Starting phenix.real_space_refine on Mon Aug 25 14:30:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h3j_51827/08_2025/9h3j_51827.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h3j_51827/08_2025/9h3j_51827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h3j_51827/08_2025/9h3j_51827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h3j_51827/08_2025/9h3j_51827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h3j_51827/08_2025/9h3j_51827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h3j_51827/08_2025/9h3j_51827.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 183 5.16 5 C 17508 2.51 5 N 4494 2.21 5 O 5400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 27585 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9013 Classifications: {'peptide': 1160} Link IDs: {'PCIS': 4, 'PTRANS': 43, 'TRANS': 1112} Chain breaks: 5 Chain: "B" Number of atoms: 9013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9013 Classifications: {'peptide': 1160} Link IDs: {'PCIS': 4, 'PTRANS': 43, 'TRANS': 1112} Chain breaks: 5 Chain: "E" Number of atoms: 9013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9013 Classifications: {'peptide': 1160} Link IDs: {'PCIS': 4, 'PTRANS': 43, 'TRANS': 1112} Chain breaks: 5 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.68, per 1000 atoms: 0.21 Number of scatterers: 27585 At special positions: 0 Unit cell: (143.84, 147.32, 160.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 183 16.00 O 5400 8.00 N 4494 7.00 C 17508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 481 " - pdb=" SG CYS A 497 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 584 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 670 " distance=2.03 Simple disulfide: pdb=" SG CYS A 695 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 812 " - pdb=" SG CYS A 834 " distance=2.03 Simple disulfide: pdb=" SG CYS A 817 " - pdb=" SG CYS A 823 " distance=2.03 Simple disulfide: pdb=" SG CYS A 924 " - pdb=" SG CYS A 935 " distance=2.03 Simple disulfide: pdb=" SG CYS A1112 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A1162 " - pdb=" SG CYS A1207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 481 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 578 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS B 695 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 812 " - pdb=" SG CYS B 834 " distance=2.03 Simple disulfide: pdb=" SG CYS B 817 " - pdb=" SG CYS B 823 " distance=2.03 Simple disulfide: pdb=" SG CYS B 924 " - pdb=" SG CYS B 935 " distance=2.03 Simple disulfide: pdb=" SG CYS B1112 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B1162 " - pdb=" SG CYS B1207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 165 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 252 " distance=2.03 Simple disulfide: pdb=" SG CYS E 286 " - pdb=" SG CYS E 296 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 356 " distance=2.03 Simple disulfide: pdb=" SG CYS E 374 " - pdb=" SG CYS E 427 " distance=2.03 Simple disulfide: pdb=" SG CYS E 386 " - pdb=" SG CYS E 601 " distance=2.03 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 548 " distance=2.03 Simple disulfide: pdb=" SG CYS E 481 " - pdb=" SG CYS E 497 " distance=2.03 Simple disulfide: pdb=" SG CYS E 483 " - pdb=" SG CYS E 563 " distance=2.03 Simple disulfide: pdb=" SG CYS E 488 " - pdb=" SG CYS E 516 " distance=2.03 Simple disulfide: pdb=" SG CYS E 506 " - pdb=" SG CYS E 518 " distance=2.03 Simple disulfide: pdb=" SG CYS E 520 " - pdb=" SG CYS E 535 " distance=2.03 Simple disulfide: pdb=" SG CYS E 558 " - pdb=" SG CYS E 565 " distance=2.03 Simple disulfide: pdb=" SG CYS E 578 " - pdb=" SG CYS E 584 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 670 " distance=2.03 Simple disulfide: pdb=" SG CYS E 695 " - pdb=" SG CYS E 719 " distance=2.03 Simple disulfide: pdb=" SG CYS E 734 " - pdb=" SG CYS E 743 " distance=2.03 Simple disulfide: pdb=" SG CYS E 812 " - pdb=" SG CYS E 834 " distance=2.03 Simple disulfide: pdb=" SG CYS E 817 " - pdb=" SG CYS E 823 " distance=2.03 Simple disulfide: pdb=" SG CYS E 924 " - pdb=" SG CYS E 935 " distance=2.03 Simple disulfide: pdb=" SG CYS E1112 " - pdb=" SG CYS E1123 " distance=2.03 Simple disulfide: pdb=" SG CYS E1162 " - pdb=" SG CYS E1207 " distance=2.03 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 Links applied NAG-ASN " NAG A1401 " - " ASN A 198 " " NAG A1402 " - " ASN A 437 " " NAG A1403 " - " ASN A 611 " " NAG A1404 " - " ASN A 635 " " NAG A1405 " - " ASN A 662 " " NAG A1407 " - " ASN A 923 " " NAG A1408 " - " ASN A1180 " " NAG A1410 " - " ASN A 682 " " NAG A1411 " - " ASN A 774 " " NAG A1412 " - " ASN A 59 " " NAG A1413 " - " ASN A1210 " " NAG B1401 " - " ASN B 198 " " NAG B1402 " - " ASN B 437 " " NAG B1403 " - " ASN B 611 " " NAG B1404 " - " ASN B 635 " " NAG B1405 " - " ASN B 662 " " NAG B1407 " - " ASN B 923 " " NAG B1408 " - " ASN B1180 " " NAG B1410 " - " ASN B 682 " " NAG B1411 " - " ASN B 774 " " NAG B1412 " - " ASN B 59 " " NAG B1413 " - " ASN B1210 " " NAG E1401 " - " ASN E 198 " " NAG E1402 " - " ASN E 437 " " NAG E1403 " - " ASN E 611 " " NAG E1404 " - " ASN E 635 " " NAG E1405 " - " ASN E 662 " " NAG E1407 " - " ASN E 923 " " NAG E1408 " - " ASN E1180 " " NAG E1410 " - " ASN E 682 " " NAG E1411 " - " ASN E 774 " " NAG E1412 " - " ASN E 59 " " NAG E1413 " - " ASN E1210 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6504 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 78 sheets defined 25.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.606A pdb=" N LYS A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.682A pdb=" N ILE A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 694 through 701 removed outlier: 3.755A pdb=" N ASN A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 783 Processing helix chain 'A' and resid 811 through 818 Processing helix chain 'A' and resid 820 through 828 Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 833 through 861 Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.710A pdb=" N GLY A 872 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 910 removed outlier: 4.148A pdb=" N LYS A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 924 removed outlier: 3.934A pdb=" N CYS A 924 " --> pdb=" O ALA A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 939 Processing helix chain 'A' and resid 950 through 964 Processing helix chain 'A' and resid 970 through 974 removed outlier: 3.910A pdb=" N ALA A 974 " --> pdb=" O THR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 989 removed outlier: 3.904A pdb=" N LEU A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 997 removed outlier: 4.050A pdb=" N LEU A 996 " --> pdb=" O THR A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1017 Processing helix chain 'A' and resid 1022 through 1045 removed outlier: 3.716A pdb=" N ASN A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1048 No H-bonds generated for 'chain 'A' and resid 1046 through 1048' Processing helix chain 'A' and resid 1056 through 1062 Processing helix chain 'A' and resid 1065 through 1113 removed outlier: 3.871A pdb=" N ARG A1075 " --> pdb=" O ALA A1071 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A1096 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.610A pdb=" N LYS B 92 " --> pdb=" O LEU B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.679A pdb=" N ILE B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.514A pdb=" N GLN B 406 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 694 through 701 removed outlier: 3.767A pdb=" N ASN B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 783 Processing helix chain 'B' and resid 811 through 818 Processing helix chain 'B' and resid 820 through 829 removed outlier: 3.747A pdb=" N GLU B 829 " --> pdb=" O GLN B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 861 Processing helix chain 'B' and resid 868 through 872 removed outlier: 3.709A pdb=" N GLY B 872 " --> pdb=" O ILE B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 910 removed outlier: 4.127A pdb=" N LYS B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 924 removed outlier: 3.927A pdb=" N CYS B 924 " --> pdb=" O ALA B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 939 Processing helix chain 'B' and resid 950 through 964 Processing helix chain 'B' and resid 970 through 974 removed outlier: 3.887A pdb=" N ALA B 974 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 989 removed outlier: 3.877A pdb=" N LEU B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 997 removed outlier: 4.012A pdb=" N LEU B 996 " --> pdb=" O THR B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1017 Processing helix chain 'B' and resid 1022 through 1045 removed outlier: 3.713A pdb=" N ASN B1035 " --> pdb=" O VAL B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1048 No H-bonds generated for 'chain 'B' and resid 1046 through 1048' Processing helix chain 'B' and resid 1056 through 1062 Processing helix chain 'B' and resid 1065 through 1113 removed outlier: 3.868A pdb=" N ARG B1075 " --> pdb=" O ALA B1071 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B1076 " --> pdb=" O GLN B1072 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B1096 " --> pdb=" O LEU B1092 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B1097 " --> pdb=" O SER B1093 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 92 removed outlier: 3.608A pdb=" N LYS E 92 " --> pdb=" O LEU E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 289 through 299 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 359 through 367 removed outlier: 3.679A pdb=" N ILE E 367 " --> pdb=" O LEU E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 382 Processing helix chain 'E' and resid 401 through 406 Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 436 through 438 No H-bonds generated for 'chain 'E' and resid 436 through 438' Processing helix chain 'E' and resid 447 through 452 Processing helix chain 'E' and resid 694 through 701 removed outlier: 3.753A pdb=" N ASN E 701 " --> pdb=" O HIS E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 779 through 783 Processing helix chain 'E' and resid 811 through 818 Processing helix chain 'E' and resid 820 through 829 removed outlier: 3.736A pdb=" N GLU E 829 " --> pdb=" O GLN E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 861 Processing helix chain 'E' and resid 868 through 872 removed outlier: 3.721A pdb=" N GLY E 872 " --> pdb=" O ILE E 869 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 910 removed outlier: 4.113A pdb=" N LYS E 909 " --> pdb=" O LEU E 905 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL E 910 " --> pdb=" O LEU E 906 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 924 removed outlier: 3.950A pdb=" N CYS E 924 " --> pdb=" O ALA E 920 " (cutoff:3.500A) Processing helix chain 'E' and resid 934 through 939 Processing helix chain 'E' and resid 950 through 964 Processing helix chain 'E' and resid 970 through 974 removed outlier: 3.872A pdb=" N ALA E 974 " --> pdb=" O THR E 971 " (cutoff:3.500A) Processing helix chain 'E' and resid 977 through 989 removed outlier: 3.861A pdb=" N LEU E 989 " --> pdb=" O ARG E 985 " (cutoff:3.500A) Processing helix chain 'E' and resid 992 through 997 removed outlier: 4.020A pdb=" N LEU E 996 " --> pdb=" O THR E 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 999 through 1017 Processing helix chain 'E' and resid 1022 through 1045 removed outlier: 3.727A pdb=" N ASN E1035 " --> pdb=" O VAL E1031 " (cutoff:3.500A) Processing helix chain 'E' and resid 1046 through 1048 No H-bonds generated for 'chain 'E' and resid 1046 through 1048' Processing helix chain 'E' and resid 1056 through 1062 Processing helix chain 'E' and resid 1065 through 1113 removed outlier: 3.882A pdb=" N ARG E1075 " --> pdb=" O ALA E1071 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU E1076 " --> pdb=" O GLN E1072 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR E1096 " --> pdb=" O LEU E1092 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU E1097 " --> pdb=" O SER E1093 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.830A pdb=" N SER A 35 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 64 removed outlier: 3.782A pdb=" N HIS A 282 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.471A pdb=" N THR A 170 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 231 through 237 removed outlier: 4.965A pdb=" N PHE A 232 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE A 223 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 213 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU A 259 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 231 through 237 removed outlier: 4.965A pdb=" N PHE A 232 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE A 223 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 213 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.794A pdb=" N SER A 110 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.172A pdb=" N VAL A 159 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A 196 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 157 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 142 through 147 Processing sheet with id=AB2, first strand: chain 'A' and resid 306 through 309 Processing sheet with id=AB3, first strand: chain 'A' and resid 320 through 323 removed outlier: 3.603A pdb=" N ARG A 668 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 664 " --> pdb=" O VAL A 634 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AB5, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.713A pdb=" N GLU A 349 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE A 387 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 595 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 369 through 375 removed outlier: 6.518A pdb=" N ALA A 369 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER A 432 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 371 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 595 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE A 387 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 600 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 466 through 470 Processing sheet with id=AB8, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AB9, first strand: chain 'A' and resid 552 through 553 Processing sheet with id=AC1, first strand: chain 'A' and resid 724 through 731 removed outlier: 4.427A pdb=" N ASN A 764 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N ALA A 728 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR A 742 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 771 through 773 Processing sheet with id=AC3, first strand: chain 'A' and resid 784 through 788 Processing sheet with id=AC4, first strand: chain 'A' and resid 792 through 802 removed outlier: 4.013A pdb=" N ILE A1130 " --> pdb=" O PHE A1145 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TYR A1147 " --> pdb=" O HIS A1128 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS A1128 " --> pdb=" O TYR A1147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 808 through 810 Processing sheet with id=AC6, first strand: chain 'A' and resid 864 through 866 removed outlier: 5.791A pdb=" N LEU A 865 " --> pdb=" O VAL B 773 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 876 through 877 Processing sheet with id=AC8, first strand: chain 'A' and resid 1161 through 1163 removed outlier: 3.537A pdb=" N ILE A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1176 through 1177 Processing sheet with id=AD1, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AD2, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.802A pdb=" N SER B 35 " --> pdb=" O ASN B 77 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 61 through 64 removed outlier: 3.786A pdb=" N HIS B 282 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AD5, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.480A pdb=" N THR B 170 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 231 through 237 removed outlier: 4.974A pdb=" N PHE B 232 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE B 223 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 213 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU B 259 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 231 through 237 removed outlier: 4.974A pdb=" N PHE B 232 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE B 223 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 213 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 110 through 114 removed outlier: 3.778A pdb=" N SER B 110 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 193 through 197 removed outlier: 7.185A pdb=" N VAL B 159 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG B 196 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE B 157 " --> pdb=" O ARG B 196 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 142 through 147 Processing sheet with id=AE2, first strand: chain 'B' and resid 306 through 309 Processing sheet with id=AE3, first strand: chain 'B' and resid 320 through 323 removed outlier: 7.042A pdb=" N VAL B 321 " --> pdb=" O ASP B 621 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 668 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 664 " --> pdb=" O VAL B 634 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 341 through 342 Processing sheet with id=AE5, first strand: chain 'B' and resid 349 through 353 removed outlier: 3.747A pdb=" N GLU B 349 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE B 387 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 595 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 369 through 375 removed outlier: 6.508A pdb=" N ALA B 369 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER B 432 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 371 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 595 " --> pdb=" O PHE B 387 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE B 387 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 600 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 466 through 470 Processing sheet with id=AE8, first strand: chain 'B' and resid 474 through 475 Processing sheet with id=AE9, first strand: chain 'B' and resid 552 through 553 Processing sheet with id=AF1, first strand: chain 'B' and resid 724 through 731 removed outlier: 4.403A pdb=" N ASN B 764 " --> pdb=" O ASN B 726 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ALA B 728 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 784 through 788 Processing sheet with id=AF3, first strand: chain 'B' and resid 792 through 802 removed outlier: 3.567A pdb=" N SER B1146 " --> pdb=" O GLY B 795 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B1130 " --> pdb=" O PHE B1145 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR B1147 " --> pdb=" O HIS B1128 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS B1128 " --> pdb=" O TYR B1147 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 808 through 810 Processing sheet with id=AF5, first strand: chain 'B' and resid 864 through 866 removed outlier: 5.774A pdb=" N LEU B 865 " --> pdb=" O VAL E 773 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'B' and resid 876 through 877 Processing sheet with id=AF7, first strand: chain 'B' and resid 1161 through 1163 removed outlier: 3.532A pdb=" N ILE B1167 " --> pdb=" O ILE B1163 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 1176 through 1177 Processing sheet with id=AF9, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AG1, first strand: chain 'E' and resid 35 through 36 removed outlier: 3.810A pdb=" N SER E 35 " --> pdb=" O ASN E 77 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 61 through 64 removed outlier: 3.794A pdb=" N HIS E 282 " --> pdb=" O ALA E 273 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AG4, first strand: chain 'E' and resid 81 through 82 removed outlier: 6.476A pdb=" N THR E 170 " --> pdb=" O THR E 251 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 231 through 237 removed outlier: 4.967A pdb=" N PHE E 232 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N PHE E 223 " --> pdb=" O PHE E 232 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR E 213 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU E 259 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 231 through 237 removed outlier: 4.967A pdb=" N PHE E 232 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N PHE E 223 " --> pdb=" O PHE E 232 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR E 213 " --> pdb=" O TYR E 220 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 110 through 114 removed outlier: 3.756A pdb=" N SER E 110 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 193 through 197 removed outlier: 7.172A pdb=" N VAL E 159 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG E 196 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE E 157 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 142 through 147 Processing sheet with id=AH1, first strand: chain 'E' and resid 306 through 309 Processing sheet with id=AH2, first strand: chain 'E' and resid 320 through 323 removed outlier: 3.538A pdb=" N ARG E 668 " --> pdb=" O ILE E 630 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR E 664 " --> pdb=" O VAL E 634 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 341 through 342 Processing sheet with id=AH4, first strand: chain 'E' and resid 349 through 353 removed outlier: 3.745A pdb=" N GLU E 349 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE E 387 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL E 595 " --> pdb=" O PHE E 387 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 369 through 375 removed outlier: 6.508A pdb=" N ALA E 369 " --> pdb=" O SER E 432 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N SER E 432 " --> pdb=" O ALA E 369 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER E 371 " --> pdb=" O TYR E 430 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL E 595 " --> pdb=" O PHE E 387 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE E 387 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR E 600 " --> pdb=" O PHE E 387 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 466 through 470 Processing sheet with id=AH7, first strand: chain 'E' and resid 474 through 475 Processing sheet with id=AH8, first strand: chain 'E' and resid 552 through 553 Processing sheet with id=AH9, first strand: chain 'E' and resid 724 through 731 removed outlier: 4.449A pdb=" N ASN E 764 " --> pdb=" O ASN E 726 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N ALA E 728 " --> pdb=" O ASN E 764 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 784 through 788 Processing sheet with id=AI2, first strand: chain 'E' and resid 792 through 802 removed outlier: 3.513A pdb=" N GLU E 799 " --> pdb=" O PHE E1142 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE E1130 " --> pdb=" O PHE E1145 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR E1147 " --> pdb=" O HIS E1128 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N HIS E1128 " --> pdb=" O TYR E1147 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 808 through 810 Processing sheet with id=AI4, first strand: chain 'E' and resid 876 through 877 Processing sheet with id=AI5, first strand: chain 'E' and resid 1161 through 1163 removed outlier: 3.533A pdb=" N ILE E1167 " --> pdb=" O ILE E1163 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 1176 through 1177 1092 hydrogen bonds defined for protein. 2964 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: 7.10 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8773 1.34 - 1.46: 6563 1.46 - 1.58: 12642 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 28206 Sorted by residual: bond pdb=" CA PRO A 968 " pdb=" C PRO A 968 " ideal model delta sigma weight residual 1.517 1.527 -0.010 9.30e-03 1.16e+04 1.08e+00 bond pdb=" N PRO B 303 " pdb=" CA PRO B 303 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.31e-02 5.83e+03 5.29e-01 bond pdb=" C PRO B 303 " pdb=" O PRO B 303 " ideal model delta sigma weight residual 1.246 1.240 0.006 8.50e-03 1.38e+04 4.54e-01 bond pdb=" CA ILE E 397 " pdb=" C ILE E 397 " ideal model delta sigma weight residual 1.528 1.522 0.005 8.50e-03 1.38e+04 4.10e-01 bond pdb=" C ILE A 788 " pdb=" O ILE A 788 " ideal model delta sigma weight residual 1.240 1.232 0.008 1.26e-02 6.30e+03 4.05e-01 ... (remaining 28201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 36904 1.02 - 2.04: 1246 2.04 - 3.07: 221 3.07 - 4.09: 50 4.09 - 5.11: 18 Bond angle restraints: 38439 Sorted by residual: angle pdb=" C ASN A 375 " pdb=" N ASN A 376 " pdb=" CA ASN A 376 " ideal model delta sigma weight residual 121.54 126.06 -4.52 1.91e+00 2.74e-01 5.59e+00 angle pdb=" C ASN E 375 " pdb=" N ASN E 376 " pdb=" CA ASN E 376 " ideal model delta sigma weight residual 121.54 125.98 -4.44 1.91e+00 2.74e-01 5.40e+00 angle pdb=" C ASN B 375 " pdb=" N ASN B 376 " pdb=" CA ASN B 376 " ideal model delta sigma weight residual 121.54 125.97 -4.43 1.91e+00 2.74e-01 5.38e+00 angle pdb=" N VAL E 738 " pdb=" CA VAL E 738 " pdb=" C VAL E 738 " ideal model delta sigma weight residual 109.34 113.76 -4.42 2.08e+00 2.31e-01 4.51e+00 angle pdb=" N SER B 602 " pdb=" CA SER B 602 " pdb=" C SER B 602 " ideal model delta sigma weight residual 110.80 115.29 -4.49 2.13e+00 2.20e-01 4.43e+00 ... (remaining 38434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 16306 17.60 - 35.20: 765 35.20 - 52.80: 142 52.80 - 70.40: 26 70.40 - 88.00: 14 Dihedral angle restraints: 17253 sinusoidal: 7092 harmonic: 10161 Sorted by residual: dihedral pdb=" CA CYS B 601 " pdb=" C CYS B 601 " pdb=" N SER B 602 " pdb=" CA SER B 602 " ideal model delta harmonic sigma weight residual 180.00 151.78 28.22 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA CYS A 601 " pdb=" C CYS A 601 " pdb=" N SER A 602 " pdb=" CA SER A 602 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA CYS E 601 " pdb=" C CYS E 601 " pdb=" N SER E 602 " pdb=" CA SER E 602 " ideal model delta harmonic sigma weight residual 180.00 152.35 27.65 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 17250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3566 0.048 - 0.096: 695 0.096 - 0.144: 191 0.144 - 0.193: 12 0.193 - 0.241: 3 Chirality restraints: 4467 Sorted by residual: chirality pdb=" C1 NAG E1408 " pdb=" ND2 ASN E1180 " pdb=" C2 NAG E1408 " pdb=" O5 NAG E1408 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG B1408 " pdb=" ND2 ASN B1180 " pdb=" C2 NAG B1408 " pdb=" O5 NAG B1408 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1 NAG A1408 " pdb=" ND2 ASN A1180 " pdb=" C2 NAG A1408 " pdb=" O5 NAG A1408 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4464 not shown) Planarity restraints: 4944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 325 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO B 326 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 326 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 326 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 325 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO E 326 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 326 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 326 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 325 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO A 326 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " 0.031 5.00e-02 4.00e+02 ... (remaining 4941 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 18107 3.05 - 3.51: 27760 3.51 - 3.97: 42363 3.97 - 4.44: 49460 4.44 - 4.90: 78095 Nonbonded interactions: 215785 Sorted by model distance: nonbonded pdb=" N VAL A1179 " pdb=" O VAL A1179 " model vdw 2.586 2.496 nonbonded pdb=" N VAL E1179 " pdb=" O VAL E1179 " model vdw 2.588 2.496 nonbonded pdb=" N VAL B1179 " pdb=" O VAL B1179 " model vdw 2.590 2.496 nonbonded pdb=" N THR E 793 " pdb=" O THR E 793 " model vdw 2.605 2.496 nonbonded pdb=" O PHE E 358 " pdb=" OG1 THR E 603 " model vdw 2.608 3.040 ... (remaining 215780 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 26.090 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 : 0.002 0.019 28308 Z= 0.105 Angle : 0.477 5.335 38676 Z= 0.255 Chirality : 0.041 0.241 4467 Planarity : 0.003 0.057 4911 Dihedral : 10.734 88.002 10542 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.13 % Allowed : 5.54 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -0.36 (0.14), residues: 3444 helix: 1.92 (0.20), residues: 756 sheet: 0.05 (0.20), residues: 660 loop : -1.25 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 583 TYR 0.009 0.001 TYR A 620 PHE 0.009 0.001 PHE B 113 TRP 0.005 0.001 TRP E 336 HIS 0.002 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00211 (28206) covalent geometry : angle 0.46882 (38439) SS BOND : bond 0.00171 ( 69) SS BOND : angle 0.72605 ( 138) hydrogen bonds : bond 0.19357 ( 1017) hydrogen bonds : angle 7.57296 ( 2964) link_NAG-ASN : bond 0.00501 ( 33) link_NAG-ASN : angle 1.68895 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 153 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9325 (mpp) cc_final: 0.8803 (mpp) REVERT: A 358 PHE cc_start: 0.6772 (m-80) cc_final: 0.6075 (m-80) REVERT: A 368 GLN cc_start: 0.9297 (tp40) cc_final: 0.8932 (tm-30) REVERT: A 409 LYS cc_start: 0.9181 (tppt) cc_final: 0.8967 (tppp) REVERT: A 412 TYR cc_start: 0.7104 (m-80) cc_final: 0.6398 (m-80) REVERT: A 843 GLU cc_start: 0.9416 (tt0) cc_final: 0.9180 (tm-30) REVERT: A 933 LEU cc_start: 0.9416 (tp) cc_final: 0.9198 (tp) REVERT: A 1014 ILE cc_start: 0.9453 (mt) cc_final: 0.9251 (mm) REVERT: A 1068 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9193 (mm-30) REVERT: A 1203 MET cc_start: 0.8998 (tpp) cc_final: 0.8631 (mmm) REVERT: B 118 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7730 (mm) REVERT: B 248 MET cc_start: 0.9276 (mpp) cc_final: 0.8729 (mpp) REVERT: B 291 MET cc_start: 0.9008 (tpt) cc_final: 0.8780 (tpt) REVERT: B 358 PHE cc_start: 0.6327 (m-80) cc_final: 0.5841 (m-80) REVERT: B 368 GLN cc_start: 0.9239 (tp40) cc_final: 0.8864 (tm-30) REVERT: B 385 MET cc_start: 0.8412 (ptp) cc_final: 0.8108 (mtm) REVERT: B 402 LYS cc_start: 0.8716 (tptm) cc_final: 0.8514 (tptt) REVERT: B 689 MET cc_start: 0.9274 (ttm) cc_final: 0.9068 (ttp) REVERT: B 849 ASP cc_start: 0.9060 (m-30) cc_final: 0.8814 (m-30) REVERT: B 860 MET cc_start: 0.9127 (mmp) cc_final: 0.8829 (tpp) REVERT: B 933 LEU cc_start: 0.9453 (tp) cc_final: 0.9208 (tp) REVERT: B 1068 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9193 (mm-30) REVERT: B 1106 MET cc_start: 0.9364 (mtm) cc_final: 0.9132 (mtt) REVERT: E 118 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7860 (mm) REVERT: E 215 GLU cc_start: 0.9177 (pp20) cc_final: 0.8857 (pp20) REVERT: E 248 MET cc_start: 0.9258 (mpp) cc_final: 0.8773 (mpp) REVERT: E 358 PHE cc_start: 0.6833 (m-80) cc_final: 0.6148 (m-80) REVERT: E 364 MET cc_start: 0.9319 (mmm) cc_final: 0.9116 (mmm) REVERT: E 368 GLN cc_start: 0.9257 (tp40) cc_final: 0.8663 (tp-100) REVERT: E 382 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9090 (mt) REVERT: E 412 TYR cc_start: 0.7055 (m-80) cc_final: 0.6824 (m-80) REVERT: E 594 ASP cc_start: 0.8919 (m-30) cc_final: 0.8699 (t70) REVERT: E 849 ASP cc_start: 0.9144 (m-30) cc_final: 0.8841 (m-30) REVERT: E 933 LEU cc_start: 0.9483 (tp) cc_final: 0.9212 (tp) REVERT: E 1200 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8455 (t0) outliers start: 95 outliers final: 51 residues processed: 244 average time/residue: 0.1528 time to fit residues: 60.9436 Evaluate side-chains 177 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 601 CYS Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 812 CYS Chi-restraints excluded: chain E residue 873 ILE Chi-restraints excluded: chain E residue 1200 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN A1058 GLN A1200 ASN B 406 GLN ** B 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN B1200 ASN E 316 GLN ** E 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.079429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.052042 restraints weight = 98148.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.053448 restraints weight = 51974.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.054359 restraints weight = 35766.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.054868 restraints weight = 28732.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.055106 restraints weight = 25328.405| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 28308 Z= 0.208 Angle : 0.559 6.880 38676 Z= 0.293 Chirality : 0.044 0.256 4467 Planarity : 0.003 0.059 4911 Dihedral : 6.133 59.726 4643 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.70 % Allowed : 7.72 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.28 (0.14), residues: 3444 helix: 1.94 (0.20), residues: 744 sheet: 0.07 (0.20), residues: 696 loop : -1.14 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.016 0.001 TYR A 195 PHE 0.017 0.001 PHE B 762 TRP 0.008 0.001 TRP B 184 HIS 0.003 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00469 (28206) covalent geometry : angle 0.54834 (38439) SS BOND : bond 0.00425 ( 69) SS BOND : angle 1.06370 ( 138) hydrogen bonds : bond 0.04515 ( 1017) hydrogen bonds : angle 5.69516 ( 2964) link_NAG-ASN : bond 0.00546 ( 33) link_NAG-ASN : angle 1.95162 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 119 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9299 (mpp) cc_final: 0.8649 (mpp) REVERT: A 358 PHE cc_start: 0.6795 (m-80) cc_final: 0.6377 (m-80) REVERT: A 360 MET cc_start: 0.9176 (mmm) cc_final: 0.8506 (mmm) REVERT: A 409 LYS cc_start: 0.9411 (tppt) cc_final: 0.9124 (tppp) REVERT: A 551 LEU cc_start: 0.8138 (tp) cc_final: 0.7661 (tt) REVERT: A 860 MET cc_start: 0.8640 (tpp) cc_final: 0.8309 (tpp) REVERT: A 1203 MET cc_start: 0.8328 (tpp) cc_final: 0.8055 (mmm) REVERT: B 118 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 248 MET cc_start: 0.9126 (mpp) cc_final: 0.8439 (mpp) REVERT: B 295 MET cc_start: 0.9171 (mtp) cc_final: 0.8901 (mtp) REVERT: B 358 PHE cc_start: 0.6430 (m-80) cc_final: 0.6074 (m-80) REVERT: B 360 MET cc_start: 0.9295 (mmm) cc_final: 0.8546 (mmm) REVERT: B 364 MET cc_start: 0.9043 (mmm) cc_final: 0.8742 (mmm) REVERT: B 385 MET cc_start: 0.8059 (ptp) cc_final: 0.7796 (mtm) REVERT: B 409 LYS cc_start: 0.9422 (tppt) cc_final: 0.9051 (tppp) REVERT: B 689 MET cc_start: 0.8722 (ttm) cc_final: 0.8461 (ttp) REVERT: B 849 ASP cc_start: 0.8363 (m-30) cc_final: 0.8082 (m-30) REVERT: B 1106 MET cc_start: 0.9114 (mtm) cc_final: 0.8886 (mtt) REVERT: E 118 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7943 (mm) REVERT: E 248 MET cc_start: 0.9224 (mpp) cc_final: 0.8693 (mpp) REVERT: E 291 MET cc_start: 0.8996 (tpt) cc_final: 0.8732 (tpp) REVERT: E 358 PHE cc_start: 0.6854 (m-80) cc_final: 0.6327 (m-80) REVERT: E 360 MET cc_start: 0.9205 (mmm) cc_final: 0.8874 (mmm) REVERT: E 368 GLN cc_start: 0.8753 (tp40) cc_final: 0.8484 (tp-100) REVERT: E 409 LYS cc_start: 0.9440 (tppt) cc_final: 0.8886 (ttmm) REVERT: E 412 TYR cc_start: 0.6999 (m-80) cc_final: 0.6030 (m-80) REVERT: E 849 ASP cc_start: 0.8621 (m-30) cc_final: 0.8320 (m-30) REVERT: E 1200 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8280 (t0) outliers start: 82 outliers final: 58 residues processed: 196 average time/residue: 0.1439 time to fit residues: 47.6157 Evaluate side-chains 170 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 109 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 601 CYS Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1058 GLN Chi-restraints excluded: chain E residue 1068 GLU Chi-restraints excluded: chain E residue 1200 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 217 optimal weight: 3.9990 chunk 270 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 209 optimal weight: 0.0010 chunk 51 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN B 269 GLN B 455 ASN B 796 ASN B1058 GLN E 455 ASN E 596 ASN E 796 ASN E1058 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.080351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.052473 restraints weight = 96096.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.053810 restraints weight = 52218.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.054662 restraints weight = 36655.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.055147 restraints weight = 29697.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055483 restraints weight = 26398.006| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28308 Z= 0.213 Angle : 0.557 7.124 38676 Z= 0.292 Chirality : 0.044 0.265 4467 Planarity : 0.003 0.060 4911 Dihedral : 6.013 59.789 4634 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.00 % Allowed : 8.97 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.28 (0.14), residues: 3444 helix: 1.96 (0.20), residues: 747 sheet: -0.08 (0.20), residues: 723 loop : -1.11 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.011 0.001 TYR B 784 PHE 0.017 0.001 PHE B 762 TRP 0.007 0.001 TRP B 184 HIS 0.004 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00480 (28206) covalent geometry : angle 0.54719 (38439) SS BOND : bond 0.00316 ( 69) SS BOND : angle 0.99717 ( 138) hydrogen bonds : bond 0.04111 ( 1017) hydrogen bonds : angle 5.40841 ( 2964) link_NAG-ASN : bond 0.00537 ( 33) link_NAG-ASN : angle 1.93148 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 112 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9273 (mpp) cc_final: 0.8605 (mpp) REVERT: A 358 PHE cc_start: 0.6855 (m-80) cc_final: 0.6292 (m-80) REVERT: A 360 MET cc_start: 0.9397 (mmm) cc_final: 0.8676 (mmm) REVERT: A 364 MET cc_start: 0.9137 (mmm) cc_final: 0.8799 (mmm) REVERT: A 385 MET cc_start: 0.8166 (mtm) cc_final: 0.7888 (mtm) REVERT: A 409 LYS cc_start: 0.9325 (tppt) cc_final: 0.8714 (ttmm) REVERT: A 551 LEU cc_start: 0.8140 (tp) cc_final: 0.7680 (tt) REVERT: A 860 MET cc_start: 0.8609 (tpp) cc_final: 0.8290 (tpp) REVERT: A 917 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8752 (m-10) REVERT: A 1203 MET cc_start: 0.8402 (tpp) cc_final: 0.8102 (mmm) REVERT: B 118 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7803 (mm) REVERT: B 248 MET cc_start: 0.9078 (mpp) cc_final: 0.8361 (mpp) REVERT: B 295 MET cc_start: 0.9143 (mtp) cc_final: 0.8867 (mtp) REVERT: B 358 PHE cc_start: 0.6499 (m-80) cc_final: 0.6082 (m-80) REVERT: B 360 MET cc_start: 0.9264 (mmm) cc_final: 0.8850 (mmm) REVERT: B 385 MET cc_start: 0.8093 (ptp) cc_final: 0.7839 (mtm) REVERT: B 689 MET cc_start: 0.8746 (ttm) cc_final: 0.8487 (ttp) REVERT: B 846 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 849 ASP cc_start: 0.8366 (m-30) cc_final: 0.8076 (m-30) REVERT: E 118 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7941 (mm) REVERT: E 195 TYR cc_start: 0.7506 (t80) cc_final: 0.7279 (t80) REVERT: E 248 MET cc_start: 0.9238 (mpp) cc_final: 0.8634 (mpp) REVERT: E 358 PHE cc_start: 0.6887 (m-80) cc_final: 0.6349 (m-80) REVERT: E 409 LYS cc_start: 0.9450 (tppt) cc_final: 0.8878 (ttmm) REVERT: E 849 ASP cc_start: 0.8638 (m-30) cc_final: 0.8333 (m-30) REVERT: E 1200 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8298 (t0) outliers start: 91 outliers final: 63 residues processed: 200 average time/residue: 0.1323 time to fit residues: 45.1895 Evaluate side-chains 176 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 109 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 917 PHE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1201 VAL Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 601 CYS Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 812 CYS Chi-restraints excluded: chain E residue 1200 ASN Chi-restraints excluded: chain E residue 1201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 14 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 157 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 332 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 146 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN A 581 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN B 471 GLN B1058 GLN E 368 GLN E 596 ASN ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.078991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.051620 restraints weight = 98679.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.052997 restraints weight = 52663.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.053819 restraints weight = 36519.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054317 restraints weight = 29593.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054584 restraints weight = 26219.485| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28308 Z= 0.226 Angle : 0.562 6.427 38676 Z= 0.293 Chirality : 0.044 0.269 4467 Planarity : 0.003 0.060 4911 Dihedral : 6.076 59.968 4633 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.10 % Allowed : 10.29 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.29 (0.14), residues: 3444 helix: 2.00 (0.20), residues: 747 sheet: -0.16 (0.19), residues: 747 loop : -1.11 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 362 TYR 0.013 0.001 TYR B 412 PHE 0.017 0.001 PHE B 762 TRP 0.007 0.001 TRP E 184 HIS 0.004 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00509 (28206) covalent geometry : angle 0.55275 (38439) SS BOND : bond 0.00315 ( 69) SS BOND : angle 0.88527 ( 138) hydrogen bonds : bond 0.03971 ( 1017) hydrogen bonds : angle 5.23595 ( 2964) link_NAG-ASN : bond 0.00535 ( 33) link_NAG-ASN : angle 1.88255 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 111 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9276 (mpp) cc_final: 0.8569 (mpp) REVERT: A 358 PHE cc_start: 0.6855 (m-80) cc_final: 0.6463 (m-80) REVERT: A 360 MET cc_start: 0.9371 (mmm) cc_final: 0.8971 (mmm) REVERT: A 363 LEU cc_start: 0.9381 (tt) cc_final: 0.9159 (mt) REVERT: A 409 LYS cc_start: 0.9245 (tppt) cc_final: 0.8936 (tppp) REVERT: A 551 LEU cc_start: 0.8182 (tp) cc_final: 0.7713 (tt) REVERT: A 846 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8432 (tm-30) REVERT: A 860 MET cc_start: 0.8526 (tpp) cc_final: 0.8276 (tpp) REVERT: A 917 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.8761 (m-10) REVERT: A 1203 MET cc_start: 0.8652 (tpp) cc_final: 0.8386 (mmm) REVERT: B 118 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7823 (mm) REVERT: B 295 MET cc_start: 0.9115 (mtp) cc_final: 0.8875 (mtp) REVERT: B 358 PHE cc_start: 0.6589 (m-80) cc_final: 0.6172 (m-80) REVERT: B 360 MET cc_start: 0.9242 (mmm) cc_final: 0.8911 (mmm) REVERT: B 364 MET cc_start: 0.8962 (mmm) cc_final: 0.8749 (mmm) REVERT: B 409 LYS cc_start: 0.9368 (tppt) cc_final: 0.9040 (tppp) REVERT: B 689 MET cc_start: 0.8798 (ttm) cc_final: 0.8537 (ttp) REVERT: B 846 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8317 (tm-30) REVERT: B 849 ASP cc_start: 0.8352 (m-30) cc_final: 0.8051 (m-30) REVERT: B 1176 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: E 118 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7803 (mm) REVERT: E 195 TYR cc_start: 0.7512 (t80) cc_final: 0.7296 (t80) REVERT: E 248 MET cc_start: 0.9239 (mpp) cc_final: 0.8584 (mpp) REVERT: E 358 PHE cc_start: 0.7014 (m-80) cc_final: 0.6502 (m-80) REVERT: E 409 LYS cc_start: 0.9431 (tppt) cc_final: 0.8816 (ttmm) REVERT: E 849 ASP cc_start: 0.8568 (m-30) cc_final: 0.8266 (m-30) REVERT: E 1200 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8330 (t0) REVERT: E 1204 MET cc_start: 0.8619 (mtp) cc_final: 0.8263 (mtp) outliers start: 94 outliers final: 65 residues processed: 201 average time/residue: 0.1388 time to fit residues: 47.2582 Evaluate side-chains 176 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 106 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 917 PHE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1201 VAL Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 601 CYS Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 812 CYS Chi-restraints excluded: chain E residue 1068 GLU Chi-restraints excluded: chain E residue 1200 ASN Chi-restraints excluded: chain E residue 1201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 101 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 320 optimal weight: 9.9990 chunk 229 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 308 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 263 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 596 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 ASN A1058 GLN B1058 GLN E 269 GLN E 368 GLN E 455 ASN ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.079610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.052625 restraints weight = 100501.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.054124 restraints weight = 52115.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.054975 restraints weight = 35317.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.055481 restraints weight = 27893.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.055808 restraints weight = 24610.529| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28308 Z= 0.091 Angle : 0.503 9.255 38676 Z= 0.262 Chirality : 0.043 0.402 4467 Planarity : 0.003 0.057 4911 Dihedral : 5.749 57.593 4633 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.44 % Allowed : 11.41 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.14 (0.14), residues: 3444 helix: 2.11 (0.20), residues: 747 sheet: 0.19 (0.20), residues: 708 loop : -1.11 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 362 TYR 0.012 0.001 TYR A 162 PHE 0.013 0.001 PHE E 290 TRP 0.011 0.001 TRP B 336 HIS 0.003 0.001 HIS E1128 Details of bonding type rmsd covalent geometry : bond 0.00192 (28206) covalent geometry : angle 0.49496 (38439) SS BOND : bond 0.00206 ( 69) SS BOND : angle 0.74939 ( 138) hydrogen bonds : bond 0.03323 ( 1017) hydrogen bonds : angle 4.82450 ( 2964) link_NAG-ASN : bond 0.00525 ( 33) link_NAG-ASN : angle 1.73977 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 117 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9312 (mpp) cc_final: 0.8666 (mpp) REVERT: A 358 PHE cc_start: 0.6659 (m-80) cc_final: 0.6401 (m-80) REVERT: A 360 MET cc_start: 0.9292 (mmm) cc_final: 0.8847 (mmm) REVERT: A 363 LEU cc_start: 0.9365 (tt) cc_final: 0.9053 (mt) REVERT: A 364 MET cc_start: 0.9124 (mmm) cc_final: 0.8701 (mmm) REVERT: A 409 LYS cc_start: 0.9215 (tppt) cc_final: 0.8934 (tppp) REVERT: A 860 MET cc_start: 0.8508 (tpp) cc_final: 0.8044 (tpp) REVERT: A 917 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8499 (m-10) REVERT: A 933 LEU cc_start: 0.9129 (tp) cc_final: 0.8911 (tp) REVERT: B 118 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7707 (mm) REVERT: B 248 MET cc_start: 0.9274 (mpp) cc_final: 0.8696 (mpp) REVERT: B 402 LYS cc_start: 0.9072 (tptt) cc_final: 0.8711 (tptt) REVERT: B 409 LYS cc_start: 0.9409 (tppt) cc_final: 0.8968 (tppp) REVERT: B 689 MET cc_start: 0.8706 (ttm) cc_final: 0.8442 (ttp) REVERT: B 846 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 849 ASP cc_start: 0.8396 (m-30) cc_final: 0.8084 (m-30) REVERT: E 118 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7755 (mm) REVERT: E 195 TYR cc_start: 0.7477 (t80) cc_final: 0.7128 (t80) REVERT: E 215 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8790 (tt0) REVERT: E 248 MET cc_start: 0.9270 (mpp) cc_final: 0.8622 (mpp) REVERT: E 358 PHE cc_start: 0.6842 (m-80) cc_final: 0.6460 (m-80) REVERT: E 849 ASP cc_start: 0.8567 (m-30) cc_final: 0.8250 (m-30) REVERT: E 1200 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8225 (t0) outliers start: 74 outliers final: 45 residues processed: 186 average time/residue: 0.1379 time to fit residues: 42.8038 Evaluate side-chains 155 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 105 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 917 PHE Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 812 CYS Chi-restraints excluded: chain E residue 1200 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 75 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 339 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 336 optimal weight: 7.9990 chunk 320 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 chunk 318 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 GLN A1058 GLN B1044 GLN B1058 GLN E 471 GLN E 596 ASN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.077935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.050740 restraints weight = 100886.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.052085 restraints weight = 54042.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.053012 restraints weight = 37886.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.053514 restraints weight = 30328.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.053723 restraints weight = 26769.478| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 28308 Z= 0.289 Angle : 0.614 10.457 38676 Z= 0.316 Chirality : 0.045 0.550 4467 Planarity : 0.004 0.060 4911 Dihedral : 6.004 55.382 4619 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.64 % Allowed : 12.56 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.27 (0.14), residues: 3444 helix: 1.99 (0.20), residues: 747 sheet: -0.09 (0.19), residues: 747 loop : -1.12 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 324 TYR 0.017 0.001 TYR E 412 PHE 0.019 0.001 PHE B 762 TRP 0.005 0.001 TRP E 184 HIS 0.004 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00648 (28206) covalent geometry : angle 0.60489 (38439) SS BOND : bond 0.00391 ( 69) SS BOND : angle 0.95076 ( 138) hydrogen bonds : bond 0.03967 ( 1017) hydrogen bonds : angle 5.07898 ( 2964) link_NAG-ASN : bond 0.00737 ( 33) link_NAG-ASN : angle 2.02423 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 109 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9270 (mpp) cc_final: 0.8506 (mpp) REVERT: A 358 PHE cc_start: 0.6878 (m-80) cc_final: 0.6525 (m-80) REVERT: A 360 MET cc_start: 0.9337 (mmm) cc_final: 0.8807 (mmm) REVERT: A 363 LEU cc_start: 0.9401 (tt) cc_final: 0.9090 (mt) REVERT: A 364 MET cc_start: 0.9165 (mmm) cc_final: 0.8717 (mmm) REVERT: A 385 MET cc_start: 0.8511 (mmm) cc_final: 0.8281 (tpp) REVERT: A 551 LEU cc_start: 0.8117 (tp) cc_final: 0.7739 (tt) REVERT: A 846 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8404 (tm-30) REVERT: A 860 MET cc_start: 0.8626 (tpp) cc_final: 0.8151 (tpp) REVERT: A 1176 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: B 118 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7758 (mm) REVERT: B 248 MET cc_start: 0.9142 (mpp) cc_final: 0.8463 (mpp) REVERT: B 385 MET cc_start: 0.8325 (mmm) cc_final: 0.8074 (tpp) REVERT: B 409 LYS cc_start: 0.9298 (tppt) cc_final: 0.8990 (tptp) REVERT: B 689 MET cc_start: 0.8762 (ttm) cc_final: 0.8480 (ttp) REVERT: B 846 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8357 (tm-30) REVERT: B 849 ASP cc_start: 0.8401 (m-30) cc_final: 0.8103 (m-30) REVERT: B 1176 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: E 118 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7877 (mm) REVERT: E 195 TYR cc_start: 0.7561 (t80) cc_final: 0.7281 (t80) REVERT: E 248 MET cc_start: 0.9268 (mpp) cc_final: 0.8585 (mpp) REVERT: E 358 PHE cc_start: 0.7036 (m-80) cc_final: 0.6534 (m-80) REVERT: E 551 LEU cc_start: 0.7842 (tp) cc_final: 0.7436 (tt) REVERT: E 846 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8390 (tm-30) REVERT: E 849 ASP cc_start: 0.8567 (m-30) cc_final: 0.8256 (m-30) outliers start: 80 outliers final: 56 residues processed: 184 average time/residue: 0.1385 time to fit residues: 43.0210 Evaluate side-chains 165 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 105 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 812 CYS Chi-restraints excluded: chain E residue 1068 GLU Chi-restraints excluded: chain E residue 1201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 283 optimal weight: 7.9990 chunk 211 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 123 optimal weight: 0.0060 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN B1058 GLN ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 GLN E1200 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.081260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.053503 restraints weight = 95805.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054897 restraints weight = 52088.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055745 restraints weight = 36549.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056320 restraints weight = 29735.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.056487 restraints weight = 26150.534| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 28308 Z= 0.104 Angle : 0.520 10.228 38676 Z= 0.271 Chirality : 0.043 0.347 4467 Planarity : 0.003 0.057 4911 Dihedral : 5.667 53.078 4616 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.31 % Allowed : 12.96 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.16 (0.14), residues: 3444 helix: 2.06 (0.20), residues: 750 sheet: 0.18 (0.19), residues: 726 loop : -1.13 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 362 TYR 0.010 0.001 TYR E 162 PHE 0.018 0.001 PHE B 358 TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS E1128 Details of bonding type rmsd covalent geometry : bond 0.00233 (28206) covalent geometry : angle 0.51060 (38439) SS BOND : bond 0.00223 ( 69) SS BOND : angle 1.03624 ( 138) hydrogen bonds : bond 0.03428 ( 1017) hydrogen bonds : angle 4.77509 ( 2964) link_NAG-ASN : bond 0.00567 ( 33) link_NAG-ASN : angle 1.73631 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 105 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9245 (mpp) cc_final: 0.8525 (mpp) REVERT: A 360 MET cc_start: 0.9311 (mmm) cc_final: 0.8927 (mmm) REVERT: A 363 LEU cc_start: 0.9343 (tt) cc_final: 0.9126 (mt) REVERT: A 364 MET cc_start: 0.9140 (mmm) cc_final: 0.8685 (mmp) REVERT: A 385 MET cc_start: 0.8556 (mmm) cc_final: 0.8285 (mmt) REVERT: A 846 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8393 (tm-30) REVERT: A 860 MET cc_start: 0.8474 (tpp) cc_final: 0.8057 (tpp) REVERT: A 917 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.8594 (m-10) REVERT: A 933 LEU cc_start: 0.9199 (tp) cc_final: 0.8966 (tp) REVERT: A 993 MET cc_start: 0.8616 (mmm) cc_final: 0.8277 (tpt) REVERT: B 118 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7746 (mm) REVERT: B 364 MET cc_start: 0.8895 (mmm) cc_final: 0.8547 (mmm) REVERT: B 409 LYS cc_start: 0.9405 (tppt) cc_final: 0.9043 (tptp) REVERT: B 689 MET cc_start: 0.8710 (ttm) cc_final: 0.8437 (ttp) REVERT: B 846 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8278 (tm-30) REVERT: B 849 ASP cc_start: 0.8368 (m-30) cc_final: 0.8058 (m-30) REVERT: E 118 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7824 (mm) REVERT: E 195 TYR cc_start: 0.7443 (t80) cc_final: 0.7133 (t80) REVERT: E 248 MET cc_start: 0.9264 (mpp) cc_final: 0.8565 (mpp) REVERT: E 358 PHE cc_start: 0.6598 (m-80) cc_final: 0.6344 (m-80) REVERT: E 385 MET cc_start: 0.8699 (mmm) cc_final: 0.8427 (tpp) REVERT: E 846 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8366 (tm-30) REVERT: E 849 ASP cc_start: 0.8554 (m-30) cc_final: 0.8209 (m-30) outliers start: 70 outliers final: 53 residues processed: 171 average time/residue: 0.1448 time to fit residues: 41.3924 Evaluate side-chains 159 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 103 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 917 PHE Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 812 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 91 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 248 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN B1058 GLN ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.080968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.053185 restraints weight = 96600.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.054501 restraints weight = 52505.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.055349 restraints weight = 37164.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.055882 restraints weight = 30297.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.056111 restraints weight = 26809.154| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28308 Z= 0.133 Angle : 0.521 11.717 38676 Z= 0.269 Chirality : 0.044 0.610 4467 Planarity : 0.003 0.058 4911 Dihedral : 5.705 55.463 4616 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.24 % Allowed : 12.86 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.10 (0.14), residues: 3444 helix: 2.29 (0.20), residues: 732 sheet: 0.18 (0.19), residues: 729 loop : -1.12 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 362 TYR 0.010 0.001 TYR B1211 PHE 0.021 0.001 PHE B 358 TRP 0.008 0.001 TRP A 184 HIS 0.003 0.001 HIS E1128 Details of bonding type rmsd covalent geometry : bond 0.00303 (28206) covalent geometry : angle 0.50783 (38439) SS BOND : bond 0.00249 ( 69) SS BOND : angle 0.94018 ( 138) hydrogen bonds : bond 0.03406 ( 1017) hydrogen bonds : angle 4.71846 ( 2964) link_NAG-ASN : bond 0.00672 ( 33) link_NAG-ASN : angle 2.14956 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 108 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9236 (mpp) cc_final: 0.8504 (mpp) REVERT: A 360 MET cc_start: 0.9315 (mmm) cc_final: 0.8914 (mmm) REVERT: A 364 MET cc_start: 0.9161 (mmm) cc_final: 0.8840 (mmp) REVERT: A 385 MET cc_start: 0.8475 (mmm) cc_final: 0.7974 (mmm) REVERT: A 551 LEU cc_start: 0.8224 (tp) cc_final: 0.7794 (tt) REVERT: A 630 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 846 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 860 MET cc_start: 0.8475 (tpp) cc_final: 0.8043 (tpp) REVERT: A 933 LEU cc_start: 0.9218 (tp) cc_final: 0.8993 (tp) REVERT: A 993 MET cc_start: 0.8519 (mmm) cc_final: 0.8003 (mmm) REVERT: A 1203 MET cc_start: 0.9062 (tpp) cc_final: 0.8832 (tpp) REVERT: B 118 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7795 (mm) REVERT: B 248 MET cc_start: 0.9033 (mpp) cc_final: 0.8623 (mpp) REVERT: B 364 MET cc_start: 0.8959 (mmm) cc_final: 0.8660 (mmm) REVERT: B 409 LYS cc_start: 0.9400 (tppt) cc_final: 0.9026 (tptp) REVERT: B 689 MET cc_start: 0.8729 (ttm) cc_final: 0.8454 (ttp) REVERT: B 849 ASP cc_start: 0.8350 (m-30) cc_final: 0.8050 (m-30) REVERT: E 118 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7870 (mm) REVERT: E 195 TYR cc_start: 0.7425 (t80) cc_final: 0.7147 (t80) REVERT: E 248 MET cc_start: 0.9225 (mpp) cc_final: 0.8529 (mpp) REVERT: E 358 PHE cc_start: 0.6614 (m-80) cc_final: 0.6316 (m-80) REVERT: E 385 MET cc_start: 0.8720 (mmm) cc_final: 0.8264 (tpp) REVERT: E 551 LEU cc_start: 0.8028 (tp) cc_final: 0.7517 (tt) REVERT: E 846 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8366 (tm-30) REVERT: E 849 ASP cc_start: 0.8529 (m-30) cc_final: 0.8187 (m-30) outliers start: 68 outliers final: 58 residues processed: 171 average time/residue: 0.1496 time to fit residues: 43.2083 Evaluate side-chains 167 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 106 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 812 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 53 optimal weight: 0.9980 chunk 296 optimal weight: 10.0000 chunk 335 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 303 optimal weight: 0.6980 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.080767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.053033 restraints weight = 96829.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.054371 restraints weight = 52738.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.055217 restraints weight = 37140.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.055735 restraints weight = 30138.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055977 restraints weight = 26747.686| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28308 Z= 0.166 Angle : 0.533 12.932 38676 Z= 0.277 Chirality : 0.043 0.487 4467 Planarity : 0.003 0.058 4911 Dihedral : 5.714 58.144 4616 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.24 % Allowed : 13.16 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.11 (0.14), residues: 3444 helix: 2.29 (0.20), residues: 732 sheet: 0.19 (0.19), residues: 729 loop : -1.14 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 362 TYR 0.010 0.001 TYR B1147 PHE 0.021 0.001 PHE B 358 TRP 0.006 0.001 TRP A 336 HIS 0.003 0.001 HIS E1128 Details of bonding type rmsd covalent geometry : bond 0.00376 (28206) covalent geometry : angle 0.52109 (38439) SS BOND : bond 0.00270 ( 69) SS BOND : angle 0.91910 ( 138) hydrogen bonds : bond 0.03508 ( 1017) hydrogen bonds : angle 4.74754 ( 2964) link_NAG-ASN : bond 0.00554 ( 33) link_NAG-ASN : angle 2.12255 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 107 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9224 (mpp) cc_final: 0.8491 (mpp) REVERT: A 551 LEU cc_start: 0.8260 (tp) cc_final: 0.7810 (tt) REVERT: A 630 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8269 (mp) REVERT: A 846 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8623 (tm-30) REVERT: A 860 MET cc_start: 0.8532 (tpp) cc_final: 0.8089 (tpp) REVERT: A 993 MET cc_start: 0.8495 (mmm) cc_final: 0.7958 (mmm) REVERT: B 118 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7792 (mm) REVERT: B 248 MET cc_start: 0.9078 (mpp) cc_final: 0.8621 (mpp) REVERT: B 360 MET cc_start: 0.9180 (mmm) cc_final: 0.8812 (mmm) REVERT: B 402 LYS cc_start: 0.9107 (tptt) cc_final: 0.8904 (tptt) REVERT: B 689 MET cc_start: 0.8760 (ttm) cc_final: 0.8484 (ttp) REVERT: B 846 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8335 (tm-30) REVERT: B 849 ASP cc_start: 0.8321 (m-30) cc_final: 0.8019 (m-30) REVERT: B 1176 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: E 118 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7895 (mm) REVERT: E 195 TYR cc_start: 0.7440 (t80) cc_final: 0.7173 (t80) REVERT: E 215 GLU cc_start: 0.8914 (tt0) cc_final: 0.8640 (tt0) REVERT: E 248 MET cc_start: 0.9231 (mpp) cc_final: 0.8522 (mpp) REVERT: E 358 PHE cc_start: 0.6647 (m-80) cc_final: 0.6327 (m-80) REVERT: E 385 MET cc_start: 0.8717 (mmm) cc_final: 0.8308 (mmm) REVERT: E 551 LEU cc_start: 0.8076 (tp) cc_final: 0.7545 (tt) REVERT: E 846 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8403 (tm-30) REVERT: E 849 ASP cc_start: 0.8551 (m-30) cc_final: 0.8210 (m-30) outliers start: 68 outliers final: 58 residues processed: 171 average time/residue: 0.1359 time to fit residues: 39.1956 Evaluate side-chains 165 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 103 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 812 CYS Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 812 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 37 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A1058 GLN B1058 GLN ** E 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 861 ASN E1058 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.068244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.043739 restraints weight = 117162.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.045245 restraints weight = 56523.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.046221 restraints weight = 36299.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.046789 restraints weight = 27678.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.047202 restraints weight = 23588.549| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 28308 Z= 0.270 Angle : 0.611 13.879 38676 Z= 0.314 Chirality : 0.045 0.476 4467 Planarity : 0.003 0.059 4911 Dihedral : 6.031 58.420 4616 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.21 % Allowed : 13.62 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.30 (0.14), residues: 3444 helix: 1.89 (0.20), residues: 768 sheet: -0.04 (0.19), residues: 753 loop : -1.18 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 362 TYR 0.012 0.001 TYR B 784 PHE 0.018 0.001 PHE B 358 TRP 0.006 0.001 TRP B 261 HIS 0.005 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00608 (28206) covalent geometry : angle 0.59951 (38439) SS BOND : bond 0.00375 ( 69) SS BOND : angle 1.01327 ( 138) hydrogen bonds : bond 0.03962 ( 1017) hydrogen bonds : angle 4.99059 ( 2964) link_NAG-ASN : bond 0.00622 ( 33) link_NAG-ASN : angle 2.24167 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 103 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.9292 (mpp) cc_final: 0.8558 (mpp) REVERT: A 385 MET cc_start: 0.8419 (mmm) cc_final: 0.7990 (mmm) REVERT: A 551 LEU cc_start: 0.8484 (tp) cc_final: 0.7987 (tt) REVERT: A 846 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8665 (tm-30) REVERT: A 860 MET cc_start: 0.8552 (tpp) cc_final: 0.8156 (tpp) REVERT: A 993 MET cc_start: 0.8520 (mmm) cc_final: 0.7985 (mmm) REVERT: B 118 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7654 (mm) REVERT: B 197 ARG cc_start: 0.8861 (ttt180) cc_final: 0.8395 (ptm160) REVERT: B 248 MET cc_start: 0.9330 (mpp) cc_final: 0.8855 (mpp) REVERT: B 689 MET cc_start: 0.8828 (ttm) cc_final: 0.8550 (ttp) REVERT: B 849 ASP cc_start: 0.8425 (m-30) cc_final: 0.8129 (m-30) REVERT: B 1176 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: E 118 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7753 (mm) REVERT: E 248 MET cc_start: 0.9271 (mpp) cc_final: 0.8562 (mpp) REVERT: E 364 MET cc_start: 0.9204 (mmm) cc_final: 0.8434 (mpp) REVERT: E 385 MET cc_start: 0.8753 (mmm) cc_final: 0.8466 (mmt) REVERT: E 551 LEU cc_start: 0.8309 (tp) cc_final: 0.7750 (tt) REVERT: E 846 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8458 (tm-30) REVERT: E 849 ASP cc_start: 0.8566 (m-30) cc_final: 0.8265 (m-30) outliers start: 67 outliers final: 55 residues processed: 165 average time/residue: 0.1585 time to fit residues: 44.3525 Evaluate side-chains 162 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 104 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 812 CYS Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 565 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1206 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 616 VAL Chi-restraints excluded: chain E residue 689 MET Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 812 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 210 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 229 optimal weight: 0.5980 chunk 330 optimal weight: 4.9990 chunk 335 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A1058 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.045155 restraints weight = 114316.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.046767 restraints weight = 53413.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.047794 restraints weight = 33795.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.048443 restraints weight = 25508.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048813 restraints weight = 21500.469| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 28308 Z= 0.117 Angle : 0.537 13.441 38676 Z= 0.278 Chirality : 0.043 0.412 4467 Planarity : 0.003 0.057 4911 Dihedral : 5.583 53.819 4613 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.04 % Allowed : 13.95 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: -0.16 (0.14), residues: 3444 helix: 2.08 (0.20), residues: 750 sheet: 0.32 (0.20), residues: 690 loop : -1.18 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 324 TYR 0.010 0.001 TYR E 162 PHE 0.021 0.001 PHE B 358 TRP 0.010 0.001 TRP B 336 HIS 0.003 0.001 HIS E1128 Details of bonding type rmsd covalent geometry : bond 0.00265 (28206) covalent geometry : angle 0.52441 (38439) SS BOND : bond 0.00233 ( 69) SS BOND : angle 1.07505 ( 138) hydrogen bonds : bond 0.03498 ( 1017) hydrogen bonds : angle 4.71446 ( 2964) link_NAG-ASN : bond 0.00555 ( 33) link_NAG-ASN : angle 2.05449 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4066.12 seconds wall clock time: 71 minutes 14.98 seconds (4274.98 seconds total)