.6870 (m) cc_final: 0.6347 (p) REVERT: C 1145 GLN cc_start: 0.8357 (tt0) cc_final: 0.8004 (mt0) REVERT: C 1244 MET cc_start: 0.5611 (ptp) cc_final: 0.5033 (mmt) REVERT: C 1467 MET cc_start: 0.8652 (mtm) cc_final: 0.8370 (mtm) REVERT: D 139 ASP cc_start: 0.7710 (m-30) cc_final: 0.7508 (m-30) REVERT: D 240 HIS cc_start: 0.6913 (m-70) cc_final: 0.6592 (m170) REVERT: D 352 GLN cc_start: 0.8015 (tt0) cc_final: 0.7618 (mt0) REVERT: D 464 GLU cc_start: 0.7280 (tp30) cc_final: 0.6837 (mm-30) REVERT: D 594 ARG cc_start: 0.6945 (mtp180) cc_final: 0.6661 (mtp85) REVERT: D 663 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7668 (mmtp) REVERT: D 731 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7815 (mptt) REVERT: D 829 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7229 (mm-30) REVERT: D 870 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7995 (mtt180) REVERT: D 875 MET cc_start: 0.8610 (ptt) cc_final: 0.8037 (ptp) REVERT: D 1062 GLU cc_start: 0.8205 (tt0) cc_final: 0.7913 (tt0) REVERT: D 1064 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7690 (mttt) REVERT: D 1085 ARG cc_start: 0.5888 (ttt90) cc_final: 0.5205 (tpt170) REVERT: D 1105 THR cc_start: 0.6873 (m) cc_final: 0.6361 (p) REVERT: D 1145 GLN cc_start: 0.8357 (tt0) cc_final: 0.7997 (mt0) REVERT: D 1150 MET cc_start: 0.8590 (tpp) cc_final: 0.8356 (mtp) REVERT: D 1244 MET cc_start: 0.5606 (ptp) cc_final: 0.5031 (mmt) REVERT: D 1467 MET cc_start: 0.8642 (mtm) cc_final: 0.8356 (mtm) outliers start: 71 outliers final: 51 residues processed: 488 average time/residue: 0.9184 time to fit residues: 532.6696 Evaluate side-chains 473 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 418 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 302 optimal weight: 0.9980 chunk 304 optimal weight: 0.9990 chunk 82 optimal weight: 0.0570 chunk 259 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 374 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 179 optimal weight: 9.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 893 GLN A1463 HIS B 514 HIS B 893 GLN B1463 HIS C 514 HIS C 893 GLN C1463 HIS D 514 HIS D 893 GLN D1463 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.137449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114356 restraints weight = 58671.473| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.56 r_work: 0.3228 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 43672 Z= 0.120 Angle : 0.510 7.158 59380 Z= 0.266 Chirality : 0.039 0.193 6740 Planarity : 0.004 0.047 7504 Dihedral : 7.883 83.526 7056 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 1.62 % Allowed : 16.89 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.12), residues: 5432 helix: 2.11 (0.09), residues: 3008 sheet: -1.00 (0.24), residues: 380 loop : -0.45 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 159 TYR 0.013 0.001 TYR C 917 PHE 0.018 0.001 PHE C1068 TRP 0.008 0.001 TRP B 726 HIS 0.007 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00271 (43668) covalent geometry : angle 0.51002 (59372) SS BOND : bond 0.00030 ( 4) SS BOND : angle 0.34952 ( 8) hydrogen bonds : bond 0.03832 ( 2299) hydrogen bonds : angle 3.81069 ( 6741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 425 time to evaluate : 1.780 Fit side-chains REVERT: A 70 MET cc_start: 0.6015 (ppp) cc_final: 0.5497 (ppp) REVERT: A 77 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7397 (mmtt) REVERT: A 240 HIS cc_start: 0.6999 (m-70) cc_final: 0.6735 (m90) REVERT: A 352 GLN cc_start: 0.8013 (tt0) cc_final: 0.7635 (mt0) REVERT: A 388 LEU cc_start: 0.8023 (tp) cc_final: 0.7791 (tp) REVERT: A 594 ARG cc_start: 0.6967 (mtp180) cc_final: 0.6679 (mtp85) REVERT: A 663 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7579 (mttp) REVERT: A 731 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7820 (mttp) REVERT: A 829 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7236 (mm-30) REVERT: A 870 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7994 (mtt180) REVERT: A 875 MET cc_start: 0.8604 (ptt) cc_final: 0.8029 (ptp) REVERT: A 996 ASN cc_start: 0.8330 (m-40) cc_final: 0.7974 (m-40) REVERT: A 1062 GLU cc_start: 0.8134 (tt0) cc_final: 0.7783 (tt0) REVERT: A 1085 ARG cc_start: 0.5965 (ttt90) cc_final: 0.5267 (tpt170) REVERT: A 1105 THR cc_start: 0.6886 (m) cc_final: 0.6363 (p) REVERT: A 1145 GLN cc_start: 0.8318 (tt0) cc_final: 0.7950 (mt0) REVERT: A 1244 MET cc_start: 0.5583 (ptp) cc_final: 0.5027 (mmt) REVERT: A 1467 MET cc_start: 0.8675 (mtm) cc_final: 0.8406 (mtm) REVERT: B 240 HIS cc_start: 0.6980 (m-70) cc_final: 0.6725 (m90) REVERT: B 352 GLN cc_start: 0.7922 (tt0) cc_final: 0.7579 (mt0) REVERT: B 388 LEU cc_start: 0.8028 (tp) cc_final: 0.7802 (tp) REVERT: B 594 ARG cc_start: 0.6978 (mtp180) cc_final: 0.6693 (mtp85) REVERT: B 663 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7678 (mmtp) REVERT: B 731 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7794 (mptt) REVERT: B 829 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7250 (mm-30) REVERT: B 870 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7999 (mtt180) REVERT: B 875 MET cc_start: 0.8609 (ptt) cc_final: 0.8041 (ptp) REVERT: B 1062 GLU cc_start: 0.8240 (tt0) cc_final: 0.7952 (tt0) REVERT: B 1064 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7681 (mttt) REVERT: B 1085 ARG cc_start: 0.5965 (ttt90) cc_final: 0.5264 (tpt170) REVERT: B 1105 THR cc_start: 0.6891 (m) cc_final: 0.6383 (p) REVERT: B 1145 GLN cc_start: 0.8335 (tt0) cc_final: 0.7981 (mt0) REVERT: B 1244 MET cc_start: 0.5586 (ptp) cc_final: 0.5041 (mmt) REVERT: B 1467 MET cc_start: 0.8660 (mtm) cc_final: 0.8383 (mtm) REVERT: C 77 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7407 (mmtt) REVERT: C 240 HIS cc_start: 0.6907 (m-70) cc_final: 0.6646 (m90) REVERT: C 352 GLN cc_start: 0.7959 (tt0) cc_final: 0.7593 (mt0) REVERT: C 594 ARG cc_start: 0.6934 (mtp180) cc_final: 0.6644 (mtp85) REVERT: C 663 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7585 (mttt) REVERT: C 731 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7802 (mptt) REVERT: C 829 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7228 (mm-30) REVERT: C 870 ARG cc_start: 0.8347 (mtt180) cc_final: 0.8013 (mtt180) REVERT: C 875 MET cc_start: 0.8603 (ptt) cc_final: 0.8029 (ptp) REVERT: C 1062 GLU cc_start: 0.8131 (tt0) cc_final: 0.7776 (tt0) REVERT: C 1085 ARG cc_start: 0.5966 (ttt90) cc_final: 0.5263 (tpt170) REVERT: C 1105 THR cc_start: 0.6867 (m) cc_final: 0.6341 (p) REVERT: C 1145 GLN cc_start: 0.8363 (tt0) cc_final: 0.8029 (mt0) REVERT: C 1244 MET cc_start: 0.5612 (ptp) cc_final: 0.5039 (mmt) REVERT: C 1467 MET cc_start: 0.8653 (mtm) cc_final: 0.8372 (mtm) REVERT: D 240 HIS cc_start: 0.6976 (m-70) cc_final: 0.6716 (m90) REVERT: D 352 GLN cc_start: 0.7969 (tt0) cc_final: 0.7599 (mt0) REVERT: D 594 ARG cc_start: 0.6961 (mtp180) cc_final: 0.6675 (mtp85) REVERT: D 663 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7668 (mmtp) REVERT: D 829 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7247 (mm-30) REVERT: D 870 ARG cc_start: 0.8344 (mtt180) cc_final: 0.8010 (mtt180) REVERT: D 875 MET cc_start: 0.8610 (ptt) cc_final: 0.8039 (ptp) REVERT: D 1062 GLU cc_start: 0.8211 (tt0) cc_final: 0.7921 (tt0) REVERT: D 1064 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7682 (mttt) REVERT: D 1085 ARG cc_start: 0.5965 (ttt90) cc_final: 0.5267 (tpt170) REVERT: D 1105 THR cc_start: 0.6868 (m) cc_final: 0.6358 (p) REVERT: D 1145 GLN cc_start: 0.8354 (tt0) cc_final: 0.8001 (mt0) REVERT: D 1150 MET cc_start: 0.8567 (tpp) cc_final: 0.8238 (mtp) REVERT: D 1244 MET cc_start: 0.5604 (ptp) cc_final: 0.5043 (mmt) REVERT: D 1467 MET cc_start: 0.8649 (mtm) cc_final: 0.8362 (mtm) outliers start: 69 outliers final: 52 residues processed: 476 average time/residue: 0.8471 time to fit residues: 479.9958 Evaluate side-chains 465 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 409 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1239 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 167 optimal weight: 6.9990 chunk 231 optimal weight: 0.8980 chunk 347 optimal weight: 5.9990 chunk 367 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 324 optimal weight: 0.6980 chunk 475 optimal weight: 5.9990 chunk 235 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 HIS A 893 GLN A1463 HIS B 514 HIS B 893 GLN B1463 HIS C 514 HIS C 893 GLN C1463 HIS D 514 HIS D 893 GLN D1463 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114820 restraints weight = 58914.197| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.54 r_work: 0.3232 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43672 Z= 0.118 Angle : 0.506 7.316 59380 Z= 0.265 Chirality : 0.039 0.187 6740 Planarity : 0.004 0.048 7504 Dihedral : 7.841 83.211 7056 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 1.65 % Allowed : 17.14 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.12), residues: 5432 helix: 2.10 (0.09), residues: 3008 sheet: -0.96 (0.24), residues: 380 loop : -0.43 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 341 TYR 0.013 0.001 TYR A 917 PHE 0.015 0.001 PHE B1068 TRP 0.008 0.001 TRP D 726 HIS 0.007 0.001 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.00265 (43668) covalent geometry : angle 0.50647 (59372) SS BOND : bond 0.00034 ( 4) SS BOND : angle 0.36635 ( 8) hydrogen bonds : bond 0.03809 ( 2299) hydrogen bonds : angle 3.80681 ( 6741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15771.63 seconds wall clock time: 269 minutes 8.08 seconds (16148.08 seconds total)