Starting phenix.real_space_refine on Mon Jul 6 00:03:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q9i_13870/07_2026/7q9i_13870.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9i_13870/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7q9i_13870/07_2026/7q9i_13870.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q9i_13870/07_2026/7q9i_13870.cif" model { file = "/net/cci-nas-00/data/ceres_data/7q9i_13870/07_2026/7q9i_13870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9i_13870/07_2026/7q9i_13870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q9i_13870/07_2026/7q9i_13870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9i_13870/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 9 Time building chain proxies: 6.73, per 1000 atoms: 0.22 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: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.27 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: 10.12 Time building geometry restraints manager: 3.68 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: 17340 17.73 - 35.47: 748 35.47 - 53.20: 161 53.20 - 70.93: 34 70.93 - 88.66: 13 Dihedral angle restraints: 18296 sinusoidal: 7069 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 18293 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.750 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 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 : 10.889 88.664 10965 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/Z covalent geometry : bond 0.00372 / 0.20 (31689) covalent geometry : angle 0.57441 / 0.31 (43124) SS BOND : bond 0.00456 / 0.28 ( 51) SS BOND : angle 0.97249 / 0.69 ( 102) hydrogen bonds : bond 0.14148 / 9.30 ( 1286) hydrogen bonds : angle 7.52308 / 5.25 ( 3654) link_BETA1-4 : bond 0.00219 / 0.17 ( 12) link_BETA1-4 : angle 1.37744 / 0.94 ( 36) link_NAG-ASN : bond 0.00333 / 0.23 ( 41) link_NAG-ASN : angle 3.04984 / 2.15 ( 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 : 1.035 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: 0.2051 time to fit residues: 254.5902 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 : 1.069 ------------------------------------------------------------------------------- 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... 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 268 GLN B 610 GLN B 910 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.120666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.073439 restraints weight = 111651.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.075998 restraints weight = 69383.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.077839 restraints weight = 49229.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.079114 restraints weight = 38207.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.080054 restraints weight = 31829.481| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 0.091 31793 Z= 0.194 Angle : 0.686 23.266 43385 Z= 0.355 Chirality : 0.046 0.394 4983 Planarity : 0.004 0.046 5509 Dihedral : 4.660 29.441 4184 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 0.30 % Allowed : 1.82 % Favored : 97.88 % 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: -0.30 (0.13), residues: 3827 helix: 0.94 (0.19), residues: 702 sheet: -0.09 (0.15), residues: 1059 loop : -0.61 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 564 TYR 0.022 0.002 TYR H 111 PHE 0.042 0.002 PHE A 562 TRP 0.025 0.001 TRP J 52 HIS 0.007 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (31689) covalent geometry : angle 0.64978 / 0.35 (43124) SS BOND : bond 0.00597 / 0.43 ( 51) SS BOND : angle 1.80172 / 1.14 ( 102) hydrogen bonds : bond 0.04654 / 3.07 ( 1286) hydrogen bonds : angle 6.20736 / 4.32 ( 3654) link_BETA1-4 : bond 0.00197 / 0.15 ( 12) link_BETA1-4 : angle 1.13161 / 0.75 ( 36) link_NAG-ASN : bond 0.00698 / 0.53 ( 41) link_NAG-ASN : angle 3.84689 / 2.55 ( 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 573 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 563 time to evaluate : 1.220 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: symmetry clash revert: symmetry clash REVERT: A 204 TYR cc_start: 0.6788 (m-80) cc_final: 0.6247 (m-10) REVERT: A 225 PRO cc_start: 0.7622 (Cg_exo) cc_final: 0.6773 (Cg_endo) REVERT: A 409 PRO cc_start: 0.8486 (Cg_endo) cc_final: 0.8223 (Cg_exo) REVERT: A 420 TYR cc_start: 0.7845 (t80) cc_final: 0.6732 (t80) REVERT: A 453 PHE cc_start: 0.9329 (m-80) cc_final: 0.8931 (m-80) REVERT: A 529 ASN cc_start: 0.9633 (m-40) cc_final: 0.9329 (p0) REVERT: A 568 ASP cc_start: 0.9570 (m-30) cc_final: 0.8588 (t0) REVERT: A 609 TYR cc_start: 0.8391 (m-80) cc_final: 0.8146 (m-80) REVERT: A 737 MET cc_start: 0.9018 (tpt) cc_final: 0.8633 (tpp) REVERT: A 745 GLU cc_start: 0.9003 (mp0) cc_final: 0.8384 (tt0) REVERT: A 760 LEU cc_start: 0.9395 (mt) cc_final: 0.9038 (mt) REVERT: A 773 LYS cc_start: 0.9462 (mttm) cc_final: 0.9213 (mtpp) REVERT: A 779 PHE cc_start: 0.8903 (m-80) cc_final: 0.8394 (m-80) REVERT: A 818 LEU cc_start: 0.9665 (mt) cc_final: 0.9134 (mt) REVERT: A 903 PHE cc_start: 0.8697 (m-80) cc_final: 0.8405 (m-10) REVERT: A 908 VAL cc_start: 0.7910 (t) cc_final: 0.7640 (t) REVERT: A 916 ASN cc_start: 0.9160 (m-40) cc_final: 0.8949 (m110) REVERT: A 918 LYS cc_start: 0.9739 (mttt) cc_final: 0.9394 (tppt) REVERT: A 932 GLN cc_start: 0.9152 (mt0) cc_final: 0.8423 (tm-30) REVERT: A 935 LEU cc_start: 0.9755 (mt) cc_final: 0.9276 (pp) REVERT: A 954 GLN cc_start: 0.9514 (mt0) cc_final: 0.9278 (mt0) REVERT: A 957 ASN cc_start: 0.9572 (m110) cc_final: 0.9365 (m110) REVERT: A 966 ASN cc_start: 0.9287 (p0) cc_final: 0.8390 (t0) REVERT: A 999 GLN cc_start: 0.9261 (tp-100) cc_final: 0.8929 (tp-100) REVERT: A 1002 GLN cc_start: 0.9468 (tp-100) cc_final: 0.9150 (tp-100) REVERT: A 1007 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8979 (tp40) REVERT: A 1047 MET cc_start: 0.7729 (ttm) cc_final: 0.7161 (mtt) REVERT: A 1116 ASN cc_start: 0.9449 (m-40) cc_final: 0.9085 (m110) REVERT: B 106 PHE cc_start: 0.8370 (m-80) cc_final: 0.7954 (m-80) REVERT: B 117 LEU cc_start: 0.9802 (tp) cc_final: 0.9503 (tp) REVERT: B 118 LEU cc_start: 0.9505 (tp) cc_final: 0.9266 (tp) REVERT: B 168 PHE cc_start: 0.9002 (t80) cc_final: 0.8661 (t80) REVERT: B 177 MET cc_start: -0.1413 (ttm) cc_final: -0.4676 (mmt) REVERT: B 272 PHE cc_start: 0.7948 (m-80) cc_final: 0.7337 (m-80) REVERT: B 362 TYR cc_start: 0.9522 (m-80) cc_final: 0.9156 (m-80) REVERT: B 384 LEU cc_start: 0.9643 (mm) cc_final: 0.9097 (mp) REVERT: B 529 ASN cc_start: 0.9385 (p0) cc_final: 0.9151 (p0) REVERT: B 555 LYS cc_start: 0.8444 (tptt) cc_final: 0.7898 (ttpt) REVERT: B 565 ASP cc_start: 0.9113 (t0) cc_final: 0.8369 (p0) REVERT: B 608 LEU cc_start: 0.8790 (tp) cc_final: 0.8534 (mm) REVERT: B 655 ASN cc_start: 0.8486 (m-40) cc_final: 0.7888 (t0) REVERT: B 660 ASP cc_start: 0.8264 (t0) cc_final: 0.8063 (t0) REVERT: B 717 ILE cc_start: 0.8262 (mm) cc_final: 0.7446 (mm) REVERT: B 762 ARG cc_start: 0.9476 (ttm110) cc_final: 0.9144 (ptm160) REVERT: B 770 GLU cc_start: 0.8960 (tp30) cc_final: 0.8358 (tp30) REVERT: B 774 ASN cc_start: 0.9437 (m-40) cc_final: 0.8842 (m-40) REVERT: B 865 GLU cc_start: 0.9213 (tt0) cc_final: 0.8842 (mp0) REVERT: B 910 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8143 (pp30) REVERT: B 920 ILE cc_start: 0.9706 (mt) cc_final: 0.9446 (pt) REVERT: B 930 LYS cc_start: 0.9450 (mtmt) cc_final: 0.9137 (mttt) REVERT: B 954 GLN cc_start: 0.8860 (tp-100) cc_final: 0.8227 (pt0) REVERT: B 961 LYS cc_start: 0.9682 (mttt) cc_final: 0.9261 (mmtm) REVERT: B 989 GLN cc_start: 0.8658 (mm-40) cc_final: 0.7709 (mm-40) REVERT: B 1001 LEU cc_start: 0.9183 (mt) cc_final: 0.8809 (mt) REVERT: B 1002 GLN cc_start: 0.9346 (tp-100) cc_final: 0.9099 (tp-100) REVERT: B 1009 LEU cc_start: 0.9446 (mt) cc_final: 0.9192 (mt) REVERT: B 1051 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8706 (mm-40) REVERT: B 1064 TYR cc_start: 0.8996 (t80) cc_final: 0.8789 (t80) REVERT: B 1106 PHE cc_start: 0.8843 (t80) cc_final: 0.8363 (t80) REVERT: C 53 ASP cc_start: 0.8669 (m-30) cc_final: 0.8454 (m-30) REVERT: C 55 PHE cc_start: 0.7876 (m-80) cc_final: 0.7644 (m-10) REVERT: C 58 PHE cc_start: 0.9236 (m-10) cc_final: 0.8989 (m-80) REVERT: C 177 MET cc_start: -0.0242 (ttm) cc_final: -0.1195 (ttt) REVERT: C 189 LEU cc_start: 0.9587 (tp) cc_final: 0.9348 (tp) REVERT: C 223 LEU cc_start: 0.9257 (mp) cc_final: 0.9006 (mp) REVERT: C 348 TYR cc_start: 0.9225 (p90) cc_final: 0.8900 (p90) REVERT: C 377 TYR cc_start: 0.7787 (m-80) cc_final: 0.7172 (m-80) REVERT: C 707 ASN cc_start: 0.9121 (p0) cc_final: 0.8404 (t0) REVERT: C 733 VAL cc_start: 0.9169 (t) cc_final: 0.8814 (t) REVERT: C 737 MET cc_start: 0.9445 (tpt) cc_final: 0.9113 (mmm) REVERT: C 774 ASN cc_start: 0.9386 (m110) cc_final: 0.9167 (m110) REVERT: C 779 PHE cc_start: 0.9167 (m-80) cc_final: 0.8682 (m-10) REVERT: C 799 PHE cc_start: 0.8757 (m-80) cc_final: 0.8551 (m-80) REVERT: C 803 LEU cc_start: 0.9673 (mt) cc_final: 0.9309 (pp) REVERT: C 816 GLU cc_start: 0.9186 (mt-10) cc_final: 0.7979 (mt-10) REVERT: C 819 LEU cc_start: 0.9607 (mt) cc_final: 0.9329 (mt) REVERT: C 858 LEU cc_start: 0.9146 (mt) cc_final: 0.8871 (tp) REVERT: C 918 LYS cc_start: 0.9608 (mttt) cc_final: 0.9307 (mptt) REVERT: C 961 LYS cc_start: 0.9300 (mttt) cc_final: 0.8968 (mmtt) REVERT: C 1000 SER cc_start: 0.9372 (t) cc_final: 0.9168 (m) REVERT: C 1009 LEU cc_start: 0.9480 (mt) cc_final: 0.9192 (mt) REVERT: C 1015 ILE cc_start: 0.9623 (mm) cc_final: 0.9333 (tt) REVERT: C 1028 GLU cc_start: 0.8796 (tp30) cc_final: 0.8569 (tp30) REVERT: C 1051 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8223 (tp-100) REVERT: C 1085 HIS cc_start: 0.8786 (m-70) cc_final: 0.8515 (m-70) REVERT: H 34 MET cc_start: 0.3184 (mpp) cc_final: 0.2816 (mpp) outliers start: 10 outliers final: 0 residues processed: 568 average time/residue: 0.1794 time to fit residues: 165.6889 Evaluate side-chains 421 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 420 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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: 9.9990 chunk 351 optimal weight: 30.0000 chunk 132 optimal weight: 9.9990 chunk 240 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 314 ASN B 447 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN B 801 GLN B 821 ASN B 869 GLN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.110944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.064887 restraints weight = 121226.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.066917 restraints weight = 76997.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.068236 restraints weight = 55011.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069183 restraints weight = 43467.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.069855 restraints weight = 36952.490| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 31793 Z= 0.351 Angle : 0.842 24.506 43385 Z= 0.447 Chirality : 0.048 0.317 4983 Planarity : 0.006 0.083 5509 Dihedral : 5.343 23.856 4184 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 0.12 % Allowed : 3.58 % Favored : 96.30 % 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: -1.00 (0.13), residues: 3827 helix: -0.72 (0.18), residues: 693 sheet: -0.24 (0.16), residues: 986 loop : -0.79 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 354 TYR 0.037 0.002 TYR C 738 PHE 0.034 0.003 PHE B 903 TRP 0.013 0.002 TRP B 64 HIS 0.011 0.002 HIS C1055 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.35 (31689) covalent geometry : angle 0.81137 / 0.44 (43124) SS BOND : bond 0.00764 / 0.55 ( 51) SS BOND : angle 2.50113 / 1.61 ( 102) hydrogen bonds : bond 0.05554 / 3.69 ( 1286) hydrogen bonds : angle 6.56746 / 4.56 ( 3654) link_BETA1-4 : bond 0.00937 / 0.78 ( 12) link_BETA1-4 : angle 1.93216 / 1.29 ( 36) link_NAG-ASN : bond 0.00661 / 0.47 ( 41) link_NAG-ASN : angle 3.63143 / 2.47 ( 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 488 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 484 time to evaluate : 1.095 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: 0.8459 (p) cc_final: 0.7348 (m) REVERT: A 420 TYR cc_start: 0.8599 (t80) cc_final: 0.7784 (t80) REVERT: A 529 ASN cc_start: 0.9619 (m-40) cc_final: 0.9269 (p0) REVERT: A 532 LYS cc_start: 0.9280 (mttt) cc_final: 0.9017 (ptmt) REVERT: A 543 LEU cc_start: 0.9366 (mm) cc_final: 0.9132 (mt) REVERT: A 568 ASP cc_start: 0.9669 (m-30) cc_final: 0.8743 (t0) REVERT: A 660 ASP cc_start: 0.8815 (t0) cc_final: 0.8467 (t70) REVERT: A 737 MET cc_start: 0.9033 (tpt) cc_final: 0.8768 (tpp) REVERT: A 738 TYR cc_start: 0.9127 (t80) cc_final: 0.8825 (t80) REVERT: A 744 THR cc_start: 0.8882 (m) cc_final: 0.8679 (p) REVERT: A 760 LEU cc_start: 0.9561 (mt) cc_final: 0.8779 (mt) REVERT: A 918 LYS cc_start: 0.9736 (mttt) cc_final: 0.9335 (tppt) REVERT: A 919 LEU cc_start: 0.9374 (mp) cc_final: 0.8934 (mp) REVERT: A 954 GLN cc_start: 0.9584 (mt0) cc_final: 0.9300 (mt0) REVERT: A 957 ASN cc_start: 0.9441 (m110) cc_final: 0.9160 (m110) REVERT: A 970 ILE cc_start: 0.9013 (pt) cc_final: 0.8713 (pt) REVERT: A 989 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8531 (mt0) REVERT: A 999 GLN cc_start: 0.9289 (tp-100) cc_final: 0.8739 (tp-100) REVERT: A 1002 GLN cc_start: 0.9512 (tp40) cc_final: 0.9130 (tp-100) REVERT: A 1007 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8513 (tm-30) REVERT: A 1047 MET cc_start: 0.8264 (ttm) cc_final: 0.7092 (mtt) REVERT: A 1078 ILE cc_start: 0.9118 (mm) cc_final: 0.8838 (tp) REVERT: A 1085 HIS cc_start: 0.9332 (m90) cc_final: 0.9088 (m-70) REVERT: A 1116 ASN cc_start: 0.9377 (m-40) cc_final: 0.9051 (m110) REVERT: A 1124 ASP cc_start: 0.8373 (p0) cc_final: 0.8160 (p0) REVERT: B 177 MET cc_start: 0.0018 (ttm) cc_final: -0.3834 (mmt) REVERT: B 272 PHE cc_start: 0.8694 (m-80) cc_final: 0.7799 (m-10) REVERT: B 290 LEU cc_start: 0.9435 (tt) cc_final: 0.9231 (mt) REVERT: B 315 PHE cc_start: 0.8792 (t80) cc_final: 0.8553 (t80) REVERT: B 362 TYR cc_start: 0.9531 (m-80) cc_final: 0.9105 (m-80) REVERT: B 384 LEU cc_start: 0.9630 (mm) cc_final: 0.9101 (mp) REVERT: B 529 ASN cc_start: 0.9455 (p0) cc_final: 0.9236 (p0) REVERT: B 565 ASP cc_start: 0.9255 (t0) cc_final: 0.8615 (p0) REVERT: B 608 LEU cc_start: 0.9020 (tp) cc_final: 0.8614 (mm) REVERT: B 655 ASN cc_start: 0.8554 (m-40) cc_final: 0.7843 (t0) REVERT: B 660 ASP cc_start: 0.8977 (t0) cc_final: 0.8759 (t70) REVERT: B 717 ILE cc_start: 0.8333 (mm) cc_final: 0.7730 (mm) REVERT: B 865 GLU cc_start: 0.9419 (tt0) cc_final: 0.9047 (mp0) REVERT: B 930 LYS cc_start: 0.9442 (mtmt) cc_final: 0.9077 (mttt) REVERT: B 999 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8776 (tm-30) REVERT: B 1001 LEU cc_start: 0.9246 (mt) cc_final: 0.8747 (mt) REVERT: B 1009 LEU cc_start: 0.9560 (mt) cc_final: 0.9224 (mt) REVERT: C 177 MET cc_start: 0.2819 (ttm) cc_final: 0.2316 (ttp) REVERT: C 223 LEU cc_start: 0.9128 (mp) cc_final: 0.8781 (tp) REVERT: C 272 PHE cc_start: 0.8370 (m-10) cc_final: 0.8073 (m-10) REVERT: C 309 ILE cc_start: 0.9100 (tt) cc_final: 0.8852 (tp) REVERT: C 321 GLU cc_start: 0.9211 (tp30) cc_final: 0.8607 (tp30) REVERT: C 348 TYR cc_start: 0.9313 (p90) cc_final: 0.9032 (p90) REVERT: C 377 TYR cc_start: 0.7952 (m-80) cc_final: 0.7340 (m-80) REVERT: C 431 ILE cc_start: 0.9803 (mt) cc_final: 0.9583 (tp) REVERT: C 707 ASN cc_start: 0.9290 (p0) cc_final: 0.8859 (t0) REVERT: C 711 ILE cc_start: 0.9778 (mt) cc_final: 0.9575 (tt) REVERT: C 733 VAL cc_start: 0.9358 (t) cc_final: 0.9050 (p) REVERT: C 737 MET cc_start: 0.9254 (tpt) cc_final: 0.8869 (tpp) REVERT: C 738 TYR cc_start: 0.9501 (t80) cc_final: 0.9277 (t80) REVERT: C 803 LEU cc_start: 0.9812 (mt) cc_final: 0.9264 (pp) REVERT: C 817 ASP cc_start: 0.9458 (m-30) cc_final: 0.9254 (m-30) REVERT: C 918 LYS cc_start: 0.9684 (mttt) cc_final: 0.9292 (mptt) REVERT: C 947 ASP cc_start: 0.9208 (m-30) cc_final: 0.8990 (p0) REVERT: C 948 VAL cc_start: 0.9307 (t) cc_final: 0.8818 (t) REVERT: C 961 LYS cc_start: 0.9379 (mttt) cc_final: 0.8781 (mmmt) REVERT: C 962 GLN cc_start: 0.9053 (mm110) cc_final: 0.8718 (mm110) REVERT: C 1009 LEU cc_start: 0.9687 (mt) cc_final: 0.9450 (mm) REVERT: C 1011 ARG cc_start: 0.9378 (tpp-160) cc_final: 0.8622 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9219 (pt0) cc_final: 0.8947 (pp20) REVERT: C 1015 ILE cc_start: 0.9731 (mm) cc_final: 0.9436 (mt) REVERT: H 34 MET cc_start: 0.2600 (mpp) cc_final: 0.2231 (mpp) outliers start: 4 outliers final: 0 residues processed: 486 average time/residue: 0.1731 time to fit residues: 138.5658 Evaluate side-chains 376 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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: 3.9990 chunk 356 optimal weight: 50.0000 chunk 271 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 239 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 374 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 99 ASN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.110853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067600 restraints weight = 123075.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070053 restraints weight = 75809.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.071454 restraints weight = 48031.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.072289 restraints weight = 34551.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.072380 restraints weight = 31726.195| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31793 Z= 0.235 Angle : 0.678 22.504 43385 Z= 0.358 Chirality : 0.045 0.294 4983 Planarity : 0.004 0.056 5509 Dihedral : 5.057 26.913 4184 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.32 % Rotamer: Outliers : 0.12 % Allowed : 2.41 % Favored : 97.47 % 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: -0.42 (0.18), residues: 696 sheet: -0.08 (0.15), residues: 1015 loop : -0.79 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 454 TYR 0.029 0.002 TYR C 310 PHE 0.021 0.002 PHE A 562 TRP 0.021 0.001 TRP L 34 HIS 0.006 0.001 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.23 (31689) covalent geometry : angle 0.64962 / 0.35 (43124) SS BOND : bond 0.00558 / 0.41 ( 51) SS BOND : angle 1.73859 / 1.10 ( 102) hydrogen bonds : bond 0.04725 / 3.14 ( 1286) hydrogen bonds : angle 6.14623 / 4.27 ( 3654) link_BETA1-4 : bond 0.00321 / 0.26 ( 12) link_BETA1-4 : angle 1.39250 / 0.97 ( 36) link_NAG-ASN : bond 0.00514 / 0.38 ( 41) link_NAG-ASN : angle 3.35800 / 2.24 ( 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 474 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 470 time to evaluate : 0.805 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: 0.8629 (t80) cc_final: 0.8010 (t80) REVERT: A 453 PHE cc_start: 0.9551 (m-10) cc_final: 0.9271 (m-80) REVERT: A 529 ASN cc_start: 0.9678 (m-40) cc_final: 0.9404 (p0) REVERT: A 532 LYS cc_start: 0.9229 (mttt) cc_final: 0.8989 (ptmt) REVERT: A 559 PHE cc_start: 0.8373 (p90) cc_final: 0.8124 (p90) REVERT: A 737 MET cc_start: 0.9078 (tpt) cc_final: 0.8809 (tpp) REVERT: A 760 LEU cc_start: 0.9209 (mt) cc_final: 0.8741 (mt) REVERT: A 818 LEU cc_start: 0.9591 (mt) cc_final: 0.9297 (mt) REVERT: A 918 LYS cc_start: 0.9718 (mttt) cc_final: 0.9198 (tppt) REVERT: A 935 LEU cc_start: 0.9669 (mt) cc_final: 0.9344 (pp) REVERT: A 957 ASN cc_start: 0.9244 (m110) cc_final: 0.8997 (m110) REVERT: A 970 ILE cc_start: 0.9176 (pt) cc_final: 0.8715 (pt) REVERT: A 977 ILE cc_start: 0.9476 (pt) cc_final: 0.8886 (mm) REVERT: A 989 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8428 (mt0) REVERT: A 999 GLN cc_start: 0.9283 (tp-100) cc_final: 0.8696 (tp-100) REVERT: A 1002 GLN cc_start: 0.9514 (tp40) cc_final: 0.9092 (tp-100) REVERT: A 1007 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8534 (tm-30) REVERT: A 1047 MET cc_start: 0.7998 (ttm) cc_final: 0.7176 (mtt) REVERT: A 1116 ASN cc_start: 0.9443 (m-40) cc_final: 0.9100 (m110) REVERT: A 1124 ASP cc_start: 0.8386 (p0) cc_final: 0.8186 (p0) REVERT: B 41 LYS cc_start: 0.7109 (tttt) cc_final: 0.6805 (tptt) REVERT: B 177 MET cc_start: 0.2591 (ttm) cc_final: -0.2147 (mmt) REVERT: B 315 PHE cc_start: 0.8627 (t80) cc_final: 0.8414 (t80) REVERT: B 362 TYR cc_start: 0.9504 (m-80) cc_final: 0.9030 (m-80) REVERT: B 384 LEU cc_start: 0.9682 (mm) cc_final: 0.9264 (mt) REVERT: B 529 ASN cc_start: 0.9440 (p0) cc_final: 0.9217 (p0) REVERT: B 565 ASP cc_start: 0.9222 (t0) cc_final: 0.8670 (p0) REVERT: B 655 ASN cc_start: 0.8622 (m-40) cc_final: 0.7798 (t0) REVERT: B 660 ASP cc_start: 0.9043 (t0) cc_final: 0.8580 (p0) REVERT: B 717 ILE cc_start: 0.8382 (mm) cc_final: 0.7756 (mm) REVERT: B 865 GLU cc_start: 0.9426 (tt0) cc_final: 0.9057 (mp0) REVERT: B 957 ASN cc_start: 0.9271 (m110) cc_final: 0.8943 (m110) REVERT: B 958 THR cc_start: 0.9560 (p) cc_final: 0.9296 (p) REVERT: B 999 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8730 (tm-30) REVERT: B 1001 LEU cc_start: 0.9292 (mt) cc_final: 0.8849 (mt) REVERT: B 1009 LEU cc_start: 0.9556 (mt) cc_final: 0.9315 (mt) REVERT: B 1064 TYR cc_start: 0.8909 (t80) cc_final: 0.8516 (t80) REVERT: C 53 ASP cc_start: 0.8790 (m-30) cc_final: 0.8590 (m-30) REVERT: C 58 PHE cc_start: 0.9503 (m-10) cc_final: 0.9058 (m-80) REVERT: C 177 MET cc_start: 0.3482 (ttm) cc_final: 0.2856 (ttp) REVERT: C 223 LEU cc_start: 0.9010 (mp) cc_final: 0.8760 (mp) REVERT: C 272 PHE cc_start: 0.8233 (m-10) cc_final: 0.7882 (m-10) REVERT: C 315 PHE cc_start: 0.7990 (t80) cc_final: 0.7421 (t80) REVERT: C 348 TYR cc_start: 0.9282 (p90) cc_final: 0.9021 (p90) REVERT: C 377 TYR cc_start: 0.7707 (m-80) cc_final: 0.7170 (m-80) REVERT: C 707 ASN cc_start: 0.9250 (p0) cc_final: 0.8820 (t0) REVERT: C 711 ILE cc_start: 0.9705 (mt) cc_final: 0.9491 (tt) REVERT: C 733 VAL cc_start: 0.9330 (t) cc_final: 0.9039 (p) REVERT: C 734 ASP cc_start: 0.8717 (t0) cc_final: 0.8051 (t0) REVERT: C 736 THR cc_start: 0.8848 (m) cc_final: 0.8630 (p) REVERT: C 737 MET cc_start: 0.9274 (tpt) cc_final: 0.8698 (tpt) REVERT: C 738 TYR cc_start: 0.9393 (t80) cc_final: 0.9141 (t80) REVERT: C 761 ASN cc_start: 0.9582 (m110) cc_final: 0.9368 (m110) REVERT: C 786 TYR cc_start: 0.8274 (m-10) cc_final: 0.7333 (m-10) REVERT: C 803 LEU cc_start: 0.9746 (mt) cc_final: 0.9322 (pp) REVERT: C 816 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9067 (mp0) REVERT: C 817 ASP cc_start: 0.9270 (m-30) cc_final: 0.9040 (m-30) REVERT: C 918 LYS cc_start: 0.9674 (mttt) cc_final: 0.9300 (mptt) REVERT: C 961 LYS cc_start: 0.9230 (mttt) cc_final: 0.8780 (mttt) REVERT: C 1009 LEU cc_start: 0.9672 (mt) cc_final: 0.9450 (mm) REVERT: C 1011 ARG cc_start: 0.9285 (tpp-160) cc_final: 0.8663 (tpp-160) REVERT: C 1014 GLU cc_start: 0.8994 (pt0) cc_final: 0.8685 (pp20) REVERT: C 1015 ILE cc_start: 0.9754 (mm) cc_final: 0.9464 (mt) REVERT: H 83 MET cc_start: -0.6669 (ptt) cc_final: -0.6977 (ptt) REVERT: E 73 ASP cc_start: 0.4852 (m-30) cc_final: 0.4566 (p0) outliers start: 4 outliers final: 1 residues processed: 472 average time/residue: 0.1676 time to fit residues: 132.2486 Evaluate side-chains 375 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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: 40.0000 chunk 276 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 307 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 610 GLN ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN ** C 946 GLN ** 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 ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.113093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.069303 restraints weight = 120873.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072288 restraints weight = 70444.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.073500 restraints weight = 43401.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.074183 restraints weight = 31723.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.074613 restraints weight = 28950.961| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 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 : 0.003 0.065 31793 Z= 0.139 Angle : 0.603 22.444 43385 Z= 0.314 Chirality : 0.044 0.265 4983 Planarity : 0.004 0.041 5509 Dihedral : 4.680 24.068 4184 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 0.06 % Allowed : 2.06 % Favored : 97.88 % 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: -0.42 (0.13), residues: 3827 helix: 0.49 (0.19), residues: 687 sheet: 0.06 (0.15), residues: 1058 loop : -0.68 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 19 TYR 0.022 0.001 TYR A 366 PHE 0.030 0.002 PHE A 556 TRP 0.021 0.001 TRP L 34 HIS 0.006 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (31689) covalent geometry : angle 0.57301 / 0.31 (43124) SS BOND : bond 0.00375 / 0.28 ( 51) SS BOND : angle 1.89628 / 1.22 ( 102) hydrogen bonds : bond 0.04107 / 2.72 ( 1286) hydrogen bonds : angle 5.75166 / 4.01 ( 3654) link_BETA1-4 : bond 0.00378 / 0.26 ( 12) link_BETA1-4 : angle 1.12162 / 0.80 ( 36) link_NAG-ASN : bond 0.00412 / 0.30 ( 41) link_NAG-ASN : angle 3.13055 / 2.10 ( 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 488 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 486 time to evaluate : 0.855 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 311 GLN cc_start: 0.9208 (pp30) cc_final: 0.8972 (pp30) REVERT: A 420 TYR cc_start: 0.8247 (t80) cc_final: 0.7447 (t80) REVERT: A 453 PHE cc_start: 0.9522 (m-10) cc_final: 0.9227 (m-80) REVERT: A 529 ASN cc_start: 0.9631 (m-40) cc_final: 0.9390 (p0) REVERT: A 568 ASP cc_start: 0.9726 (m-30) cc_final: 0.8706 (t0) REVERT: A 737 MET cc_start: 0.9081 (tpt) cc_final: 0.8733 (tpp) REVERT: A 759 GLN cc_start: 0.9360 (pp30) cc_final: 0.9128 (pp30) REVERT: A 760 LEU cc_start: 0.9100 (mt) cc_final: 0.8849 (mt) REVERT: A 818 LEU cc_start: 0.9592 (mt) cc_final: 0.9256 (mt) REVERT: A 918 LYS cc_start: 0.9674 (mttt) cc_final: 0.9298 (tppt) REVERT: A 935 LEU cc_start: 0.9785 (mt) cc_final: 0.9412 (pp) REVERT: A 957 ASN cc_start: 0.9194 (m110) cc_final: 0.8923 (m110) REVERT: A 970 ILE cc_start: 0.9162 (pt) cc_final: 0.8602 (pt) REVERT: A 977 ILE cc_start: 0.9335 (pt) cc_final: 0.8515 (mm) REVERT: A 989 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8331 (mt0) REVERT: A 1002 GLN cc_start: 0.9527 (tp40) cc_final: 0.9142 (tp-100) REVERT: A 1003 THR cc_start: 0.9586 (m) cc_final: 0.9283 (p) REVERT: A 1007 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8783 (tm-30) REVERT: A 1047 MET cc_start: 0.7982 (ttm) cc_final: 0.7311 (mtt) REVERT: A 1049 PHE cc_start: 0.8772 (m-10) cc_final: 0.8496 (m-10) REVERT: A 1092 PHE cc_start: 0.8730 (m-10) cc_final: 0.8411 (m-10) REVERT: A 1116 ASN cc_start: 0.9422 (m-40) cc_final: 0.9052 (m110) REVERT: B 102 ARG cc_start: 0.8620 (mmt90) cc_final: 0.7590 (mmp80) REVERT: B 177 MET cc_start: 0.2985 (ttm) cc_final: -0.3735 (mmt) REVERT: B 315 PHE cc_start: 0.8637 (t80) cc_final: 0.8422 (t80) REVERT: B 362 TYR cc_start: 0.9472 (m-80) cc_final: 0.9109 (m-80) REVERT: B 384 LEU cc_start: 0.9682 (mm) cc_final: 0.9245 (mt) REVERT: B 529 ASN cc_start: 0.9434 (p0) cc_final: 0.9216 (p0) REVERT: B 565 ASP cc_start: 0.9147 (t0) cc_final: 0.8610 (p0) REVERT: B 655 ASN cc_start: 0.8667 (m-40) cc_final: 0.7851 (t0) REVERT: B 660 ASP cc_start: 0.9082 (t0) cc_final: 0.8606 (p0) REVERT: B 717 ILE cc_start: 0.8359 (mm) cc_final: 0.7584 (mm) REVERT: B 774 ASN cc_start: 0.8994 (m110) cc_final: 0.8681 (m110) REVERT: B 865 GLU cc_start: 0.9364 (tt0) cc_final: 0.8928 (mp0) REVERT: B 870 TYR cc_start: 0.9162 (m-80) cc_final: 0.8937 (m-80) REVERT: B 903 PHE cc_start: 0.8241 (m-10) cc_final: 0.8002 (m-10) REVERT: B 910 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8415 (pp30) REVERT: B 951 GLN cc_start: 0.9264 (tp-100) cc_final: 0.8837 (tp40) REVERT: B 957 ASN cc_start: 0.9328 (m110) cc_final: 0.8926 (m-40) REVERT: B 999 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8720 (tm-30) REVERT: B 1001 LEU cc_start: 0.9323 (mt) cc_final: 0.9050 (mt) REVERT: B 1009 LEU cc_start: 0.9550 (mt) cc_final: 0.9224 (mt) REVERT: B 1051 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8266 (mm-40) REVERT: B 1064 TYR cc_start: 0.8943 (t80) cc_final: 0.8465 (t80) REVERT: B 1106 PHE cc_start: 0.9003 (t80) cc_final: 0.8601 (t80) REVERT: C 53 ASP cc_start: 0.8747 (m-30) cc_final: 0.8530 (m-30) REVERT: C 177 MET cc_start: 0.3639 (ttm) cc_final: 0.3001 (ttp) REVERT: C 189 LEU cc_start: 0.9643 (tp) cc_final: 0.8995 (tp) REVERT: C 223 LEU cc_start: 0.9013 (mp) cc_final: 0.8710 (mp) REVERT: C 272 PHE cc_start: 0.8097 (m-10) cc_final: 0.7731 (m-10) REVERT: C 315 PHE cc_start: 0.7947 (t80) cc_final: 0.7254 (t80) REVERT: C 348 TYR cc_start: 0.9240 (p90) cc_final: 0.8957 (p90) REVERT: C 377 TYR cc_start: 0.7503 (m-80) cc_final: 0.6845 (m-80) REVERT: C 711 ILE cc_start: 0.9628 (mt) cc_final: 0.9387 (tt) REVERT: C 733 VAL cc_start: 0.9295 (t) cc_final: 0.9037 (p) REVERT: C 734 ASP cc_start: 0.8794 (t0) cc_final: 0.8405 (t0) REVERT: C 737 MET cc_start: 0.9103 (tpt) cc_final: 0.8611 (tpt) REVERT: C 738 TYR cc_start: 0.9332 (t80) cc_final: 0.8893 (t80) REVERT: C 761 ASN cc_start: 0.9559 (m110) cc_final: 0.9324 (m110) REVERT: C 770 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9299 (mt-10) REVERT: C 786 TYR cc_start: 0.7919 (m-10) cc_final: 0.7625 (m-10) REVERT: C 803 LEU cc_start: 0.9764 (mt) cc_final: 0.9352 (pp) REVERT: C 816 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8263 (mp0) REVERT: C 817 ASP cc_start: 0.9163 (m-30) cc_final: 0.8946 (m-30) REVERT: C 918 LYS cc_start: 0.9650 (mttt) cc_final: 0.9261 (mptt) REVERT: C 947 ASP cc_start: 0.9270 (m-30) cc_final: 0.8937 (p0) REVERT: C 948 VAL cc_start: 0.9299 (t) cc_final: 0.8839 (t) REVERT: C 961 LYS cc_start: 0.9125 (mttt) cc_final: 0.8697 (mttt) REVERT: C 1009 LEU cc_start: 0.9606 (mt) cc_final: 0.9375 (mm) REVERT: C 1011 ARG cc_start: 0.9211 (tpp-160) cc_final: 0.8686 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9036 (pt0) cc_final: 0.8827 (pp20) REVERT: C 1015 ILE cc_start: 0.9714 (mm) cc_final: 0.9490 (tt) REVERT: C 1021 LEU cc_start: 0.9463 (mt) cc_final: 0.9216 (mt) REVERT: C 1031 LEU cc_start: 0.9537 (mp) cc_final: 0.9186 (mp) REVERT: C 1051 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8427 (tp-100) REVERT: H 34 MET cc_start: 0.2524 (mpp) cc_final: 0.2000 (mpp) REVERT: H 83 MET cc_start: -0.6587 (ptt) cc_final: -0.7019 (ptt) outliers start: 2 outliers final: 0 residues processed: 487 average time/residue: 0.1638 time to fit residues: 132.8618 Evaluate side-chains 399 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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: 1.9990 chunk 112 optimal weight: 20.0000 chunk 166 optimal weight: 0.7980 chunk 308 optimal weight: 4.9990 chunk 253 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 231 optimal weight: 0.9980 chunk 362 optimal weight: 50.0000 chunk 217 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 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** C 962 GLN ** 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 E 82 GLN ** 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 = 0.4037 r_free = 0.4037 target = 0.111642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.067311 restraints weight = 123716.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.068883 restraints weight = 76463.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.070434 restraints weight = 52524.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.071591 restraints weight = 35397.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.071609 restraints weight = 32853.112| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31793 Z= 0.203 Angle : 0.636 21.591 43385 Z= 0.336 Chirality : 0.044 0.258 4983 Planarity : 0.004 0.053 5509 Dihedral : 4.770 23.791 4184 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 0.03 % Allowed : 2.06 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.13), residues: 3827 helix: 0.08 (0.19), residues: 693 sheet: 0.01 (0.15), residues: 1040 loop : -0.68 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 214 TYR 0.025 0.002 TYR A 263 PHE 0.030 0.002 PHE A 756 TRP 0.027 0.001 TRP L 34 HIS 0.013 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (31689) covalent geometry : angle 0.61001 / 0.33 (43124) SS BOND : bond 0.00536 / 0.41 ( 51) SS BOND : angle 1.73612 / 1.09 ( 102) hydrogen bonds : bond 0.04412 / 2.92 ( 1286) hydrogen bonds : angle 5.87385 / 4.09 ( 3654) link_BETA1-4 : bond 0.00198 / 0.15 ( 12) link_BETA1-4 : angle 1.34610 / 0.94 ( 36) link_NAG-ASN : bond 0.00446 / 0.34 ( 41) link_NAG-ASN : angle 3.06362 / 2.05 ( 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 454 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 1.009 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: A 311 GLN cc_start: 0.9368 (pp30) cc_final: 0.9005 (pp30) REVERT: A 420 TYR cc_start: 0.8619 (t80) cc_final: 0.7667 (t80) REVERT: A 453 PHE cc_start: 0.9544 (m-10) cc_final: 0.9253 (m-80) REVERT: A 529 ASN cc_start: 0.9612 (m-40) cc_final: 0.9308 (p0) REVERT: A 694 MET cc_start: 0.8901 (ppp) cc_final: 0.8244 (ppp) REVERT: A 734 ASP cc_start: 0.8673 (t0) cc_final: 0.8306 (t0) REVERT: A 737 MET cc_start: 0.9237 (tpt) cc_final: 0.9003 (tpp) REVERT: A 753 TYR cc_start: 0.9332 (m-10) cc_final: 0.9110 (m-80) REVERT: A 760 LEU cc_start: 0.9378 (mt) cc_final: 0.8968 (mt) REVERT: A 818 LEU cc_start: 0.9619 (mt) cc_final: 0.9348 (mt) REVERT: A 918 LYS cc_start: 0.9648 (mttt) cc_final: 0.9328 (tptp) REVERT: A 922 ASN cc_start: 0.9562 (m-40) cc_final: 0.9014 (m110) REVERT: A 935 LEU cc_start: 0.9675 (mt) cc_final: 0.9298 (pp) REVERT: A 957 ASN cc_start: 0.9192 (m110) cc_final: 0.8929 (m110) REVERT: A 970 ILE cc_start: 0.9170 (pt) cc_final: 0.8672 (pt) REVERT: A 977 ILE cc_start: 0.9438 (pt) cc_final: 0.9083 (pt) REVERT: A 989 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8441 (mt0) REVERT: A 1002 GLN cc_start: 0.9544 (tp40) cc_final: 0.9092 (tp-100) REVERT: A 1003 THR cc_start: 0.9513 (m) cc_final: 0.9257 (p) REVERT: A 1007 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8482 (tm-30) REVERT: A 1049 PHE cc_start: 0.8801 (m-10) cc_final: 0.8600 (m-10) REVERT: A 1092 PHE cc_start: 0.8901 (m-10) cc_final: 0.8424 (m-10) REVERT: A 1116 ASN cc_start: 0.9420 (m-40) cc_final: 0.9067 (m110) REVERT: B 58 PHE cc_start: 0.9101 (m-80) cc_final: 0.8810 (m-80) REVERT: B 153 MET cc_start: 0.8037 (ppp) cc_final: 0.7549 (pmm) REVERT: B 177 MET cc_start: 0.2750 (ttm) cc_final: -0.1813 (mmt) REVERT: B 287 ASP cc_start: 0.8413 (m-30) cc_final: 0.7864 (m-30) REVERT: B 315 PHE cc_start: 0.8609 (t80) cc_final: 0.8329 (t80) REVERT: B 362 TYR cc_start: 0.9540 (m-80) cc_final: 0.9045 (m-80) REVERT: B 384 LEU cc_start: 0.9718 (mm) cc_final: 0.9256 (mt) REVERT: B 529 ASN cc_start: 0.9438 (p0) cc_final: 0.9213 (p0) REVERT: B 565 ASP cc_start: 0.9046 (t0) cc_final: 0.8617 (p0) REVERT: B 655 ASN cc_start: 0.8749 (m-40) cc_final: 0.7974 (t0) REVERT: B 694 MET cc_start: 0.8670 (ppp) cc_final: 0.8455 (ppp) REVERT: B 717 ILE cc_start: 0.8515 (mm) cc_final: 0.7860 (mm) REVERT: B 774 ASN cc_start: 0.8778 (m110) cc_final: 0.8564 (m-40) REVERT: B 865 GLU cc_start: 0.9426 (tt0) cc_final: 0.8900 (mp0) REVERT: B 951 GLN cc_start: 0.9279 (tp-100) cc_final: 0.8765 (tp40) REVERT: B 957 ASN cc_start: 0.9358 (m110) cc_final: 0.9029 (m-40) REVERT: B 999 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8668 (tm-30) REVERT: B 1001 LEU cc_start: 0.9324 (mt) cc_final: 0.9085 (mm) REVERT: B 1009 LEU cc_start: 0.9604 (mt) cc_final: 0.9256 (mt) REVERT: B 1014 GLU cc_start: 0.9216 (tt0) cc_final: 0.8379 (mm-30) REVERT: B 1028 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8154 (mt-10) REVERT: B 1051 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8026 (mt0) REVERT: B 1064 TYR cc_start: 0.8825 (t80) cc_final: 0.8505 (t80) REVERT: C 53 ASP cc_start: 0.8855 (m-30) cc_final: 0.8642 (m-30) REVERT: C 58 PHE cc_start: 0.9381 (m-10) cc_final: 0.8991 (m-80) REVERT: C 223 LEU cc_start: 0.9144 (mp) cc_final: 0.8869 (tp) REVERT: C 272 PHE cc_start: 0.8402 (m-10) cc_final: 0.7999 (m-10) REVERT: C 310 TYR cc_start: 0.8332 (m-80) cc_final: 0.8051 (m-80) REVERT: C 315 PHE cc_start: 0.8022 (t80) cc_final: 0.7396 (t80) REVERT: C 348 TYR cc_start: 0.9289 (p90) cc_final: 0.9000 (p90) REVERT: C 377 TYR cc_start: 0.7507 (m-80) cc_final: 0.6838 (m-80) REVERT: C 647 LEU cc_start: 0.9317 (tp) cc_final: 0.9077 (pp) REVERT: C 711 ILE cc_start: 0.9666 (mt) cc_final: 0.9391 (tt) REVERT: C 733 VAL cc_start: 0.9363 (t) cc_final: 0.9044 (p) REVERT: C 734 ASP cc_start: 0.8870 (t0) cc_final: 0.8302 (t0) REVERT: C 736 THR cc_start: 0.8859 (m) cc_final: 0.8638 (p) REVERT: C 737 MET cc_start: 0.9065 (tpt) cc_final: 0.8361 (tpt) REVERT: C 738 TYR cc_start: 0.9427 (t80) cc_final: 0.9158 (t80) REVERT: C 761 ASN cc_start: 0.9595 (m110) cc_final: 0.9368 (m110) REVERT: C 786 TYR cc_start: 0.8449 (m-10) cc_final: 0.7713 (m-10) REVERT: C 799 PHE cc_start: 0.9231 (m-10) cc_final: 0.9027 (m-10) REVERT: C 816 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8447 (mp0) REVERT: C 916 ASN cc_start: 0.9473 (m110) cc_final: 0.9227 (m110) REVERT: C 918 LYS cc_start: 0.9677 (mttt) cc_final: 0.9302 (mptt) REVERT: C 947 ASP cc_start: 0.9276 (m-30) cc_final: 0.8858 (p0) REVERT: C 948 VAL cc_start: 0.9420 (t) cc_final: 0.8971 (t) REVERT: C 961 LYS cc_start: 0.9207 (mttt) cc_final: 0.8774 (mttt) REVERT: C 992 ARG cc_start: 0.8705 (mtt180) cc_final: 0.8123 (mpp80) REVERT: C 1009 LEU cc_start: 0.9639 (mt) cc_final: 0.9378 (mm) REVERT: C 1011 ARG cc_start: 0.9246 (tpp-160) cc_final: 0.8575 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9097 (pt0) cc_final: 0.8755 (pp20) REVERT: C 1015 ILE cc_start: 0.9754 (mm) cc_final: 0.9478 (mt) REVERT: C 1021 LEU cc_start: 0.9467 (mt) cc_final: 0.9231 (mt) REVERT: C 1031 LEU cc_start: 0.9621 (mp) cc_final: 0.9229 (mp) REVERT: C 1051 GLN cc_start: 0.8790 (tp-100) cc_final: 0.8216 (mm-40) REVERT: H 34 MET cc_start: 0.2687 (mpp) cc_final: 0.2048 (mpp) REVERT: H 83 MET cc_start: -0.6201 (ptt) cc_final: -0.6609 (ptt) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.1549 time to fit residues: 117.5196 Evaluate side-chains 376 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 6.9990 chunk 349 optimal weight: 50.0000 chunk 370 optimal weight: 30.0000 chunk 282 optimal weight: 3.9990 chunk 178 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 304 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 HIS ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** B1045 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 C 318 GLN 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** ** C 954 GLN ** 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 = 0.4013 r_free = 0.4013 target = 0.110290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.065877 restraints weight = 125334.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.066668 restraints weight = 80358.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.068052 restraints weight = 59336.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.068985 restraints weight = 40120.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.069219 restraints weight = 34668.553| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31793 Z= 0.219 Angle : 0.652 20.767 43385 Z= 0.344 Chirality : 0.045 0.245 4983 Planarity : 0.004 0.056 5509 Dihedral : 4.922 22.005 4184 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.81 % 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: -0.70 (0.13), residues: 3827 helix: -0.19 (0.19), residues: 690 sheet: -0.10 (0.15), residues: 1027 loop : -0.68 (0.14), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 352 TYR 0.025 0.002 TYR C 738 PHE 0.024 0.002 PHE B 43 TRP 0.025 0.001 TRP L 34 HIS 0.010 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.22 (31689) covalent geometry : angle 0.62818 / 0.34 (43124) SS BOND : bond 0.00424 / 0.31 ( 51) SS BOND : angle 1.39406 / 0.89 ( 102) hydrogen bonds : bond 0.04482 / 2.98 ( 1286) hydrogen bonds : angle 5.93342 / 4.14 ( 3654) link_BETA1-4 : bond 0.00219 / 0.15 ( 12) link_BETA1-4 : angle 1.34521 / 0.96 ( 36) link_NAG-ASN : bond 0.00429 / 0.32 ( 41) link_NAG-ASN : angle 3.04606 / 2.00 ( 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 438 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 437 time to evaluate : 1.218 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 311 GLN cc_start: 0.9414 (pp30) cc_final: 0.9071 (pp30) REVERT: A 420 TYR cc_start: 0.8260 (t80) cc_final: 0.7335 (t80) REVERT: A 453 PHE cc_start: 0.9537 (m-10) cc_final: 0.9314 (m-80) REVERT: A 529 ASN cc_start: 0.9655 (m-40) cc_final: 0.9310 (p0) REVERT: A 582 LEU cc_start: 0.8919 (mp) cc_final: 0.8701 (mm) REVERT: A 694 MET cc_start: 0.8904 (ppp) cc_final: 0.8410 (ppp) REVERT: A 737 MET cc_start: 0.9216 (tpt) cc_final: 0.8991 (tpp) REVERT: A 759 GLN cc_start: 0.9420 (pp30) cc_final: 0.9120 (pp30) REVERT: A 760 LEU cc_start: 0.9436 (mt) cc_final: 0.8991 (mt) REVERT: A 774 ASN cc_start: 0.9219 (m110) cc_final: 0.9004 (m110) REVERT: A 818 LEU cc_start: 0.9605 (mt) cc_final: 0.9345 (mt) REVERT: A 918 LYS cc_start: 0.9647 (mttt) cc_final: 0.9270 (tppt) REVERT: A 935 LEU cc_start: 0.9699 (mt) cc_final: 0.9354 (pp) REVERT: A 957 ASN cc_start: 0.9161 (m110) cc_final: 0.8925 (m110) REVERT: A 977 ILE cc_start: 0.9564 (pt) cc_final: 0.9057 (mm) REVERT: A 989 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8489 (mp10) REVERT: A 1001 LEU cc_start: 0.9260 (mt) cc_final: 0.9015 (mt) REVERT: A 1002 GLN cc_start: 0.9544 (tp40) cc_final: 0.9119 (tp-100) REVERT: A 1003 THR cc_start: 0.9477 (m) cc_final: 0.9248 (m) REVERT: A 1007 GLN cc_start: 0.9436 (mm-40) cc_final: 0.8509 (tm-30) REVERT: A 1047 MET cc_start: 0.7953 (tpp) cc_final: 0.7544 (mtt) REVERT: A 1060 LEU cc_start: 0.9473 (mp) cc_final: 0.9262 (mp) REVERT: A 1116 ASN cc_start: 0.9406 (m-40) cc_final: 0.9050 (m110) REVERT: B 58 PHE cc_start: 0.9196 (m-80) cc_final: 0.8594 (m-80) REVERT: B 177 MET cc_start: 0.2802 (ttm) cc_final: -0.1965 (mmt) REVERT: B 216 LEU cc_start: 0.7831 (tp) cc_final: 0.7367 (pt) REVERT: B 315 PHE cc_start: 0.8503 (t80) cc_final: 0.8239 (t80) REVERT: B 362 TYR cc_start: 0.9526 (m-80) cc_final: 0.9059 (m-80) REVERT: B 384 LEU cc_start: 0.9709 (mm) cc_final: 0.9234 (mt) REVERT: B 565 ASP cc_start: 0.9070 (t0) cc_final: 0.8624 (p0) REVERT: B 589 PHE cc_start: 0.8583 (p90) cc_final: 0.8375 (p90) REVERT: B 655 ASN cc_start: 0.8815 (m-40) cc_final: 0.8029 (t0) REVERT: B 717 ILE cc_start: 0.8513 (mm) cc_final: 0.7852 (mm) REVERT: B 752 GLN cc_start: 0.8593 (mt0) cc_final: 0.8315 (mt0) REVERT: B 774 ASN cc_start: 0.8774 (m110) cc_final: 0.8540 (m-40) REVERT: B 781 GLN cc_start: 0.8917 (mm110) cc_final: 0.8249 (tm-30) REVERT: B 951 GLN cc_start: 0.9237 (tp-100) cc_final: 0.8684 (tp-100) REVERT: B 952 ASN cc_start: 0.9538 (t0) cc_final: 0.9308 (t0) REVERT: B 956 LEU cc_start: 0.9749 (mt) cc_final: 0.9542 (mt) REVERT: B 957 ASN cc_start: 0.9291 (m110) cc_final: 0.8915 (m-40) REVERT: B 975 ASN cc_start: 0.9602 (m-40) cc_final: 0.9162 (t0) REVERT: B 976 ASP cc_start: 0.9425 (t70) cc_final: 0.8878 (t0) REVERT: B 980 ARG cc_start: 0.9088 (ptm160) cc_final: 0.8486 (ptm160) REVERT: B 999 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8724 (tm-30) REVERT: B 1009 LEU cc_start: 0.9515 (mt) cc_final: 0.9166 (mt) REVERT: B 1014 GLU cc_start: 0.9196 (tt0) cc_final: 0.8374 (mm-30) REVERT: B 1031 LEU cc_start: 0.8560 (mp) cc_final: 0.8355 (mp) REVERT: B 1051 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8154 (mt0) REVERT: B 1064 TYR cc_start: 0.8826 (t80) cc_final: 0.8565 (t80) REVERT: C 58 PHE cc_start: 0.9388 (m-10) cc_final: 0.9020 (m-80) REVERT: C 128 ILE cc_start: 0.9847 (pt) cc_final: 0.9575 (mm) REVERT: C 223 LEU cc_start: 0.9096 (mp) cc_final: 0.8825 (tp) REVERT: C 272 PHE cc_start: 0.8514 (m-10) cc_final: 0.8083 (m-10) REVERT: C 348 TYR cc_start: 0.9276 (p90) cc_final: 0.9014 (p90) REVERT: C 377 TYR cc_start: 0.7505 (m-80) cc_final: 0.6885 (m-80) REVERT: C 647 LEU cc_start: 0.9337 (tp) cc_final: 0.9080 (pp) REVERT: C 711 ILE cc_start: 0.9652 (mt) cc_final: 0.9314 (tt) REVERT: C 733 VAL cc_start: 0.9387 (t) cc_final: 0.9103 (p) REVERT: C 734 ASP cc_start: 0.8784 (t0) cc_final: 0.8253 (t0) REVERT: C 737 MET cc_start: 0.8886 (tpt) cc_final: 0.8240 (tpt) REVERT: C 762 ARG cc_start: 0.8842 (mtm-85) cc_final: 0.8331 (mtt-85) REVERT: C 770 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9279 (mt-10) REVERT: C 786 TYR cc_start: 0.8632 (m-10) cc_final: 0.8128 (m-10) REVERT: C 816 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8873 (mp0) REVERT: C 916 ASN cc_start: 0.9423 (m110) cc_final: 0.9154 (m110) REVERT: C 918 LYS cc_start: 0.9660 (mttt) cc_final: 0.9256 (mptt) REVERT: C 961 LYS cc_start: 0.9228 (mttt) cc_final: 0.8788 (mttt) REVERT: C 992 ARG cc_start: 0.8804 (mtt180) cc_final: 0.8227 (mpp80) REVERT: C 1011 ARG cc_start: 0.9234 (tpp-160) cc_final: 0.8557 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9236 (pt0) cc_final: 0.8856 (pp20) REVERT: C 1015 ILE cc_start: 0.9760 (mm) cc_final: 0.9464 (mt) REVERT: C 1021 LEU cc_start: 0.9479 (mt) cc_final: 0.9243 (mt) REVERT: C 1031 LEU cc_start: 0.9666 (mp) cc_final: 0.9307 (mp) REVERT: H 34 MET cc_start: 0.2507 (mpp) cc_final: 0.1685 (mpp) REVERT: H 83 MET cc_start: -0.6158 (ptt) cc_final: -0.6440 (ptt) outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.1697 time to fit residues: 123.8880 Evaluate side-chains 360 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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: 7.9990 chunk 206 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 377 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 322 optimal weight: 6.9990 chunk 360 optimal weight: 40.0000 chunk 125 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 GLN A 687 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 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** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 ASN ** 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 ** 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 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** 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 = 0.3959 r_free = 0.3959 target = 0.106355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.059712 restraints weight = 127864.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.061266 restraints weight = 79747.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.062538 restraints weight = 57424.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.063485 restraints weight = 45339.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.063782 restraints weight = 39015.582| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 31793 Z= 0.333 Angle : 0.779 19.731 43385 Z= 0.416 Chirality : 0.047 0.238 4983 Planarity : 0.005 0.068 5509 Dihedral : 5.462 26.318 4184 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.62 % Favored : 94.36 % Rotamer: Outliers : 0.03 % Allowed : 1.28 % Favored : 98.69 % 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: -1.27 (0.13), residues: 3827 helix: -1.27 (0.17), residues: 693 sheet: -0.34 (0.16), residues: 1033 loop : -0.88 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 574 TYR 0.039 0.002 TYR A 738 PHE 0.051 0.003 PHE C 797 TRP 0.024 0.002 TRP L 34 HIS 0.013 0.002 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.33 (31689) covalent geometry : angle 0.75575 / 0.41 (43124) SS BOND : bond 0.00569 / 0.41 ( 51) SS BOND : angle 1.56579 / 1.01 ( 102) hydrogen bonds : bond 0.05344 / 3.56 ( 1286) hydrogen bonds : angle 6.40173 / 4.46 ( 3654) link_BETA1-4 : bond 0.00389 / 0.28 ( 12) link_BETA1-4 : angle 1.80417 / 1.23 ( 36) link_NAG-ASN : bond 0.00877 / 0.66 ( 41) link_NAG-ASN : angle 3.27974 / 2.17 ( 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 407 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 406 time to evaluate : 1.133 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: A 377 TYR cc_start: 0.9285 (m-80) cc_final: 0.8825 (m-80) REVERT: A 420 TYR cc_start: 0.8673 (t80) cc_final: 0.7590 (t80) REVERT: A 453 PHE cc_start: 0.9666 (m-10) cc_final: 0.9461 (m-10) REVERT: A 529 ASN cc_start: 0.9635 (m-40) cc_final: 0.9328 (p0) REVERT: A 694 MET cc_start: 0.8995 (ppp) cc_final: 0.8633 (ppp) REVERT: A 737 MET cc_start: 0.9327 (tpt) cc_final: 0.8969 (tpp) REVERT: A 738 TYR cc_start: 0.9255 (t80) cc_final: 0.8921 (t80) REVERT: A 739 ILE cc_start: 0.9568 (mm) cc_final: 0.9266 (tp) REVERT: A 753 TYR cc_start: 0.9575 (m-10) cc_final: 0.9365 (m-10) REVERT: A 759 GLN cc_start: 0.9452 (pp30) cc_final: 0.9097 (pp30) REVERT: A 760 LEU cc_start: 0.9520 (mt) cc_final: 0.9260 (mt) REVERT: A 893 ILE cc_start: 0.8966 (tp) cc_final: 0.8708 (tp) REVERT: A 918 LYS cc_start: 0.9742 (mttt) cc_final: 0.9384 (tppt) REVERT: A 957 ASN cc_start: 0.9398 (m110) cc_final: 0.8983 (m110) REVERT: A 958 THR cc_start: 0.9728 (p) cc_final: 0.9453 (p) REVERT: A 961 LYS cc_start: 0.9459 (mttt) cc_final: 0.8945 (mttm) REVERT: A 989 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8487 (mp10) REVERT: A 1002 GLN cc_start: 0.9565 (tp40) cc_final: 0.9178 (tp-100) REVERT: A 1003 THR cc_start: 0.9485 (m) cc_final: 0.9251 (p) REVERT: A 1100 PHE cc_start: 0.9198 (m-80) cc_final: 0.8905 (m-80) REVERT: A 1116 ASN cc_start: 0.9375 (m-40) cc_final: 0.9004 (m110) REVERT: B 58 PHE cc_start: 0.9233 (m-80) cc_final: 0.8638 (m-80) REVERT: B 177 MET cc_start: 0.3199 (ttm) cc_final: -0.2012 (mmt) REVERT: B 362 TYR cc_start: 0.9602 (m-80) cc_final: 0.9198 (m-80) REVERT: B 384 LEU cc_start: 0.9756 (mm) cc_final: 0.9308 (mt) REVERT: B 551 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9104 (mm-30) REVERT: B 565 ASP cc_start: 0.9091 (t0) cc_final: 0.8848 (p0) REVERT: B 610 GLN cc_start: 0.8464 (tp-100) cc_final: 0.8149 (tp-100) REVERT: B 655 ASN cc_start: 0.8903 (m-40) cc_final: 0.8189 (t0) REVERT: B 752 GLN cc_start: 0.8718 (mt0) cc_final: 0.8451 (mt0) REVERT: B 774 ASN cc_start: 0.8842 (m110) cc_final: 0.8571 (m110) REVERT: B 957 ASN cc_start: 0.9239 (m110) cc_final: 0.8965 (m110) REVERT: B 975 ASN cc_start: 0.9591 (m-40) cc_final: 0.9263 (t0) REVERT: B 999 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8700 (tm-30) REVERT: B 1001 LEU cc_start: 0.9367 (mm) cc_final: 0.9022 (mm) REVERT: B 1014 GLU cc_start: 0.9314 (tt0) cc_final: 0.8598 (mm-30) REVERT: B 1051 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8342 (mt0) REVERT: B 1100 PHE cc_start: 0.9342 (m-80) cc_final: 0.9086 (m-80) REVERT: C 128 ILE cc_start: 0.9804 (pt) cc_final: 0.9483 (mm) REVERT: C 223 LEU cc_start: 0.9218 (mp) cc_final: 0.8990 (tp) REVERT: C 272 PHE cc_start: 0.8766 (m-10) cc_final: 0.8225 (m-10) REVERT: C 377 TYR cc_start: 0.7855 (m-80) cc_final: 0.7330 (m-80) REVERT: C 647 LEU cc_start: 0.9406 (tp) cc_final: 0.8864 (pp) REVERT: C 733 VAL cc_start: 0.9429 (t) cc_final: 0.9183 (t) REVERT: C 734 ASP cc_start: 0.8663 (t0) cc_final: 0.8311 (t0) REVERT: C 737 MET cc_start: 0.8962 (tpt) cc_final: 0.8511 (tpt) REVERT: C 762 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8421 (mtt-85) REVERT: C 771 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8828 (mm110) REVERT: C 816 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8967 (mp0) REVERT: C 918 LYS cc_start: 0.9616 (mttt) cc_final: 0.9232 (mptt) REVERT: C 961 LYS cc_start: 0.9307 (mttt) cc_final: 0.8822 (mttt) REVERT: C 962 GLN cc_start: 0.9071 (mm110) cc_final: 0.8608 (mm110) REVERT: C 975 ASN cc_start: 0.9568 (m110) cc_final: 0.8908 (p0) REVERT: C 1014 GLU cc_start: 0.9249 (pt0) cc_final: 0.8786 (pp20) REVERT: C 1015 ILE cc_start: 0.9773 (mm) cc_final: 0.9462 (mt) REVERT: C 1021 LEU cc_start: 0.9460 (mt) cc_final: 0.9234 (mt) REVERT: C 1031 LEU cc_start: 0.9693 (mp) cc_final: 0.9464 (mp) REVERT: H 34 MET cc_start: 0.3226 (mpp) cc_final: 0.2164 (mpp) REVERT: H 83 MET cc_start: -0.6127 (ptt) cc_final: -0.6329 (ptt) REVERT: E 73 ASP cc_start: 0.5014 (m-30) cc_final: 0.4736 (p0) outliers start: 1 outliers final: 0 residues processed: 406 average time/residue: 0.1721 time to fit residues: 116.2744 Evaluate side-chains 335 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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: 0.0010 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 190 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 207 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 343 optimal weight: 0.7980 chunk 378 optimal weight: 50.0000 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN A 975 ASN A1007 GLN ** A1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B1002 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 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 999 GLN ** 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 = 0.4053 r_free = 0.4053 target = 0.112928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.068949 restraints weight = 123552.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.071059 restraints weight = 73991.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.072985 restraints weight = 47005.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.073588 restraints weight = 33485.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.073612 restraints weight = 28475.470| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31793 Z= 0.124 Angle : 0.616 19.864 43385 Z= 0.317 Chirality : 0.046 0.354 4983 Planarity : 0.004 0.064 5509 Dihedral : 4.843 22.606 4184 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 0.06 % Allowed : 0.66 % Favored : 99.28 % 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: -0.60 (0.13), residues: 3827 helix: 0.05 (0.19), residues: 692 sheet: 0.00 (0.16), residues: 938 loop : -0.68 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 812 TYR 0.033 0.001 TYR B 738 PHE 0.031 0.002 PHE C 797 TRP 0.022 0.001 TRP L 34 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (31689) covalent geometry : angle 0.59506 / 0.31 (43124) SS BOND : bond 0.00385 / 0.29 ( 51) SS BOND : angle 1.22415 / 0.79 ( 102) hydrogen bonds : bond 0.03966 / 2.67 ( 1286) hydrogen bonds : angle 5.74974 / 4.03 ( 3654) link_BETA1-4 : bond 0.00298 / 0.20 ( 12) link_BETA1-4 : angle 1.11968 / 0.79 ( 36) link_NAG-ASN : bond 0.00417 / 0.32 ( 41) link_NAG-ASN : angle 2.85321 / 1.92 ( 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 462 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 460 time to evaluate : 1.037 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: A 295 GLU cc_start: 0.9140 (mp0) cc_final: 0.8576 (mp0) REVERT: A 311 GLN cc_start: 0.9298 (pp30) cc_final: 0.8999 (pp30) REVERT: A 377 TYR cc_start: 0.9257 (m-80) cc_final: 0.8816 (m-80) REVERT: A 420 TYR cc_start: 0.8215 (t80) cc_final: 0.7052 (t80) REVERT: A 453 PHE cc_start: 0.9561 (m-10) cc_final: 0.9346 (m-10) REVERT: A 529 ASN cc_start: 0.9691 (m-40) cc_final: 0.9412 (p0) REVERT: A 568 ASP cc_start: 0.9749 (m-30) cc_final: 0.9186 (t0) REVERT: A 694 MET cc_start: 0.8921 (ppp) cc_final: 0.8632 (ppp) REVERT: A 737 MET cc_start: 0.9145 (tpt) cc_final: 0.8728 (tpp) REVERT: A 748 ASN cc_start: 0.8624 (t0) cc_final: 0.8412 (t0) REVERT: A 759 GLN cc_start: 0.9455 (pp30) cc_final: 0.9121 (pp30) REVERT: A 760 LEU cc_start: 0.9348 (mt) cc_final: 0.9145 (mt) REVERT: A 818 LEU cc_start: 0.9490 (mt) cc_final: 0.9187 (mt) REVERT: A 897 MET cc_start: 0.6964 (mpp) cc_final: 0.6734 (mpp) REVERT: A 903 PHE cc_start: 0.8853 (m-80) cc_final: 0.8605 (m-10) REVERT: A 918 LYS cc_start: 0.9657 (mttt) cc_final: 0.9282 (tppt) REVERT: A 935 LEU cc_start: 0.9634 (mm) cc_final: 0.9399 (pp) REVERT: A 954 GLN cc_start: 0.9209 (mt0) cc_final: 0.8993 (pt0) REVERT: A 957 ASN cc_start: 0.9090 (m110) cc_final: 0.8663 (m-40) REVERT: A 958 THR cc_start: 0.9691 (p) cc_final: 0.9392 (p) REVERT: A 961 LYS cc_start: 0.9306 (mttt) cc_final: 0.8818 (mttm) REVERT: A 977 ILE cc_start: 0.9614 (pt) cc_final: 0.9192 (mm) REVERT: A 989 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8382 (mp10) REVERT: A 994 ILE cc_start: 0.9204 (mt) cc_final: 0.8959 (mt) REVERT: A 1001 LEU cc_start: 0.9373 (mt) cc_final: 0.9131 (mt) REVERT: A 1002 GLN cc_start: 0.9474 (tp40) cc_final: 0.9015 (tp-100) REVERT: A 1116 ASN cc_start: 0.9372 (m-40) cc_final: 0.9044 (m-40) REVERT: B 58 PHE cc_start: 0.9205 (m-80) cc_final: 0.8765 (m-80) REVERT: B 106 PHE cc_start: 0.8839 (m-80) cc_final: 0.8355 (m-80) REVERT: B 117 LEU cc_start: 0.9772 (tp) cc_final: 0.9497 (tp) REVERT: B 119 ILE cc_start: 0.8969 (pt) cc_final: 0.8617 (pt) REVERT: B 177 MET cc_start: 0.3318 (ttm) cc_final: -0.1476 (mmt) REVERT: B 216 LEU cc_start: 0.8130 (tp) cc_final: 0.7636 (pt) REVERT: B 273 LEU cc_start: 0.9233 (tp) cc_final: 0.9003 (tp) REVERT: B 315 PHE cc_start: 0.8395 (t80) cc_final: 0.8173 (t80) REVERT: B 362 TYR cc_start: 0.9453 (m-80) cc_final: 0.9027 (m-80) REVERT: B 384 LEU cc_start: 0.9737 (mm) cc_final: 0.9277 (mt) REVERT: B 565 ASP cc_start: 0.8944 (t0) cc_final: 0.8505 (p0) REVERT: B 738 TYR cc_start: 0.8620 (t80) cc_final: 0.8408 (t80) REVERT: B 752 GLN cc_start: 0.8710 (mt0) cc_final: 0.8398 (mt0) REVERT: B 774 ASN cc_start: 0.8965 (m110) cc_final: 0.8711 (m-40) REVERT: B 781 GLN cc_start: 0.8677 (mm110) cc_final: 0.8195 (tm-30) REVERT: B 956 LEU cc_start: 0.9677 (mt) cc_final: 0.9426 (mt) REVERT: B 957 ASN cc_start: 0.9353 (m110) cc_final: 0.9034 (m110) REVERT: B 975 ASN cc_start: 0.9671 (m-40) cc_final: 0.9166 (t0) REVERT: B 999 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8767 (tm-30) REVERT: B 1001 LEU cc_start: 0.9456 (mm) cc_final: 0.9038 (mm) REVERT: B 1014 GLU cc_start: 0.9133 (tt0) cc_final: 0.8214 (mm-30) REVERT: B 1051 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8383 (mt0) REVERT: B 1064 TYR cc_start: 0.8848 (t80) cc_final: 0.8158 (t80) REVERT: C 53 ASP cc_start: 0.8880 (m-30) cc_final: 0.8669 (m-30) REVERT: C 223 LEU cc_start: 0.9059 (mp) cc_final: 0.8786 (tp) REVERT: C 272 PHE cc_start: 0.8507 (m-10) cc_final: 0.7997 (m-10) REVERT: C 321 GLU cc_start: 0.9339 (tp30) cc_final: 0.8765 (tp30) REVERT: C 348 TYR cc_start: 0.9272 (p90) cc_final: 0.8878 (p90) REVERT: C 377 TYR cc_start: 0.7566 (m-80) cc_final: 0.6987 (m-80) REVERT: C 647 LEU cc_start: 0.9345 (tp) cc_final: 0.8855 (pp) REVERT: C 711 ILE cc_start: 0.9418 (mp) cc_final: 0.9055 (tt) REVERT: C 733 VAL cc_start: 0.9449 (t) cc_final: 0.9168 (p) REVERT: C 734 ASP cc_start: 0.8890 (t0) cc_final: 0.8542 (t0) REVERT: C 737 MET cc_start: 0.8822 (tpt) cc_final: 0.8578 (tpp) REVERT: C 749 LEU cc_start: 0.9751 (tt) cc_final: 0.9521 (tt) REVERT: C 762 ARG cc_start: 0.8962 (mtm-85) cc_final: 0.8191 (mtt180) REVERT: C 767 ILE cc_start: 0.9796 (mt) cc_final: 0.9426 (mt) REVERT: C 770 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9163 (mt-10) REVERT: C 771 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8812 (mm-40) REVERT: C 799 PHE cc_start: 0.9013 (m-10) cc_final: 0.8744 (m-10) REVERT: C 816 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8827 (mt-10) REVERT: C 916 ASN cc_start: 0.9328 (m110) cc_final: 0.9069 (m110) REVERT: C 918 LYS cc_start: 0.9585 (mttt) cc_final: 0.9207 (mptt) REVERT: C 947 ASP cc_start: 0.9068 (m-30) cc_final: 0.8828 (m-30) REVERT: C 961 LYS cc_start: 0.9136 (mttt) cc_final: 0.8678 (mmtt) REVERT: C 989 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8273 (mm-40) REVERT: C 992 ARG cc_start: 0.8869 (mpp80) cc_final: 0.8369 (tpp80) REVERT: C 1011 ARG cc_start: 0.9176 (tpp-160) cc_final: 0.8860 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9219 (pt0) cc_final: 0.8913 (pp20) REVERT: C 1021 LEU cc_start: 0.9411 (mt) cc_final: 0.9167 (mt) REVERT: C 1031 LEU cc_start: 0.9563 (mp) cc_final: 0.9148 (mp) REVERT: C 1051 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8739 (mm-40) outliers start: 2 outliers final: 0 residues processed: 460 average time/residue: 0.1661 time to fit residues: 127.1214 Evaluate side-chains 370 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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: 7.9990 chunk 338 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 chunk 296 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 236 optimal weight: 0.0670 chunk 265 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN 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** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.111238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.067461 restraints weight = 124357.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.070133 restraints weight = 74241.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071829 restraints weight = 44958.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.072392 restraints weight = 32097.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.072610 restraints weight = 30199.246| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 0.055 31793 Z= 0.123 Angle : 0.603 19.512 43385 Z= 0.311 Chirality : 0.045 0.282 4983 Planarity : 0.004 0.065 5509 Dihedral : 4.666 22.504 4184 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.76 % 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: -0.44 (0.13), residues: 3827 helix: 0.34 (0.19), residues: 688 sheet: 0.09 (0.16), residues: 994 loop : -0.64 (0.14), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 980 TYR 0.034 0.001 TYR B 738 PHE 0.049 0.002 PHE C 272 TRP 0.031 0.001 TRP F 90 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (31689) covalent geometry : angle 0.58268 / 0.31 (43124) SS BOND : bond 0.00401 / 0.30 ( 51) SS BOND : angle 1.10149 / 0.70 ( 102) hydrogen bonds : bond 0.03807 / 2.56 ( 1286) hydrogen bonds : angle 5.63602 / 3.94 ( 3654) link_BETA1-4 : bond 0.00317 / 0.23 ( 12) link_BETA1-4 : angle 1.11760 / 0.80 ( 36) link_NAG-ASN : bond 0.00414 / 0.32 ( 41) link_NAG-ASN : angle 2.77004 / 1.86 ( 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 442 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 441 time to evaluate : 0.901 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: A 295 GLU cc_start: 0.9117 (mp0) cc_final: 0.8559 (mp0) REVERT: A 311 GLN cc_start: 0.9319 (pp30) cc_final: 0.8980 (pp30) REVERT: A 325 ARG cc_start: 0.7207 (mmt180) cc_final: 0.7004 (mmp-170) REVERT: A 377 TYR cc_start: 0.9253 (m-80) cc_final: 0.8962 (m-80) REVERT: A 420 TYR cc_start: 0.8358 (t80) cc_final: 0.7280 (t80) REVERT: A 422 LEU cc_start: 0.9579 (tp) cc_final: 0.9291 (tp) REVERT: A 453 PHE cc_start: 0.9547 (m-10) cc_final: 0.9345 (m-10) REVERT: A 529 ASN cc_start: 0.9716 (m-40) cc_final: 0.9452 (p0) REVERT: A 568 ASP cc_start: 0.9746 (m-30) cc_final: 0.9181 (t0) REVERT: A 694 MET cc_start: 0.8926 (ppp) cc_final: 0.8607 (ppp) REVERT: A 737 MET cc_start: 0.9087 (tpt) cc_final: 0.8701 (tpp) REVERT: A 893 ILE cc_start: 0.8944 (tp) cc_final: 0.8704 (tp) REVERT: A 897 MET cc_start: 0.6804 (mpp) cc_final: 0.6467 (mmp) REVERT: A 903 PHE cc_start: 0.8911 (m-80) cc_final: 0.8657 (m-10) REVERT: A 918 LYS cc_start: 0.9610 (mttt) cc_final: 0.9166 (tptp) REVERT: A 922 ASN cc_start: 0.9388 (m-40) cc_final: 0.8781 (m110) REVERT: A 957 ASN cc_start: 0.9087 (m110) cc_final: 0.8857 (m110) REVERT: A 977 ILE cc_start: 0.9583 (pt) cc_final: 0.9214 (mm) REVERT: A 989 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8610 (mp10) REVERT: A 994 ILE cc_start: 0.9199 (mt) cc_final: 0.8715 (mt) REVERT: A 1001 LEU cc_start: 0.9340 (mt) cc_final: 0.9046 (mt) REVERT: A 1002 GLN cc_start: 0.9507 (tp40) cc_final: 0.8985 (tp-100) REVERT: A 1116 ASN cc_start: 0.9338 (m-40) cc_final: 0.8970 (m-40) REVERT: B 58 PHE cc_start: 0.9229 (m-80) cc_final: 0.8784 (m-80) REVERT: B 106 PHE cc_start: 0.8836 (m-80) cc_final: 0.8344 (m-80) REVERT: B 117 LEU cc_start: 0.9769 (tp) cc_final: 0.9491 (tp) REVERT: B 119 ILE cc_start: 0.8967 (pt) cc_final: 0.8590 (pt) REVERT: B 177 MET cc_start: 0.3335 (ttm) cc_final: -0.1412 (mmt) REVERT: B 204 TYR cc_start: 0.5406 (m-10) cc_final: 0.5041 (m-80) REVERT: B 315 PHE cc_start: 0.8440 (t80) cc_final: 0.8221 (t80) REVERT: B 362 TYR cc_start: 0.9495 (m-80) cc_final: 0.9083 (m-80) REVERT: B 384 LEU cc_start: 0.9747 (mm) cc_final: 0.9293 (mt) REVERT: B 529 ASN cc_start: 0.9397 (p0) cc_final: 0.9179 (p0) REVERT: B 565 ASP cc_start: 0.8952 (t0) cc_final: 0.8484 (p0) REVERT: B 752 GLN cc_start: 0.8679 (mt0) cc_final: 0.8421 (mt0) REVERT: B 774 ASN cc_start: 0.8983 (m110) cc_final: 0.8598 (m-40) REVERT: B 781 GLN cc_start: 0.8784 (mm110) cc_final: 0.8333 (tm-30) REVERT: B 903 PHE cc_start: 0.7198 (m-80) cc_final: 0.6846 (m-10) REVERT: B 951 GLN cc_start: 0.9176 (tp-100) cc_final: 0.8801 (tp40) REVERT: B 952 ASN cc_start: 0.9542 (t0) cc_final: 0.9301 (t0) REVERT: B 956 LEU cc_start: 0.9719 (mt) cc_final: 0.9496 (mt) REVERT: B 957 ASN cc_start: 0.9370 (m110) cc_final: 0.9063 (m110) REVERT: B 999 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8774 (tm-30) REVERT: B 1001 LEU cc_start: 0.9429 (mm) cc_final: 0.8897 (mm) REVERT: B 1014 GLU cc_start: 0.9100 (tt0) cc_final: 0.8193 (mm-30) REVERT: B 1051 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8253 (mt0) REVERT: B 1064 TYR cc_start: 0.8730 (t80) cc_final: 0.8169 (t80) REVERT: C 223 LEU cc_start: 0.9082 (mp) cc_final: 0.8792 (tp) REVERT: C 272 PHE cc_start: 0.8318 (m-10) cc_final: 0.8040 (m-10) REVERT: C 321 GLU cc_start: 0.9347 (tp30) cc_final: 0.8777 (tp30) REVERT: C 351 ASN cc_start: 0.9471 (t0) cc_final: 0.9230 (m110) REVERT: C 377 TYR cc_start: 0.7589 (m-80) cc_final: 0.7010 (m-80) REVERT: C 647 LEU cc_start: 0.9189 (tp) cc_final: 0.8559 (pp) REVERT: C 711 ILE cc_start: 0.9348 (mp) cc_final: 0.8980 (tt) REVERT: C 733 VAL cc_start: 0.9484 (t) cc_final: 0.9194 (p) REVERT: C 734 ASP cc_start: 0.8831 (t0) cc_final: 0.8526 (t0) REVERT: C 737 MET cc_start: 0.8758 (tpt) cc_final: 0.8528 (tpp) REVERT: C 752 GLN cc_start: 0.8838 (mt0) cc_final: 0.8590 (mt0) REVERT: C 767 ILE cc_start: 0.9818 (mt) cc_final: 0.9437 (mt) REVERT: C 770 GLU cc_start: 0.9555 (mt-10) cc_final: 0.9163 (mt-10) REVERT: C 771 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8641 (mm-40) REVERT: C 799 PHE cc_start: 0.8926 (m-10) cc_final: 0.8564 (m-10) REVERT: C 916 ASN cc_start: 0.9303 (m110) cc_final: 0.9048 (m110) REVERT: C 918 LYS cc_start: 0.9601 (mttt) cc_final: 0.9193 (mptt) REVERT: C 947 ASP cc_start: 0.9043 (m-30) cc_final: 0.8777 (m-30) REVERT: C 954 GLN cc_start: 0.9417 (mp10) cc_final: 0.9178 (pm20) REVERT: C 961 LYS cc_start: 0.9161 (mttt) cc_final: 0.8728 (mmtt) REVERT: C 989 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8283 (mm-40) REVERT: C 1009 LEU cc_start: 0.9392 (mm) cc_final: 0.9126 (mm) REVERT: C 1011 ARG cc_start: 0.9211 (tpp-160) cc_final: 0.8832 (tpp-160) REVERT: C 1014 GLU cc_start: 0.9196 (pt0) cc_final: 0.8823 (pp20) REVERT: C 1021 LEU cc_start: 0.9407 (mt) cc_final: 0.9186 (mt) REVERT: C 1028 GLU cc_start: 0.8413 (tp30) cc_final: 0.7618 (tp30) REVERT: H 34 MET cc_start: 0.2914 (mpp) cc_final: 0.2545 (mpp) REVERT: H 83 MET cc_start: -0.6408 (ptt) cc_final: -0.6826 (ptt) outliers start: 1 outliers final: 0 residues processed: 441 average time/residue: 0.1715 time to fit residues: 127.3061 Evaluate side-chains 361 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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: 3.9990 chunk 159 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 301 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 898 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** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.110428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.063756 restraints weight = 123715.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.065812 restraints weight = 75304.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067170 restraints weight = 53275.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.068214 restraints weight = 42192.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.068829 restraints weight = 35794.105| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31793 Z= 0.171 Angle : 0.615 18.862 43385 Z= 0.322 Chirality : 0.045 0.220 4983 Planarity : 0.006 0.277 5509 Dihedral : 4.771 36.078 4184 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.71 % 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: -0.50 (0.13), residues: 3827 helix: 0.15 (0.19), residues: 694 sheet: 0.06 (0.16), residues: 994 loop : -0.64 (0.14), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 574 TYR 0.041 0.001 TYR B 738 PHE 0.043 0.002 PHE C 272 TRP 0.021 0.001 TRP F 90 HIS 0.007 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (31689) covalent geometry : angle 0.59573 / 0.32 (43124) SS BOND : bond 0.00438 / 0.33 ( 51) SS BOND : angle 1.18331 / 0.76 ( 102) hydrogen bonds : bond 0.04050 / 2.74 ( 1286) hydrogen bonds : angle 5.70432 / 3.98 ( 3654) link_BETA1-4 : bond 0.00192 / 0.13 ( 12) link_BETA1-4 : angle 1.26241 / 0.88 ( 36) link_NAG-ASN : bond 0.00426 / 0.33 ( 41) link_NAG-ASN : angle 2.74324 / 1.83 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5890.62 seconds wall clock time: 102 minutes 43.65 seconds (6163.65 seconds total)