Starting phenix.real_space_refine on Fri Mar 6 13:29:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q9i_13870/03_2026/7q9i_13870.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9i_13870/03_2026/7q9i_13870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q9i_13870/03_2026/7q9i_13870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9i_13870/03_2026/7q9i_13870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q9i_13870/03_2026/7q9i_13870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9i_13870/03_2026/7q9i_13870.map" } resolution = 4.9 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= 0.002 sd= 0.023 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 138 5.16 5 C 19693 2.51 5 N 5098 2.21 5 O 6037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30966 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8290 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 53, 'TRANS': 1008} Chain breaks: 6 Chain: "B" Number of atoms: 8267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8267 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Chain: "C" Number of atoms: 8273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8273 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 53, 'TRANS': 1005} Chain breaks: 6 Chain: "H" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 983 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 983 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "J" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 983 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.27, per 1000 atoms: 0.20 Number of scatterers: 30966 At special positions: 0 Unit cell: (205.84, 192.56, 190.9, 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 138 16.00 O 6037 8.00 N 5098 7.00 C 19693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.02 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.02 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.02 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 106 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 106 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 87 " distance=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 340 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 279 " " NAG A1304 " - " ASN A 600 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 328 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 340 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 328 " " NAG C1309 " - " ASN C 340 " " NAG D 1 " - " ASN A 714 " " NAG G 1 " - " ASN A 798 " " NAG I 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG N 1 " - " ASN B 714 " " NAG O 1 " - " ASN B 798 " " NAG P 1 " - " ASN B1095 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN C 714 " " NAG S 1 " - " ASN C 798 " " NAG T 1 " - " ASN C1095 " " NAG U 1 " - " ASN C1131 " Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 938.5 milliseconds 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7178 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 72 sheets defined 22.2% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.290A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.592A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.301A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 405' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.521A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.043A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1031 removed outlier: 4.331A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.235A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.692A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.199A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.833A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 907 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.002A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.594A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.061A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.948A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.555A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.485A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.896A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.835A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 909 through 916 removed outlier: 3.908A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.801A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.524A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1031 removed outlier: 3.945A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.852A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 26 through 30 Processing helix chain 'K' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.421A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.816A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.917A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.917A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.889A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 3.913A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.533A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.146A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.024A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.382A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.507A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.586A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 260 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.786A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.896A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.896A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 308 through 315 removed outlier: 5.368A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.793A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ASN B 539 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.793A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ASN B 539 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AD1, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.730A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD3, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.659A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.994A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AD6, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AD7, first strand: chain 'B' and resid 715 through 725 removed outlier: 7.083A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.434A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.517A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AE2, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.735A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.857A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.902A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.902A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 141 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 143 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.288A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 321 through 325 removed outlier: 3.864A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.743A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.731A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.385A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AF6, first strand: chain 'C' and resid 715 through 725 removed outlier: 6.978A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.397A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.527A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.776A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.204A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.709A pdb=" N VAL L 70 " --> pdb=" O CYS L 22 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.519A pdb=" N ILE L 47 " --> pdb=" O TRP L 34 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AG7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.775A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.203A pdb=" N VAL E 115 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 4 through 5 removed outlier: 4.709A pdb=" N VAL F 70 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.519A pdb=" N ILE F 47 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN F 36 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU F 45 " --> pdb=" O GLN F 36 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AH4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AH5, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.776A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.203A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 4 through 5 removed outlier: 4.710A pdb=" N VAL K 70 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.518A pdb=" N ILE K 47 " --> pdb=" O TRP K 34 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN K 36 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU K 45 " --> pdb=" O GLN K 36 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 9 through 12 1379 hydrogen bonds defined for protein. 3654 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: 8.35 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: 9846 1.34 - 1.46: 7862 1.46 - 1.58: 13807 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 31689 Sorted by residual: bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C ILE B 802 " pdb=" N LEU B 803 " ideal model delta sigma weight residual 1.331 1.274 0.057 2.83e-02 1.25e+03 4.10e+00 bond pdb=" CA GLN B 318 " pdb=" CB GLN B 318 " ideal model delta sigma weight residual 1.530 1.561 -0.032 1.58e-02 4.01e+03 3.98e+00 ... (remaining 31684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 42408 1.87 - 3.74: 679 3.74 - 5.61: 35 5.61 - 7.48: 1 7.48 - 9.35: 1 Bond angle restraints: 43124 Sorted by residual: angle pdb=" C VAL B 317 " pdb=" N GLN B 318 " pdb=" CA GLN B 318 " ideal model delta sigma weight residual 121.80 131.15 -9.35 2.44e+00 1.68e-01 1.47e+01 angle pdb=" N GLN B 318 " pdb=" CA GLN B 318 " pdb=" CB GLN B 318 " ideal model delta sigma weight residual 110.37 116.19 -5.82 1.78e+00 3.16e-01 1.07e+01 angle pdb=" N THR B 615 " pdb=" CA THR B 615 " pdb=" C THR B 615 " ideal model delta sigma weight residual 114.62 110.93 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" C CYS F 22 " pdb=" N GLY F 23 " pdb=" CA GLY F 23 " ideal model delta sigma weight residual 122.29 119.46 2.83 8.90e-01 1.26e+00 1.01e+01 angle pdb=" C CYS L 22 " pdb=" N GLY L 23 " pdb=" CA GLY L 23 " ideal model delta sigma weight residual 122.29 119.47 2.82 8.90e-01 1.26e+00 1.01e+01 ... (remaining 43119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 18311 17.73 - 35.47: 840 35.47 - 53.20: 202 53.20 - 70.93: 43 70.93 - 88.66: 13 Dihedral angle restraints: 19409 sinusoidal: 8182 harmonic: 11227 Sorted by residual: dihedral pdb=" CA LYS B 525 " pdb=" C LYS B 525 " pdb=" N LYS B 526 " pdb=" CA LYS B 526 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ILE B 329 " pdb=" C ILE B 329 " pdb=" N THR B 330 " pdb=" CA THR B 330 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CB CYS C1079 " pdb=" SG CYS C1079 " pdb=" SG CYS C1123 " pdb=" CB CYS C1123 " ideal model delta sinusoidal sigma weight residual -86.00 -125.70 39.70 1 1.00e+01 1.00e-02 2.21e+01 ... (remaining 19406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4080 0.051 - 0.102: 685 0.102 - 0.154: 209 0.154 - 0.205: 7 0.205 - 0.256: 2 Chirality restraints: 4983 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.43e+00 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.48e+00 ... (remaining 4980 not shown) Planarity restraints: 5550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 328 " -0.016 2.00e-02 2.50e+03 1.65e-02 3.39e+00 pdb=" CG ASN A 328 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 328 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 328 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 585 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A 586 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 586 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 586 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1049 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A1050 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1050 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1050 " -0.024 5.00e-02 4.00e+02 ... (remaining 5547 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3552 2.75 - 3.29: 30318 3.29 - 3.83: 51650 3.83 - 4.36: 64357 4.36 - 4.90: 107875 Nonbonded interactions: 257752 Sorted by model distance: nonbonded pdb=" O GLN B 52 " pdb=" OD1 ASP B 53 " model vdw 2.216 3.040 nonbonded pdb=" O LYS C 961 " pdb=" OG SER C 964 " model vdw 2.220 3.040 nonbonded pdb=" O PRO A 57 " pdb=" OG SER A 60 " model vdw 2.225 3.040 nonbonded pdb=" O ALA A 876 " pdb=" OG1 THR A 880 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.241 3.040 ... (remaining 257747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 617 or resid 638 through 1309)) selection = (chain 'B' and resid 13 through 1309) selection = (chain 'C' and (resid 13 through 617 or resid 638 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 28.390 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 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 : 0.004 0.057 31793 Z= 0.195 Angle : 0.598 15.702 43385 Z= 0.318 Chirality : 0.044 0.256 4983 Planarity : 0.004 0.043 5509 Dihedral : 11.095 88.664 12078 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 0.80 % Allowed : 4.08 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 3827 helix: 1.38 (0.21), residues: 665 sheet: -0.28 (0.15), residues: 1045 loop : -0.68 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.013 0.001 TYR A 366 PHE 0.016 0.001 PHE C 303 TRP 0.010 0.001 TRP C 64 HIS 0.004 0.001 HIS A 652 Details of bonding type rmsd covalent geometry : bond 0.00372 (31689) covalent geometry : angle 0.57441 (43124) SS BOND : bond 0.00456 ( 51) SS BOND : angle 0.97249 ( 102) hydrogen bonds : bond 0.14148 ( 1286) hydrogen bonds : angle 7.52308 ( 3654) link_BETA1-4 : bond 0.00219 ( 12) link_BETA1-4 : angle 1.37744 ( 36) link_NAG-ASN : bond 0.00333 ( 41) link_NAG-ASN : angle 3.04984 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 764 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8535 (p) cc_final: 0.7776 (m) REVERT: A 52 GLN cc_start: 0.8906 (tt0) cc_final: 0.8633 (tp-100) REVERT: A 225 PRO cc_start: 0.7868 (Cg_exo) cc_final: 0.7531 (Cg_endo) REVERT: A 325 ARG cc_start: 0.7445 (mmp-170) cc_final: 0.6716 (tpp80) REVERT: A 409 PRO cc_start: 0.8921 (Cg_endo) cc_final: 0.8192 (Cg_exo) REVERT: A 420 TYR cc_start: 0.8317 (t80) cc_final: 0.7555 (t80) REVERT: A 453 PHE cc_start: 0.9268 (m-80) cc_final: 0.8909 (m-80) REVERT: A 457 ASN cc_start: 0.9590 (m-40) cc_final: 0.9210 (t0) REVERT: A 529 ASN cc_start: 0.9611 (m-40) cc_final: 0.9282 (p0) REVERT: A 568 ASP cc_start: 0.9469 (m-30) cc_final: 0.8404 (t0) REVERT: A 715 PHE cc_start: 0.8027 (p90) cc_final: 0.7575 (p90) REVERT: A 727 SER cc_start: 0.9209 (p) cc_final: 0.8908 (t) REVERT: A 729 THR cc_start: 0.9126 (m) cc_final: 0.8862 (t) REVERT: A 737 MET cc_start: 0.9023 (tpt) cc_final: 0.8665 (tpp) REVERT: A 745 GLU cc_start: 0.8846 (mp0) cc_final: 0.7997 (tt0) REVERT: A 756 PHE cc_start: 0.8706 (m-10) cc_final: 0.7967 (m-10) REVERT: A 774 ASN cc_start: 0.9334 (m-40) cc_final: 0.9108 (m-40) REVERT: A 779 PHE cc_start: 0.8912 (m-80) cc_final: 0.8546 (m-80) REVERT: A 816 GLU cc_start: 0.9349 (mt-10) cc_final: 0.9101 (mt-10) REVERT: A 823 VAL cc_start: 0.8696 (t) cc_final: 0.7642 (t) REVERT: A 903 PHE cc_start: 0.9069 (m-80) cc_final: 0.8485 (m-10) REVERT: A 908 VAL cc_start: 0.8460 (t) cc_final: 0.8084 (t) REVERT: A 910 GLN cc_start: 0.8295 (pt0) cc_final: 0.8070 (pp30) REVERT: A 918 LYS cc_start: 0.9715 (mttt) cc_final: 0.9499 (tptp) REVERT: A 932 GLN cc_start: 0.9189 (mt0) cc_final: 0.8810 (tm-30) REVERT: A 944 LYS cc_start: 0.9523 (mttt) cc_final: 0.9314 (mmmm) REVERT: A 998 LEU cc_start: 0.9530 (tp) cc_final: 0.9238 (pp) REVERT: A 1007 GLN cc_start: 0.9487 (mm-40) cc_final: 0.8915 (tp40) REVERT: A 1085 HIS cc_start: 0.9135 (m-70) cc_final: 0.8853 (m90) REVERT: A 1116 ASN cc_start: 0.9302 (m-40) cc_final: 0.8971 (m110) REVERT: B 128 ILE cc_start: 0.9548 (mt) cc_final: 0.9329 (mp) REVERT: B 177 MET cc_start: -0.1518 (ttm) cc_final: -0.5036 (mmt) REVERT: B 223 LEU cc_start: 0.9031 (mp) cc_final: 0.8673 (mm) REVERT: B 272 PHE cc_start: 0.7941 (m-80) cc_final: 0.7366 (m-80) REVERT: B 297 LYS cc_start: 0.9482 (mttt) cc_final: 0.9199 (mtpp) REVERT: B 340 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8768 (m-40) REVERT: B 565 ASP cc_start: 0.9027 (t0) cc_final: 0.8214 (p0) REVERT: B 609 TYR cc_start: 0.9030 (m-80) cc_final: 0.8655 (m-80) REVERT: B 655 ASN cc_start: 0.8385 (m-40) cc_final: 0.7830 (t0) REVERT: B 717 ILE cc_start: 0.8235 (mm) cc_final: 0.7314 (mm) REVERT: B 774 ASN cc_start: 0.9285 (m-40) cc_final: 0.8796 (m-40) REVERT: B 865 GLU cc_start: 0.9256 (tt0) cc_final: 0.8994 (pm20) REVERT: B 928 ILE cc_start: 0.9003 (mm) cc_final: 0.8465 (pt) REVERT: B 930 LYS cc_start: 0.9454 (mtmt) cc_final: 0.9112 (mttt) REVERT: B 932 GLN cc_start: 0.8915 (mt0) cc_final: 0.8437 (tm-30) REVERT: B 944 LYS cc_start: 0.9489 (mttt) cc_final: 0.9203 (mtmt) REVERT: B 961 LYS cc_start: 0.9699 (mttt) cc_final: 0.9438 (mmtm) REVERT: B 963 LEU cc_start: 0.8472 (mt) cc_final: 0.8054 (mt) REVERT: B 989 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8598 (mm110) REVERT: B 1015 ILE cc_start: 0.9403 (mm) cc_final: 0.9191 (mm) REVERT: B 1028 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7002 (mt-10) REVERT: B 1051 GLN cc_start: 0.8602 (mm-40) cc_final: 0.7647 (mm-40) REVERT: B 1069 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: B 1085 HIS cc_start: 0.7776 (m-70) cc_final: 0.7527 (m90) REVERT: B 1106 PHE cc_start: 0.8762 (t80) cc_final: 0.7646 (t80) REVERT: C 44 ARG cc_start: 0.4263 (OUTLIER) cc_final: 0.4053 (mpt-90) REVERT: C 55 PHE cc_start: 0.8084 (m-80) cc_final: 0.6844 (m-80) REVERT: C 56 LEU cc_start: 0.9213 (tp) cc_final: 0.9000 (tp) REVERT: C 58 PHE cc_start: 0.9071 (m-10) cc_final: 0.8757 (m-80) REVERT: C 128 ILE cc_start: 0.9549 (mt) cc_final: 0.9245 (mt) REVERT: C 177 MET cc_start: -0.0392 (ttm) cc_final: -0.1286 (ttt) REVERT: C 223 LEU cc_start: 0.9351 (mp) cc_final: 0.8986 (mp) REVERT: C 348 TYR cc_start: 0.9122 (p90) cc_final: 0.8821 (p90) REVERT: C 707 ASN cc_start: 0.9029 (p0) cc_final: 0.8319 (t0) REVERT: C 744 THR cc_start: 0.9566 (m) cc_final: 0.9305 (p) REVERT: C 761 ASN cc_start: 0.9120 (m110) cc_final: 0.8651 (m110) REVERT: C 799 PHE cc_start: 0.8586 (m-80) cc_final: 0.8380 (m-80) REVERT: C 819 LEU cc_start: 0.9623 (mt) cc_final: 0.9363 (mt) REVERT: C 858 LEU cc_start: 0.8935 (mt) cc_final: 0.8528 (tt) REVERT: C 918 LYS cc_start: 0.9566 (mttt) cc_final: 0.9202 (mptt) REVERT: C 961 LYS cc_start: 0.9365 (mttt) cc_final: 0.9036 (mmtt) REVERT: C 983 PRO cc_start: 0.8240 (Cg_exo) cc_final: 0.7848 (Cg_endo) REVERT: C 1000 SER cc_start: 0.9425 (t) cc_final: 0.9179 (m) REVERT: C 1015 ILE cc_start: 0.9632 (mm) cc_final: 0.9253 (tp) REVERT: C 1073 THR cc_start: 0.9053 (m) cc_final: 0.8439 (p) REVERT: C 1106 PHE cc_start: 0.8762 (t80) cc_final: 0.8176 (t80) REVERT: C 1108 GLU cc_start: 0.9106 (tt0) cc_final: 0.8680 (pp20) REVERT: C 1110 GLN cc_start: 0.9614 (mt0) cc_final: 0.9200 (mm110) REVERT: H 32 TYR cc_start: 0.8822 (m-80) cc_final: 0.8503 (m-80) REVERT: E 34 MET cc_start: -0.4603 (mmm) cc_final: -0.4894 (mmt) outliers start: 27 outliers final: 8 residues processed: 787 average time/residue: 0.1997 time to fit residues: 247.6299 Evaluate side-chains 496 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 485 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.0270 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN A1008 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 164 ASN B 610 GLN ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS C 672 GLN C 774 ASN C 801 GLN C 869 GLN C 910 GLN C 923 GLN C 932 GLN C1008 GLN ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS K 96 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.120296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072991 restraints weight = 111356.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.075622 restraints weight = 68376.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.077524 restraints weight = 48130.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.078862 restraints weight = 37088.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.079762 restraints weight = 30659.401| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31793 Z= 0.199 Angle : 0.683 23.792 43385 Z= 0.355 Chirality : 0.046 0.366 4983 Planarity : 0.004 0.047 5509 Dihedral : 6.491 57.328 5297 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 0.27 % Allowed : 1.70 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 3827 helix: 1.02 (0.19), residues: 694 sheet: -0.10 (0.15), residues: 1062 loop : -0.59 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 564 TYR 0.022 0.002 TYR H 111 PHE 0.040 0.002 PHE A 562 TRP 0.023 0.001 TRP J 52 HIS 0.006 0.001 HIS B 652 Details of bonding type rmsd covalent geometry : bond 0.00390 (31689) covalent geometry : angle 0.64306 (43124) SS BOND : bond 0.00906 ( 51) SS BOND : angle 1.91818 ( 102) hydrogen bonds : bond 0.04677 ( 1286) hydrogen bonds : angle 6.21112 ( 3654) link_BETA1-4 : bond 0.00664 ( 12) link_BETA1-4 : angle 1.25979 ( 36) link_NAG-ASN : bond 0.00630 ( 41) link_NAG-ASN : angle 4.01458 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 560 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.6754 (m-80) cc_final: 0.6214 (m-10) REVERT: A 225 PRO cc_start: 0.7668 (Cg_exo) cc_final: 0.6816 (Cg_endo) REVERT: A 409 PRO cc_start: 0.8528 (Cg_endo) cc_final: 0.8270 (Cg_exo) REVERT: A 420 TYR cc_start: 0.7838 (t80) cc_final: 0.6739 (t80) REVERT: A 453 PHE cc_start: 0.9328 (m-80) cc_final: 0.8926 (m-80) REVERT: A 529 ASN cc_start: 0.9615 (m-40) cc_final: 0.9315 (p0) REVERT: A 568 ASP cc_start: 0.9548 (m-30) cc_final: 0.8513 (t0) REVERT: A 609 TYR cc_start: 0.8384 (m-80) cc_final: 0.8150 (m-80) REVERT: A 737 MET cc_start: 0.9026 (tpt) cc_final: 0.8632 (tpp) REVERT: A 745 GLU cc_start: 0.9030 (mp0) cc_final: 0.8406 (tt0) REVERT: A 760 LEU cc_start: 0.9396 (mt) cc_final: 0.9039 (mt) REVERT: A 773 LYS cc_start: 0.9445 (mttm) cc_final: 0.9177 (mtpp) REVERT: A 779 PHE cc_start: 0.8892 (m-80) cc_final: 0.8385 (m-80) REVERT: A 818 LEU cc_start: 0.9671 (mt) cc_final: 0.9147 (mt) REVERT: A 903 PHE cc_start: 0.8702 (m-80) cc_final: 0.8403 (m-10) REVERT: A 908 VAL cc_start: 0.7920 (t) cc_final: 0.7647 (t) REVERT: A 918 LYS cc_start: 0.9731 (mttt) cc_final: 0.9388 (tppt) REVERT: A 932 GLN cc_start: 0.9152 (mt0) cc_final: 0.8441 (tm-30) REVERT: A 935 LEU cc_start: 0.9752 (mt) cc_final: 0.9281 (pp) REVERT: A 954 GLN cc_start: 0.9507 (mt0) cc_final: 0.9273 (mt0) REVERT: A 957 ASN cc_start: 0.9558 (m110) cc_final: 0.9344 (m110) REVERT: A 966 ASN cc_start: 0.9295 (p0) cc_final: 0.8275 (t0) REVERT: A 999 GLN cc_start: 0.9254 (tp-100) cc_final: 0.8937 (tp-100) REVERT: A 1002 GLN cc_start: 0.9441 (tp-100) cc_final: 0.9128 (tp-100) REVERT: A 1007 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8914 (tm-30) REVERT: A 1047 MET cc_start: 0.7667 (ttm) cc_final: 0.7094 (mtt) REVERT: A 1116 ASN cc_start: 0.9447 (m-40) cc_final: 0.9076 (m110) REVERT: A 1124 ASP cc_start: 0.8260 (p0) cc_final: 0.8002 (p0) REVERT: B 106 PHE cc_start: 0.8353 (m-80) cc_final: 0.7914 (m-80) REVERT: B 117 LEU cc_start: 0.9786 (tp) cc_final: 0.9435 (tp) REVERT: B 168 PHE cc_start: 0.9023 (t80) cc_final: 0.8677 (t80) REVERT: B 177 MET cc_start: -0.1599 (ttm) cc_final: -0.4793 (mmt) REVERT: B 272 PHE cc_start: 0.8016 (m-80) cc_final: 0.7364 (m-80) REVERT: B 362 TYR cc_start: 0.9520 (m-80) cc_final: 0.9159 (m-80) REVERT: B 384 LEU cc_start: 0.9636 (mm) cc_final: 0.9097 (mp) REVERT: B 529 ASN cc_start: 0.9368 (p0) cc_final: 0.9119 (p0) REVERT: B 555 LYS cc_start: 0.8398 (tptt) cc_final: 0.7998 (ttpt) REVERT: B 565 ASP cc_start: 0.9180 (t0) cc_final: 0.8308 (p0) REVERT: B 608 LEU cc_start: 0.8797 (tp) cc_final: 0.8545 (mm) REVERT: B 655 ASN cc_start: 0.8503 (m-40) cc_final: 0.7905 (t0) REVERT: B 660 ASP cc_start: 0.8298 (t0) cc_final: 0.8093 (t0) REVERT: B 717 ILE cc_start: 0.8247 (mm) cc_final: 0.7454 (mm) REVERT: B 762 ARG cc_start: 0.9462 (ttm110) cc_final: 0.9130 (ptm160) REVERT: B 770 GLU cc_start: 0.8896 (tp30) cc_final: 0.8277 (tp30) REVERT: B 774 ASN cc_start: 0.9378 (m-40) cc_final: 0.8751 (m-40) REVERT: B 865 GLU cc_start: 0.9209 (tt0) cc_final: 0.8840 (mp0) REVERT: B 920 ILE cc_start: 0.9682 (mt) cc_final: 0.9415 (pt) REVERT: B 930 LYS cc_start: 0.9442 (mtmt) cc_final: 0.9139 (mttt) REVERT: B 961 LYS cc_start: 0.9690 (mttt) cc_final: 0.9270 (mmtm) REVERT: B 989 GLN cc_start: 0.8692 (mm-40) cc_final: 0.7727 (mm-40) REVERT: B 1001 LEU cc_start: 0.9159 (mt) cc_final: 0.8772 (mt) REVERT: B 1002 GLN cc_start: 0.9305 (tp-100) cc_final: 0.9060 (tp-100) REVERT: B 1009 LEU cc_start: 0.9455 (mt) cc_final: 0.9187 (mt) REVERT: B 1051 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8694 (mm-40) REVERT: B 1106 PHE cc_start: 0.8821 (t80) cc_final: 0.8317 (t80) REVERT: C 53 ASP cc_start: 0.8729 (m-30) cc_final: 0.8452 (m-30) REVERT: C 55 PHE cc_start: 0.8211 (m-80) cc_final: 0.7235 (m-10) REVERT: C 58 PHE cc_start: 0.9254 (m-10) cc_final: 0.8918 (m-80) REVERT: C 177 MET cc_start: -0.0485 (ttm) cc_final: -0.1393 (ttt) REVERT: C 189 LEU cc_start: 0.9575 (tp) cc_final: 0.9329 (tp) REVERT: C 223 LEU cc_start: 0.9250 (mp) cc_final: 0.9005 (mp) REVERT: C 348 TYR cc_start: 0.9215 (p90) cc_final: 0.8887 (p90) REVERT: C 377 TYR cc_start: 0.7836 (m-80) cc_final: 0.7220 (m-80) REVERT: C 707 ASN cc_start: 0.9111 (p0) cc_final: 0.8394 (t0) REVERT: C 733 VAL cc_start: 0.9122 (t) cc_final: 0.8747 (t) REVERT: C 737 MET cc_start: 0.9445 (tpt) cc_final: 0.9112 (mmm) REVERT: C 774 ASN cc_start: 0.9367 (m110) cc_final: 0.9144 (m110) REVERT: C 779 PHE cc_start: 0.9144 (m-80) cc_final: 0.8678 (m-10) REVERT: C 799 PHE cc_start: 0.8743 (m-80) cc_final: 0.8529 (m-80) REVERT: C 803 LEU cc_start: 0.9679 (mt) cc_final: 0.9312 (pp) REVERT: C 816 GLU cc_start: 0.9161 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 819 LEU cc_start: 0.9634 (mt) cc_final: 0.9354 (mt) REVERT: C 858 LEU cc_start: 0.9208 (mt) cc_final: 0.8903 (tp) REVERT: C 918 LYS cc_start: 0.9598 (mttt) cc_final: 0.9289 (mptt) REVERT: C 961 LYS cc_start: 0.9324 (mttt) cc_final: 0.8977 (mmtt) REVERT: C 1000 SER cc_start: 0.9375 (t) cc_final: 0.9167 (m) REVERT: C 1009 LEU cc_start: 0.9495 (mt) cc_final: 0.9196 (mt) REVERT: C 1011 ARG cc_start: 0.9067 (tpp80) cc_final: 0.8808 (tpp-160) REVERT: C 1015 ILE cc_start: 0.9626 (mm) cc_final: 0.9336 (tt) REVERT: C 1028 GLU cc_start: 0.8798 (tp30) cc_final: 0.8580 (tp30) REVERT: C 1051 GLN cc_start: 0.9164 (tp-100) cc_final: 0.8206 (tp-100) REVERT: C 1085 HIS cc_start: 0.8743 (m-70) cc_final: 0.8470 (m-70) REVERT: H 34 MET cc_start: 0.3163 (mpp) cc_final: 0.2946 (mpp) outliers start: 9 outliers final: 1 residues processed: 564 average time/residue: 0.1920 time to fit residues: 175.2999 Evaluate side-chains 420 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 193 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 240 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN A 484 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN A1002 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 314 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN B 853 ASN B 869 GLN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 GLN B 950 ASN B1002 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 604 GLN C 687 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN C 853 ASN C 904 ASN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN C 950 ASN C1055 HIS ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.110290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.064519 restraints weight = 121525.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.066202 restraints weight = 76532.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.067598 restraints weight = 55306.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.068648 restraints weight = 43768.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.069347 restraints weight = 37058.923| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 31793 Z= 0.349 Angle : 0.864 24.716 43385 Z= 0.457 Chirality : 0.049 0.322 4983 Planarity : 0.006 0.082 5509 Dihedral : 6.490 45.357 5297 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.34 % Favored : 95.61 % Rotamer: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 3827 helix: -0.91 (0.18), residues: 687 sheet: -0.19 (0.16), residues: 983 loop : -0.84 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 992 TYR 0.040 0.002 TYR C 738 PHE 0.041 0.003 PHE C 556 TRP 0.016 0.002 TRP L 34 HIS 0.013 0.003 HIS C1055 Details of bonding type rmsd covalent geometry : bond 0.00666 (31689) covalent geometry : angle 0.83329 (43124) SS BOND : bond 0.00702 ( 51) SS BOND : angle 2.50225 ( 102) hydrogen bonds : bond 0.05756 ( 1286) hydrogen bonds : angle 6.65480 ( 3654) link_BETA1-4 : bond 0.00513 ( 12) link_BETA1-4 : angle 1.87327 ( 36) link_NAG-ASN : bond 0.00674 ( 41) link_NAG-ASN : angle 3.72368 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 483 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8487 (p) cc_final: 0.7437 (m) REVERT: A 420 TYR cc_start: 0.8682 (t80) cc_final: 0.7943 (t80) REVERT: A 529 ASN cc_start: 0.9642 (m-40) cc_final: 0.9285 (p0) REVERT: A 532 LYS cc_start: 0.9276 (mttt) cc_final: 0.9014 (ptmt) REVERT: A 543 LEU cc_start: 0.9371 (mm) cc_final: 0.9149 (mt) REVERT: A 568 ASP cc_start: 0.9702 (m-30) cc_final: 0.8805 (t0) REVERT: A 660 ASP cc_start: 0.8820 (t0) cc_final: 0.8527 (t70) REVERT: A 735 CYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7585 (m) REVERT: A 738 TYR cc_start: 0.9157 (t80) cc_final: 0.8820 (t80) REVERT: A 760 LEU cc_start: 0.9592 (mt) cc_final: 0.8846 (mt) REVERT: A 773 LYS cc_start: 0.9503 (mttm) cc_final: 0.9278 (mtpp) REVERT: A 918 LYS cc_start: 0.9753 (mttt) cc_final: 0.9344 (tppt) REVERT: A 919 LEU cc_start: 0.9391 (mp) cc_final: 0.8951 (mp) REVERT: A 954 GLN cc_start: 0.9618 (mt0) cc_final: 0.9313 (mt0) REVERT: A 957 ASN cc_start: 0.9302 (m110) cc_final: 0.9060 (m110) REVERT: A 970 ILE cc_start: 0.8935 (pt) cc_final: 0.8615 (pt) REVERT: A 989 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8481 (mt0) REVERT: A 999 GLN cc_start: 0.9288 (tp-100) cc_final: 0.8741 (tp-100) REVERT: A 1002 GLN cc_start: 0.9546 (tp40) cc_final: 0.9173 (tp-100) REVERT: A 1007 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8533 (tm-30) REVERT: A 1047 MET cc_start: 0.8285 (ttm) cc_final: 0.7378 (mtt) REVERT: A 1078 ILE cc_start: 0.9154 (mm) cc_final: 0.8802 (tp) REVERT: A 1085 HIS cc_start: 0.9252 (m90) cc_final: 0.8880 (m-70) REVERT: A 1092 PHE cc_start: 0.8605 (m-10) cc_final: 0.8298 (m-10) REVERT: A 1100 PHE cc_start: 0.9027 (m-80) cc_final: 0.8781 (m-80) REVERT: A 1116 ASN cc_start: 0.9376 (m-40) cc_final: 0.9061 (m110) REVERT: A 1124 ASP cc_start: 0.8385 (p0) cc_final: 0.8177 (p0) REVERT: B 41 LYS cc_start: 0.7906 (tttt) cc_final: 0.7506 (tptt) REVERT: B 153 MET cc_start: 0.8115 (tmm) cc_final: 0.7847 (mtt) REVERT: B 177 MET cc_start: 0.0323 (ttm) cc_final: -0.3570 (mmt) REVERT: B 272 PHE cc_start: 0.8707 (m-80) cc_final: 0.7806 (m-10) REVERT: B 315 PHE cc_start: 0.8752 (t80) cc_final: 0.8504 (t80) REVERT: B 362 TYR cc_start: 0.9530 (m-80) cc_final: 0.9103 (m-80) REVERT: B 384 LEU cc_start: 0.9633 (mm) cc_final: 0.9098 (mp) REVERT: B 529 ASN cc_start: 0.9449 (p0) cc_final: 0.9240 (p0) REVERT: B 565 ASP cc_start: 0.9224 (t0) cc_final: 0.8578 (p0) REVERT: B 608 LEU cc_start: 0.8967 (tp) cc_final: 0.8613 (mm) REVERT: B 655 ASN cc_start: 0.8543 (m-40) cc_final: 0.7896 (t0) REVERT: B 660 ASP cc_start: 0.9021 (t0) cc_final: 0.8813 (t70) REVERT: B 717 ILE cc_start: 0.8456 (mm) cc_final: 0.7774 (mm) REVERT: B 728 MET cc_start: 0.9327 (mtm) cc_final: 0.8818 (mpp) REVERT: B 739 ILE cc_start: 0.9369 (mt) cc_final: 0.9128 (mt) REVERT: B 865 GLU cc_start: 0.9453 (tt0) cc_final: 0.9060 (mp0) REVERT: B 930 LYS cc_start: 0.9500 (mtmt) cc_final: 0.9134 (mttt) REVERT: B 989 GLN cc_start: 0.9331 (mm-40) cc_final: 0.9121 (mp10) REVERT: B 999 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8838 (tm-30) REVERT: B 1009 LEU cc_start: 0.9551 (mt) cc_final: 0.9186 (mt) REVERT: B 1014 GLU cc_start: 0.9305 (tt0) cc_final: 0.8861 (mm-30) REVERT: C 177 MET cc_start: 0.3121 (ttm) cc_final: 0.2620 (ttp) REVERT: C 223 LEU cc_start: 0.9123 (mp) cc_final: 0.8781 (tp) REVERT: C 321 GLU cc_start: 0.9259 (tp30) cc_final: 0.8690 (tp30) REVERT: C 348 TYR cc_start: 0.9314 (p90) cc_final: 0.9027 (p90) REVERT: C 377 TYR cc_start: 0.7940 (m-80) cc_final: 0.7401 (m-80) REVERT: C 431 ILE cc_start: 0.9799 (mt) cc_final: 0.9581 (tp) REVERT: C 696 LEU cc_start: 0.9152 (tp) cc_final: 0.8944 (pt) REVERT: C 707 ASN cc_start: 0.9269 (p0) cc_final: 0.8796 (t0) REVERT: C 733 VAL cc_start: 0.9419 (t) cc_final: 0.9178 (p) REVERT: C 737 MET cc_start: 0.9238 (tpt) cc_final: 0.8881 (tpp) REVERT: C 738 TYR cc_start: 0.9539 (t80) cc_final: 0.9325 (t80) REVERT: C 802 ILE cc_start: 0.9805 (pt) cc_final: 0.9603 (pt) REVERT: C 803 LEU cc_start: 0.9786 (mt) cc_final: 0.9216 (pp) REVERT: C 918 LYS cc_start: 0.9671 (mttt) cc_final: 0.9315 (mptt) REVERT: C 948 VAL cc_start: 0.9312 (t) cc_final: 0.8777 (t) REVERT: C 961 LYS cc_start: 0.9373 (mttt) cc_final: 0.8783 (mmmt) REVERT: C 962 GLN cc_start: 0.9120 (mm110) cc_final: 0.8750 (mm110) REVERT: C 992 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8358 (mpp80) REVERT: C 1009 LEU cc_start: 0.9674 (mt) cc_final: 0.9417 (mm) REVERT: C 1011 ARG cc_start: 0.9175 (tpp80) cc_final: 0.8882 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9376 (pt0) cc_final: 0.9063 (pp20) REVERT: C 1015 ILE cc_start: 0.9739 (mm) cc_final: 0.9403 (mt) REVERT: H 34 MET cc_start: 0.2630 (mpp) cc_final: 0.2207 (mpp) REVERT: E 73 ASP cc_start: 0.4636 (m-30) cc_final: 0.4293 (p0) outliers start: 8 outliers final: 3 residues processed: 486 average time/residue: 0.1812 time to fit residues: 143.6571 Evaluate side-chains 377 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 373 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 208 optimal weight: 0.9980 chunk 356 optimal weight: 50.0000 chunk 271 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 282 optimal weight: 0.5980 chunk 138 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 374 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A 975 ASN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 774 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN C 962 GLN ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.115546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.070130 restraints weight = 117887.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.072654 restraints weight = 70328.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.074444 restraints weight = 48676.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.075651 restraints weight = 37220.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.076572 restraints weight = 30814.228| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 31793 Z= 0.134 Angle : 0.620 22.999 43385 Z= 0.320 Chirality : 0.045 0.302 4983 Planarity : 0.004 0.043 5509 Dihedral : 5.588 45.684 5297 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.72 % Favored : 97.26 % Rotamer: Outliers : 0.15 % Allowed : 1.70 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.13), residues: 3827 helix: 0.34 (0.19), residues: 692 sheet: -0.01 (0.15), residues: 1031 loop : -0.67 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 78 TYR 0.029 0.001 TYR B 263 PHE 0.030 0.002 PHE C 272 TRP 0.021 0.001 TRP L 34 HIS 0.006 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00284 (31689) covalent geometry : angle 0.58931 (43124) SS BOND : bond 0.00410 ( 51) SS BOND : angle 1.64620 ( 102) hydrogen bonds : bond 0.04205 ( 1286) hydrogen bonds : angle 5.87136 ( 3654) link_BETA1-4 : bond 0.00359 ( 12) link_BETA1-4 : angle 1.15916 ( 36) link_NAG-ASN : bond 0.00437 ( 41) link_NAG-ASN : angle 3.33819 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 510 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 TYR cc_start: 0.8613 (t80) cc_final: 0.7705 (t80) REVERT: A 453 PHE cc_start: 0.9612 (m-10) cc_final: 0.9292 (m-80) REVERT: A 529 ASN cc_start: 0.9647 (m-40) cc_final: 0.9358 (p0) REVERT: A 532 LYS cc_start: 0.9224 (mttt) cc_final: 0.8988 (ptmt) REVERT: A 568 ASP cc_start: 0.9691 (m-30) cc_final: 0.8730 (t0) REVERT: A 737 MET cc_start: 0.8304 (tpp) cc_final: 0.7807 (tpp) REVERT: A 756 PHE cc_start: 0.8427 (m-10) cc_final: 0.8162 (m-10) REVERT: A 760 LEU cc_start: 0.9301 (mt) cc_final: 0.9061 (mt) REVERT: A 770 GLU cc_start: 0.9374 (pt0) cc_final: 0.9147 (pt0) REVERT: A 771 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8919 (mm-40) REVERT: A 918 LYS cc_start: 0.9695 (mttt) cc_final: 0.9277 (tppt) REVERT: A 932 GLN cc_start: 0.9322 (mt0) cc_final: 0.8749 (tm-30) REVERT: A 957 ASN cc_start: 0.9240 (m110) cc_final: 0.8991 (m110) REVERT: A 966 ASN cc_start: 0.9397 (p0) cc_final: 0.8894 (m-40) REVERT: A 976 ASP cc_start: 0.9528 (t0) cc_final: 0.9299 (t0) REVERT: A 977 ILE cc_start: 0.9394 (pt) cc_final: 0.8505 (mm) REVERT: A 989 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8431 (mt0) REVERT: A 999 GLN cc_start: 0.9271 (tp-100) cc_final: 0.8610 (tp-100) REVERT: A 1002 GLN cc_start: 0.9502 (tp40) cc_final: 0.9017 (tp-100) REVERT: A 1007 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8810 (tm-30) REVERT: A 1047 MET cc_start: 0.7821 (ttm) cc_final: 0.7017 (mtt) REVERT: A 1085 HIS cc_start: 0.9316 (m90) cc_final: 0.8787 (m-70) REVERT: A 1086 PHE cc_start: 0.8661 (m-80) cc_final: 0.8230 (m-10) REVERT: A 1116 ASN cc_start: 0.9393 (m-40) cc_final: 0.9027 (m110) REVERT: A 1124 ASP cc_start: 0.8328 (p0) cc_final: 0.8118 (p0) REVERT: B 102 ARG cc_start: 0.8479 (mmt90) cc_final: 0.7486 (mmp80) REVERT: B 177 MET cc_start: 0.1414 (ttm) cc_final: -0.4071 (mmt) REVERT: B 362 TYR cc_start: 0.9481 (m-80) cc_final: 0.9161 (m-80) REVERT: B 384 LEU cc_start: 0.9684 (mm) cc_final: 0.9232 (mp) REVERT: B 529 ASN cc_start: 0.9440 (p0) cc_final: 0.9197 (p0) REVERT: B 555 LYS cc_start: 0.8351 (tptt) cc_final: 0.7770 (ttpt) REVERT: B 565 ASP cc_start: 0.9190 (t0) cc_final: 0.8686 (p0) REVERT: B 608 LEU cc_start: 0.8817 (tp) cc_final: 0.8534 (mm) REVERT: B 655 ASN cc_start: 0.8648 (m-40) cc_final: 0.7815 (t0) REVERT: B 717 ILE cc_start: 0.8408 (mm) cc_final: 0.7781 (mm) REVERT: B 728 MET cc_start: 0.9147 (mtm) cc_final: 0.8691 (mpp) REVERT: B 774 ASN cc_start: 0.8925 (m110) cc_final: 0.8640 (m110) REVERT: B 781 GLN cc_start: 0.8867 (mm110) cc_final: 0.8652 (mm110) REVERT: B 802 ILE cc_start: 0.8394 (pt) cc_final: 0.8043 (pt) REVERT: B 865 GLU cc_start: 0.9355 (tt0) cc_final: 0.8967 (mp0) REVERT: B 903 PHE cc_start: 0.7541 (m-10) cc_final: 0.7301 (m-80) REVERT: B 920 ILE cc_start: 0.9674 (mt) cc_final: 0.9418 (pt) REVERT: B 926 SER cc_start: 0.9609 (m) cc_final: 0.8933 (p) REVERT: B 930 LYS cc_start: 0.9417 (mtmt) cc_final: 0.8922 (mttt) REVERT: B 957 ASN cc_start: 0.9286 (m110) cc_final: 0.8895 (m110) REVERT: B 989 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8717 (mp10) REVERT: B 999 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8664 (tm-30) REVERT: B 1014 GLU cc_start: 0.9129 (tt0) cc_final: 0.8697 (mm-30) REVERT: B 1064 TYR cc_start: 0.9163 (t80) cc_final: 0.8516 (t80) REVERT: B 1106 PHE cc_start: 0.8989 (t80) cc_final: 0.8581 (t80) REVERT: C 53 ASP cc_start: 0.8846 (m-30) cc_final: 0.8593 (m-30) REVERT: C 58 PHE cc_start: 0.9420 (m-10) cc_final: 0.9034 (m-80) REVERT: C 128 ILE cc_start: 0.9779 (pt) cc_final: 0.9565 (mm) REVERT: C 177 MET cc_start: 0.2536 (ttm) cc_final: 0.1892 (ttp) REVERT: C 189 LEU cc_start: 0.9634 (tp) cc_final: 0.8939 (tp) REVERT: C 223 LEU cc_start: 0.8968 (mp) cc_final: 0.8659 (mp) REVERT: C 295 GLU cc_start: 0.8591 (mp0) cc_final: 0.8288 (mp0) REVERT: C 315 PHE cc_start: 0.7673 (t80) cc_final: 0.7430 (t80) REVERT: C 321 GLU cc_start: 0.9210 (tp30) cc_final: 0.8577 (tp30) REVERT: C 348 TYR cc_start: 0.9243 (p90) cc_final: 0.8939 (p90) REVERT: C 377 TYR cc_start: 0.7777 (m-80) cc_final: 0.7217 (m-80) REVERT: C 431 ILE cc_start: 0.9800 (mt) cc_final: 0.9596 (tt) REVERT: C 559 PHE cc_start: 0.7448 (p90) cc_final: 0.7164 (p90) REVERT: C 733 VAL cc_start: 0.9248 (t) cc_final: 0.8963 (p) REVERT: C 734 ASP cc_start: 0.8890 (t0) cc_final: 0.8348 (t0) REVERT: C 736 THR cc_start: 0.8764 (m) cc_final: 0.8501 (p) REVERT: C 737 MET cc_start: 0.9336 (tpt) cc_final: 0.8724 (tpt) REVERT: C 738 TYR cc_start: 0.9318 (t80) cc_final: 0.8893 (t80) REVERT: C 761 ASN cc_start: 0.9609 (m110) cc_final: 0.9380 (m110) REVERT: C 770 GLU cc_start: 0.9565 (mt-10) cc_final: 0.9323 (mt-10) REVERT: C 781 GLN cc_start: 0.8450 (mt0) cc_final: 0.8063 (tm-30) REVERT: C 786 TYR cc_start: 0.7932 (m-10) cc_final: 0.6845 (m-10) REVERT: C 803 LEU cc_start: 0.9759 (mt) cc_final: 0.9360 (pp) REVERT: C 816 GLU cc_start: 0.8924 (mt-10) cc_final: 0.7827 (mp0) REVERT: C 885 PHE cc_start: 0.7995 (p90) cc_final: 0.6901 (p90) REVERT: C 916 ASN cc_start: 0.9166 (m-40) cc_final: 0.8956 (m110) REVERT: C 918 LYS cc_start: 0.9625 (mttt) cc_final: 0.9292 (mptt) REVERT: C 961 LYS cc_start: 0.9154 (mttt) cc_final: 0.8708 (mttt) REVERT: C 1009 LEU cc_start: 0.9605 (mt) cc_final: 0.9365 (mm) REVERT: C 1011 ARG cc_start: 0.8883 (tpp80) cc_final: 0.8653 (tpp-160) REVERT: C 1021 LEU cc_start: 0.9452 (mt) cc_final: 0.9230 (mt) REVERT: C 1031 LEU cc_start: 0.9476 (mp) cc_final: 0.9238 (mp) REVERT: C 1051 GLN cc_start: 0.8682 (tp-100) cc_final: 0.7948 (tp40) REVERT: C 1124 ASP cc_start: 0.8357 (p0) cc_final: 0.8148 (p0) REVERT: H 83 MET cc_start: -0.6767 (ptt) cc_final: -0.7113 (ptt) outliers start: 5 outliers final: 2 residues processed: 514 average time/residue: 0.1779 time to fit residues: 151.1093 Evaluate side-chains 417 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 415 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 338 optimal weight: 50.0000 chunk 324 optimal weight: 50.0000 chunk 276 optimal weight: 0.6980 chunk 220 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 ASN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN C1007 GLN ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.113078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.068869 restraints weight = 121073.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070806 restraints weight = 73300.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.072180 restraints weight = 49337.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.073339 restraints weight = 34789.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.073337 restraints weight = 31743.891| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31793 Z= 0.186 Angle : 0.621 22.832 43385 Z= 0.327 Chirality : 0.044 0.276 4983 Planarity : 0.004 0.050 5509 Dihedral : 5.292 43.071 5297 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 0.06 % Allowed : 2.09 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 3827 helix: 0.22 (0.19), residues: 683 sheet: 0.09 (0.15), residues: 1051 loop : -0.66 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 574 TYR 0.036 0.002 TYR B 914 PHE 0.030 0.002 PHE A 562 TRP 0.021 0.001 TRP L 34 HIS 0.006 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00366 (31689) covalent geometry : angle 0.59202 (43124) SS BOND : bond 0.00609 ( 51) SS BOND : angle 1.67692 ( 102) hydrogen bonds : bond 0.04315 ( 1286) hydrogen bonds : angle 5.86111 ( 3654) link_BETA1-4 : bond 0.00258 ( 12) link_BETA1-4 : angle 1.34699 ( 36) link_NAG-ASN : bond 0.00424 ( 41) link_NAG-ASN : angle 3.19086 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 465 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7668 (pmm) cc_final: 0.7432 (pmm) REVERT: A 325 ARG cc_start: 0.7330 (mmt180) cc_final: 0.6064 (mmp-170) REVERT: A 420 TYR cc_start: 0.8384 (t80) cc_final: 0.7532 (t80) REVERT: A 453 PHE cc_start: 0.9530 (m-10) cc_final: 0.9246 (m-80) REVERT: A 529 ASN cc_start: 0.9579 (m-40) cc_final: 0.9203 (p0) REVERT: A 532 LYS cc_start: 0.9303 (mttt) cc_final: 0.8974 (ptmt) REVERT: A 568 ASP cc_start: 0.9750 (m-30) cc_final: 0.8867 (t0) REVERT: A 737 MET cc_start: 0.8498 (tpp) cc_final: 0.7820 (tpp) REVERT: A 759 GLN cc_start: 0.9305 (pp30) cc_final: 0.9029 (pp30) REVERT: A 760 LEU cc_start: 0.9314 (mt) cc_final: 0.8759 (mt) REVERT: A 818 LEU cc_start: 0.9611 (mt) cc_final: 0.9281 (mt) REVERT: A 918 LYS cc_start: 0.9664 (mttt) cc_final: 0.9291 (tppt) REVERT: A 935 LEU cc_start: 0.9778 (mt) cc_final: 0.9378 (pp) REVERT: A 957 ASN cc_start: 0.9216 (m110) cc_final: 0.8964 (m110) REVERT: A 970 ILE cc_start: 0.8886 (pt) cc_final: 0.8531 (pt) REVERT: A 977 ILE cc_start: 0.9368 (pt) cc_final: 0.9002 (pt) REVERT: A 989 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8376 (mt0) REVERT: A 1001 LEU cc_start: 0.9399 (mt) cc_final: 0.9113 (mt) REVERT: A 1002 GLN cc_start: 0.9494 (tp40) cc_final: 0.9073 (tp-100) REVERT: A 1003 THR cc_start: 0.9608 (m) cc_final: 0.9323 (p) REVERT: A 1007 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8793 (tm-30) REVERT: A 1047 MET cc_start: 0.7901 (ttm) cc_final: 0.7172 (mtt) REVERT: A 1049 PHE cc_start: 0.8777 (m-10) cc_final: 0.8519 (m-10) REVERT: A 1092 PHE cc_start: 0.8690 (m-10) cc_final: 0.8405 (m-10) REVERT: A 1116 ASN cc_start: 0.9433 (m-40) cc_final: 0.9092 (m110) REVERT: A 1124 ASP cc_start: 0.8378 (p0) cc_final: 0.8176 (p0) REVERT: B 41 LYS cc_start: 0.7665 (tttt) cc_final: 0.7314 (tptt) REVERT: B 177 MET cc_start: 0.3071 (ttm) cc_final: -0.2079 (mmt) REVERT: B 315 PHE cc_start: 0.8503 (t80) cc_final: 0.8245 (t80) REVERT: B 362 TYR cc_start: 0.9500 (m-80) cc_final: 0.9108 (m-80) REVERT: B 384 LEU cc_start: 0.9691 (mm) cc_final: 0.9250 (mt) REVERT: B 529 ASN cc_start: 0.9444 (p0) cc_final: 0.9215 (p0) REVERT: B 565 ASP cc_start: 0.9193 (t0) cc_final: 0.8651 (p0) REVERT: B 655 ASN cc_start: 0.8652 (m-40) cc_final: 0.7817 (t0) REVERT: B 717 ILE cc_start: 0.8369 (mm) cc_final: 0.7727 (mm) REVERT: B 728 MET cc_start: 0.9239 (mtm) cc_final: 0.8670 (mpp) REVERT: B 774 ASN cc_start: 0.8780 (m110) cc_final: 0.8520 (m-40) REVERT: B 781 GLN cc_start: 0.8985 (mm110) cc_final: 0.8135 (tm-30) REVERT: B 865 GLU cc_start: 0.9405 (tt0) cc_final: 0.8912 (mp0) REVERT: B 930 LYS cc_start: 0.9408 (mtmt) cc_final: 0.8939 (mttt) REVERT: B 957 ASN cc_start: 0.9314 (m110) cc_final: 0.8977 (m-40) REVERT: B 989 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8780 (mp10) REVERT: B 999 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8748 (tm-30) REVERT: B 1002 GLN cc_start: 0.9367 (tp-100) cc_final: 0.9153 (tp-100) REVERT: B 1009 LEU cc_start: 0.9518 (mt) cc_final: 0.9208 (mt) REVERT: B 1014 GLU cc_start: 0.9150 (tt0) cc_final: 0.8796 (mm-30) REVERT: B 1015 ILE cc_start: 0.9550 (tp) cc_final: 0.9337 (tp) REVERT: B 1064 TYR cc_start: 0.8903 (t80) cc_final: 0.8494 (t80) REVERT: C 53 ASP cc_start: 0.8873 (m-30) cc_final: 0.8651 (m-30) REVERT: C 58 PHE cc_start: 0.9399 (m-10) cc_final: 0.8992 (m-80) REVERT: C 177 MET cc_start: 0.3543 (ttm) cc_final: 0.2934 (ttp) REVERT: C 223 LEU cc_start: 0.9104 (mp) cc_final: 0.8777 (tp) REVERT: C 272 PHE cc_start: 0.8317 (m-10) cc_final: 0.7985 (m-10) REVERT: C 315 PHE cc_start: 0.7929 (t80) cc_final: 0.7296 (t80) REVERT: C 348 TYR cc_start: 0.9244 (p90) cc_final: 0.8973 (p90) REVERT: C 377 TYR cc_start: 0.7496 (m-80) cc_final: 0.6880 (m-80) REVERT: C 431 ILE cc_start: 0.9737 (mt) cc_final: 0.9518 (tt) REVERT: C 733 VAL cc_start: 0.9278 (t) cc_final: 0.8986 (p) REVERT: C 734 ASP cc_start: 0.8951 (t0) cc_final: 0.8576 (t0) REVERT: C 737 MET cc_start: 0.9269 (tpt) cc_final: 0.8775 (tpt) REVERT: C 738 TYR cc_start: 0.9396 (t80) cc_final: 0.9089 (t80) REVERT: C 761 ASN cc_start: 0.9610 (m110) cc_final: 0.9374 (m110) REVERT: C 767 ILE cc_start: 0.9871 (mt) cc_final: 0.9578 (mt) REVERT: C 770 GLU cc_start: 0.9559 (mt-10) cc_final: 0.9050 (mt-10) REVERT: C 781 GLN cc_start: 0.8586 (mt0) cc_final: 0.8141 (tm-30) REVERT: C 786 TYR cc_start: 0.8385 (m-10) cc_final: 0.7428 (m-10) REVERT: C 802 ILE cc_start: 0.9808 (pt) cc_final: 0.9588 (pt) REVERT: C 803 LEU cc_start: 0.9529 (mt) cc_final: 0.9264 (pp) REVERT: C 918 LYS cc_start: 0.9657 (mttt) cc_final: 0.9277 (mptt) REVERT: C 961 LYS cc_start: 0.9192 (mttt) cc_final: 0.8744 (mttt) REVERT: C 1009 LEU cc_start: 0.9625 (mt) cc_final: 0.9328 (mm) REVERT: C 1021 LEU cc_start: 0.9480 (mt) cc_final: 0.9253 (mt) REVERT: C 1051 GLN cc_start: 0.8263 (tp-100) cc_final: 0.7533 (mm-40) REVERT: C 1124 ASP cc_start: 0.8252 (p0) cc_final: 0.8008 (p0) REVERT: H 32 TYR cc_start: 0.9308 (m-80) cc_final: 0.8982 (m-80) REVERT: H 34 MET cc_start: 0.2107 (mpp) cc_final: 0.1738 (mpp) REVERT: H 83 MET cc_start: -0.6772 (ptt) cc_final: -0.7089 (ptt) REVERT: K 89 VAL cc_start: 0.2212 (p) cc_final: 0.1804 (p) outliers start: 2 outliers final: 1 residues processed: 466 average time/residue: 0.1774 time to fit residues: 136.9519 Evaluate side-chains 383 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 70 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 253 optimal weight: 30.0000 chunk 118 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 chunk 362 optimal weight: 40.0000 chunk 217 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN B 687 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1007 GLN C1051 GLN ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.107234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060564 restraints weight = 124312.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062332 restraints weight = 78191.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.063676 restraints weight = 57084.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.064498 restraints weight = 45207.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065075 restraints weight = 38549.802| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 31793 Z= 0.335 Angle : 0.797 21.765 43385 Z= 0.426 Chirality : 0.048 0.323 4983 Planarity : 0.005 0.086 5509 Dihedral : 5.905 45.500 5297 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 3827 helix: -1.20 (0.17), residues: 693 sheet: -0.19 (0.16), residues: 1010 loop : -0.85 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1088 TYR 0.052 0.002 TYR B 738 PHE 0.033 0.003 PHE A 797 TRP 0.029 0.002 TRP L 34 HIS 0.015 0.002 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00640 (31689) covalent geometry : angle 0.77295 (43124) SS BOND : bond 0.00694 ( 51) SS BOND : angle 1.68861 ( 102) hydrogen bonds : bond 0.05441 ( 1286) hydrogen bonds : angle 6.47999 ( 3654) link_BETA1-4 : bond 0.00413 ( 12) link_BETA1-4 : angle 1.88774 ( 36) link_NAG-ASN : bond 0.00968 ( 41) link_NAG-ASN : angle 3.36276 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ARG cc_start: 0.7595 (mmt180) cc_final: 0.6509 (tpp-160) REVERT: A 354 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7643 (ttp80) REVERT: A 420 TYR cc_start: 0.8419 (t80) cc_final: 0.7374 (t80) REVERT: A 453 PHE cc_start: 0.9668 (m-10) cc_final: 0.9434 (m-80) REVERT: A 529 ASN cc_start: 0.9646 (m-40) cc_final: 0.9207 (p0) REVERT: A 532 LYS cc_start: 0.9337 (mttt) cc_final: 0.8980 (ptmt) REVERT: A 694 MET cc_start: 0.8973 (tmm) cc_final: 0.8328 (ppp) REVERT: A 733 VAL cc_start: 0.9024 (t) cc_final: 0.8727 (m) REVERT: A 734 ASP cc_start: 0.8700 (t0) cc_final: 0.8493 (t0) REVERT: A 737 MET cc_start: 0.8681 (tpp) cc_final: 0.8244 (tpp) REVERT: A 760 LEU cc_start: 0.9431 (mt) cc_final: 0.9173 (mt) REVERT: A 761 ASN cc_start: 0.9242 (m-40) cc_final: 0.8956 (p0) REVERT: A 774 ASN cc_start: 0.9199 (m110) cc_final: 0.8914 (m110) REVERT: A 916 ASN cc_start: 0.9588 (t0) cc_final: 0.9378 (t0) REVERT: A 918 LYS cc_start: 0.9668 (mttt) cc_final: 0.9393 (tptp) REVERT: A 954 GLN cc_start: 0.9296 (mt0) cc_final: 0.9056 (pt0) REVERT: A 957 ASN cc_start: 0.9239 (m110) cc_final: 0.8781 (m110) REVERT: A 958 THR cc_start: 0.9719 (p) cc_final: 0.9389 (p) REVERT: A 961 LYS cc_start: 0.9418 (mttt) cc_final: 0.8909 (mttm) REVERT: A 977 ILE cc_start: 0.9548 (pt) cc_final: 0.9276 (pt) REVERT: A 989 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8663 (mt0) REVERT: A 1001 LEU cc_start: 0.9334 (mt) cc_final: 0.9057 (mt) REVERT: A 1002 GLN cc_start: 0.9521 (tp40) cc_final: 0.9107 (tp-100) REVERT: A 1003 THR cc_start: 0.9544 (m) cc_final: 0.9305 (m) REVERT: A 1007 GLN cc_start: 0.9390 (mm-40) cc_final: 0.8555 (tm-30) REVERT: A 1010 ILE cc_start: 0.9400 (mt) cc_final: 0.9152 (mt) REVERT: A 1116 ASN cc_start: 0.9458 (m-40) cc_final: 0.9135 (m110) REVERT: B 119 ILE cc_start: 0.9023 (pt) cc_final: 0.8807 (pt) REVERT: B 177 MET cc_start: 0.2399 (ttm) cc_final: -0.2868 (mmt) REVERT: B 204 TYR cc_start: 0.6019 (m-10) cc_final: 0.5812 (m-10) REVERT: B 362 TYR cc_start: 0.9587 (m-80) cc_final: 0.9127 (m-80) REVERT: B 384 LEU cc_start: 0.9723 (mm) cc_final: 0.9327 (mt) REVERT: B 565 ASP cc_start: 0.9120 (t0) cc_final: 0.8887 (p0) REVERT: B 655 ASN cc_start: 0.8805 (m-40) cc_final: 0.8053 (t0) REVERT: B 717 ILE cc_start: 0.8717 (mm) cc_final: 0.8062 (mm) REVERT: B 728 MET cc_start: 0.9250 (mtm) cc_final: 0.9010 (mtm) REVERT: B 774 ASN cc_start: 0.8750 (m110) cc_final: 0.8482 (m110) REVERT: B 903 PHE cc_start: 0.8178 (m-10) cc_final: 0.7876 (m-10) REVERT: B 957 ASN cc_start: 0.9253 (m110) cc_final: 0.8963 (m110) REVERT: B 989 GLN cc_start: 0.9442 (mm-40) cc_final: 0.8842 (mp10) REVERT: B 999 GLN cc_start: 0.9285 (tm-30) cc_final: 0.8763 (tm-30) REVERT: B 1014 GLU cc_start: 0.9223 (tt0) cc_final: 0.8842 (mm-30) REVERT: C 58 PHE cc_start: 0.9469 (m-10) cc_final: 0.9016 (m-80) REVERT: C 177 MET cc_start: 0.2554 (ttm) cc_final: 0.1994 (ttp) REVERT: C 223 LEU cc_start: 0.9204 (mp) cc_final: 0.8969 (tp) REVERT: C 272 PHE cc_start: 0.8740 (m-10) cc_final: 0.8250 (m-10) REVERT: C 348 TYR cc_start: 0.9347 (p90) cc_final: 0.9040 (p90) REVERT: C 377 TYR cc_start: 0.7851 (m-80) cc_final: 0.7335 (m-80) REVERT: C 431 ILE cc_start: 0.9691 (mt) cc_final: 0.9485 (tp) REVERT: C 647 LEU cc_start: 0.9255 (tp) cc_final: 0.8944 (pp) REVERT: C 733 VAL cc_start: 0.9300 (t) cc_final: 0.8964 (p) REVERT: C 734 ASP cc_start: 0.8574 (t0) cc_final: 0.7876 (t0) REVERT: C 737 MET cc_start: 0.8923 (tpt) cc_final: 0.7946 (tpt) REVERT: C 762 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8382 (mtt-85) REVERT: C 767 ILE cc_start: 0.9863 (mt) cc_final: 0.9608 (mt) REVERT: C 770 GLU cc_start: 0.9589 (mt-10) cc_final: 0.9383 (mt-10) REVERT: C 771 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8741 (mm110) REVERT: C 781 GLN cc_start: 0.8684 (mt0) cc_final: 0.8451 (mt0) REVERT: C 786 TYR cc_start: 0.8678 (m-10) cc_final: 0.7979 (m-10) REVERT: C 816 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8403 (mt-10) REVERT: C 918 LYS cc_start: 0.9659 (mttt) cc_final: 0.9262 (mptt) REVERT: C 961 LYS cc_start: 0.9309 (mttt) cc_final: 0.8896 (mttt) REVERT: C 975 ASN cc_start: 0.9506 (m110) cc_final: 0.8805 (p0) REVERT: C 992 ARG cc_start: 0.8882 (mtt180) cc_final: 0.8379 (mpp80) REVERT: C 1009 LEU cc_start: 0.9696 (mt) cc_final: 0.9434 (mm) REVERT: C 1011 ARG cc_start: 0.9340 (tpp-160) cc_final: 0.8754 (mmt-90) REVERT: C 1021 LEU cc_start: 0.9483 (mt) cc_final: 0.9279 (mt) REVERT: C 1051 GLN cc_start: 0.8279 (tp40) cc_final: 0.7630 (mm-40) REVERT: H 34 MET cc_start: 0.2507 (mpp) cc_final: 0.1826 (mpp) REVERT: E 73 ASP cc_start: 0.4814 (m-30) cc_final: 0.4537 (p0) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.1802 time to fit residues: 129.0706 Evaluate side-chains 348 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 378 optimal weight: 30.0000 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 349 optimal weight: 50.0000 chunk 370 optimal weight: 6.9990 chunk 282 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 304 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN A 610 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.110935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.065550 restraints weight = 123755.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.068003 restraints weight = 73195.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.069699 restraints weight = 50742.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.070946 restraints weight = 39063.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071763 restraints weight = 32202.441| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 31793 Z= 0.142 Angle : 0.616 21.513 43385 Z= 0.319 Chirality : 0.045 0.251 4983 Planarity : 0.004 0.039 5509 Dihedral : 5.228 43.472 5297 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.13), residues: 3827 helix: -0.11 (0.19), residues: 682 sheet: 0.05 (0.16), residues: 1032 loop : -0.68 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 574 TYR 0.027 0.001 TYR B 738 PHE 0.031 0.002 PHE B 43 TRP 0.024 0.001 TRP L 34 HIS 0.008 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00302 (31689) covalent geometry : angle 0.58812 (43124) SS BOND : bond 0.00399 ( 51) SS BOND : angle 1.76022 ( 102) hydrogen bonds : bond 0.04174 ( 1286) hydrogen bonds : angle 5.84960 ( 3654) link_BETA1-4 : bond 0.00230 ( 12) link_BETA1-4 : angle 1.22246 ( 36) link_NAG-ASN : bond 0.00400 ( 41) link_NAG-ASN : angle 3.07249 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 465 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 TYR cc_start: 0.8129 (t80) cc_final: 0.7099 (t80) REVERT: A 453 PHE cc_start: 0.9628 (m-10) cc_final: 0.9306 (m-80) REVERT: A 529 ASN cc_start: 0.9645 (m-40) cc_final: 0.9254 (p0) REVERT: A 532 LYS cc_start: 0.9298 (mttt) cc_final: 0.9008 (ptmt) REVERT: A 582 LEU cc_start: 0.8987 (mp) cc_final: 0.8780 (mm) REVERT: A 734 ASP cc_start: 0.8560 (t0) cc_final: 0.8310 (t0) REVERT: A 737 MET cc_start: 0.8484 (tpp) cc_final: 0.8036 (tpp) REVERT: A 760 LEU cc_start: 0.9239 (mt) cc_final: 0.9033 (mt) REVERT: A 761 ASN cc_start: 0.9191 (m-40) cc_final: 0.8860 (p0) REVERT: A 767 ILE cc_start: 0.9196 (mm) cc_final: 0.8960 (mm) REVERT: A 893 ILE cc_start: 0.8858 (tp) cc_final: 0.8612 (tp) REVERT: A 918 LYS cc_start: 0.9641 (mttt) cc_final: 0.9403 (tptp) REVERT: A 957 ASN cc_start: 0.9175 (m110) cc_final: 0.8946 (m110) REVERT: A 970 ILE cc_start: 0.9137 (pt) cc_final: 0.8637 (pt) REVERT: A 977 ILE cc_start: 0.9522 (pt) cc_final: 0.9041 (mm) REVERT: A 989 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8205 (mp10) REVERT: A 994 ILE cc_start: 0.9229 (mt) cc_final: 0.8968 (mt) REVERT: A 1001 LEU cc_start: 0.9437 (mt) cc_final: 0.9198 (mt) REVERT: A 1002 GLN cc_start: 0.9533 (tp40) cc_final: 0.9132 (tp-100) REVERT: A 1003 THR cc_start: 0.9526 (m) cc_final: 0.9305 (m) REVERT: A 1007 GLN cc_start: 0.9442 (mm-40) cc_final: 0.8534 (tm-30) REVERT: A 1047 MET cc_start: 0.8498 (tpp) cc_final: 0.7783 (mmm) REVERT: A 1078 ILE cc_start: 0.8809 (mm) cc_final: 0.8599 (mm) REVERT: A 1116 ASN cc_start: 0.9431 (m-40) cc_final: 0.9102 (m110) REVERT: B 153 MET cc_start: 0.7313 (pmm) cc_final: 0.7099 (pmm) REVERT: B 177 MET cc_start: 0.2412 (ttm) cc_final: -0.2607 (mmt) REVERT: B 204 TYR cc_start: 0.5331 (m-10) cc_final: 0.5130 (m-10) REVERT: B 273 LEU cc_start: 0.9162 (tp) cc_final: 0.8914 (tp) REVERT: B 274 LEU cc_start: 0.8947 (mt) cc_final: 0.8722 (tt) REVERT: B 362 TYR cc_start: 0.9555 (m-80) cc_final: 0.9103 (m-80) REVERT: B 384 LEU cc_start: 0.9720 (mm) cc_final: 0.9319 (mt) REVERT: B 565 ASP cc_start: 0.8979 (t0) cc_final: 0.8503 (p0) REVERT: B 655 ASN cc_start: 0.8839 (m-40) cc_final: 0.8069 (t0) REVERT: B 717 ILE cc_start: 0.8455 (mm) cc_final: 0.7768 (mm) REVERT: B 728 MET cc_start: 0.9208 (mtm) cc_final: 0.8950 (mtm) REVERT: B 774 ASN cc_start: 0.8855 (m110) cc_final: 0.8633 (m-40) REVERT: B 781 GLN cc_start: 0.8921 (mm110) cc_final: 0.8344 (tm-30) REVERT: B 865 GLU cc_start: 0.9360 (tt0) cc_final: 0.8955 (mp0) REVERT: B 952 ASN cc_start: 0.9479 (t0) cc_final: 0.9234 (t0) REVERT: B 956 LEU cc_start: 0.9699 (mt) cc_final: 0.9466 (mt) REVERT: B 957 ASN cc_start: 0.9336 (m110) cc_final: 0.8962 (m110) REVERT: B 998 LEU cc_start: 0.9506 (pp) cc_final: 0.9243 (pp) REVERT: B 999 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8835 (tm-30) REVERT: B 1001 LEU cc_start: 0.9446 (mm) cc_final: 0.8999 (mm) REVERT: B 1014 GLU cc_start: 0.8969 (tt0) cc_final: 0.7970 (mm-30) REVERT: B 1015 ILE cc_start: 0.9592 (tt) cc_final: 0.9368 (pt) REVERT: B 1028 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8063 (mt-10) REVERT: B 1031 LEU cc_start: 0.8542 (mp) cc_final: 0.8323 (mp) REVERT: B 1064 TYR cc_start: 0.8953 (t80) cc_final: 0.8622 (t80) REVERT: C 58 PHE cc_start: 0.9355 (m-10) cc_final: 0.8984 (m-80) REVERT: C 177 MET cc_start: 0.3536 (ttm) cc_final: 0.2933 (ttp) REVERT: C 223 LEU cc_start: 0.9057 (mp) cc_final: 0.8762 (tp) REVERT: C 272 PHE cc_start: 0.8517 (m-10) cc_final: 0.8178 (m-10) REVERT: C 315 PHE cc_start: 0.7955 (t80) cc_final: 0.7190 (t80) REVERT: C 321 GLU cc_start: 0.9220 (tp30) cc_final: 0.8482 (tp30) REVERT: C 348 TYR cc_start: 0.9253 (p90) cc_final: 0.8911 (p90) REVERT: C 377 TYR cc_start: 0.7701 (m-80) cc_final: 0.6904 (m-80) REVERT: C 647 LEU cc_start: 0.9317 (tp) cc_final: 0.8931 (pp) REVERT: C 733 VAL cc_start: 0.9348 (t) cc_final: 0.9050 (p) REVERT: C 734 ASP cc_start: 0.8819 (t0) cc_final: 0.8548 (t0) REVERT: C 737 MET cc_start: 0.8881 (tpt) cc_final: 0.8655 (tpp) REVERT: C 738 TYR cc_start: 0.9404 (t80) cc_final: 0.9197 (t80) REVERT: C 762 ARG cc_start: 0.8932 (mtm-85) cc_final: 0.8067 (mtt180) REVERT: C 767 ILE cc_start: 0.9823 (mt) cc_final: 0.9286 (mt) REVERT: C 770 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9011 (mt-10) REVERT: C 771 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8646 (mm-40) REVERT: C 781 GLN cc_start: 0.8605 (mt0) cc_final: 0.8250 (tm-30) REVERT: C 786 TYR cc_start: 0.8455 (m-10) cc_final: 0.7821 (m-10) REVERT: C 918 LYS cc_start: 0.9654 (mttt) cc_final: 0.9232 (mptt) REVERT: C 961 LYS cc_start: 0.9142 (mttt) cc_final: 0.8700 (mttt) REVERT: C 1011 ARG cc_start: 0.9237 (tpp-160) cc_final: 0.8920 (tpp-160) REVERT: C 1021 LEU cc_start: 0.9467 (mt) cc_final: 0.9264 (mt) REVERT: C 1051 GLN cc_start: 0.8419 (tp-100) cc_final: 0.7601 (tp-100) REVERT: H 34 MET cc_start: 0.2352 (mpp) cc_final: 0.1684 (mpp) REVERT: H 83 MET cc_start: -0.6279 (ptt) cc_final: -0.6746 (ptt) REVERT: E 73 ASP cc_start: 0.4820 (m-30) cc_final: 0.4475 (p0) outliers start: 1 outliers final: 0 residues processed: 465 average time/residue: 0.1795 time to fit residues: 137.3328 Evaluate side-chains 393 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 234 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 377 optimal weight: 50.0000 chunk 128 optimal weight: 10.0000 chunk 322 optimal weight: 3.9990 chunk 360 optimal weight: 50.0000 chunk 125 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 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 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN A 925 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS B 268 GLN B 761 ASN B 946 GLN ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.105347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.059500 restraints weight = 128531.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060505 restraints weight = 81094.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.061804 restraints weight = 58691.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.062478 restraints weight = 46916.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.063297 restraints weight = 40670.812| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 31793 Z= 0.368 Angle : 0.845 20.509 43385 Z= 0.453 Chirality : 0.049 0.274 4983 Planarity : 0.006 0.091 5509 Dihedral : 6.084 47.254 5297 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 25.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 0.03 % Allowed : 1.34 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 3827 helix: -1.58 (0.17), residues: 699 sheet: -0.44 (0.16), residues: 1022 loop : -0.93 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 270 TYR 0.053 0.002 TYR B 738 PHE 0.035 0.003 PHE A 797 TRP 0.027 0.002 TRP B 64 HIS 0.014 0.002 HIS B 652 Details of bonding type rmsd covalent geometry : bond 0.00704 (31689) covalent geometry : angle 0.82163 (43124) SS BOND : bond 0.00560 ( 51) SS BOND : angle 1.94404 ( 102) hydrogen bonds : bond 0.05628 ( 1286) hydrogen bonds : angle 6.65937 ( 3654) link_BETA1-4 : bond 0.00421 ( 12) link_BETA1-4 : angle 2.09362 ( 36) link_NAG-ASN : bond 0.00746 ( 41) link_NAG-ASN : angle 3.26950 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9130 (tp) cc_final: 0.8842 (mt) REVERT: A 377 TYR cc_start: 0.9339 (m-80) cc_final: 0.8881 (m-80) REVERT: A 420 TYR cc_start: 0.8466 (t80) cc_final: 0.7381 (t80) REVERT: A 453 PHE cc_start: 0.9678 (m-10) cc_final: 0.9475 (m-10) REVERT: A 529 ASN cc_start: 0.9698 (m-40) cc_final: 0.9197 (p0) REVERT: A 532 LYS cc_start: 0.9382 (mttt) cc_final: 0.9126 (ptmt) REVERT: A 582 LEU cc_start: 0.8933 (mp) cc_final: 0.8694 (mm) REVERT: A 734 ASP cc_start: 0.8876 (t0) cc_final: 0.8619 (t0) REVERT: A 737 MET cc_start: 0.8740 (tpp) cc_final: 0.8394 (tpp) REVERT: A 767 ILE cc_start: 0.9344 (mm) cc_final: 0.9120 (mm) REVERT: A 893 ILE cc_start: 0.8942 (tp) cc_final: 0.8733 (tp) REVERT: A 897 MET cc_start: 0.7331 (mpp) cc_final: 0.7106 (mpp) REVERT: A 918 LYS cc_start: 0.9691 (mttt) cc_final: 0.9422 (tptp) REVERT: A 957 ASN cc_start: 0.9357 (m110) cc_final: 0.9012 (m-40) REVERT: A 958 THR cc_start: 0.9729 (p) cc_final: 0.9482 (p) REVERT: A 961 LYS cc_start: 0.9489 (mttt) cc_final: 0.9050 (mttm) REVERT: A 977 ILE cc_start: 0.9673 (pt) cc_final: 0.9274 (mm) REVERT: A 989 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8484 (mp10) REVERT: A 1001 LEU cc_start: 0.9380 (mt) cc_final: 0.9092 (mt) REVERT: A 1002 GLN cc_start: 0.9566 (tp40) cc_final: 0.9218 (tp-100) REVERT: A 1003 THR cc_start: 0.9495 (m) cc_final: 0.9220 (p) REVERT: A 1100 PHE cc_start: 0.9296 (m-80) cc_final: 0.9016 (m-80) REVERT: A 1116 ASN cc_start: 0.9360 (m-40) cc_final: 0.9002 (m110) REVERT: B 118 LEU cc_start: 0.9680 (tt) cc_final: 0.9396 (tp) REVERT: B 119 ILE cc_start: 0.9003 (pt) cc_final: 0.8803 (pt) REVERT: B 177 MET cc_start: 0.3139 (ttm) cc_final: -0.2114 (mmt) REVERT: B 362 TYR cc_start: 0.9513 (m-80) cc_final: 0.9105 (m-80) REVERT: B 384 LEU cc_start: 0.9721 (mm) cc_final: 0.9270 (mt) REVERT: B 610 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8224 (tp-100) REVERT: B 694 MET cc_start: 0.8684 (ppp) cc_final: 0.8466 (ppp) REVERT: B 752 GLN cc_start: 0.8743 (mt0) cc_final: 0.8480 (mt0) REVERT: B 774 ASN cc_start: 0.8789 (m110) cc_final: 0.8442 (m110) REVERT: B 952 ASN cc_start: 0.9561 (t0) cc_final: 0.9321 (m110) REVERT: B 975 ASN cc_start: 0.9606 (m-40) cc_final: 0.9248 (t0) REVERT: B 999 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8830 (tm-30) REVERT: B 1001 LEU cc_start: 0.9483 (mm) cc_final: 0.9013 (mm) REVERT: B 1014 GLU cc_start: 0.9250 (tt0) cc_final: 0.8877 (mm-30) REVERT: B 1064 TYR cc_start: 0.8819 (t80) cc_final: 0.8523 (t80) REVERT: C 177 MET cc_start: 0.4491 (ttm) cc_final: 0.3923 (ttp) REVERT: C 223 LEU cc_start: 0.9213 (mp) cc_final: 0.8989 (tp) REVERT: C 272 PHE cc_start: 0.8919 (m-10) cc_final: 0.8620 (m-10) REVERT: C 377 TYR cc_start: 0.7827 (m-80) cc_final: 0.7309 (m-80) REVERT: C 559 PHE cc_start: 0.8394 (p90) cc_final: 0.8166 (p90) REVERT: C 647 LEU cc_start: 0.9410 (tp) cc_final: 0.8886 (pp) REVERT: C 728 MET cc_start: 0.9081 (ptm) cc_final: 0.8017 (tmm) REVERT: C 733 VAL cc_start: 0.9401 (t) cc_final: 0.9181 (t) REVERT: C 734 ASP cc_start: 0.8648 (t0) cc_final: 0.8326 (t0) REVERT: C 737 MET cc_start: 0.8835 (tpt) cc_final: 0.8383 (tpt) REVERT: C 762 ARG cc_start: 0.8914 (mtm-85) cc_final: 0.8460 (mtt-85) REVERT: C 770 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9166 (mt-10) REVERT: C 781 GLN cc_start: 0.8822 (mt0) cc_final: 0.8455 (mt0) REVERT: C 918 LYS cc_start: 0.9594 (mttt) cc_final: 0.9203 (mptt) REVERT: C 975 ASN cc_start: 0.9520 (m110) cc_final: 0.8828 (p0) REVERT: C 989 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8586 (mm-40) REVERT: C 1011 ARG cc_start: 0.9462 (tpp-160) cc_final: 0.9004 (mmt-90) REVERT: C 1051 GLN cc_start: 0.8171 (tp-100) cc_final: 0.7683 (tp-100) REVERT: H 34 MET cc_start: 0.2400 (mpp) cc_final: 0.1753 (mpp) REVERT: H 83 MET cc_start: -0.5843 (ptt) cc_final: -0.6148 (ptt) outliers start: 1 outliers final: 0 residues processed: 407 average time/residue: 0.1800 time to fit residues: 121.2317 Evaluate side-chains 331 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 202 optimal weight: 0.0570 chunk 46 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 310 optimal weight: 0.9990 chunk 343 optimal weight: 9.9990 chunk 378 optimal weight: 50.0000 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN ** A1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.110071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.064775 restraints weight = 126326.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067167 restraints weight = 74918.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.068885 restraints weight = 51702.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070092 restraints weight = 39601.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070836 restraints weight = 32777.709| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31793 Z= 0.142 Angle : 0.640 20.553 43385 Z= 0.332 Chirality : 0.046 0.333 4983 Planarity : 0.004 0.050 5509 Dihedral : 5.433 50.881 5297 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 0.06 % Allowed : 0.54 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.13), residues: 3827 helix: -0.41 (0.19), residues: 689 sheet: -0.16 (0.16), residues: 1001 loop : -0.74 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 237 TYR 0.033 0.001 TYR B 204 PHE 0.040 0.002 PHE C 756 TRP 0.020 0.001 TRP L 34 HIS 0.006 0.001 HIS B1061 Details of bonding type rmsd covalent geometry : bond 0.00301 (31689) covalent geometry : angle 0.61426 (43124) SS BOND : bond 0.00382 ( 51) SS BOND : angle 1.41094 ( 102) hydrogen bonds : bond 0.04220 ( 1286) hydrogen bonds : angle 5.98520 ( 3654) link_BETA1-4 : bond 0.00247 ( 12) link_BETA1-4 : angle 1.29371 ( 36) link_NAG-ASN : bond 0.00545 ( 41) link_NAG-ASN : angle 3.15395 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 451 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8207 (pmm) cc_final: 0.8006 (pmm) REVERT: A 354 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7518 (ttp80) REVERT: A 377 TYR cc_start: 0.9319 (m-80) cc_final: 0.8922 (m-80) REVERT: A 420 TYR cc_start: 0.7987 (t80) cc_final: 0.7155 (t80) REVERT: A 453 PHE cc_start: 0.9652 (m-10) cc_final: 0.9409 (m-10) REVERT: A 529 ASN cc_start: 0.9681 (m-40) cc_final: 0.9180 (p0) REVERT: A 532 LYS cc_start: 0.9329 (mttt) cc_final: 0.9097 (ptmt) REVERT: A 568 ASP cc_start: 0.9734 (m-30) cc_final: 0.8702 (t0) REVERT: A 582 LEU cc_start: 0.8887 (mp) cc_final: 0.8633 (mm) REVERT: A 737 MET cc_start: 0.8741 (tpp) cc_final: 0.8374 (tpp) REVERT: A 767 ILE cc_start: 0.9258 (mm) cc_final: 0.9009 (mm) REVERT: A 897 MET cc_start: 0.7010 (mpp) cc_final: 0.6789 (mpp) REVERT: A 918 LYS cc_start: 0.9661 (mttt) cc_final: 0.9142 (tppt) REVERT: A 935 LEU cc_start: 0.9784 (mt) cc_final: 0.9435 (pp) REVERT: A 957 ASN cc_start: 0.9133 (m110) cc_final: 0.8746 (m110) REVERT: A 958 THR cc_start: 0.9696 (p) cc_final: 0.9411 (p) REVERT: A 961 LYS cc_start: 0.9332 (mttt) cc_final: 0.8840 (mttm) REVERT: A 977 ILE cc_start: 0.9618 (pt) cc_final: 0.9155 (mm) REVERT: A 989 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8370 (mp10) REVERT: A 994 ILE cc_start: 0.9305 (mt) cc_final: 0.8974 (mt) REVERT: A 1002 GLN cc_start: 0.9496 (tp40) cc_final: 0.9084 (tp-100) REVERT: A 1047 MET cc_start: 0.8604 (tpp) cc_final: 0.8130 (mmm) REVERT: A 1060 LEU cc_start: 0.9501 (mp) cc_final: 0.9294 (mp) REVERT: A 1078 ILE cc_start: 0.8913 (mm) cc_final: 0.8710 (mm) REVERT: A 1116 ASN cc_start: 0.9406 (m-40) cc_final: 0.9106 (m110) REVERT: B 58 PHE cc_start: 0.9199 (m-80) cc_final: 0.8581 (m-80) REVERT: B 118 LEU cc_start: 0.9655 (tt) cc_final: 0.9374 (tp) REVERT: B 177 MET cc_start: 0.2967 (ttm) cc_final: -0.1934 (mmt) REVERT: B 204 TYR cc_start: 0.5567 (m-10) cc_final: 0.5252 (m-10) REVERT: B 273 LEU cc_start: 0.9235 (tp) cc_final: 0.8991 (tp) REVERT: B 274 LEU cc_start: 0.8805 (mt) cc_final: 0.8588 (tp) REVERT: B 362 TYR cc_start: 0.9461 (m-80) cc_final: 0.9069 (m-80) REVERT: B 384 LEU cc_start: 0.9732 (mm) cc_final: 0.9340 (mt) REVERT: B 565 ASP cc_start: 0.9004 (t0) cc_final: 0.8477 (p0) REVERT: B 752 GLN cc_start: 0.8785 (mt0) cc_final: 0.8468 (mt0) REVERT: B 781 GLN cc_start: 0.8886 (mm110) cc_final: 0.8394 (tm-30) REVERT: B 816 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8377 (mm-30) REVERT: B 952 ASN cc_start: 0.9522 (t0) cc_final: 0.9213 (t0) REVERT: B 957 ASN cc_start: 0.9368 (m110) cc_final: 0.8993 (m110) REVERT: B 975 ASN cc_start: 0.9667 (m-40) cc_final: 0.9202 (t0) REVERT: B 998 LEU cc_start: 0.9474 (pp) cc_final: 0.9182 (pp) REVERT: B 999 GLN cc_start: 0.9306 (tm-30) cc_final: 0.8838 (tm-30) REVERT: B 1001 LEU cc_start: 0.9490 (mm) cc_final: 0.9050 (mm) REVERT: B 1014 GLU cc_start: 0.9050 (tt0) cc_final: 0.8148 (mm-30) REVERT: B 1031 LEU cc_start: 0.8538 (mp) cc_final: 0.8324 (mp) REVERT: B 1051 GLN cc_start: 0.9027 (tt0) cc_final: 0.8555 (tt0) REVERT: B 1064 TYR cc_start: 0.8995 (t80) cc_final: 0.8475 (t80) REVERT: C 58 PHE cc_start: 0.9366 (m-10) cc_final: 0.8984 (m-80) REVERT: C 177 MET cc_start: 0.4688 (ttm) cc_final: 0.4168 (ttp) REVERT: C 223 LEU cc_start: 0.9077 (mp) cc_final: 0.8811 (tp) REVERT: C 272 PHE cc_start: 0.8591 (m-10) cc_final: 0.8180 (m-10) REVERT: C 310 TYR cc_start: 0.8786 (m-80) cc_final: 0.8285 (m-80) REVERT: C 321 GLU cc_start: 0.9320 (tp30) cc_final: 0.8733 (tp30) REVERT: C 377 TYR cc_start: 0.7738 (m-80) cc_final: 0.7150 (m-80) REVERT: C 647 LEU cc_start: 0.9334 (tp) cc_final: 0.8867 (pp) REVERT: C 733 VAL cc_start: 0.9363 (t) cc_final: 0.9076 (p) REVERT: C 734 ASP cc_start: 0.8977 (t0) cc_final: 0.8651 (t0) REVERT: C 737 MET cc_start: 0.8826 (tpt) cc_final: 0.8609 (tpp) REVERT: C 767 ILE cc_start: 0.9765 (mt) cc_final: 0.9484 (mt) REVERT: C 770 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9060 (mt-10) REVERT: C 816 GLU cc_start: 0.8624 (mp0) cc_final: 0.7970 (mp0) REVERT: C 914 TYR cc_start: 0.7757 (m-80) cc_final: 0.7421 (m-80) REVERT: C 918 LYS cc_start: 0.9578 (mttt) cc_final: 0.9151 (tptp) REVERT: C 961 LYS cc_start: 0.9155 (mttt) cc_final: 0.8704 (mttt) REVERT: C 989 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8535 (mm-40) REVERT: C 1011 ARG cc_start: 0.9273 (tpp-160) cc_final: 0.8737 (mmt180) REVERT: C 1021 LEU cc_start: 0.9435 (mt) cc_final: 0.9217 (mt) REVERT: C 1031 LEU cc_start: 0.9500 (mp) cc_final: 0.9298 (mp) REVERT: H 34 MET cc_start: 0.2122 (mpp) cc_final: 0.1884 (mpp) REVERT: H 83 MET cc_start: -0.6133 (ptt) cc_final: -0.6590 (ptt) outliers start: 2 outliers final: 0 residues processed: 451 average time/residue: 0.1755 time to fit residues: 130.9585 Evaluate side-chains 356 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 146 optimal weight: 6.9990 chunk 338 optimal weight: 30.0000 chunk 113 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 105 optimal weight: 0.0570 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN ** C 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN C1051 GLN ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.107316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.062981 restraints weight = 123694.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064582 restraints weight = 79977.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065921 restraints weight = 50576.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066694 restraints weight = 39382.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066655 restraints weight = 37330.323| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31793 Z= 0.271 Angle : 0.718 19.930 43385 Z= 0.382 Chirality : 0.046 0.223 4983 Planarity : 0.005 0.068 5509 Dihedral : 5.695 56.425 5297 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.77 % Favored : 94.20 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.13), residues: 3827 helix: -0.93 (0.18), residues: 687 sheet: -0.35 (0.16), residues: 1019 loop : -0.83 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 564 TYR 0.044 0.002 TYR B 738 PHE 0.034 0.002 PHE C1039 TRP 0.021 0.002 TRP L 34 HIS 0.010 0.001 HIS B1061 Details of bonding type rmsd covalent geometry : bond 0.00522 (31689) covalent geometry : angle 0.69472 (43124) SS BOND : bond 0.00526 ( 51) SS BOND : angle 1.57916 ( 102) hydrogen bonds : bond 0.04932 ( 1286) hydrogen bonds : angle 6.29523 ( 3654) link_BETA1-4 : bond 0.00203 ( 12) link_BETA1-4 : angle 1.58973 ( 36) link_NAG-ASN : bond 0.00537 ( 41) link_NAG-ASN : angle 3.14794 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 404 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8668 (mp) cc_final: 0.8255 (mp) REVERT: A 354 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7336 (ttp80) REVERT: A 377 TYR cc_start: 0.9172 (m-80) cc_final: 0.8605 (m-80) REVERT: A 420 TYR cc_start: 0.8210 (t80) cc_final: 0.7186 (t80) REVERT: A 529 ASN cc_start: 0.9732 (m-40) cc_final: 0.9215 (p0) REVERT: A 532 LYS cc_start: 0.9362 (mttt) cc_final: 0.9115 (ptmt) REVERT: A 568 ASP cc_start: 0.9762 (m-30) cc_final: 0.9030 (t0) REVERT: A 582 LEU cc_start: 0.8918 (mp) cc_final: 0.8685 (mm) REVERT: A 737 MET cc_start: 0.8784 (tpp) cc_final: 0.8548 (tpp) REVERT: A 748 ASN cc_start: 0.8612 (t0) cc_final: 0.8410 (t0) REVERT: A 897 MET cc_start: 0.7179 (mpp) cc_final: 0.6946 (mpp) REVERT: A 918 LYS cc_start: 0.9699 (mttt) cc_final: 0.9335 (tppt) REVERT: A 957 ASN cc_start: 0.9210 (m110) cc_final: 0.8821 (m110) REVERT: A 958 THR cc_start: 0.9716 (p) cc_final: 0.9372 (p) REVERT: A 961 LYS cc_start: 0.9436 (mttt) cc_final: 0.8983 (mttm) REVERT: A 989 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8508 (mp10) REVERT: A 1002 GLN cc_start: 0.9569 (tp40) cc_final: 0.9187 (tp-100) REVERT: A 1116 ASN cc_start: 0.9392 (m-40) cc_final: 0.9039 (m110) REVERT: B 58 PHE cc_start: 0.9245 (m-80) cc_final: 0.8689 (m-80) REVERT: B 118 LEU cc_start: 0.9626 (tt) cc_final: 0.9382 (tp) REVERT: B 153 MET cc_start: 0.7720 (pmm) cc_final: 0.7488 (pmm) REVERT: B 177 MET cc_start: 0.4212 (ttm) cc_final: -0.0378 (mmt) REVERT: B 362 TYR cc_start: 0.9413 (m-80) cc_final: 0.9030 (m-80) REVERT: B 384 LEU cc_start: 0.9701 (mm) cc_final: 0.9252 (mt) REVERT: B 565 ASP cc_start: 0.9055 (t0) cc_final: 0.8744 (p0) REVERT: B 610 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7671 (tp-100) REVERT: B 694 MET cc_start: 0.8571 (ppp) cc_final: 0.8300 (ppp) REVERT: B 752 GLN cc_start: 0.8819 (mt0) cc_final: 0.8601 (mt0) REVERT: B 781 GLN cc_start: 0.8922 (mm110) cc_final: 0.8449 (tm-30) REVERT: B 797 PHE cc_start: 0.9117 (m-10) cc_final: 0.8729 (m-10) REVERT: B 952 ASN cc_start: 0.9532 (t0) cc_final: 0.9256 (t0) REVERT: B 957 ASN cc_start: 0.9298 (m110) cc_final: 0.8892 (m110) REVERT: B 975 ASN cc_start: 0.9709 (m-40) cc_final: 0.9372 (t0) REVERT: B 999 GLN cc_start: 0.9342 (tm-30) cc_final: 0.8801 (tm-30) REVERT: B 1014 GLU cc_start: 0.9292 (tt0) cc_final: 0.8653 (mm-30) REVERT: B 1031 LEU cc_start: 0.8861 (mp) cc_final: 0.8652 (mp) REVERT: B 1051 GLN cc_start: 0.8799 (tt0) cc_final: 0.8464 (tt0) REVERT: B 1064 TYR cc_start: 0.8912 (t80) cc_final: 0.8540 (t80) REVERT: C 58 PHE cc_start: 0.9420 (m-10) cc_final: 0.9032 (m-80) REVERT: C 177 MET cc_start: 0.5627 (ttm) cc_final: 0.5213 (ttp) REVERT: C 223 LEU cc_start: 0.9139 (mp) cc_final: 0.8912 (tp) REVERT: C 272 PHE cc_start: 0.8725 (m-10) cc_final: 0.8322 (m-10) REVERT: C 377 TYR cc_start: 0.7682 (m-80) cc_final: 0.7181 (m-80) REVERT: C 559 PHE cc_start: 0.8370 (p90) cc_final: 0.8140 (p90) REVERT: C 647 LEU cc_start: 0.9253 (tp) cc_final: 0.8596 (pp) REVERT: C 728 MET cc_start: 0.9463 (ptm) cc_final: 0.8849 (ppp) REVERT: C 733 VAL cc_start: 0.9419 (t) cc_final: 0.9189 (t) REVERT: C 734 ASP cc_start: 0.8577 (t0) cc_final: 0.8217 (t0) REVERT: C 767 ILE cc_start: 0.9776 (mt) cc_final: 0.9521 (mt) REVERT: C 770 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9159 (mt-10) REVERT: C 799 PHE cc_start: 0.9284 (m-80) cc_final: 0.8843 (m-10) REVERT: C 816 GLU cc_start: 0.9039 (mp0) cc_final: 0.8225 (mp0) REVERT: C 918 LYS cc_start: 0.9621 (mttt) cc_final: 0.9249 (mptt) REVERT: C 954 GLN cc_start: 0.9614 (mp10) cc_final: 0.9306 (mp10) REVERT: C 957 ASN cc_start: 0.9405 (m-40) cc_final: 0.9157 (m-40) REVERT: C 961 LYS cc_start: 0.9257 (mttt) cc_final: 0.8825 (mttt) REVERT: C 993 LEU cc_start: 0.9225 (mt) cc_final: 0.9020 (mt) REVERT: C 1011 ARG cc_start: 0.9377 (tpp-160) cc_final: 0.8865 (mmt180) REVERT: C 1021 LEU cc_start: 0.9479 (mt) cc_final: 0.9243 (mt) REVERT: C 1051 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: H 83 MET cc_start: -0.6042 (ptt) cc_final: -0.6589 (ptt) REVERT: E 73 ASP cc_start: 0.4797 (m-30) cc_final: 0.4438 (p0) outliers start: 3 outliers final: 1 residues processed: 405 average time/residue: 0.1773 time to fit residues: 119.3877 Evaluate side-chains 327 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 310 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 262 optimal weight: 6.9990 chunk 301 optimal weight: 0.0770 chunk 139 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.112144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067458 restraints weight = 125810.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.070569 restraints weight = 76589.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.071370 restraints weight = 47260.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.072056 restraints weight = 34875.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.072207 restraints weight = 32837.479| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.6791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31793 Z= 0.126 Angle : 0.617 19.950 43385 Z= 0.320 Chirality : 0.045 0.223 4983 Planarity : 0.004 0.048 5509 Dihedral : 5.225 56.736 5297 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.13), residues: 3827 helix: -0.08 (0.19), residues: 687 sheet: -0.12 (0.16), residues: 1025 loop : -0.72 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 237 TYR 0.036 0.001 TYR B 738 PHE 0.028 0.002 PHE C 756 TRP 0.020 0.001 TRP L 34 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00269 (31689) covalent geometry : angle 0.59432 (43124) SS BOND : bond 0.00401 ( 51) SS BOND : angle 1.35457 ( 102) hydrogen bonds : bond 0.03993 ( 1286) hydrogen bonds : angle 5.84929 ( 3654) link_BETA1-4 : bond 0.00265 ( 12) link_BETA1-4 : angle 1.18635 ( 36) link_NAG-ASN : bond 0.00416 ( 41) link_NAG-ASN : angle 2.89001 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6555.65 seconds wall clock time: 113 minutes 41.95 seconds (6821.95 seconds total)