Starting phenix.real_space_refine on Tue Aug 26 23:17:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srd_40727/08_2025/8srd_40727.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srd_40727/08_2025/8srd_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 { model { file = "/net/cci-nas-00/data/ceres_data/8srd_40727/08_2025/8srd_40727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srd_40727/08_2025/8srd_40727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8srd_40727/08_2025/8srd_40727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srd_40727/08_2025/8srd_40727.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42686 Number of models: 1 Model: "" Number of chains: 8 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: "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: "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} Restraints were copied for chains: B, C Time building chain proxies: 14.08, per 1000 atoms: 0.33 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=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.02 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 376 " distance=0.00 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 399 " distance=0.00 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 446 " distance=0.00 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 609 " distance=0.00 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 676 " distance=0.00 Simple disulfide: pdb=" SG CYS B 817 " - pdb=" SG CYS B 817 " distance=0.00 Simple disulfide: pdb=" SG CYS B 857 " - pdb=" SG CYS B 857 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.02 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B 997 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.02 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B 997 " distance=2.02 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B1006 " distance=0.00 Simple disulfide: pdb=" SG CYS B1060 " - pdb=" SG CYS B1060 " distance=0.00 Simple disulfide: pdb=" SG CYS B1090 " - pdb=" SG CYS B1090 " distance=0.00 Simple disulfide: pdb=" SG CYS B1245 " - pdb=" SG CYS B1245 " distance=0.00 Simple disulfide: pdb=" SG CYS B1291 " - pdb=" SG CYS B1291 " distance=0.00 Simple disulfide: pdb=" SG CYS B1424 " - pdb=" SG CYS B1424 " distance=0.00 Simple disulfide: pdb=" SG CYS B1439 " - pdb=" SG CYS B1439 " distance=0.00 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 2.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.91 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: 13.13 Time building geometry restraints manager: 4.04 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: 24310 17.80 - 35.61: 1972 35.61 - 53.41: 381 53.41 - 71.21: 96 71.21 - 89.02: 60 Dihedral angle restraints: 26819 sinusoidal: 10911 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 26816 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: 2.02 - 2.60: 382 2.60 - 3.17: 33245 3.17 - 3.75: 65807 3.75 - 4.32: 91845 4.32 - 4.90: 153559 Nonbonded interactions: 344838 Sorted by model distance: nonbonded pdb=" SG CYS D 997 " pdb=" SG CYS D1006 " model vdw 2.024 3.760 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 ... (remaining 344833 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: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 48.360 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.450 ------------------------------------------------------------------------------- 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 43671 Z= 0.697 Angle : 1.758 11.751 59393 Z= 1.160 Chirality : 0.098 0.603 6740 Planarity : 0.011 0.055 7504 Dihedral : 14.224 89.018 16476 Min Nonbonded Distance : 2.024 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 aren 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 0.00661 ( 3) SS BOND : angle 0.39716 ( 21) 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 : 1.700 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: 0.5893 (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: 0.7446 (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: 0.8146 (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: 0.6668 (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: 0.6115 (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: 0.5851 (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: 0.7405 (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: 0.6668 (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: 0.7027 (mt0) REVERT: D 1248 TYR cc_start: 0.6887 (t80) cc_final: 0.6648 (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: 0.8221 time to fit residues: 1074.0794 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 : 1.530 ------------------------------------------------------------------------------- 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 C 957 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 D 992 ASN D1045 GLN D1056 ASN D1129 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.145018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121203 restraints weight = 58633.257| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.63 r_work: 0.3354 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43671 Z= 0.151 Angle : 0.582 8.493 59393 Z= 0.308 Chirality : 0.041 0.216 6740 Planarity : 0.004 0.045 7504 Dihedral : 9.085 88.869 7068 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.75 % Allowed : 9.57 % Favored : 87.68 % 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 aren not related in a simple way. whole: 0.80 (0.11), residues: 5432 helix: 1.71 (0.09), residues: 2972 sheet: -0.49 (0.23), residues: 396 loop : -1.01 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 159 TYR 0.017 0.002 TYR D 979 PHE 0.022 0.002 PHE A1083 TRP 0.011 0.001 TRP C 606 HIS 0.007 0.001 HIS A 514 Details of bonding type rmsd covalent geometry : bond 0.00315 (43668) covalent geometry : angle 0.58204 (59372) SS BOND : bond 0.00079 ( 3) SS BOND : angle 0.36072 ( 21) hydrogen bonds : bond 0.05005 ( 2299) hydrogen bonds : angle 4.39821 ( 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 805 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 688 time to evaluate : 1.839 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: 0.7670 (mtp85) REVERT: A 174 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7628 (mtm180) REVERT: A 352 GLN cc_start: 0.7850 (tt0) cc_final: 0.7279 (mt0) REVERT: A 365 GLN cc_start: 0.6756 (mt0) cc_final: 0.5851 (mp10) REVERT: A 410 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7352 (mtpt) REVERT: A 456 MET cc_start: 0.7250 (mtt) cc_final: 0.6998 (mtp) REVERT: A 594 ARG cc_start: 0.6861 (mtp180) cc_final: 0.6560 (mtp85) REVERT: A 618 HIS cc_start: 0.6839 (t70) cc_final: 0.6157 (m170) REVERT: A 663 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7341 (mttm) REVERT: A 666 GLU cc_start: 0.7525 (pt0) cc_final: 0.7213 (tt0) REVERT: A 731 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7631 (mmmt) REVERT: A 829 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6973 (mm-30) REVERT: A 833 SER cc_start: 0.7706 (t) cc_final: 0.7465 (p) REVERT: A 870 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7805 (mtp85) REVERT: A 875 MET cc_start: 0.8365 (ptt) cc_final: 0.7985 (ptp) REVERT: A 1005 GLU cc_start: 0.6514 (mt-10) cc_final: 0.5929 (tt0) REVERT: A 1050 ASP cc_start: 0.7828 (m-30) cc_final: 0.7554 (m-30) REVERT: A 1062 GLU cc_start: 0.8004 (tt0) cc_final: 0.7631 (tt0) REVERT: A 1064 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7886 (mttt) REVERT: A 1085 ARG cc_start: 0.5607 (ttt90) cc_final: 0.5206 (tpt170) REVERT: A 1105 THR cc_start: 0.6999 (m) cc_final: 0.6619 (p) REVERT: A 1122 ARG cc_start: 0.6871 (mtm-85) cc_final: 0.6518 (mtm-85) REVERT: A 1125 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6057 (pp20) REVERT: A 1145 GLN cc_start: 0.8446 (tt0) cc_final: 0.7867 (mt0) REVERT: A 1244 MET cc_start: 0.5995 (ptp) cc_final: 0.5751 (ptp) REVERT: A 1453 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8385 (mp) REVERT: B 78 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7690 (mtp85) REVERT: B 174 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7635 (mtm180) REVERT: B 352 GLN cc_start: 0.7840 (tt0) cc_final: 0.7337 (mt0) REVERT: B 365 GLN cc_start: 0.6776 (mt0) cc_final: 0.5875 (mp10) REVERT: B 410 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7360 (mtpt) REVERT: B 456 MET cc_start: 0.7265 (mtt) cc_final: 0.7008 (mtp) REVERT: B 473 ILE cc_start: 0.7939 (mt) cc_final: 0.7734 (mp) REVERT: B 594 ARG cc_start: 0.6850 (mtp180) cc_final: 0.6556 (mtp85) REVERT: B 618 HIS cc_start: 0.6806 (t70) cc_final: 0.6122 (m170) REVERT: B 663 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7326 (mttm) REVERT: B 731 LYS cc_start: 0.7864 (ttpt) cc_final: 0.7598 (mmmt) REVERT: B 829 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7015 (mm-30) REVERT: B 833 SER cc_start: 0.7650 (t) cc_final: 0.7424 (p) REVERT: B 870 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7811 (mtp85) REVERT: B 875 MET cc_start: 0.8370 (ptt) cc_final: 0.8000 (ptp) REVERT: B 1005 GLU cc_start: 0.6600 (mt-10) cc_final: 0.5967 (tt0) REVERT: B 1050 ASP cc_start: 0.7869 (m-30) cc_final: 0.7602 (m-30) REVERT: B 1062 GLU cc_start: 0.7988 (tt0) cc_final: 0.7627 (tt0) REVERT: B 1064 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7810 (mttt) REVERT: B 1085 ARG cc_start: 0.5627 (ttt90) cc_final: 0.5263 (tpt90) REVERT: B 1105 THR cc_start: 0.7017 (m) cc_final: 0.6628 (p) REVERT: B 1122 ARG cc_start: 0.6858 (mtm-85) cc_final: 0.6502 (mtm-85) REVERT: B 1125 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6046 (pp20) REVERT: B 1145 GLN cc_start: 0.8446 (tt0) cc_final: 0.7876 (mt0) REVERT: B 1389 GLU cc_start: 0.8225 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 1453 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 78 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7682 (mtp85) REVERT: C 174 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7642 (mtm180) REVERT: C 352 GLN cc_start: 0.7841 (tt0) cc_final: 0.7345 (mt0) REVERT: C 365 GLN cc_start: 0.6775 (mt0) cc_final: 0.5865 (mp10) REVERT: C 410 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7353 (mtpt) REVERT: C 456 MET cc_start: 0.7250 (mtt) cc_final: 0.6991 (mtp) REVERT: C 594 ARG cc_start: 0.6820 (mtp180) cc_final: 0.6529 (mtp85) REVERT: C 618 HIS cc_start: 0.6817 (t70) cc_final: 0.6130 (m170) REVERT: C 663 LYS cc_start: 0.7961 (mmmt) cc_final: 0.7335 (mttm) REVERT: C 731 LYS cc_start: 0.7865 (ttpt) cc_final: 0.7603 (mmmt) REVERT: C 829 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7001 (mm-30) REVERT: C 833 SER cc_start: 0.7653 (t) cc_final: 0.7436 (p) REVERT: C 870 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7808 (mtp85) REVERT: C 875 MET cc_start: 0.8374 (ptt) cc_final: 0.8000 (ptp) REVERT: C 1005 GLU cc_start: 0.6590 (mt-10) cc_final: 0.5954 (tt0) REVERT: C 1050 ASP cc_start: 0.7875 (m-30) cc_final: 0.7617 (m-30) REVERT: C 1062 GLU cc_start: 0.7980 (tt0) cc_final: 0.7607 (tt0) REVERT: C 1064 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7822 (mttt) REVERT: C 1085 ARG cc_start: 0.5610 (ttt90) cc_final: 0.5246 (tpt90) REVERT: C 1105 THR cc_start: 0.7011 (m) cc_final: 0.6626 (p) REVERT: C 1122 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6534 (mtm-85) REVERT: C 1125 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6048 (pp20) REVERT: C 1145 GLN cc_start: 0.8437 (tt0) cc_final: 0.7846 (mt0) REVERT: C 1389 GLU cc_start: 0.8208 (mt-10) cc_final: 0.8003 (mt-10) REVERT: C 1453 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8380 (mp) REVERT: D 78 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7683 (mtp85) REVERT: D 174 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7638 (mtm180) REVERT: D 352 GLN cc_start: 0.7835 (tt0) cc_final: 0.7338 (mt0) REVERT: D 365 GLN cc_start: 0.6785 (mt0) cc_final: 0.5879 (mp10) REVERT: D 410 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7372 (mtpt) REVERT: D 456 MET cc_start: 0.7278 (mtt) cc_final: 0.7028 (mtp) REVERT: D 473 ILE cc_start: 0.7938 (mt) cc_final: 0.7737 (mp) REVERT: D 594 ARG cc_start: 0.6855 (mtp180) cc_final: 0.6567 (mtp85) REVERT: D 618 HIS cc_start: 0.6809 (t70) cc_final: 0.6122 (m170) REVERT: D 663 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7330 (mttm) REVERT: D 731 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7591 (mmmt) REVERT: D 829 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7005 (mm-30) REVERT: D 833 SER cc_start: 0.7660 (t) cc_final: 0.7433 (p) REVERT: D 870 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7815 (mtp85) REVERT: D 875 MET cc_start: 0.8377 (ptt) cc_final: 0.8006 (ptp) REVERT: D 1005 GLU cc_start: 0.6420 (mt-10) cc_final: 0.5925 (tt0) REVERT: D 1050 ASP cc_start: 0.7848 (m-30) cc_final: 0.7573 (m-30) REVERT: D 1062 GLU cc_start: 0.7996 (tt0) cc_final: 0.7628 (tt0) REVERT: D 1064 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7815 (mttt) REVERT: D 1085 ARG cc_start: 0.5615 (ttt90) cc_final: 0.5252 (tpt90) REVERT: D 1105 THR cc_start: 0.6999 (m) cc_final: 0.6605 (p) REVERT: D 1122 ARG cc_start: 0.6871 (mtm-85) cc_final: 0.6515 (mtm-85) REVERT: D 1125 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6045 (pp20) REVERT: D 1145 GLN cc_start: 0.8434 (tt0) cc_final: 0.7855 (mt0) REVERT: D 1453 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8396 (mp) outliers start: 117 outliers final: 27 residues processed: 776 average time/residue: 0.9046 time to fit residues: 839.3650 Evaluate side-chains 551 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 508 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 410 LYS 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 323 LEU Chi-restraints excluded: chain B residue 410 LYS 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 323 LEU Chi-restraints excluded: chain C residue 410 LYS 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 323 LEU Chi-restraints excluded: chain D residue 410 LYS 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: 2.9990 chunk 161 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 399 optimal weight: 2.9990 chunk 494 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 chunk 522 optimal weight: 1.9990 chunk 355 optimal weight: 0.9990 chunk 417 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN A 514 HIS A 813 HIS A 893 GLN A 957 GLN A 992 ASN A1255 HIS A1282 ASN A1456 GLN A1463 HIS B 284 GLN B 514 HIS B 813 HIS B 893 GLN B 957 GLN B 992 ASN B1255 HIS B1282 ASN B1456 GLN B1463 HIS C 284 GLN C 514 HIS C 813 HIS C 893 GLN C 992 ASN C1255 HIS C1282 ASN C1456 GLN C1463 HIS D 284 GLN D 514 HIS D 813 HIS D 893 GLN D1255 HIS D1282 ASN D1456 GLN D1463 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110354 restraints weight = 58850.391| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.53 r_work: 0.3183 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43671 Z= 0.233 Angle : 0.662 9.481 59393 Z= 0.348 Chirality : 0.045 0.178 6740 Planarity : 0.005 0.049 7504 Dihedral : 9.015 88.436 7056 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.46 % Allowed : 11.81 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.11), residues: 5432 helix: 1.67 (0.09), residues: 2988 sheet: -0.63 (0.23), residues: 384 loop : -0.82 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1008 TYR 0.022 0.002 TYR D 917 PHE 0.022 0.002 PHE A 798 TRP 0.014 0.002 TRP B1216 HIS 0.010 0.002 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.00523 (43668) covalent geometry : angle 0.66215 (59372) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.36729 ( 21) hydrogen bonds : bond 0.05155 ( 2299) hydrogen bonds : angle 4.29956 ( 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 702 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 555 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6150 (ppp) cc_final: 0.5696 (ppp) REVERT: A 139 ASP cc_start: 0.7645 (m-30) cc_final: 0.7380 (m-30) REVERT: A 174 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7676 (mtp180) REVERT: A 352 GLN cc_start: 0.7885 (tt0) cc_final: 0.7589 (mt0) REVERT: A 365 GLN cc_start: 0.7161 (mt0) cc_final: 0.6249 (mp10) REVERT: A 456 MET cc_start: 0.7693 (mtt) cc_final: 0.7489 (mtp) REVERT: A 506 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7026 (ttt-90) REVERT: A 592 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6335 (tp-100) REVERT: A 594 ARG cc_start: 0.7058 (mtp180) cc_final: 0.6661 (mtp85) REVERT: A 618 HIS cc_start: 0.7201 (t70) cc_final: 0.6539 (m170) REVERT: A 638 GLU cc_start: 0.7801 (pt0) cc_final: 0.7591 (mm-30) REVERT: A 663 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7573 (mttt) REVERT: A 731 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7611 (mttp) REVERT: A 829 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7159 (mm-30) REVERT: A 875 MET cc_start: 0.8663 (ptt) cc_final: 0.8228 (ptt) REVERT: A 996 ASN cc_start: 0.8291 (m-40) cc_final: 0.7912 (m-40) REVERT: A 1062 GLU cc_start: 0.8030 (tt0) cc_final: 0.7738 (tt0) REVERT: A 1064 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7770 (mttt) REVERT: A 1065 ASP cc_start: 0.7612 (p0) cc_final: 0.7379 (p0) REVERT: A 1085 ARG cc_start: 0.5697 (ttt90) cc_final: 0.5221 (tpt90) REVERT: A 1105 THR cc_start: 0.6998 (m) cc_final: 0.6493 (p) REVERT: A 1127 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7145 (pt0) REVERT: A 1145 GLN cc_start: 0.8583 (tt0) cc_final: 0.8019 (mt0) REVERT: A 1164 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8521 (mt) REVERT: A 1204 VAL cc_start: 0.8323 (t) cc_final: 0.8104 (p) REVERT: A 1453 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 70 MET cc_start: 0.6092 (ppp) cc_final: 0.5660 (ppp) REVERT: B 139 ASP cc_start: 0.7664 (m-30) cc_final: 0.7397 (m-30) REVERT: B 174 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7649 (mtp180) REVERT: B 352 GLN cc_start: 0.7886 (tt0) cc_final: 0.7590 (mt0) REVERT: B 365 GLN cc_start: 0.7128 (mt0) cc_final: 0.6234 (mp10) REVERT: B 456 MET cc_start: 0.7659 (mtt) cc_final: 0.7445 (mtp) REVERT: B 473 ILE cc_start: 0.8056 (mt) cc_final: 0.7844 (mp) REVERT: B 506 ARG cc_start: 0.7488 (mtp85) cc_final: 0.7041 (ttt-90) REVERT: B 592 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6335 (tp-100) REVERT: B 594 ARG cc_start: 0.7019 (mtp180) cc_final: 0.6626 (mtp85) REVERT: B 618 HIS cc_start: 0.7169 (t70) cc_final: 0.6514 (m170) REVERT: B 638 GLU cc_start: 0.7820 (pt0) cc_final: 0.7598 (mm-30) REVERT: B 663 LYS cc_start: 0.8270 (mmmt) cc_final: 0.8036 (mptt) REVERT: B 731 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7605 (mttp) REVERT: B 829 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7210 (mm-30) REVERT: B 875 MET cc_start: 0.8631 (ptt) cc_final: 0.8187 (ptt) REVERT: B 996 ASN cc_start: 0.8297 (m-40) cc_final: 0.7926 (m-40) REVERT: B 1062 GLU cc_start: 0.8099 (tt0) cc_final: 0.7827 (tt0) REVERT: B 1064 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7773 (mttt) REVERT: B 1065 ASP cc_start: 0.7618 (p0) cc_final: 0.7395 (p0) REVERT: B 1085 ARG cc_start: 0.5734 (ttt90) cc_final: 0.5159 (tpt170) REVERT: B 1105 THR cc_start: 0.6977 (m) cc_final: 0.6464 (p) REVERT: B 1127 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7138 (pt0) REVERT: B 1145 GLN cc_start: 0.8599 (tt0) cc_final: 0.8036 (mt0) REVERT: B 1164 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8522 (mt) REVERT: B 1204 VAL cc_start: 0.8320 (t) cc_final: 0.8096 (p) REVERT: C 70 MET cc_start: 0.6143 (ppp) cc_final: 0.5689 (ppp) REVERT: C 139 ASP cc_start: 0.7658 (m-30) cc_final: 0.7390 (m-30) REVERT: C 174 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7655 (mtp180) REVERT: C 352 GLN cc_start: 0.7899 (tt0) cc_final: 0.7598 (mt0) REVERT: C 365 GLN cc_start: 0.7134 (mt0) cc_final: 0.6234 (mp10) REVERT: C 506 ARG cc_start: 0.7483 (mtp85) cc_final: 0.7033 (ttt-90) REVERT: C 592 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6278 (tp-100) REVERT: C 594 ARG cc_start: 0.7052 (mtp180) cc_final: 0.6654 (mtp85) REVERT: C 618 HIS cc_start: 0.7116 (t70) cc_final: 0.6464 (m170) REVERT: C 638 GLU cc_start: 0.7789 (pt0) cc_final: 0.7587 (mm-30) REVERT: C 663 LYS cc_start: 0.8241 (mmmt) cc_final: 0.7619 (mttt) REVERT: C 731 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7608 (mttp) REVERT: C 829 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7206 (mm-30) REVERT: C 875 MET cc_start: 0.8631 (ptt) cc_final: 0.8183 (ptt) REVERT: C 996 ASN cc_start: 0.8303 (m-40) cc_final: 0.7927 (m-40) REVERT: C 1062 GLU cc_start: 0.8073 (tt0) cc_final: 0.7802 (tt0) REVERT: C 1064 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7769 (mttt) REVERT: C 1065 ASP cc_start: 0.7602 (p0) cc_final: 0.7376 (p0) REVERT: C 1085 ARG cc_start: 0.5737 (ttt90) cc_final: 0.5211 (tpt90) REVERT: C 1105 THR cc_start: 0.7001 (m) cc_final: 0.6496 (p) REVERT: C 1127 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7143 (pt0) REVERT: C 1145 GLN cc_start: 0.8563 (tt0) cc_final: 0.8014 (mt0) REVERT: C 1204 VAL cc_start: 0.8332 (t) cc_final: 0.8107 (p) REVERT: C 1453 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8496 (mp) REVERT: D 70 MET cc_start: 0.6092 (ppp) cc_final: 0.5661 (ppp) REVERT: D 139 ASP cc_start: 0.7648 (m-30) cc_final: 0.7383 (m-30) REVERT: D 174 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7675 (mtp180) REVERT: D 352 GLN cc_start: 0.7909 (tt0) cc_final: 0.7599 (mt0) REVERT: D 365 GLN cc_start: 0.7133 (mt0) cc_final: 0.6228 (mp10) REVERT: D 456 MET cc_start: 0.7650 (mtt) cc_final: 0.7439 (mtp) REVERT: D 473 ILE cc_start: 0.8062 (mt) cc_final: 0.7857 (mp) REVERT: D 506 ARG cc_start: 0.7490 (mtp85) cc_final: 0.7042 (ttt-90) REVERT: D 592 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6314 (tp40) REVERT: D 594 ARG cc_start: 0.7022 (mtp180) cc_final: 0.6623 (mtp85) REVERT: D 618 HIS cc_start: 0.7176 (t70) cc_final: 0.6530 (m170) REVERT: D 638 GLU cc_start: 0.7804 (pt0) cc_final: 0.7587 (mm-30) REVERT: D 663 LYS cc_start: 0.8261 (mmmt) cc_final: 0.8026 (mptt) REVERT: D 731 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7613 (mttp) REVERT: D 829 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7197 (mm-30) REVERT: D 875 MET cc_start: 0.8630 (ptt) cc_final: 0.8184 (ptt) REVERT: D 1062 GLU cc_start: 0.8070 (tt0) cc_final: 0.7802 (tt0) REVERT: D 1064 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7793 (mttt) REVERT: D 1065 ASP cc_start: 0.7632 (p0) cc_final: 0.7408 (p0) REVERT: D 1085 ARG cc_start: 0.5723 (ttt90) cc_final: 0.5203 (tpt90) REVERT: D 1105 THR cc_start: 0.6967 (m) cc_final: 0.6457 (p) REVERT: D 1127 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7160 (pt0) REVERT: D 1145 GLN cc_start: 0.8566 (tt0) cc_final: 0.8011 (mt0) REVERT: D 1164 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8507 (mt) REVERT: D 1204 VAL cc_start: 0.8321 (t) cc_final: 0.8098 (p) REVERT: D 1453 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8497 (mp) outliers start: 147 outliers final: 61 residues processed: 667 average time/residue: 0.8896 time to fit residues: 705.8882 Evaluate side-chains 536 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 461 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 181 THR 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 479 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 634 SER 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 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 181 THR Chi-restraints excluded: chain B residue 248 THR 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 1154 LEU Chi-restraints excluded: chain B residue 1164 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 C residue 78 ARG Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 248 THR 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 622 ILE Chi-restraints excluded: chain C residue 634 SER 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 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 181 THR Chi-restraints excluded: chain D residue 248 THR 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 622 ILE 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 1154 LEU Chi-restraints excluded: chain D residue 1164 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 178 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 326 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 140 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 395 optimal weight: 0.8980 chunk 234 optimal weight: 0.5980 chunk 272 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 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 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 = 0.3648 r_free = 0.3648 target = 0.135837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112136 restraints weight = 58433.477| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.52 r_work: 0.3200 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43671 Z= 0.125 Angle : 0.521 8.076 59393 Z= 0.273 Chirality : 0.039 0.175 6740 Planarity : 0.004 0.047 7504 Dihedral : 8.493 86.046 7056 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 2.85 % Allowed : 13.83 % Favored : 83.33 % 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 aren not related in a simple way. whole: 1.18 (0.11), residues: 5432 helix: 1.93 (0.09), residues: 2992 sheet: -0.76 (0.24), residues: 372 loop : -0.63 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 159 TYR 0.014 0.001 TYR D 799 PHE 0.024 0.001 PHE D1068 TRP 0.010 0.001 TRP C 726 HIS 0.010 0.001 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.00277 (43668) covalent geometry : angle 0.52079 (59372) SS BOND : bond 0.00005 ( 3) SS BOND : angle 0.23406 ( 21) hydrogen bonds : bond 0.04161 ( 2299) hydrogen bonds : angle 4.00157 ( 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 606 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 485 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7587 (m-30) cc_final: 0.7317 (m-30) REVERT: A 240 HIS cc_start: 0.6700 (m-70) cc_final: 0.6392 (m170) REVERT: A 352 GLN cc_start: 0.7822 (tt0) cc_final: 0.7519 (mt0) REVERT: A 365 GLN cc_start: 0.7072 (mt0) cc_final: 0.6182 (mp10) REVERT: A 502 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7107 (pt0) REVERT: A 506 ARG cc_start: 0.7459 (mtp85) cc_final: 0.6962 (ttt-90) REVERT: A 594 ARG cc_start: 0.7006 (mtp180) cc_final: 0.6600 (mtp85) REVERT: A 618 HIS cc_start: 0.7154 (t70) cc_final: 0.6591 (m170) REVERT: A 663 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7660 (mttt) REVERT: A 731 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7674 (mptt) REVERT: A 829 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7095 (mm-30) REVERT: A 870 ARG cc_start: 0.8360 (mtt180) cc_final: 0.8089 (mtt90) REVERT: A 875 MET cc_start: 0.8603 (ptt) cc_final: 0.8139 (ptp) REVERT: A 996 ASN cc_start: 0.8284 (m-40) cc_final: 0.7891 (m-40) REVERT: A 1062 GLU cc_start: 0.8088 (tt0) cc_final: 0.7803 (tt0) REVERT: A 1064 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7697 (mttt) REVERT: A 1085 ARG cc_start: 0.5800 (ttt90) cc_final: 0.5187 (tpt170) REVERT: A 1105 THR cc_start: 0.6883 (m) cc_final: 0.6397 (p) REVERT: A 1145 GLN cc_start: 0.8507 (tt0) cc_final: 0.8038 (mt0) REVERT: A 1164 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8553 (mt) REVERT: B 139 ASP cc_start: 0.7650 (m-30) cc_final: 0.7396 (m-30) REVERT: B 240 HIS cc_start: 0.6744 (m-70) cc_final: 0.6476 (m170) REVERT: B 352 GLN cc_start: 0.7829 (tt0) cc_final: 0.7523 (mt0) REVERT: B 365 GLN cc_start: 0.7035 (mt0) cc_final: 0.6136 (mp10) REVERT: B 502 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: B 506 ARG cc_start: 0.7427 (mtp85) cc_final: 0.6933 (ttt-90) REVERT: B 594 ARG cc_start: 0.6986 (mtp180) cc_final: 0.6592 (mtp85) REVERT: B 596 THR cc_start: 0.7795 (m) cc_final: 0.7591 (t) REVERT: B 618 HIS cc_start: 0.7130 (t70) cc_final: 0.6510 (m170) REVERT: B 663 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7698 (mmtp) REVERT: B 731 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7637 (mttp) REVERT: B 829 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7157 (mm-30) REVERT: B 870 ARG cc_start: 0.8341 (mtt180) cc_final: 0.8071 (mtt90) REVERT: B 875 MET cc_start: 0.8599 (ptt) cc_final: 0.8135 (ptp) REVERT: B 996 ASN cc_start: 0.8313 (m-40) cc_final: 0.7924 (m-40) REVERT: B 1062 GLU cc_start: 0.8090 (tt0) cc_final: 0.7805 (tt0) REVERT: B 1064 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7716 (mttt) REVERT: B 1085 ARG cc_start: 0.5801 (ttt90) cc_final: 0.5207 (tpt170) REVERT: B 1105 THR cc_start: 0.6897 (m) cc_final: 0.6432 (p) REVERT: B 1126 ARG cc_start: 0.7279 (ttm110) cc_final: 0.7017 (mtp-110) REVERT: B 1145 GLN cc_start: 0.8500 (tt0) cc_final: 0.8007 (mt0) REVERT: B 1164 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8544 (mt) REVERT: B 1204 VAL cc_start: 0.8212 (t) cc_final: 0.8007 (p) REVERT: C 139 ASP cc_start: 0.7579 (m-30) cc_final: 0.7317 (m-30) REVERT: C 240 HIS cc_start: 0.6667 (m-70) cc_final: 0.6370 (m170) REVERT: C 352 GLN cc_start: 0.7821 (tt0) cc_final: 0.7531 (mt0) REVERT: C 365 GLN cc_start: 0.7083 (mt0) cc_final: 0.6191 (mp10) REVERT: C 506 ARG cc_start: 0.7474 (mtp85) cc_final: 0.6974 (ttt-90) REVERT: C 594 ARG cc_start: 0.7000 (mtp180) cc_final: 0.6668 (mtp85) REVERT: C 618 HIS cc_start: 0.7161 (t70) cc_final: 0.6584 (m170) REVERT: C 663 LYS cc_start: 0.8291 (mmmt) cc_final: 0.7673 (mttt) REVERT: C 731 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7644 (mttp) REVERT: C 829 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7108 (mm-30) REVERT: C 870 ARG cc_start: 0.8349 (mtt180) cc_final: 0.8074 (mtt90) REVERT: C 875 MET cc_start: 0.8610 (ptt) cc_final: 0.8155 (ptp) REVERT: C 996 ASN cc_start: 0.8290 (m-40) cc_final: 0.7896 (m-40) REVERT: C 1062 GLU cc_start: 0.8086 (tt0) cc_final: 0.7798 (tt0) REVERT: C 1064 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7705 (mttt) REVERT: C 1085 ARG cc_start: 0.5792 (ttt90) cc_final: 0.5194 (tpt170) REVERT: C 1105 THR cc_start: 0.6900 (m) cc_final: 0.6421 (p) REVERT: C 1145 GLN cc_start: 0.8511 (tt0) cc_final: 0.8046 (mt0) REVERT: C 1204 VAL cc_start: 0.8237 (t) cc_final: 0.8031 (p) REVERT: D 139 ASP cc_start: 0.7622 (m-30) cc_final: 0.7368 (m-30) REVERT: D 240 HIS cc_start: 0.6717 (m-70) cc_final: 0.6442 (m170) REVERT: D 352 GLN cc_start: 0.7857 (tt0) cc_final: 0.7516 (mt0) REVERT: D 365 GLN cc_start: 0.7076 (mt0) cc_final: 0.6165 (mp10) REVERT: D 502 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7124 (pt0) REVERT: D 506 ARG cc_start: 0.7425 (mtp85) cc_final: 0.6929 (ttt-90) REVERT: D 594 ARG cc_start: 0.7004 (mtp180) cc_final: 0.6613 (mtp85) REVERT: D 596 THR cc_start: 0.7833 (m) cc_final: 0.7613 (t) REVERT: D 618 HIS cc_start: 0.7144 (t70) cc_final: 0.6571 (m170) REVERT: D 663 LYS cc_start: 0.8284 (mmmt) cc_final: 0.7698 (mmtp) REVERT: D 731 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7652 (mttp) REVERT: D 829 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7164 (mm-30) REVERT: D 870 ARG cc_start: 0.8336 (mtt180) cc_final: 0.8067 (mtt90) REVERT: D 875 MET cc_start: 0.8601 (ptt) cc_final: 0.8139 (ptp) REVERT: D 996 ASN cc_start: 0.8310 (m-40) cc_final: 0.7924 (m-40) REVERT: D 1062 GLU cc_start: 0.8099 (tt0) cc_final: 0.7813 (tt0) REVERT: D 1064 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7722 (mttt) REVERT: D 1085 ARG cc_start: 0.5787 (ttt90) cc_final: 0.5176 (tpt170) REVERT: D 1105 THR cc_start: 0.6888 (m) cc_final: 0.6417 (p) REVERT: D 1126 ARG cc_start: 0.7274 (ttm110) cc_final: 0.6996 (mtp-110) REVERT: D 1145 GLN cc_start: 0.8466 (tt0) cc_final: 0.7989 (mt0) REVERT: D 1164 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8548 (mt) outliers start: 121 outliers final: 53 residues processed: 578 average time/residue: 0.8878 time to fit residues: 616.6276 Evaluate side-chains 515 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 452 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 323 LEU 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 831 THR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 248 THR 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 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 1154 LEU Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 248 THR 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 574 VAL 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 1039 ASP Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 248 THR 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 733 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 1039 ASP Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1164 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 516 optimal weight: 0.0270 chunk 7 optimal weight: 2.9990 chunk 505 optimal weight: 4.9990 chunk 394 optimal weight: 0.9980 chunk 274 optimal weight: 3.9990 chunk 477 optimal weight: 9.9990 chunk 403 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.7842 ------------------------------------------------------------------------------- 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110739 restraints weight = 58783.907| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.52 r_work: 0.3175 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 43671 Z= 0.194 Angle : 0.590 7.967 59393 Z= 0.309 Chirality : 0.042 0.186 6740 Planarity : 0.005 0.052 7504 Dihedral : 8.657 86.406 7056 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.16 % Favored : 95.77 % Rotamer: Outliers : 3.36 % Allowed : 14.09 % Favored : 82.55 % 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 aren not related in a simple way. whole: 1.04 (0.11), residues: 5432 helix: 1.80 (0.09), residues: 3000 sheet: -0.83 (0.24), residues: 388 loop : -0.65 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 341 TYR 0.021 0.002 TYR C 917 PHE 0.021 0.002 PHE D 604 TRP 0.012 0.002 TRP D1216 HIS 0.009 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00447 (43668) covalent geometry : angle 0.59018 (59372) SS BOND : bond 0.00025 ( 3) SS BOND : angle 0.26315 ( 21) hydrogen bonds : bond 0.04669 ( 2299) hydrogen bonds : angle 4.10376 ( 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 609 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 466 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.5806 (ttm110) REVERT: A 70 MET cc_start: 0.6193 (ppp) cc_final: 0.5673 (ppp) REVERT: A 77 LYS cc_start: 0.7719 (mtmt) cc_final: 0.7457 (mmtt) REVERT: A 139 ASP cc_start: 0.7597 (m-30) cc_final: 0.7357 (m-30) REVERT: A 240 HIS cc_start: 0.6914 (m-70) cc_final: 0.6692 (m-70) REVERT: A 272 ILE cc_start: 0.8292 (mm) cc_final: 0.7996 (mt) REVERT: A 352 GLN cc_start: 0.7859 (tt0) cc_final: 0.7562 (mt0) REVERT: A 365 GLN cc_start: 0.7210 (mt0) cc_final: 0.6261 (mp10) REVERT: A 506 ARG cc_start: 0.7523 (mtp85) cc_final: 0.7011 (ttt-90) REVERT: A 577 ASP cc_start: 0.7197 (t0) cc_final: 0.6785 (t70) REVERT: A 594 ARG cc_start: 0.6962 (mtp180) cc_final: 0.6550 (mtp85) REVERT: A 618 HIS cc_start: 0.7260 (t70) cc_final: 0.6549 (m170) REVERT: A 663 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7585 (mttt) REVERT: A 731 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7689 (mttp) REVERT: A 829 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7148 (mm-30) REVERT: A 875 MET cc_start: 0.8670 (ptt) cc_final: 0.8104 (ptp) REVERT: A 930 MET cc_start: 0.8570 (mtt) cc_final: 0.8309 (mtt) REVERT: A 996 ASN cc_start: 0.8243 (m-40) cc_final: 0.7876 (m-40) REVERT: A 1005 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6899 (mt-10) REVERT: A 1062 GLU cc_start: 0.8050 (tt0) cc_final: 0.7726 (tt0) REVERT: A 1064 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7678 (mttt) REVERT: A 1085 ARG cc_start: 0.5809 (ttt90) cc_final: 0.5186 (tpt170) REVERT: A 1105 THR cc_start: 0.6870 (m) cc_final: 0.6372 (p) REVERT: A 1126 ARG cc_start: 0.7268 (ttm110) cc_final: 0.7004 (mtp-110) REVERT: A 1145 GLN cc_start: 0.8455 (tt0) cc_final: 0.7983 (mt0) REVERT: A 1150 MET cc_start: 0.8868 (tpp) cc_final: 0.8221 (mtp) REVERT: A 1164 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8584 (mt) REVERT: B 70 MET cc_start: 0.6192 (ppp) cc_final: 0.5668 (ppp) REVERT: B 77 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7518 (mmtt) REVERT: B 139 ASP cc_start: 0.7658 (m-30) cc_final: 0.7424 (m-30) REVERT: B 240 HIS cc_start: 0.6975 (m-70) cc_final: 0.6771 (m-70) REVERT: B 272 ILE cc_start: 0.8258 (mm) cc_final: 0.8003 (mt) REVERT: B 352 GLN cc_start: 0.7935 (tt0) cc_final: 0.7594 (mt0) REVERT: B 365 GLN cc_start: 0.7200 (mt0) cc_final: 0.6234 (mp10) REVERT: B 506 ARG cc_start: 0.7508 (mtp85) cc_final: 0.6997 (ttt-90) REVERT: B 592 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6225 (tp40) REVERT: B 594 ARG cc_start: 0.6961 (mtp180) cc_final: 0.6541 (mtp85) REVERT: B 618 HIS cc_start: 0.7290 (t70) cc_final: 0.6536 (m170) REVERT: B 663 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7642 (mmtp) REVERT: B 731 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7619 (mttp) REVERT: B 829 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7187 (mm-30) REVERT: B 875 MET cc_start: 0.8659 (ptt) cc_final: 0.8090 (ptp) REVERT: B 996 ASN cc_start: 0.8269 (m-40) cc_final: 0.7912 (m-40) REVERT: B 1005 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6857 (mt-10) REVERT: B 1062 GLU cc_start: 0.8073 (tt0) cc_final: 0.7749 (tt0) REVERT: B 1064 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7660 (mttt) REVERT: B 1085 ARG cc_start: 0.5757 (ttt90) cc_final: 0.5137 (tpt170) REVERT: B 1105 THR cc_start: 0.6859 (m) cc_final: 0.6373 (p) REVERT: B 1126 ARG cc_start: 0.7233 (ttm110) cc_final: 0.6973 (mtp-110) REVERT: B 1145 GLN cc_start: 0.8510 (tt0) cc_final: 0.8008 (mt0) REVERT: B 1150 MET cc_start: 0.8397 (mtp) cc_final: 0.8170 (mtp) REVERT: B 1164 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8581 (mt) REVERT: B 1204 VAL cc_start: 0.8262 (t) cc_final: 0.8052 (p) REVERT: B 1244 MET cc_start: 0.6094 (ptt) cc_final: 0.5200 (tpt) REVERT: C 69 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.5817 (ttm110) REVERT: C 70 MET cc_start: 0.6153 (ppp) cc_final: 0.5588 (ppp) REVERT: C 77 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7476 (mmtt) REVERT: C 139 ASP cc_start: 0.7565 (m-30) cc_final: 0.7323 (m-30) REVERT: C 272 ILE cc_start: 0.8257 (mm) cc_final: 0.8008 (mt) REVERT: C 352 GLN cc_start: 0.7888 (tt0) cc_final: 0.7577 (mt0) REVERT: C 365 GLN cc_start: 0.7228 (mt0) cc_final: 0.6274 (mp10) REVERT: C 506 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7016 (ttt-90) REVERT: C 577 ASP cc_start: 0.7193 (t0) cc_final: 0.6783 (t70) REVERT: C 592 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.6035 (tp40) REVERT: C 594 ARG cc_start: 0.6971 (mtp180) cc_final: 0.6565 (mtp85) REVERT: C 618 HIS cc_start: 0.7257 (t70) cc_final: 0.6528 (m170) REVERT: C 663 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7579 (mttt) REVERT: C 731 LYS cc_start: 0.7959 (ttpt) cc_final: 0.7642 (mttp) REVERT: C 829 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7155 (mm-30) REVERT: C 875 MET cc_start: 0.8678 (ptt) cc_final: 0.8112 (ptp) REVERT: C 996 ASN cc_start: 0.8254 (m-40) cc_final: 0.7897 (m-40) REVERT: C 1062 GLU cc_start: 0.8062 (tt0) cc_final: 0.7742 (tt0) REVERT: C 1064 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7699 (mttt) REVERT: C 1085 ARG cc_start: 0.5819 (ttt90) cc_final: 0.5191 (tpt170) REVERT: C 1105 THR cc_start: 0.6874 (m) cc_final: 0.6377 (p) REVERT: C 1126 ARG cc_start: 0.7253 (ttm110) cc_final: 0.6988 (mtp-110) REVERT: C 1145 GLN cc_start: 0.8500 (tt0) cc_final: 0.8009 (mt0) REVERT: C 1204 VAL cc_start: 0.8288 (t) cc_final: 0.8067 (p) REVERT: C 1244 MET cc_start: 0.5995 (ptt) cc_final: 0.5107 (tpt) REVERT: D 70 MET cc_start: 0.6202 (ppp) cc_final: 0.5668 (ppp) REVERT: D 77 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7509 (mmtt) REVERT: D 139 ASP cc_start: 0.7652 (m-30) cc_final: 0.7417 (m-30) REVERT: D 272 ILE cc_start: 0.8245 (mm) cc_final: 0.7987 (mt) REVERT: D 352 GLN cc_start: 0.7933 (tt0) cc_final: 0.7586 (mt0) REVERT: D 365 GLN cc_start: 0.7214 (mt0) cc_final: 0.6248 (mp10) REVERT: D 506 ARG cc_start: 0.7510 (mtp85) cc_final: 0.6991 (ttt-90) REVERT: D 577 ASP cc_start: 0.7286 (t0) cc_final: 0.6845 (t70) REVERT: D 592 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6222 (tp40) REVERT: D 594 ARG cc_start: 0.6954 (mtp180) cc_final: 0.6528 (mtp85) REVERT: D 618 HIS cc_start: 0.7280 (t70) cc_final: 0.6540 (m170) REVERT: D 663 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7652 (mmtp) REVERT: D 731 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7636 (mttp) REVERT: D 829 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7198 (mm-30) REVERT: D 875 MET cc_start: 0.8669 (ptt) cc_final: 0.8099 (ptp) REVERT: D 996 ASN cc_start: 0.8370 (m-40) cc_final: 0.7980 (m-40) REVERT: D 1062 GLU cc_start: 0.8075 (tt0) cc_final: 0.7752 (tt0) REVERT: D 1064 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7684 (mttt) REVERT: D 1085 ARG cc_start: 0.5815 (ttt90) cc_final: 0.5187 (tpt170) REVERT: D 1105 THR cc_start: 0.6862 (m) cc_final: 0.6370 (p) REVERT: D 1126 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6960 (mtp-110) REVERT: D 1145 GLN cc_start: 0.8491 (tt0) cc_final: 0.7992 (mt0) REVERT: D 1164 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8576 (mt) REVERT: D 1244 MET cc_start: 0.6117 (ptt) cc_final: 0.5197 (tpt) REVERT: D 1394 MET cc_start: 0.7825 (mtt) cc_final: 0.7623 (mtt) outliers start: 143 outliers final: 69 residues processed: 572 average time/residue: 0.9215 time to fit residues: 630.0164 Evaluate side-chains 526 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 443 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG 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 447 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 561 ASP 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 1005 GLU 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 1277 VAL 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 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 1005 GLU Chi-restraints excluded: chain B residue 1064 LYS 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 1277 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 69 ARG 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 447 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 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 1164 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1277 VAL 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 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 1154 LEU Chi-restraints excluded: chain D residue 1164 LEU Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1277 VAL 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: 1.9990 chunk 141 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 427 optimal weight: 0.2980 chunk 258 optimal weight: 2.9990 chunk 538 optimal weight: 0.8980 chunk 114 optimal weight: 0.0060 chunk 333 optimal weight: 0.6980 chunk 403 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 514 HIS A 893 GLN A1463 HIS B 514 HIS B 893 GLN B1080 HIS B1463 HIS C 448 ASN C 514 HIS C 893 GLN C1463 HIS D 448 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 = 0.3650 r_free = 0.3650 target = 0.136203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113737 restraints weight = 58916.786| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.57 r_work: 0.3180 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 43671 Z= 0.106 Angle : 0.489 8.133 59393 Z= 0.256 Chirality : 0.038 0.168 6740 Planarity : 0.004 0.047 7504 Dihedral : 8.112 83.890 7056 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 2.30 % Allowed : 15.59 % Favored : 82.10 % 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 aren not related in a simple way. whole: 1.32 (0.12), residues: 5432 helix: 2.04 (0.09), residues: 3008 sheet: -1.00 (0.24), residues: 376 loop : -0.49 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 341 TYR 0.011 0.001 TYR C 799 PHE 0.017 0.001 PHE C1068 TRP 0.011 0.001 TRP B1124 HIS 0.007 0.001 HIS B1463 Details of bonding type rmsd covalent geometry : bond 0.00230 (43668) covalent geometry : angle 0.48907 (59372) SS BOND : bond 0.00062 ( 3) SS BOND : angle 0.28094 ( 21) hydrogen bonds : bond 0.03784 ( 2299) hydrogen bonds : angle 3.86717 ( 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 567 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 469 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7619 (m-30) cc_final: 0.7400 (m-30) REVERT: A 240 HIS cc_start: 0.6966 (m-70) cc_final: 0.6648 (m170) REVERT: A 272 ILE cc_start: 0.8289 (mm) cc_final: 0.8031 (mt) REVERT: A 352 GLN cc_start: 0.7861 (tt0) cc_final: 0.7570 (mt0) REVERT: A 506 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7007 (ttt-90) REVERT: A 594 ARG cc_start: 0.6948 (mtp180) cc_final: 0.6547 (mtp85) REVERT: A 618 HIS cc_start: 0.7291 (t70) cc_final: 0.6679 (m170) REVERT: A 663 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7646 (mttt) REVERT: A 731 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7805 (mttp) REVERT: A 829 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7236 (mm-30) REVERT: A 875 MET cc_start: 0.8608 (ptt) cc_final: 0.8142 (ptp) REVERT: A 996 ASN cc_start: 0.8391 (m-40) cc_final: 0.8064 (m-40) REVERT: A 1062 GLU cc_start: 0.8225 (tt0) cc_final: 0.7943 (tt0) REVERT: A 1064 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7620 (mttt) REVERT: A 1085 ARG cc_start: 0.5902 (ttt90) cc_final: 0.5175 (tpt170) REVERT: A 1105 THR cc_start: 0.6895 (m) cc_final: 0.6441 (p) REVERT: A 1145 GLN cc_start: 0.8470 (tt0) cc_final: 0.8092 (mt0) REVERT: A 1150 MET cc_start: 0.8731 (tpp) cc_final: 0.8352 (mtp) REVERT: A 1244 MET cc_start: 0.5839 (ptp) cc_final: 0.5188 (mmt) REVERT: A 1480 ARG cc_start: 0.7653 (ttp80) cc_final: 0.7135 (ttp80) REVERT: B 77 LYS cc_start: 0.7659 (mtmt) cc_final: 0.7400 (mmtt) REVERT: B 139 ASP cc_start: 0.7655 (m-30) cc_final: 0.7430 (m-30) REVERT: B 240 HIS cc_start: 0.6911 (m-70) cc_final: 0.6603 (m170) REVERT: B 352 GLN cc_start: 0.7845 (tt0) cc_final: 0.7568 (mt0) REVERT: B 436 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5860 (mmmm) REVERT: B 506 ARG cc_start: 0.7517 (mtp85) cc_final: 0.7010 (ttt-90) REVERT: B 594 ARG cc_start: 0.6922 (mtp180) cc_final: 0.6516 (mtp85) REVERT: B 618 HIS cc_start: 0.7256 (t70) cc_final: 0.6671 (m170) REVERT: B 663 LYS cc_start: 0.8278 (mmmt) cc_final: 0.7697 (mmtp) REVERT: B 731 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7690 (mptt) REVERT: B 829 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7243 (mm-30) REVERT: B 875 MET cc_start: 0.8604 (ptt) cc_final: 0.8144 (ptp) REVERT: B 996 ASN cc_start: 0.8385 (m-40) cc_final: 0.8040 (m-40) REVERT: B 1062 GLU cc_start: 0.8261 (tt0) cc_final: 0.7905 (tt0) REVERT: B 1064 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7667 (mttt) REVERT: B 1085 ARG cc_start: 0.5828 (ttt90) cc_final: 0.5116 (tpt170) REVERT: B 1105 THR cc_start: 0.6891 (m) cc_final: 0.6422 (p) REVERT: B 1126 ARG cc_start: 0.7426 (ttm110) cc_final: 0.7212 (mtp-110) REVERT: B 1145 GLN cc_start: 0.8532 (tt0) cc_final: 0.8100 (mt0) REVERT: B 1480 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7128 (ttp80) REVERT: C 77 LYS cc_start: 0.7672 (mtmt) cc_final: 0.7413 (mmtt) REVERT: C 139 ASP cc_start: 0.7651 (m-30) cc_final: 0.7427 (m-30) REVERT: C 240 HIS cc_start: 0.7546 (m-70) cc_final: 0.7320 (m170) REVERT: C 352 GLN cc_start: 0.7871 (tt0) cc_final: 0.7587 (mt0) REVERT: C 436 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5935 (mmmm) REVERT: C 506 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7006 (ttt-90) REVERT: C 594 ARG cc_start: 0.6948 (mtp180) cc_final: 0.6549 (mtp85) REVERT: C 618 HIS cc_start: 0.7259 (t70) cc_final: 0.6630 (m170) REVERT: C 663 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7652 (mttt) REVERT: C 731 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7692 (mptt) REVERT: C 829 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7213 (mm-30) REVERT: C 870 ARG cc_start: 0.8376 (mtt180) cc_final: 0.8053 (mtt90) REVERT: C 875 MET cc_start: 0.8601 (ptt) cc_final: 0.8137 (ptp) REVERT: C 996 ASN cc_start: 0.8388 (m-40) cc_final: 0.8044 (m-40) REVERT: C 1062 GLU cc_start: 0.8218 (tt0) cc_final: 0.7939 (tt0) REVERT: C 1064 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7620 (mttt) REVERT: C 1085 ARG cc_start: 0.5911 (ttt90) cc_final: 0.5197 (tpt170) REVERT: C 1105 THR cc_start: 0.6892 (m) cc_final: 0.6425 (p) REVERT: C 1145 GLN cc_start: 0.8489 (tt0) cc_final: 0.8109 (mt0) REVERT: C 1480 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7112 (ttp80) REVERT: D 77 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7415 (mmtt) REVERT: D 139 ASP cc_start: 0.7634 (m-30) cc_final: 0.7411 (m-30) REVERT: D 240 HIS cc_start: 0.7515 (m-70) cc_final: 0.7296 (m170) REVERT: D 352 GLN cc_start: 0.7879 (tt0) cc_final: 0.7583 (mt0) REVERT: D 506 ARG cc_start: 0.7534 (mtp85) cc_final: 0.7020 (ttt-90) REVERT: D 594 ARG cc_start: 0.6905 (mtp180) cc_final: 0.6501 (mtp85) REVERT: D 618 HIS cc_start: 0.7256 (t70) cc_final: 0.6616 (m170) REVERT: D 663 LYS cc_start: 0.8300 (mmmt) cc_final: 0.7705 (mmtp) REVERT: D 731 LYS cc_start: 0.7968 (ttpt) cc_final: 0.7687 (mptt) REVERT: D 829 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7239 (mm-30) REVERT: D 875 MET cc_start: 0.8616 (ptt) cc_final: 0.8156 (ptp) REVERT: D 1062 GLU cc_start: 0.8245 (tt0) cc_final: 0.7875 (tt0) REVERT: D 1064 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7667 (mttt) REVERT: D 1085 ARG cc_start: 0.5873 (ttt90) cc_final: 0.5160 (tpt170) REVERT: D 1105 THR cc_start: 0.6876 (m) cc_final: 0.6404 (p) REVERT: D 1145 GLN cc_start: 0.8442 (tt0) cc_final: 0.8086 (mt0) REVERT: D 1150 MET cc_start: 0.8785 (tpp) cc_final: 0.8175 (mtp) REVERT: D 1480 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7125 (ttp80) outliers start: 98 outliers final: 44 residues processed: 544 average time/residue: 0.9510 time to fit residues: 614.5270 Evaluate side-chains 494 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 444 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 THR 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 574 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1039 ASP Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 436 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 588 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 436 LYS 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 588 VAL Chi-restraints excluded: chain C residue 679 SER Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 248 THR 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 574 VAL Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 1039 ASP Chi-restraints excluded: chain D residue 1064 LYS 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: 5.9990 chunk 64 optimal weight: 5.9990 chunk 472 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 405 optimal weight: 4.9990 chunk 264 optimal weight: 0.4980 chunk 381 optimal weight: 0.0570 chunk 85 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 336 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN A1463 HIS ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN B1463 HIS ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 893 GLN C1463 HIS ** D 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 GLN D1463 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109883 restraints weight = 58716.695| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.47 r_work: 0.3171 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 43671 Z= 0.199 Angle : 0.596 7.592 59393 Z= 0.312 Chirality : 0.042 0.179 6740 Planarity : 0.005 0.056 7504 Dihedral : 8.559 85.951 7056 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 2.49 % Allowed : 15.87 % Favored : 81.63 % 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 aren not related in a simple way. whole: 1.10 (0.11), residues: 5432 helix: 1.84 (0.09), residues: 2996 sheet: -0.85 (0.24), residues: 388 loop : -0.60 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 341 TYR 0.022 0.002 TYR A 917 PHE 0.021 0.002 PHE C 604 TRP 0.013 0.002 TRP C1216 HIS 0.009 0.001 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.00463 (43668) covalent geometry : angle 0.59600 (59372) SS BOND : bond 0.00026 ( 3) SS BOND : angle 0.27702 ( 21) hydrogen bonds : bond 0.04643 ( 2299) hydrogen bonds : angle 4.08432 ( 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 564 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 458 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7436 (mmtt) REVERT: A 81 MET cc_start: 0.7637 (ptm) cc_final: 0.7389 (ptm) REVERT: A 139 ASP cc_start: 0.7647 (m-30) cc_final: 0.7436 (m-30) REVERT: A 196 MET cc_start: 0.8665 (mmt) cc_final: 0.8352 (mmp) REVERT: A 240 HIS cc_start: 0.7011 (m-70) cc_final: 0.6800 (m90) REVERT: A 272 ILE cc_start: 0.8214 (mm) cc_final: 0.8011 (mt) REVERT: A 352 GLN cc_start: 0.7891 (tt0) cc_final: 0.7561 (mt0) REVERT: A 388 LEU cc_start: 0.8005 (tp) cc_final: 0.7757 (tp) REVERT: A 433 GLU cc_start: 0.7650 (tt0) cc_final: 0.7214 (mm-30) REVERT: A 506 ARG cc_start: 0.7486 (mtp85) cc_final: 0.6973 (ttt180) REVERT: A 577 ASP cc_start: 0.7234 (t0) cc_final: 0.6759 (t70) REVERT: A 594 ARG cc_start: 0.6923 (mtp180) cc_final: 0.6496 (mtp85) REVERT: A 663 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7568 (mttt) REVERT: A 731 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7846 (mttp) REVERT: A 829 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7186 (mm-30) REVERT: A 875 MET cc_start: 0.8715 (ptt) cc_final: 0.8188 (ptp) REVERT: A 930 MET cc_start: 0.8596 (mtt) cc_final: 0.8301 (mtt) REVERT: A 996 ASN cc_start: 0.8302 (m-40) cc_final: 0.7931 (m-40) REVERT: A 1005 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: A 1062 GLU cc_start: 0.8179 (tt0) cc_final: 0.7881 (tt0) REVERT: A 1064 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7688 (mttt) REVERT: A 1081 MET cc_start: 0.7349 (mtp) cc_final: 0.7083 (mtp) REVERT: A 1085 ARG cc_start: 0.5908 (ttt90) cc_final: 0.5149 (tpt170) REVERT: A 1105 THR cc_start: 0.6900 (m) cc_final: 0.6409 (p) REVERT: A 1130 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7369 (mm-30) REVERT: A 1145 GLN cc_start: 0.8401 (tt0) cc_final: 0.7995 (mt0) REVERT: A 1244 MET cc_start: 0.5818 (ptp) cc_final: 0.5282 (mmt) REVERT: A 1480 ARG cc_start: 0.7563 (ttp80) cc_final: 0.7017 (ttp80) REVERT: B 69 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5900 (ttm110) REVERT: B 70 MET cc_start: 0.6158 (ppp) cc_final: 0.5585 (ppp) REVERT: B 139 ASP cc_start: 0.7686 (m-30) cc_final: 0.7471 (m-30) REVERT: B 240 HIS cc_start: 0.6994 (m-70) cc_final: 0.6793 (m90) REVERT: B 272 ILE cc_start: 0.8250 (mm) cc_final: 0.7991 (mt) REVERT: B 352 GLN cc_start: 0.7826 (tt0) cc_final: 0.7524 (mt0) REVERT: B 365 GLN cc_start: 0.7023 (mt0) cc_final: 0.6077 (mp10) REVERT: B 388 LEU cc_start: 0.8028 (tp) cc_final: 0.7784 (tp) REVERT: B 433 GLU cc_start: 0.7703 (tt0) cc_final: 0.7276 (mm-30) REVERT: B 506 ARG cc_start: 0.7506 (mtp85) cc_final: 0.6990 (ttt180) REVERT: B 592 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6229 (tp40) REVERT: B 594 ARG cc_start: 0.6936 (mtp180) cc_final: 0.6536 (mtp85) REVERT: B 663 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7611 (mmtp) REVERT: B 731 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7767 (mttp) REVERT: B 829 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7150 (mm-30) REVERT: B 875 MET cc_start: 0.8729 (ptt) cc_final: 0.8206 (ptp) REVERT: B 996 ASN cc_start: 0.8293 (m-40) cc_final: 0.7920 (m-40) REVERT: B 1005 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6825 (mt-10) REVERT: B 1062 GLU cc_start: 0.8185 (tt0) cc_final: 0.7879 (tt0) REVERT: B 1064 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7684 (mttt) REVERT: B 1081 MET cc_start: 0.7429 (mtp) cc_final: 0.7183 (mtp) REVERT: B 1085 ARG cc_start: 0.5910 (ttt90) cc_final: 0.5185 (tpt170) REVERT: B 1105 THR cc_start: 0.6914 (m) cc_final: 0.6419 (p) REVERT: B 1145 GLN cc_start: 0.8488 (tt0) cc_final: 0.8019 (mt0) REVERT: B 1150 MET cc_start: 0.8481 (mtp) cc_final: 0.8248 (mtt) REVERT: B 1480 ARG cc_start: 0.7529 (ttp80) cc_final: 0.6997 (ttp80) REVERT: C 139 ASP cc_start: 0.7639 (m-30) cc_final: 0.7426 (m-30) REVERT: C 196 MET cc_start: 0.8663 (mmt) cc_final: 0.8347 (mmp) REVERT: C 352 GLN cc_start: 0.7908 (tt0) cc_final: 0.7561 (mt0) REVERT: C 365 GLN cc_start: 0.7032 (mt0) cc_final: 0.6086 (mp10) REVERT: C 388 LEU cc_start: 0.8006 (tp) cc_final: 0.7766 (tp) REVERT: C 433 GLU cc_start: 0.7672 (tt0) cc_final: 0.7245 (mm-30) REVERT: C 506 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6992 (ttt180) REVERT: C 577 ASP cc_start: 0.7227 (t0) cc_final: 0.6760 (t70) REVERT: C 594 ARG cc_start: 0.6926 (mtp180) cc_final: 0.6502 (mtp85) REVERT: C 663 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7573 (mttt) REVERT: C 731 LYS cc_start: 0.8052 (ttpt) cc_final: 0.7790 (mttp) REVERT: C 829 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7157 (mm-30) REVERT: C 875 MET cc_start: 0.8712 (ptt) cc_final: 0.8192 (ptp) REVERT: C 996 ASN cc_start: 0.8302 (m-40) cc_final: 0.7935 (m-40) REVERT: C 1062 GLU cc_start: 0.8171 (tt0) cc_final: 0.7873 (tt0) REVERT: C 1064 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7688 (mttt) REVERT: C 1081 MET cc_start: 0.7318 (mtp) cc_final: 0.7055 (mtp) REVERT: C 1085 ARG cc_start: 0.5936 (ttt90) cc_final: 0.5166 (tpt170) REVERT: C 1105 THR cc_start: 0.6907 (m) cc_final: 0.6413 (p) REVERT: C 1130 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7374 (mm-30) REVERT: C 1145 GLN cc_start: 0.8416 (tt0) cc_final: 0.7966 (mt0) REVERT: C 1150 MET cc_start: 0.8515 (mmt) cc_final: 0.8097 (mtp) REVERT: C 1480 ARG cc_start: 0.7546 (ttp80) cc_final: 0.7007 (ttp80) REVERT: D 69 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.5877 (ttm110) REVERT: D 70 MET cc_start: 0.6161 (ppp) cc_final: 0.5586 (ppp) REVERT: D 139 ASP cc_start: 0.7650 (m-30) cc_final: 0.7437 (m-30) REVERT: D 196 MET cc_start: 0.8660 (mmt) cc_final: 0.8336 (mmp) REVERT: D 272 ILE cc_start: 0.8227 (mm) cc_final: 0.7971 (mt) REVERT: D 352 GLN cc_start: 0.7836 (tt0) cc_final: 0.7532 (mt0) REVERT: D 365 GLN cc_start: 0.7050 (mt0) cc_final: 0.6102 (mp10) REVERT: D 388 LEU cc_start: 0.8004 (tp) cc_final: 0.7770 (tp) REVERT: D 433 GLU cc_start: 0.7692 (tt0) cc_final: 0.7267 (mm-30) REVERT: D 506 ARG cc_start: 0.7491 (mtp85) cc_final: 0.6980 (ttt180) REVERT: D 577 ASP cc_start: 0.7225 (t0) cc_final: 0.6792 (t70) REVERT: D 592 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6225 (tp40) REVERT: D 594 ARG cc_start: 0.6942 (mtp180) cc_final: 0.6528 (mtp85) REVERT: D 663 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7611 (mmtp) REVERT: D 731 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7752 (mttp) REVERT: D 829 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7150 (mm-30) REVERT: D 875 MET cc_start: 0.8725 (ptt) cc_final: 0.8196 (ptp) REVERT: D 996 ASN cc_start: 0.8493 (m-40) cc_final: 0.8087 (m-40) REVERT: D 1062 GLU cc_start: 0.8159 (tt0) cc_final: 0.7852 (tt0) REVERT: D 1064 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7688 (mttt) REVERT: D 1081 MET cc_start: 0.7384 (mtp) cc_final: 0.7125 (mtp) REVERT: D 1085 ARG cc_start: 0.5934 (ttt90) cc_final: 0.5170 (tpt170) REVERT: D 1105 THR cc_start: 0.6904 (m) cc_final: 0.6405 (p) REVERT: D 1145 GLN cc_start: 0.8439 (tt0) cc_final: 0.8011 (mt0) REVERT: D 1480 ARG cc_start: 0.7506 (ttp80) cc_final: 0.6985 (ttp80) outliers start: 106 outliers final: 62 residues processed: 547 average time/residue: 0.9642 time to fit residues: 624.6786 Evaluate side-chains 515 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 442 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 170 LEU Chi-restraints excluded: chain A residue 199 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 479 SER 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 1005 GLU Chi-restraints excluded: chain A residue 1039 ASP 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 1277 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 260 VAL 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 588 VAL Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 1005 GLU Chi-restraints excluded: chain B residue 1064 LYS 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 1277 VAL Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 248 THR 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 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 1064 LYS Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1277 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 199 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 588 VAL Chi-restraints excluded: chain D residue 592 GLN 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 1164 LEU Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1277 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: 5.9990 chunk 46 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 357 optimal weight: 3.9990 chunk 447 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN A1463 HIS ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN B1463 HIS ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 893 GLN C1463 HIS ** D 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 GLN D1463 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108926 restraints weight = 59999.335| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.53 r_work: 0.3151 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 43671 Z= 0.234 Angle : 0.640 7.873 59393 Z= 0.334 Chirality : 0.044 0.182 6740 Planarity : 0.005 0.054 7504 Dihedral : 8.927 84.954 7056 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 2.73 % Allowed : 15.66 % Favored : 81.61 % 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 aren not related in a simple way. whole: 0.80 (0.11), residues: 5432 helix: 1.58 (0.09), residues: 3000 sheet: -0.81 (0.24), residues: 388 loop : -0.75 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 341 TYR 0.023 0.002 TYR D 917 PHE 0.027 0.002 PHE A1068 TRP 0.015 0.002 TRP D1216 HIS 0.009 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00548 (43668) covalent geometry : angle 0.63992 (59372) SS BOND : bond 0.00038 ( 3) SS BOND : angle 0.34349 ( 21) hydrogen bonds : bond 0.04956 ( 2299) hydrogen bonds : angle 4.24973 ( 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 573 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 457 time to evaluate : 2.701 Fit side-chains REVERT: A 70 MET cc_start: 0.6200 (ppp) cc_final: 0.5663 (ppp) REVERT: A 240 HIS cc_start: 0.7295 (m-70) cc_final: 0.7044 (m90) REVERT: A 352 GLN cc_start: 0.7831 (tt0) cc_final: 0.7573 (mt0) REVERT: A 365 GLN cc_start: 0.7259 (mt0) cc_final: 0.6351 (mp10) REVERT: A 388 LEU cc_start: 0.7971 (tp) cc_final: 0.7725 (tp) REVERT: A 433 GLU cc_start: 0.7555 (tt0) cc_final: 0.7108 (mm-30) REVERT: A 506 ARG cc_start: 0.7490 (mtp85) cc_final: 0.6998 (ttt-90) REVERT: A 577 ASP cc_start: 0.7288 (t0) cc_final: 0.6863 (t70) REVERT: A 592 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6009 (tp40) REVERT: A 594 ARG cc_start: 0.7006 (mtp180) cc_final: 0.6584 (mtp85) REVERT: A 663 LYS cc_start: 0.8300 (mmmt) cc_final: 0.8044 (mptt) REVERT: A 731 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7723 (mttp) REVERT: A 829 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7319 (mm-30) REVERT: A 875 MET cc_start: 0.8694 (ptt) cc_final: 0.8219 (ptp) REVERT: A 996 ASN cc_start: 0.8296 (m-40) cc_final: 0.7961 (m-40) REVERT: A 1005 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: A 1062 GLU cc_start: 0.8127 (tt0) cc_final: 0.7864 (tt0) REVERT: A 1064 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7738 (mttt) REVERT: A 1081 MET cc_start: 0.7170 (mtp) cc_final: 0.6902 (mtp) REVERT: A 1085 ARG cc_start: 0.5889 (ttt90) cc_final: 0.5142 (tpt170) REVERT: A 1105 THR cc_start: 0.6968 (m) cc_final: 0.6483 (p) REVERT: A 1130 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7490 (mm-30) REVERT: A 1145 GLN cc_start: 0.8504 (tt0) cc_final: 0.8060 (mt0) REVERT: A 1244 MET cc_start: 0.5912 (ptp) cc_final: 0.5332 (mmt) REVERT: B 69 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.5989 (ttm110) REVERT: B 70 MET cc_start: 0.6180 (ppp) cc_final: 0.5674 (ppp) REVERT: B 240 HIS cc_start: 0.7254 (m-70) cc_final: 0.7047 (m90) REVERT: B 272 ILE cc_start: 0.8261 (mm) cc_final: 0.8043 (mt) REVERT: B 352 GLN cc_start: 0.7845 (tt0) cc_final: 0.7574 (mt0) REVERT: B 365 GLN cc_start: 0.7232 (mt0) cc_final: 0.6352 (mp10) REVERT: B 388 LEU cc_start: 0.7970 (tp) cc_final: 0.7730 (tp) REVERT: B 433 GLU cc_start: 0.7565 (tt0) cc_final: 0.7104 (mm-30) REVERT: B 506 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7002 (ttt-90) REVERT: B 577 ASP cc_start: 0.7304 (t0) cc_final: 0.6869 (t70) REVERT: B 592 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6185 (tp40) REVERT: B 594 ARG cc_start: 0.6963 (mtp180) cc_final: 0.6525 (mtp85) REVERT: B 663 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7609 (mttt) REVERT: B 731 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7725 (mttp) REVERT: B 829 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7318 (mm-30) REVERT: B 875 MET cc_start: 0.8688 (ptt) cc_final: 0.8213 (ptp) REVERT: B 996 ASN cc_start: 0.8268 (m-40) cc_final: 0.7928 (m-40) REVERT: B 1005 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: B 1062 GLU cc_start: 0.8168 (tt0) cc_final: 0.7907 (tt0) REVERT: B 1064 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7735 (mttt) REVERT: B 1081 MET cc_start: 0.7226 (mtp) cc_final: 0.6941 (mtp) REVERT: B 1085 ARG cc_start: 0.5832 (ttt90) cc_final: 0.5151 (tpt90) REVERT: B 1105 THR cc_start: 0.6951 (m) cc_final: 0.6458 (p) REVERT: B 1130 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7424 (mm-30) REVERT: B 1145 GLN cc_start: 0.8523 (tt0) cc_final: 0.8059 (mt0) REVERT: B 1150 MET cc_start: 0.8544 (mtp) cc_final: 0.8336 (mtp) REVERT: C 272 ILE cc_start: 0.8194 (mm) cc_final: 0.7972 (mt) REVERT: C 352 GLN cc_start: 0.7825 (tt0) cc_final: 0.7570 (mt0) REVERT: C 365 GLN cc_start: 0.7225 (mt0) cc_final: 0.6350 (mp10) REVERT: C 388 LEU cc_start: 0.7971 (tp) cc_final: 0.7727 (tp) REVERT: C 433 GLU cc_start: 0.7563 (tt0) cc_final: 0.7123 (mm-30) REVERT: C 506 ARG cc_start: 0.7506 (mtp85) cc_final: 0.7011 (ttt-90) REVERT: C 577 ASP cc_start: 0.7302 (t0) cc_final: 0.6871 (t70) REVERT: C 594 ARG cc_start: 0.6999 (mtp180) cc_final: 0.6576 (mtp85) REVERT: C 663 LYS cc_start: 0.8296 (mmmt) cc_final: 0.8046 (mptt) REVERT: C 731 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7731 (mttp) REVERT: C 829 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7321 (mm-30) REVERT: C 875 MET cc_start: 0.8690 (ptt) cc_final: 0.8217 (ptp) REVERT: C 996 ASN cc_start: 0.8291 (m-40) cc_final: 0.7956 (m-40) REVERT: C 1062 GLU cc_start: 0.8138 (tt0) cc_final: 0.7870 (tt0) REVERT: C 1064 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7731 (mttt) REVERT: C 1081 MET cc_start: 0.7197 (mtp) cc_final: 0.6937 (mtp) REVERT: C 1085 ARG cc_start: 0.5888 (ttt90) cc_final: 0.5151 (tpt170) REVERT: C 1105 THR cc_start: 0.6969 (m) cc_final: 0.6482 (p) REVERT: C 1130 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7481 (mm-30) REVERT: C 1145 GLN cc_start: 0.8504 (tt0) cc_final: 0.8090 (mt0) REVERT: C 1150 MET cc_start: 0.8476 (mmt) cc_final: 0.8114 (mtp) REVERT: D 69 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.5986 (ttm110) REVERT: D 70 MET cc_start: 0.6194 (ppp) cc_final: 0.5679 (ppp) REVERT: D 272 ILE cc_start: 0.8244 (mm) cc_final: 0.8026 (mt) REVERT: D 352 GLN cc_start: 0.7847 (tt0) cc_final: 0.7575 (mt0) REVERT: D 365 GLN cc_start: 0.7245 (mt0) cc_final: 0.6349 (mp10) REVERT: D 388 LEU cc_start: 0.7966 (tp) cc_final: 0.7730 (tp) REVERT: D 433 GLU cc_start: 0.7526 (tt0) cc_final: 0.7078 (mm-30) REVERT: D 506 ARG cc_start: 0.7469 (mtp85) cc_final: 0.6978 (ttt-90) REVERT: D 577 ASP cc_start: 0.7278 (t0) cc_final: 0.6843 (t70) REVERT: D 592 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6189 (tp40) REVERT: D 594 ARG cc_start: 0.6958 (mtp180) cc_final: 0.6515 (mtp85) REVERT: D 663 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7605 (mttt) REVERT: D 731 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7717 (mttp) REVERT: D 829 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7340 (mm-30) REVERT: D 875 MET cc_start: 0.8706 (ptt) cc_final: 0.8229 (ptp) REVERT: D 996 ASN cc_start: 0.8403 (m-40) cc_final: 0.8048 (m-40) REVERT: D 1062 GLU cc_start: 0.8127 (tt0) cc_final: 0.7861 (tt0) REVERT: D 1064 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7750 (mttt) REVERT: D 1081 MET cc_start: 0.7195 (mtp) cc_final: 0.6930 (mtp) REVERT: D 1085 ARG cc_start: 0.5871 (ttt90) cc_final: 0.5136 (tpt170) REVERT: D 1105 THR cc_start: 0.6944 (m) cc_final: 0.6450 (p) REVERT: D 1130 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7431 (mm-30) REVERT: D 1145 GLN cc_start: 0.8495 (tt0) cc_final: 0.8077 (mt0) outliers start: 116 outliers final: 69 residues processed: 556 average time/residue: 0.9231 time to fit residues: 611.6799 Evaluate side-chains 510 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 430 time to evaluate : 1.890 ------------------------------------------------------------------------------- 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 170 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 323 LEU 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 592 GLN Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 323 LEU 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 592 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 1005 GLU Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1277 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 199 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 LEU 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 831 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 1277 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 248 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 561 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1277 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: 0.7980 chunk 457 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 404 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 GLN A1080 HIS A1463 HIS ** B 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN B1463 HIS ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 893 GLN C1080 HIS C1463 HIS ** D 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 GLN D1080 HIS D1463 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.133564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110861 restraints weight = 58715.576| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.45 r_work: 0.3170 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43671 Z= 0.146 Angle : 0.552 7.876 59393 Z= 0.290 Chirality : 0.040 0.175 6740 Planarity : 0.004 0.053 7504 Dihedral : 8.568 84.384 7056 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 2.14 % Allowed : 16.72 % Favored : 81.14 % 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 aren not related in a simple way. whole: 1.03 (0.12), residues: 5432 helix: 1.80 (0.09), residues: 3000 sheet: -0.81 (0.24), residues: 388 loop : -0.67 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 341 TYR 0.016 0.002 TYR D 917 PHE 0.020 0.002 PHE B1068 TRP 0.012 0.001 TRP B1124 HIS 0.008 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00333 (43668) covalent geometry : angle 0.55209 (59372) SS BOND : bond 0.00059 ( 3) SS BOND : angle 0.37611 ( 21) hydrogen bonds : bond 0.04298 ( 2299) hydrogen bonds : angle 4.06244 ( 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 522 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 431 time to evaluate : 2.026 Fit side-chains REVERT: A 240 HIS cc_start: 0.7145 (m-70) cc_final: 0.6891 (m-70) REVERT: A 352 GLN cc_start: 0.7859 (tt0) cc_final: 0.7583 (mt0) REVERT: A 388 LEU cc_start: 0.7914 (tp) cc_final: 0.7638 (tp) REVERT: A 433 GLU cc_start: 0.7606 (tt0) cc_final: 0.7174 (mm-30) REVERT: A 506 ARG cc_start: 0.7469 (mtp85) cc_final: 0.6973 (ttt-90) REVERT: A 577 ASP cc_start: 0.7248 (t0) cc_final: 0.6809 (t70) REVERT: A 594 ARG cc_start: 0.6946 (mtp180) cc_final: 0.6527 (mtp85) REVERT: A 663 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7591 (mttt) REVERT: A 697 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7309 (mppt) REVERT: A 731 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7757 (mttp) REVERT: A 829 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7236 (mm-30) REVERT: A 875 MET cc_start: 0.8653 (ptt) cc_final: 0.8188 (ptp) REVERT: A 996 ASN cc_start: 0.8329 (m-40) cc_final: 0.7970 (m-40) REVERT: A 1005 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: A 1062 GLU cc_start: 0.8166 (tt0) cc_final: 0.7869 (tt0) REVERT: A 1064 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7647 (mttt) REVERT: A 1081 MET cc_start: 0.7208 (mtp) cc_final: 0.6946 (mtp) REVERT: A 1085 ARG cc_start: 0.6006 (ttt90) cc_final: 0.5250 (tpt170) REVERT: A 1105 THR cc_start: 0.6936 (m) cc_final: 0.6459 (p) REVERT: A 1127 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7050 (pt0) REVERT: A 1130 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7398 (mm-30) REVERT: A 1145 GLN cc_start: 0.8388 (tt0) cc_final: 0.7958 (mt0) REVERT: A 1150 MET cc_start: 0.8697 (tpp) cc_final: 0.8452 (mtp) REVERT: A 1244 MET cc_start: 0.5840 (ptp) cc_final: 0.5247 (mmt) REVERT: B 77 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7394 (mmtt) REVERT: B 240 HIS cc_start: 0.7213 (m-70) cc_final: 0.6946 (m-70) REVERT: B 272 ILE cc_start: 0.8251 (mm) cc_final: 0.8013 (mt) REVERT: B 352 GLN cc_start: 0.7832 (tt0) cc_final: 0.7572 (mt0) REVERT: B 388 LEU cc_start: 0.7922 (tp) cc_final: 0.7668 (tp) REVERT: B 433 GLU cc_start: 0.7631 (tt0) cc_final: 0.7202 (mm-30) REVERT: B 506 ARG cc_start: 0.7470 (mtp85) cc_final: 0.6963 (ttt-90) REVERT: B 594 ARG cc_start: 0.6913 (mtp180) cc_final: 0.6487 (mtp85) REVERT: B 663 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7571 (mttt) REVERT: B 697 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7330 (mppt) REVERT: B 731 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7753 (mttp) REVERT: B 829 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7273 (mm-30) REVERT: B 875 MET cc_start: 0.8661 (ptt) cc_final: 0.8206 (ptp) REVERT: B 996 ASN cc_start: 0.8321 (m-40) cc_final: 0.7964 (m-40) REVERT: B 1005 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: B 1062 GLU cc_start: 0.8223 (tt0) cc_final: 0.7930 (tt0) REVERT: B 1064 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7621 (mttt) REVERT: B 1081 MET cc_start: 0.7269 (mtp) cc_final: 0.6985 (mtp) REVERT: B 1085 ARG cc_start: 0.5990 (ttt90) cc_final: 0.5231 (tpt170) REVERT: B 1105 THR cc_start: 0.6906 (m) cc_final: 0.6422 (p) REVERT: B 1115 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7833 (tp) REVERT: B 1130 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7429 (mm-30) REVERT: B 1145 GLN cc_start: 0.8408 (tt0) cc_final: 0.7933 (mt0) REVERT: B 1244 MET cc_start: 0.5673 (ptt) cc_final: 0.5252 (mmt) REVERT: C 77 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7387 (mmtt) REVERT: C 272 ILE cc_start: 0.8219 (mm) cc_final: 0.7973 (mt) REVERT: C 352 GLN cc_start: 0.7873 (tt0) cc_final: 0.7584 (mt0) REVERT: C 388 LEU cc_start: 0.7913 (tp) cc_final: 0.7652 (tp) REVERT: C 433 GLU cc_start: 0.7585 (tt0) cc_final: 0.7151 (mm-30) REVERT: C 506 ARG cc_start: 0.7490 (mtp85) cc_final: 0.6996 (ttt-90) REVERT: C 577 ASP cc_start: 0.7244 (t0) cc_final: 0.6803 (t70) REVERT: C 594 ARG cc_start: 0.6917 (mtp180) cc_final: 0.6496 (mtp85) REVERT: C 663 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7595 (mttt) REVERT: C 697 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7308 (mppt) REVERT: C 731 LYS cc_start: 0.8042 (ttpt) cc_final: 0.7769 (mttp) REVERT: C 829 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7280 (mm-30) REVERT: C 875 MET cc_start: 0.8650 (ptt) cc_final: 0.8185 (ptp) REVERT: C 996 ASN cc_start: 0.8327 (m-40) cc_final: 0.7971 (m-40) REVERT: C 1062 GLU cc_start: 0.8169 (tt0) cc_final: 0.7875 (tt0) REVERT: C 1064 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7636 (mttt) REVERT: C 1081 MET cc_start: 0.7204 (mtp) cc_final: 0.6929 (mtp) REVERT: C 1085 ARG cc_start: 0.6020 (ttt90) cc_final: 0.5265 (tpt170) REVERT: C 1105 THR cc_start: 0.6943 (m) cc_final: 0.6464 (p) REVERT: C 1127 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7068 (pt0) REVERT: C 1130 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7398 (mm-30) REVERT: C 1145 GLN cc_start: 0.8383 (tt0) cc_final: 0.7961 (mt0) REVERT: C 1244 MET cc_start: 0.5670 (ptt) cc_final: 0.5249 (mmt) REVERT: D 77 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7410 (mmtt) REVERT: D 272 ILE cc_start: 0.8236 (mm) cc_final: 0.7994 (mt) REVERT: D 352 GLN cc_start: 0.7829 (tt0) cc_final: 0.7566 (mt0) REVERT: D 388 LEU cc_start: 0.7909 (tp) cc_final: 0.7639 (tp) REVERT: D 433 GLU cc_start: 0.7622 (tt0) cc_final: 0.7191 (mm-30) REVERT: D 464 GLU cc_start: 0.7379 (tp30) cc_final: 0.7029 (mm-30) REVERT: D 506 ARG cc_start: 0.7485 (mtp85) cc_final: 0.6977 (ttt-90) REVERT: D 577 ASP cc_start: 0.7208 (t0) cc_final: 0.6778 (t70) REVERT: D 594 ARG cc_start: 0.6926 (mtp180) cc_final: 0.6482 (mtp85) REVERT: D 663 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7563 (mttt) REVERT: D 697 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7312 (mppt) REVERT: D 731 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7758 (mttp) REVERT: D 829 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7298 (mm-30) REVERT: D 875 MET cc_start: 0.8669 (ptt) cc_final: 0.8214 (ptp) REVERT: D 996 ASN cc_start: 0.8447 (m-40) cc_final: 0.8060 (m-40) REVERT: D 1062 GLU cc_start: 0.8192 (tt0) cc_final: 0.7895 (tt0) REVERT: D 1064 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7638 (mttt) REVERT: D 1081 MET cc_start: 0.7259 (mtp) cc_final: 0.6966 (mtp) REVERT: D 1085 ARG cc_start: 0.6009 (ttt90) cc_final: 0.5252 (tpt170) REVERT: D 1105 THR cc_start: 0.6908 (m) cc_final: 0.6422 (p) REVERT: D 1115 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7835 (tp) REVERT: D 1127 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7054 (pt0) REVERT: D 1130 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7393 (mm-30) REVERT: D 1145 GLN cc_start: 0.8412 (tt0) cc_final: 0.7964 (mt0) REVERT: D 1150 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8221 (mtp) REVERT: D 1244 MET cc_start: 0.5683 (ptt) cc_final: 0.5248 (mmt) outliers start: 91 outliers final: 50 residues processed: 517 average time/residue: 0.9525 time to fit residues: 584.2148 Evaluate side-chains 497 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 431 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 199 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 260 VAL 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 697 LYS Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 347 ILE 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 697 LYS Chi-restraints excluded: chain B residue 831 THR Chi-restraints excluded: chain B residue 1005 GLU 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 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 248 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 347 ILE 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 697 LYS Chi-restraints excluded: chain C residue 831 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 1239 VAL Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 347 ILE 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 697 LYS Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 1004 THR Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1150 MET 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: 2.9990 chunk 304 optimal weight: 0.5980 chunk 82 optimal weight: 0.0980 chunk 259 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 374 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 179 optimal weight: 8.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3637 r_free = 0.3637 target = 0.135344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112729 restraints weight = 58676.793| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.46 r_work: 0.3199 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43671 Z= 0.116 Angle : 0.514 8.868 59393 Z= 0.271 Chirality : 0.039 0.170 6740 Planarity : 0.004 0.051 7504 Dihedral : 8.177 83.403 7056 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 1.51 % Allowed : 17.50 % Favored : 81.00 % 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 aren not related in a simple way. whole: 1.27 (0.12), residues: 5432 helix: 2.00 (0.09), residues: 3028 sheet: -0.97 (0.24), residues: 376 loop : -0.55 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 341 TYR 0.011 0.001 TYR D 917 PHE 0.018 0.001 PHE D1068 TRP 0.013 0.001 TRP B1124 HIS 0.011 0.001 HIS B 514 Details of bonding type rmsd covalent geometry : bond 0.00258 (43668) covalent geometry : angle 0.51399 (59372) SS BOND : bond 0.00093 ( 3) SS BOND : angle 0.35846 ( 21) hydrogen bonds : bond 0.03843 ( 2299) hydrogen bonds : angle 3.91019 ( 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 511 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 447 time to evaluate : 1.771 Fit side-chains REVERT: A 240 HIS cc_start: 0.7129 (m-70) cc_final: 0.6883 (m90) REVERT: A 352 GLN cc_start: 0.7905 (tt0) cc_final: 0.7594 (mt0) REVERT: A 388 LEU cc_start: 0.7848 (tp) cc_final: 0.7582 (tp) REVERT: A 433 GLU cc_start: 0.7705 (tt0) cc_final: 0.7300 (mm-30) REVERT: A 464 GLU cc_start: 0.7292 (tp30) cc_final: 0.6957 (tt0) REVERT: A 506 ARG cc_start: 0.7407 (mtp85) cc_final: 0.6905 (ttt-90) REVERT: A 577 ASP cc_start: 0.7098 (t0) cc_final: 0.6715 (t70) REVERT: A 594 ARG cc_start: 0.6864 (mtp180) cc_final: 0.6547 (mtp85) REVERT: A 618 HIS cc_start: 0.7274 (t70) cc_final: 0.6587 (m170) REVERT: A 658 MET cc_start: 0.8159 (mtp) cc_final: 0.7338 (mmm) REVERT: A 663 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7557 (mttt) REVERT: A 697 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7310 (mppt) REVERT: A 731 LYS cc_start: 0.8029 (ttpt) cc_final: 0.7750 (mttp) REVERT: A 829 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7218 (mm-30) REVERT: A 875 MET cc_start: 0.8604 (ptt) cc_final: 0.8136 (ptp) REVERT: A 996 ASN cc_start: 0.8275 (m-40) cc_final: 0.7935 (m-40) REVERT: A 1005 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6727 (mt-10) REVERT: A 1062 GLU cc_start: 0.8154 (tt0) cc_final: 0.7808 (tt0) REVERT: A 1064 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7583 (mttt) REVERT: A 1085 ARG cc_start: 0.6084 (ttt90) cc_final: 0.5271 (tpt170) REVERT: A 1105 THR cc_start: 0.6906 (m) cc_final: 0.6410 (p) REVERT: A 1127 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6946 (pt0) REVERT: A 1130 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7345 (mm-30) REVERT: A 1145 GLN cc_start: 0.8327 (tt0) cc_final: 0.7960 (mt0) REVERT: A 1244 MET cc_start: 0.5780 (ptp) cc_final: 0.5160 (mmt) REVERT: B 240 HIS cc_start: 0.7120 (m-70) cc_final: 0.6905 (m90) REVERT: B 272 ILE cc_start: 0.8213 (mm) cc_final: 0.7976 (mt) REVERT: B 352 GLN cc_start: 0.7922 (tt0) cc_final: 0.7599 (mt0) REVERT: B 388 LEU cc_start: 0.7891 (tp) cc_final: 0.7632 (tp) REVERT: B 433 GLU cc_start: 0.7651 (tt0) cc_final: 0.7227 (mm-30) REVERT: B 506 ARG cc_start: 0.7395 (mtp85) cc_final: 0.6907 (ttt-90) REVERT: B 577 ASP cc_start: 0.7230 (t0) cc_final: 0.6795 (t70) REVERT: B 594 ARG cc_start: 0.6842 (mtp180) cc_final: 0.6392 (mtp85) REVERT: B 618 HIS cc_start: 0.7311 (t70) cc_final: 0.6553 (m170) REVERT: B 663 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7562 (mmtp) REVERT: B 697 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7290 (mppt) REVERT: B 731 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7686 (mttp) REVERT: B 829 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7219 (mm-30) REVERT: B 875 MET cc_start: 0.8589 (ptt) cc_final: 0.8114 (ptp) REVERT: B 996 ASN cc_start: 0.8340 (m-40) cc_final: 0.8012 (m-40) REVERT: B 1005 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6730 (mt-10) REVERT: B 1062 GLU cc_start: 0.8171 (tt0) cc_final: 0.7828 (tt0) REVERT: B 1064 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7612 (mttt) REVERT: B 1085 ARG cc_start: 0.5997 (ttt90) cc_final: 0.5201 (tpt170) REVERT: B 1105 THR cc_start: 0.6914 (m) cc_final: 0.6441 (p) REVERT: B 1127 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6971 (pt0) REVERT: B 1130 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7281 (mm-30) REVERT: B 1145 GLN cc_start: 0.8292 (tt0) cc_final: 0.7922 (mt0) REVERT: B 1244 MET cc_start: 0.5613 (ptt) cc_final: 0.5248 (mmt) REVERT: C 352 GLN cc_start: 0.7842 (tt0) cc_final: 0.7528 (mt0) REVERT: C 388 LEU cc_start: 0.7871 (tp) cc_final: 0.7608 (tp) REVERT: C 433 GLU cc_start: 0.7678 (tt0) cc_final: 0.7262 (mm-30) REVERT: C 464 GLU cc_start: 0.7280 (tp30) cc_final: 0.6954 (tt0) REVERT: C 506 ARG cc_start: 0.7455 (mtp85) cc_final: 0.6954 (ttt-90) REVERT: C 577 ASP cc_start: 0.7115 (t0) cc_final: 0.6716 (t70) REVERT: C 594 ARG cc_start: 0.6854 (mtp180) cc_final: 0.6539 (mtp85) REVERT: C 618 HIS cc_start: 0.7235 (t70) cc_final: 0.6560 (m170) REVERT: C 658 MET cc_start: 0.8129 (mtp) cc_final: 0.7280 (mmm) REVERT: C 663 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7558 (mttt) REVERT: C 697 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7314 (mppt) REVERT: C 731 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7675 (mttp) REVERT: C 829 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7192 (mm-30) REVERT: C 875 MET cc_start: 0.8615 (ptt) cc_final: 0.8132 (ptp) REVERT: C 996 ASN cc_start: 0.8289 (m-40) cc_final: 0.7952 (m-40) REVERT: C 1062 GLU cc_start: 0.8163 (tt0) cc_final: 0.7824 (tt0) REVERT: C 1064 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7590 (mttt) REVERT: C 1085 ARG cc_start: 0.6097 (ttt90) cc_final: 0.5271 (tpt170) REVERT: C 1105 THR cc_start: 0.6909 (m) cc_final: 0.6400 (p) REVERT: C 1127 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6970 (pt0) REVERT: C 1130 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7363 (mm-30) REVERT: C 1145 GLN cc_start: 0.8326 (tt0) cc_final: 0.7951 (mt0) REVERT: C 1150 MET cc_start: 0.8601 (tpp) cc_final: 0.8054 (mtt) REVERT: C 1244 MET cc_start: 0.5613 (ptt) cc_final: 0.5218 (mmt) REVERT: D 272 ILE cc_start: 0.8196 (mm) cc_final: 0.7950 (mt) REVERT: D 352 GLN cc_start: 0.7901 (tt0) cc_final: 0.7567 (mt0) REVERT: D 388 LEU cc_start: 0.7859 (tp) cc_final: 0.7593 (tp) REVERT: D 433 GLU cc_start: 0.7638 (tt0) cc_final: 0.7212 (mm-30) REVERT: D 506 ARG cc_start: 0.7395 (mtp85) cc_final: 0.6900 (ttt-90) REVERT: D 577 ASP cc_start: 0.7195 (t0) cc_final: 0.6721 (t70) REVERT: D 594 ARG cc_start: 0.6843 (mtp180) cc_final: 0.6397 (mtp85) REVERT: D 658 MET cc_start: 0.8080 (mtp) cc_final: 0.7205 (mmm) REVERT: D 663 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7584 (mmtp) REVERT: D 697 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7275 (mppt) REVERT: D 731 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7688 (mttp) REVERT: D 829 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7229 (mm-30) REVERT: D 875 MET cc_start: 0.8590 (ptt) cc_final: 0.8097 (ptp) REVERT: D 1062 GLU cc_start: 0.8173 (tt0) cc_final: 0.7823 (tt0) REVERT: D 1064 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7623 (mttt) REVERT: D 1085 ARG cc_start: 0.6029 (ttt90) cc_final: 0.5217 (tpt170) REVERT: D 1105 THR cc_start: 0.6887 (m) cc_final: 0.6413 (p) REVERT: D 1127 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6929 (pt0) REVERT: D 1130 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7285 (mm-30) REVERT: D 1145 GLN cc_start: 0.8298 (tt0) cc_final: 0.7931 (mt0) REVERT: D 1150 MET cc_start: 0.8667 (tpp) cc_final: 0.8157 (mtt) REVERT: D 1244 MET cc_start: 0.5644 (ptt) cc_final: 0.5245 (mmt) outliers start: 64 outliers final: 38 residues processed: 503 average time/residue: 0.9379 time to fit residues: 560.8541 Evaluate side-chains 465 residues out of total 4672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 417 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 260 VAL 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 697 LYS Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1039 ASP Chi-restraints excluded: chain A residue 1064 LYS 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 248 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 347 ILE 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 697 LYS Chi-restraints excluded: chain B residue 1005 GLU 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 78 ARG Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 347 ILE 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 697 LYS Chi-restraints excluded: chain C residue 1064 LYS 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 248 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 347 ILE 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 697 LYS Chi-restraints excluded: chain D residue 1004 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 167 optimal weight: 0.9990 chunk 231 optimal weight: 0.8980 chunk 347 optimal weight: 5.9990 chunk 367 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 324 optimal weight: 0.6980 chunk 475 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN A1463 HIS B 514 HIS B 893 GLN B1463 HIS C 893 GLN C1463 HIS D 893 GLN D1463 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.134862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112047 restraints weight = 59594.279| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.50 r_work: 0.3186 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 43671 Z= 0.126 Angle : 0.524 7.644 59393 Z= 0.275 Chirality : 0.039 0.170 6740 Planarity : 0.004 0.052 7504 Dihedral : 8.131 83.431 7056 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.13 % Rotamer: Outliers : 1.67 % Allowed : 17.43 % Favored : 80.90 % 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 aren not related in a simple way. whole: 1.28 (0.12), residues: 5432 helix: 2.05 (0.09), residues: 2996 sheet: -0.86 (0.24), residues: 388 loop : -0.59 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 341 TYR 0.014 0.001 TYR A 917 PHE 0.019 0.001 PHE A1068 TRP 0.012 0.001 TRP B1124 HIS 0.010 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00284 (43668) covalent geometry : angle 0.52451 (59372) SS BOND : bond 0.00061 ( 3) SS BOND : angle 0.31098 ( 21) hydrogen bonds : bond 0.03925 ( 2299) hydrogen bonds : angle 3.90949 ( 6741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16687.48 seconds wall clock time: 284 minutes 56.30 seconds (17096.30 seconds total)