Starting phenix.real_space_refine on Sun Jul 5 23:39:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zr9_14887/07_2026/7zr9_14887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr9_14887/07_2026/7zr9_14887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zr9_14887/07_2026/7zr9_14887.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zr9_14887/07_2026/7zr9_14887.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zr9_14887/07_2026/7zr9_14887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr9_14887/07_2026/7zr9_14887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zr9_14887/07_2026/7zr9_14887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr9_14887/07_2026/7zr9_14887.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.080 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 141 5.16 5 C 19719 2.51 5 N 5108 2.21 5 O 6046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 31014 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8281 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 6 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 973 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 124} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 973 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 124} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 973 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 124} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} 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: "J" 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: "K" 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: "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: "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: "C" 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 Time building chain proxies: 6.34, per 1000 atoms: 0.20 Number of scatterers: 31014 At special positions: 0 Unit cell: (153.6, 163.2, 232.8, 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 141 16.00 O 6046 8.00 N 5108 7.00 C 19719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 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=2.02 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=2.04 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=2.03 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 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=2.02 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=2.03 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=2.03 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=1.67 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 105 " distance=2.21 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 105 " distance=2.21 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 105 " distance=2.21 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 328 " " 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 340 " " 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 328 " " NAG C1304 " - " ASN C 600 " " NAG C1305 " - " ASN C 613 " " NAG C1306 " - " ASN C 654 " " NAG C1307 " - " ASN C 706 " " NAG C1308 " - " ASN C1071 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 340 " " NAG I 1 " - " ASN B 714 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN A 714 " " NAG O 1 " - " ASN A 798 " " NAG P 1 " - " ASN A1095 " " NAG Q 1 " - " ASN A1131 " " 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: 2.25 Conformation dependent library (CDL) restraints added in 978.7 milliseconds 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7234 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 69 sheets defined 22.2% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.636A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.693A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.217A pdb=" N ARG B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.575A pdb=" N SER B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.745A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) 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: 3.544A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.161A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.616A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.542A 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 1029 removed outlier: 4.427A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.132A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.525A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.768A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) 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 883 through 888 Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.951A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 963 removed outlier: 4.066A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.594A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1029 removed outlier: 5.051A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.885A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (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 346 through 350 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 382 through 387 removed outlier: 3.735A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 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 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.572A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 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: 3.809A 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 910 through 938 removed outlier: 5.599A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) 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: 3.958A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.927A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.992A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52 through 56 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.740A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.740A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 52 through 56 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.740A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.639A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.533A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.835A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.748A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.835A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.133A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.475A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.807A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'B' and resid 651 through 652 removed outlier: 3.509A pdb=" N ALA B 691 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 699 through 701 Processing sheet with id=AB6, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AB7, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.931A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AB9, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.659A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.448A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AC3, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AC4, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.974A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.388A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.885A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 151 through 160 removed outlier: 6.834A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.455A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.195A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AD1, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AD2, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.915A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AD4, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.511A pdb=" N TYR A 486 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.503A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.700A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.700A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AD9, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.874A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 3.567A pdb=" N SER A1120 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) 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: 7.859A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.009A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.398A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 13.230A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C 141 " --> pdb=" O HIS C 242 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR C 145 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.663A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.608A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE C 101 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.313A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.892A 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: 4.244A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AF1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.863A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 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: 6.557A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (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: 5.841A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.366A 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: 3.747A pdb=" N SER C1120 " --> pdb=" O ALA C1084 " (cutoff:3.500A) removed outlier: 4.376A 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 6 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.635A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.122A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.630A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AG6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 4 through 7 removed outlier: 5.635A pdb=" N THR E 70 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N GLN E 27 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N SER E 68 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 11.582A pdb=" N VAL E 29 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N SER E 66 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.631A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AH2, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AH3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 removed outlier: 5.635A pdb=" N THR G 70 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N GLN G 27 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N SER G 68 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 11.581A pdb=" N VAL G 29 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N SER G 66 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.630A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 13 1319 hydrogen bonds defined for protein. 3480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.45 Time building geometry restraints manager: 2.90 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: 9769 1.34 - 1.46: 7184 1.46 - 1.58: 14598 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 31731 Sorted by residual: bond pdb=" CA TRP D 121 " pdb=" C TRP D 121 " ideal model delta sigma weight residual 1.520 1.398 0.121 1.16e-02 7.43e+03 1.10e+02 bond pdb=" CA TRP H 121 " pdb=" C TRP H 121 " ideal model delta sigma weight residual 1.520 1.399 0.121 1.16e-02 7.43e+03 1.09e+02 bond pdb=" CA TRP F 121 " pdb=" C TRP F 121 " ideal model delta sigma weight residual 1.520 1.399 0.121 1.16e-02 7.43e+03 1.08e+02 bond pdb=" CA CYS H 101 " pdb=" CB CYS H 101 " ideal model delta sigma weight residual 1.531 1.464 0.067 1.51e-02 4.39e+03 1.96e+01 bond pdb=" CA CYS D 101 " pdb=" CB CYS D 101 " ideal model delta sigma weight residual 1.531 1.464 0.067 1.51e-02 4.39e+03 1.94e+01 ... (remaining 31726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 42688 3.10 - 6.21: 449 6.21 - 9.31: 30 9.31 - 12.41: 7 12.41 - 15.52: 6 Bond angle restraints: 43180 Sorted by residual: angle pdb=" C CYS H 105 " pdb=" N PRO H 106 " pdb=" CA PRO H 106 " ideal model delta sigma weight residual 119.84 109.93 9.91 1.25e+00 6.40e-01 6.29e+01 angle pdb=" C CYS D 105 " pdb=" N PRO D 106 " pdb=" CA PRO D 106 " ideal model delta sigma weight residual 119.84 109.95 9.89 1.25e+00 6.40e-01 6.26e+01 angle pdb=" C CYS F 105 " pdb=" N PRO F 106 " pdb=" CA PRO F 106 " ideal model delta sigma weight residual 119.84 109.96 9.88 1.25e+00 6.40e-01 6.25e+01 angle pdb=" CA CYS D 101 " pdb=" CB CYS D 101 " pdb=" SG CYS D 101 " ideal model delta sigma weight residual 114.40 98.88 15.52 2.30e+00 1.89e-01 4.55e+01 angle pdb=" CA CYS H 101 " pdb=" CB CYS H 101 " pdb=" SG CYS H 101 " ideal model delta sigma weight residual 114.40 98.90 15.50 2.30e+00 1.89e-01 4.54e+01 ... (remaining 43175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 17524 17.85 - 35.71: 731 35.71 - 53.56: 115 53.56 - 71.41: 28 71.41 - 89.26: 18 Dihedral angle restraints: 18416 sinusoidal: 7130 harmonic: 11286 Sorted by residual: dihedral pdb=" C CYS D 101 " pdb=" N CYS D 101 " pdb=" CA CYS D 101 " pdb=" CB CYS D 101 " ideal model delta harmonic sigma weight residual -122.60 -109.26 -13.34 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" C CYS H 101 " pdb=" N CYS H 101 " pdb=" CA CYS H 101 " pdb=" CB CYS H 101 " ideal model delta harmonic sigma weight residual -122.60 -109.26 -13.34 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" C CYS F 101 " pdb=" N CYS F 101 " pdb=" CA CYS F 101 " pdb=" CB CYS F 101 " ideal model delta harmonic sigma weight residual -122.60 -109.33 -13.27 0 2.50e+00 1.60e-01 2.82e+01 ... (remaining 18413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3586 0.046 - 0.091: 909 0.091 - 0.137: 414 0.137 - 0.183: 81 0.183 - 0.229: 25 Chirality restraints: 5015 Sorted by residual: chirality pdb=" CA PRO H 53 " pdb=" N PRO H 53 " pdb=" C PRO H 53 " pdb=" CB PRO H 53 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO F 53 " pdb=" N PRO F 53 " pdb=" C PRO F 53 " pdb=" CB PRO F 53 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PRO D 53 " pdb=" N PRO D 53 " pdb=" C PRO D 53 " pdb=" CB PRO D 53 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 5012 not shown) Planarity restraints: 5555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.240 2.00e-02 2.50e+03 2.01e-01 5.03e+02 pdb=" C7 NAG B1308 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.335 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 36 " 0.058 2.00e-02 2.50e+03 3.51e-02 3.08e+01 pdb=" CG TRP L 36 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP L 36 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP L 36 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP L 36 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP L 36 " -0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP L 36 " -0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 36 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 36 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 36 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 36 " -0.058 2.00e-02 2.50e+03 3.50e-02 3.07e+01 pdb=" CG TRP E 36 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP E 36 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP E 36 " 0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP E 36 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP E 36 " 0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP E 36 " 0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 36 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 36 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 36 " -0.054 2.00e-02 2.50e+03 ... (remaining 5552 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 958 2.71 - 3.25: 30537 3.25 - 3.80: 50386 3.80 - 4.35: 63216 4.35 - 4.90: 106475 Nonbonded interactions: 251572 Sorted by model distance: nonbonded pdb=" O GLY C 877 " pdb=" OG SER C 881 " model vdw 2.158 3.040 nonbonded pdb=" O GLU A 658 " pdb=" OH TYR A 692 " model vdw 2.172 3.040 nonbonded pdb=" O GLU B 306 " pdb=" OH TYR B 310 " model vdw 2.174 3.040 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASN C 99 " pdb=" NH2 ARG C 190 " model vdw 2.178 3.120 ... (remaining 251567 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 619 or resid 638 through 1310)) selection = chain 'B' selection = (chain 'C' and (resid 13 through 619 or resid 638 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' 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' } 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: 2.950 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.930 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.007 0.365 31836 Z= 0.379 Angle : 0.908 46.727 43444 Z= 0.525 Chirality : 0.052 0.229 5015 Planarity : 0.006 0.201 5513 Dihedral : 10.569 89.264 11029 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 1.22 % Allowed : 4.90 % Favored : 93.88 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.99 % 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: -0.10 (0.13), residues: 3845 helix: 1.21 (0.20), residues: 706 sheet: 0.16 (0.15), residues: 1043 loop : -0.59 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 55 TYR 0.041 0.003 TYR F 94 PHE 0.032 0.002 PHE D 64 TRP 0.058 0.006 TRP L 36 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.36 (31731) covalent geometry : angle 0.86437 / 0.51 (43180) SS BOND : bond 0.06648 / 3.25 ( 51) SS BOND : angle 5.51113 / 4.66 ( 102) hydrogen bonds : bond 0.13466 / 8.81 ( 1272) hydrogen bonds : angle 7.13014 / 4.98 ( 3480) link_BETA1-4 : bond 0.00305 / 0.20 ( 12) link_BETA1-4 : angle 1.00810 / 0.68 ( 36) link_NAG-ASN : bond 0.00343 / 0.23 ( 42) link_NAG-ASN : angle 1.87812 / 1.33 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 378 time to evaluate : 0.903 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: B 135 PHE cc_start: 0.5455 (m-80) cc_final: 0.5006 (m-10) REVERT: B 177 MET cc_start: 0.0753 (ttm) cc_final: 0.0390 (ttp) REVERT: B 239 GLN cc_start: 0.7634 (tt0) cc_final: 0.7405 (tt0) REVERT: B 267 LEU cc_start: 0.8901 (mt) cc_final: 0.8598 (mp) REVERT: B 284 ASP cc_start: 0.7423 (t0) cc_final: 0.6941 (t0) REVERT: B 612 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8224 (p) REVERT: B 760 LEU cc_start: 0.9542 (mt) cc_final: 0.9300 (mt) REVERT: A 54 LEU cc_start: 0.8996 (mt) cc_final: 0.8621 (mm) REVERT: A 65 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: A 104 TRP cc_start: 0.7425 (m-90) cc_final: 0.7200 (m-90) REVERT: A 118 LEU cc_start: 0.8355 (tp) cc_final: 0.7756 (mp) REVERT: A 133 PHE cc_start: 0.6574 (m-80) cc_final: 0.4798 (m-80) REVERT: A 177 MET cc_start: 0.3712 (ttm) cc_final: 0.2443 (mtp) REVERT: A 221 SER cc_start: 0.7487 (t) cc_final: 0.7143 (m) REVERT: A 1139 GLN cc_start: 0.8813 (tp40) cc_final: 0.8468 (tm-30) REVERT: C 87 ASN cc_start: 0.8432 (m-40) cc_final: 0.7585 (m110) REVERT: C 143 VAL cc_start: 0.4888 (OUTLIER) cc_final: 0.4676 (p) REVERT: C 177 MET cc_start: 0.0661 (ttm) cc_final: -0.2168 (mmt) REVERT: C 263 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.5732 (m-80) REVERT: C 266 TYR cc_start: 0.7389 (m-80) cc_final: 0.7175 (m-10) REVERT: C 717 ILE cc_start: 0.9016 (mm) cc_final: 0.8808 (tt) REVERT: C 893 ILE cc_start: 0.9563 (OUTLIER) cc_final: 0.9219 (mt) REVERT: C 1020 ASN cc_start: 0.8699 (m-40) cc_final: 0.7382 (m-40) REVERT: H 39 GLN cc_start: 0.6094 (tt0) cc_final: 0.5807 (pp30) REVERT: H 81 MET cc_start: 0.4206 (tmm) cc_final: 0.3751 (ptt) REVERT: L 49 ILE cc_start: 0.7689 (mm) cc_final: 0.7121 (mm) REVERT: L 88 TYR cc_start: 0.1343 (m-80) cc_final: 0.1132 (m-80) REVERT: E 98 THR cc_start: 0.5772 (p) cc_final: 0.5224 (t) REVERT: G 4 MET cc_start: 0.4329 (mmm) cc_final: 0.3705 (mtt) outliers start: 41 outliers final: 12 residues processed: 416 average time/residue: 0.1781 time to fit residues: 119.0172 Evaluate side-chains 191 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 752 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.122268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.090822 restraints weight = 167450.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.088086 restraints weight = 134840.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.088778 restraints weight = 119989.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.088859 restraints weight = 89071.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.089069 restraints weight = 80049.527| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 31836 Z= 0.203 Angle : 0.613 8.675 43444 Z= 0.318 Chirality : 0.044 0.188 5015 Planarity : 0.004 0.092 5513 Dihedral : 4.912 58.007 4226 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.91 % Allowed : 9.01 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.09 (0.13), residues: 3845 helix: 1.51 (0.19), residues: 704 sheet: 0.13 (0.15), residues: 1039 loop : -0.43 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 325 TYR 0.038 0.001 TYR A 266 PHE 0.023 0.002 PHE A 135 TRP 0.014 0.001 TRP A 883 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (31731) covalent geometry : angle 0.60173 / 0.32 (43180) SS BOND : bond 0.00425 / 0.23 ( 51) SS BOND : angle 1.32662 / 0.90 ( 102) hydrogen bonds : bond 0.04387 / 2.96 ( 1272) hydrogen bonds : angle 5.89656 / 4.12 ( 3480) link_BETA1-4 : bond 0.00292 / 0.20 ( 12) link_BETA1-4 : angle 1.01580 / 0.64 ( 36) link_NAG-ASN : bond 0.00401 / 0.27 ( 42) link_NAG-ASN : angle 1.96196 / 1.33 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 0.969 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: B 135 PHE cc_start: 0.5383 (m-80) cc_final: 0.5075 (m-10) REVERT: B 177 MET cc_start: 0.1424 (ttm) cc_final: 0.1185 (ttp) REVERT: B 267 LEU cc_start: 0.9133 (mt) cc_final: 0.8802 (mp) REVERT: B 384 LEU cc_start: 0.8239 (mt) cc_final: 0.7685 (mt) REVERT: B 420 TYR cc_start: 0.4943 (t80) cc_final: 0.4386 (t80) REVERT: B 612 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8345 (p) REVERT: B 696 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7796 (mt) REVERT: A 65 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: A 87 ASN cc_start: 0.8785 (t0) cc_final: 0.8389 (t0) REVERT: A 177 MET cc_start: 0.3887 (ttm) cc_final: 0.3023 (mtp) REVERT: A 799 PHE cc_start: 0.8161 (m-10) cc_final: 0.7849 (m-10) REVERT: A 1139 GLN cc_start: 0.9080 (tp40) cc_final: 0.8705 (tm-30) REVERT: C 87 ASN cc_start: 0.8653 (m-40) cc_final: 0.7550 (m110) REVERT: C 118 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8000 (mt) REVERT: C 177 MET cc_start: 0.1423 (ttm) cc_final: -0.1664 (tpp) REVERT: C 203 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8792 (pt) REVERT: C 263 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.5853 (m-80) REVERT: C 266 TYR cc_start: 0.7553 (m-80) cc_final: 0.7333 (m-10) REVERT: C 899 MET cc_start: 0.9133 (tpp) cc_final: 0.8838 (tpp) REVERT: C 959 LEU cc_start: 0.9497 (tp) cc_final: 0.9295 (tp) REVERT: H 46 GLU cc_start: 0.3993 (OUTLIER) cc_final: 0.3646 (pt0) REVERT: H 63 LYS cc_start: 0.1400 (tttt) cc_final: 0.1101 (pttt) REVERT: H 81 MET cc_start: 0.4606 (tmm) cc_final: 0.3497 (ptt) REVERT: D 47 TRP cc_start: 0.2100 (t60) cc_final: 0.0516 (t60) REVERT: D 48 MET cc_start: 0.2265 (OUTLIER) cc_final: 0.0524 (ptm) REVERT: E 4 MET cc_start: 0.4698 (mmt) cc_final: 0.4424 (mmt) REVERT: G 4 MET cc_start: 0.3595 (mmm) cc_final: 0.3179 (mtt) outliers start: 64 outliers final: 33 residues processed: 236 average time/residue: 0.1724 time to fit residues: 67.9510 Evaluate side-chains 175 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 331 optimal weight: 40.0000 chunk 158 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 293 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN A 946 GLN A 975 ASN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.120755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.087907 restraints weight = 166833.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.086020 restraints weight = 128370.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.086136 restraints weight = 119297.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.086640 restraints weight = 87082.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.086643 restraints weight = 76426.594| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31836 Z= 0.230 Angle : 0.628 12.719 43444 Z= 0.323 Chirality : 0.044 0.332 5015 Planarity : 0.004 0.056 5513 Dihedral : 4.940 51.165 4216 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 3.01 % Allowed : 10.06 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.10 (0.13), residues: 3845 helix: 1.64 (0.20), residues: 702 sheet: 0.12 (0.15), residues: 1044 loop : -0.46 (0.14), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 574 TYR 0.027 0.002 TYR C 486 PHE 0.023 0.002 PHE H 64 TRP 0.025 0.002 TRP A 104 HIS 0.008 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (31731) covalent geometry : angle 0.61577 / 0.32 (43180) SS BOND : bond 0.00462 / 0.27 ( 51) SS BOND : angle 1.30219 / 0.89 ( 102) hydrogen bonds : bond 0.04242 / 2.85 ( 1272) hydrogen bonds : angle 5.78718 / 4.03 ( 3480) link_BETA1-4 : bond 0.00476 / 0.32 ( 12) link_BETA1-4 : angle 1.13736 / 0.74 ( 36) link_NAG-ASN : bond 0.00479 / 0.34 ( 42) link_NAG-ASN : angle 2.09907 / 1.45 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 153 time to evaluate : 0.768 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: B 177 MET cc_start: 0.2461 (ttm) cc_final: 0.2244 (ttt) REVERT: B 267 LEU cc_start: 0.9116 (mt) cc_final: 0.8763 (mp) REVERT: B 284 ASP cc_start: 0.7888 (t0) cc_final: 0.7356 (t0) REVERT: B 420 TYR cc_start: 0.5096 (t80) cc_final: 0.4447 (t80) REVERT: B 612 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8430 (p) REVERT: B 696 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7827 (mt) REVERT: B 805 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8757 (p0) REVERT: B 855 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8239 (pp) REVERT: A 65 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: A 153 MET cc_start: 0.4791 (mmt) cc_final: 0.4552 (mmt) REVERT: A 177 MET cc_start: 0.4843 (ttm) cc_final: 0.4302 (mtp) REVERT: C 24 LEU cc_start: 0.1462 (OUTLIER) cc_final: 0.0954 (tp) REVERT: C 87 ASN cc_start: 0.8656 (m-40) cc_final: 0.8431 (m110) REVERT: C 118 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7974 (mt) REVERT: C 177 MET cc_start: 0.2079 (ttm) cc_final: -0.0907 (mmt) REVERT: C 263 TYR cc_start: 0.6577 (OUTLIER) cc_final: 0.5855 (m-80) REVERT: C 311 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: C 899 MET cc_start: 0.9121 (tpp) cc_final: 0.8799 (tpp) REVERT: C 976 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8192 (t0) REVERT: C 1026 MET cc_start: 0.9116 (tpp) cc_final: 0.8908 (mmm) REVERT: D 48 MET cc_start: 0.1380 (mtm) cc_final: 0.0918 (ptm) REVERT: G 4 MET cc_start: 0.4638 (mmm) cc_final: 0.4236 (mtt) outliers start: 101 outliers final: 61 residues processed: 245 average time/residue: 0.1655 time to fit residues: 69.6574 Evaluate side-chains 198 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 127 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1005 VAL Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 134 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 305 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 334 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 975 ASN A 999 GLN C 577 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.121004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.088215 restraints weight = 165533.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.086214 restraints weight = 125979.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.086654 restraints weight = 111067.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.086839 restraints weight = 82069.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.086854 restraints weight = 79487.076| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31836 Z= 0.172 Angle : 0.565 10.057 43444 Z= 0.289 Chirality : 0.043 0.227 5015 Planarity : 0.004 0.073 5513 Dihedral : 4.769 53.827 4216 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.57 % Rotamer: Outliers : 2.69 % Allowed : 11.10 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: 0.16 (0.14), residues: 3845 helix: 1.80 (0.20), residues: 705 sheet: 0.11 (0.15), residues: 1028 loop : -0.43 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1011 TYR 0.035 0.001 TYR C 486 PHE 0.016 0.002 PHE C1086 TRP 0.025 0.001 TRP A 104 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (31731) covalent geometry : angle 0.55347 / 0.29 (43180) SS BOND : bond 0.00431 / 0.25 ( 51) SS BOND : angle 1.03797 / 0.71 ( 102) hydrogen bonds : bond 0.03846 / 2.59 ( 1272) hydrogen bonds : angle 5.54987 / 3.88 ( 3480) link_BETA1-4 : bond 0.00252 / 0.17 ( 12) link_BETA1-4 : angle 0.99196 / 0.64 ( 36) link_NAG-ASN : bond 0.00345 / 0.24 ( 42) link_NAG-ASN : angle 1.94895 / 1.34 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 140 time to evaluate : 1.206 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: B 177 MET cc_start: 0.2063 (ttm) cc_final: 0.1632 (ttt) REVERT: B 267 LEU cc_start: 0.9083 (mt) cc_final: 0.8740 (mp) REVERT: B 284 ASP cc_start: 0.7749 (t0) cc_final: 0.7203 (t0) REVERT: B 420 TYR cc_start: 0.5074 (t80) cc_final: 0.4370 (t80) REVERT: B 612 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8445 (p) REVERT: B 696 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7757 (mt) REVERT: B 855 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8251 (pp) REVERT: A 65 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: A 153 MET cc_start: 0.4940 (mmt) cc_final: 0.4725 (mmt) REVERT: A 177 MET cc_start: 0.5001 (ttm) cc_final: 0.4401 (mtp) REVERT: A 985 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8274 (tp30) REVERT: C 87 ASN cc_start: 0.8607 (m-40) cc_final: 0.8389 (m110) REVERT: C 118 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8001 (mt) REVERT: C 177 MET cc_start: 0.2430 (ttm) cc_final: -0.0944 (mmp) REVERT: C 263 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5720 (m-80) REVERT: C 311 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8063 (mm110) REVERT: C 976 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8154 (t0) REVERT: C 1026 MET cc_start: 0.9084 (tpp) cc_final: 0.8882 (mmm) REVERT: H 81 MET cc_start: 0.4112 (tmm) cc_final: 0.3673 (tmm) REVERT: D 48 MET cc_start: 0.1489 (mtm) cc_final: 0.0972 (ptm) REVERT: E 4 MET cc_start: 0.3641 (mmt) cc_final: 0.2921 (tpp) REVERT: G 4 MET cc_start: 0.4958 (mmm) cc_final: 0.4496 (mtt) outliers start: 90 outliers final: 57 residues processed: 218 average time/residue: 0.1681 time to fit residues: 62.6656 Evaluate side-chains 185 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 119 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 343 optimal weight: 40.0000 chunk 86 optimal weight: 3.9990 chunk 331 optimal weight: 30.0000 chunk 194 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 447 ASN A 125 ASN A 149 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A1007 GLN C 490 GLN C 537 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.112715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.083751 restraints weight = 150311.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.080791 restraints weight = 104835.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.081168 restraints weight = 90642.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.081376 restraints weight = 73455.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.081477 restraints weight = 68210.459| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.155 31836 Z= 0.338 Angle : 0.757 11.359 43444 Z= 0.388 Chirality : 0.047 0.284 5015 Planarity : 0.005 0.069 5513 Dihedral : 5.465 57.702 4216 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.27 % Allowed : 12.03 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.28 (0.13), residues: 3845 helix: 1.32 (0.20), residues: 685 sheet: -0.20 (0.15), residues: 1052 loop : -0.65 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 67 TYR 0.028 0.002 TYR C 486 PHE 0.032 0.003 PHE B1086 TRP 0.019 0.002 TRP A 64 HIS 0.011 0.002 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.34 (31731) covalent geometry : angle 0.74023 / 0.38 (43180) SS BOND : bond 0.00854 / 0.40 ( 51) SS BOND : angle 1.43315 / 0.99 ( 102) hydrogen bonds : bond 0.04776 / 3.20 ( 1272) hydrogen bonds : angle 6.21261 / 4.35 ( 3480) link_BETA1-4 : bond 0.00439 / 0.30 ( 12) link_BETA1-4 : angle 1.47160 / 0.92 ( 36) link_NAG-ASN : bond 0.00824 / 0.57 ( 42) link_NAG-ASN : angle 2.74103 / 1.96 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 124 time to evaluate : 1.224 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: B 267 LEU cc_start: 0.9022 (mt) cc_final: 0.8730 (mp) REVERT: B 284 ASP cc_start: 0.7913 (t0) cc_final: 0.7470 (t0) REVERT: B 420 TYR cc_start: 0.4702 (t80) cc_final: 0.4356 (t80) REVERT: B 696 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8208 (mt) REVERT: B 805 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8805 (p0) REVERT: A 65 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: A 153 MET cc_start: 0.5353 (mmt) cc_final: 0.4976 (mmm) REVERT: A 177 MET cc_start: 0.2609 (ttm) cc_final: 0.2340 (mtp) REVERT: C 24 LEU cc_start: 0.2291 (OUTLIER) cc_final: 0.2046 (tt) REVERT: C 62 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8260 (p) REVERT: C 118 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7960 (mt) REVERT: C 899 MET cc_start: 0.9080 (tpp) cc_final: 0.8719 (tpp) REVERT: C 976 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.7973 (t0) REVERT: C 1026 MET cc_start: 0.9182 (tpp) cc_final: 0.8773 (mmm) REVERT: C 1031 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8911 (mt) REVERT: H 63 LYS cc_start: 0.1151 (tttt) cc_final: 0.0795 (mtmt) REVERT: H 81 MET cc_start: 0.3885 (tmm) cc_final: 0.1680 (tmm) REVERT: G 4 MET cc_start: 0.3103 (mmm) cc_final: 0.2506 (mtt) outliers start: 143 outliers final: 101 residues processed: 252 average time/residue: 0.1658 time to fit residues: 71.9738 Evaluate side-chains 222 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 113 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1038 ASP Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1005 VAL Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 193 optimal weight: 0.8980 chunk 289 optimal weight: 0.7980 chunk 343 optimal weight: 20.0000 chunk 376 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 329 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 40 optimal weight: 50.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 447 ASN B 904 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.119188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.086830 restraints weight = 164839.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.084681 restraints weight = 134757.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.085155 restraints weight = 111369.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.085315 restraints weight = 87717.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.085433 restraints weight = 78810.156| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31836 Z= 0.178 Angle : 0.605 14.505 43444 Z= 0.305 Chirality : 0.044 0.242 5015 Planarity : 0.004 0.074 5513 Dihedral : 5.083 57.224 4216 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.93 % Allowed : 13.94 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.11 (0.14), residues: 3845 helix: 1.74 (0.20), residues: 685 sheet: -0.24 (0.15), residues: 1066 loop : -0.55 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.018 0.001 TYR C 486 PHE 0.029 0.002 PHE A 140 TRP 0.014 0.001 TRP A 104 HIS 0.008 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (31731) covalent geometry : angle 0.59158 / 0.30 (43180) SS BOND : bond 0.00458 / 0.25 ( 51) SS BOND : angle 1.13540 / 0.71 ( 102) hydrogen bonds : bond 0.04013 / 2.70 ( 1272) hydrogen bonds : angle 5.76582 / 4.05 ( 3480) link_BETA1-4 : bond 0.00209 / 0.15 ( 12) link_BETA1-4 : angle 1.11808 / 0.70 ( 36) link_NAG-ASN : bond 0.00418 / 0.29 ( 42) link_NAG-ASN : angle 2.16789 / 1.55 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 126 time to evaluate : 1.165 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: B 135 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: B 177 MET cc_start: 0.1968 (ttt) cc_final: 0.1532 (ttt) REVERT: B 267 LEU cc_start: 0.9056 (mt) cc_final: 0.8741 (mp) REVERT: B 420 TYR cc_start: 0.5202 (t80) cc_final: 0.4471 (t80) REVERT: B 579 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8585 (pt) REVERT: B 612 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8539 (p) REVERT: B 696 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8069 (mt) REVERT: B 855 LEU cc_start: 0.8710 (mp) cc_final: 0.8229 (pp) REVERT: A 689 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9272 (tp) REVERT: C 24 LEU cc_start: 0.2269 (OUTLIER) cc_final: 0.1917 (tt) REVERT: C 62 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8538 (p) REVERT: C 118 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7944 (mt) REVERT: C 263 TYR cc_start: 0.6415 (OUTLIER) cc_final: 0.6164 (m-80) REVERT: C 562 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8235 (p90) REVERT: C 899 MET cc_start: 0.9000 (tpp) cc_final: 0.8799 (tpp) REVERT: C 976 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8119 (t0) REVERT: C 1026 MET cc_start: 0.9092 (tpp) cc_final: 0.8718 (mmm) REVERT: C 1031 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9028 (mt) REVERT: H 81 MET cc_start: 0.3558 (tmm) cc_final: 0.1721 (tmm) REVERT: D 48 MET cc_start: -0.0343 (ptm) cc_final: -0.1244 (ptm) REVERT: E 4 MET cc_start: 0.3190 (tpt) cc_final: 0.2785 (tpp) REVERT: G 4 MET cc_start: 0.5171 (mmm) cc_final: 0.4593 (mtt) outliers start: 98 outliers final: 68 residues processed: 208 average time/residue: 0.1703 time to fit residues: 60.1868 Evaluate side-chains 197 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 117 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1038 ASP Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 115 optimal weight: 8.9990 chunk 304 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 377 optimal weight: 50.0000 chunk 255 optimal weight: 30.0000 chunk 69 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 289 optimal weight: 0.0970 chunk 138 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 164 ASN B 904 ASN A 125 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 125 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.118110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.083056 restraints weight = 165873.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.083911 restraints weight = 120620.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.084104 restraints weight = 86014.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.084104 restraints weight = 81654.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.084112 restraints weight = 72004.801| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31836 Z= 0.243 Angle : 0.650 11.581 43444 Z= 0.329 Chirality : 0.045 0.254 5015 Planarity : 0.004 0.077 5513 Dihedral : 5.127 52.982 4216 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.70 % Allowed : 13.70 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.21 (0.14), residues: 3845 helix: 1.62 (0.20), residues: 691 sheet: -0.25 (0.15), residues: 1041 loop : -0.64 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 56 TYR 0.022 0.002 TYR A 870 PHE 0.025 0.002 PHE B1086 TRP 0.021 0.002 TRP C 152 HIS 0.008 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (31731) covalent geometry : angle 0.63651 / 0.33 (43180) SS BOND : bond 0.00519 / 0.28 ( 51) SS BOND : angle 1.08954 / 0.70 ( 102) hydrogen bonds : bond 0.04200 / 2.81 ( 1272) hydrogen bonds : angle 5.86625 / 4.13 ( 3480) link_BETA1-4 : bond 0.00268 / 0.18 ( 12) link_BETA1-4 : angle 1.13317 / 0.70 ( 36) link_NAG-ASN : bond 0.00560 / 0.40 ( 42) link_NAG-ASN : angle 2.33616 / 1.68 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 120 time to evaluate : 1.221 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: B 267 LEU cc_start: 0.8998 (mt) cc_final: 0.8651 (mp) REVERT: B 420 TYR cc_start: 0.5384 (t80) cc_final: 0.4691 (t80) REVERT: B 579 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8504 (pt) REVERT: B 612 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8551 (p) REVERT: B 696 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 805 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8770 (p0) REVERT: B 855 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8147 (pp) REVERT: B 1143 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7803 (m-30) REVERT: A 177 MET cc_start: 0.1020 (mtt) cc_final: 0.0282 (mtp) REVERT: A 689 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9246 (tp) REVERT: C 24 LEU cc_start: 0.2838 (OUTLIER) cc_final: 0.2543 (tt) REVERT: C 62 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8332 (p) REVERT: C 118 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7898 (mt) REVERT: C 120 VAL cc_start: 0.7974 (m) cc_final: 0.7721 (p) REVERT: C 177 MET cc_start: 0.0514 (ttt) cc_final: 0.0048 (ttt) REVERT: C 976 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8042 (t0) REVERT: C 1026 MET cc_start: 0.9117 (tpp) cc_final: 0.8753 (mmm) REVERT: C 1031 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8834 (mt) REVERT: H 81 MET cc_start: 0.3098 (tmm) cc_final: 0.1461 (tmm) REVERT: D 48 MET cc_start: -0.0213 (ptm) cc_final: -0.1003 (ptm) REVERT: E 4 MET cc_start: 0.2969 (tpt) cc_final: 0.2523 (tpp) REVERT: G 4 MET cc_start: 0.5253 (mmm) cc_final: 0.4698 (mtt) outliers start: 124 outliers final: 89 residues processed: 229 average time/residue: 0.1649 time to fit residues: 65.0782 Evaluate side-chains 214 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 113 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 805 ASP Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1038 ASP Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1143 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 303 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 226 optimal weight: 6.9990 chunk 325 optimal weight: 0.0010 chunk 86 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 125 optimal weight: 0.0770 chunk 257 optimal weight: 0.1980 overall best weight: 0.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 904 ASN A 367 ASN A 434 ASN A 898 GLN C 898 GLN C 952 ASN C1045 HIS C1080 HIS E 91 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.120918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.089202 restraints weight = 166062.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.087963 restraints weight = 127043.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.088091 restraints weight = 101820.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.088324 restraints weight = 87569.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.088349 restraints weight = 79496.272| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31836 Z= 0.099 Angle : 0.551 11.121 43444 Z= 0.276 Chirality : 0.043 0.187 5015 Planarity : 0.004 0.070 5513 Dihedral : 4.556 53.165 4212 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.70 % Allowed : 15.94 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.14 (0.14), residues: 3845 helix: 2.02 (0.20), residues: 691 sheet: 0.02 (0.16), residues: 1023 loop : -0.49 (0.14), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 325 TYR 0.017 0.001 TYR A 366 PHE 0.020 0.001 PHE C 201 TRP 0.018 0.001 TRP C 152 HIS 0.006 0.001 HIS C1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (31731) covalent geometry : angle 0.54294 / 0.27 (43180) SS BOND : bond 0.00342 / 0.17 ( 51) SS BOND : angle 0.86473 / 0.56 ( 102) hydrogen bonds : bond 0.03402 / 2.29 ( 1272) hydrogen bonds : angle 5.30362 / 3.75 ( 3480) link_BETA1-4 : bond 0.00354 / 0.24 ( 12) link_BETA1-4 : angle 0.84642 / 0.52 ( 36) link_NAG-ASN : bond 0.00304 / 0.20 ( 42) link_NAG-ASN : angle 1.73240 / 1.22 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 147 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 PHE cc_start: 0.5983 (m-80) cc_final: 0.4843 (m-80) REVERT: B 267 LEU cc_start: 0.8970 (mt) cc_final: 0.8612 (mp) REVERT: B 420 TYR cc_start: 0.5005 (t80) cc_final: 0.4366 (t80) REVERT: B 612 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 855 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8138 (pp) REVERT: A 177 MET cc_start: 0.1240 (mtt) cc_final: 0.0413 (mtp) REVERT: C 62 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8443 (p) REVERT: C 118 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7876 (mt) REVERT: C 120 VAL cc_start: 0.8179 (m) cc_final: 0.7962 (p) REVERT: C 177 MET cc_start: -0.1421 (ttt) cc_final: -0.1785 (ttt) REVERT: C 893 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9182 (mt) REVERT: C 976 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8055 (t0) REVERT: H 81 MET cc_start: 0.3043 (tmm) cc_final: 0.1250 (tmm) REVERT: L 49 ILE cc_start: 0.7092 (mp) cc_final: 0.6797 (mm) REVERT: D 48 MET cc_start: 0.0540 (ptm) cc_final: -0.0473 (ptm) REVERT: E 4 MET cc_start: 0.2676 (tpt) cc_final: 0.2188 (tpp) REVERT: G 4 MET cc_start: 0.3627 (mmm) cc_final: 0.3206 (mtt) outliers start: 57 outliers final: 40 residues processed: 193 average time/residue: 0.1690 time to fit residues: 55.5257 Evaluate side-chains 167 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 205 optimal weight: 0.3980 chunk 48 optimal weight: 20.0000 chunk 353 optimal weight: 30.0000 chunk 158 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 237 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN C 99 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1045 HIS ** 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 = 0.4188 r_free = 0.4188 target = 0.113128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084593 restraints weight = 148643.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.081871 restraints weight = 102173.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.082318 restraints weight = 89114.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.082494 restraints weight = 71761.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.082602 restraints weight = 65643.507| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 31836 Z= 0.258 Angle : 0.647 9.796 43444 Z= 0.328 Chirality : 0.045 0.258 5015 Planarity : 0.004 0.077 5513 Dihedral : 4.806 44.945 4210 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.18 % Allowed : 16.21 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.06 (0.14), residues: 3845 helix: 1.75 (0.20), residues: 697 sheet: -0.11 (0.16), residues: 1035 loop : -0.58 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1016 TYR 0.031 0.002 TYR C 486 PHE 0.028 0.002 PHE B1086 TRP 0.024 0.002 TRP H 116 HIS 0.008 0.001 HIS C1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.26 (31731) covalent geometry : angle 0.63472 / 0.33 (43180) SS BOND : bond 0.00498 / 0.27 ( 51) SS BOND : angle 1.07654 / 0.71 ( 102) hydrogen bonds : bond 0.04024 / 2.70 ( 1272) hydrogen bonds : angle 5.63584 / 3.98 ( 3480) link_BETA1-4 : bond 0.00292 / 0.20 ( 12) link_BETA1-4 : angle 1.08580 / 0.67 ( 36) link_NAG-ASN : bond 0.00537 / 0.38 ( 42) link_NAG-ASN : angle 2.24233 / 1.61 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 117 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 267 LEU cc_start: 0.9040 (mt) cc_final: 0.8700 (mp) REVERT: B 284 ASP cc_start: 0.7551 (t0) cc_final: 0.7115 (t0) REVERT: B 420 TYR cc_start: 0.4520 (t80) cc_final: 0.4283 (t80) REVERT: B 612 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 855 LEU cc_start: 0.8652 (mp) cc_final: 0.8183 (pp) REVERT: A 65 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: A 177 MET cc_start: 0.0749 (mtt) cc_final: 0.0380 (mtt) REVERT: A 745 GLU cc_start: 0.8626 (pm20) cc_final: 0.8313 (pm20) REVERT: C 120 VAL cc_start: 0.8161 (m) cc_final: 0.7917 (p) REVERT: C 486 TYR cc_start: 0.2377 (OUTLIER) cc_final: 0.1746 (t80) REVERT: C 737 MET cc_start: 0.7901 (ppp) cc_final: 0.7593 (tmm) REVERT: C 976 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.7979 (t0) REVERT: H 81 MET cc_start: 0.3325 (tmm) cc_final: 0.2686 (tmm) REVERT: D 48 MET cc_start: 0.1161 (ptm) cc_final: 0.0109 (ptm) REVERT: D 55 PHE cc_start: 0.1346 (t80) cc_final: 0.1115 (t80) REVERT: E 4 MET cc_start: 0.2777 (tpt) cc_final: 0.2235 (tpp) REVERT: G 4 MET cc_start: 0.2402 (mmm) cc_final: 0.2065 (mtt) outliers start: 73 outliers final: 60 residues processed: 182 average time/residue: 0.1708 time to fit residues: 53.7700 Evaluate side-chains 174 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 110 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1038 ASP Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 486 TYR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 192 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 384 optimal weight: 30.0000 chunk 199 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 351 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 195 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN C 99 ASN ** C 776 GLN ** 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 = 0.4284 r_free = 0.4284 target = 0.119526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.085272 restraints weight = 164817.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.085873 restraints weight = 114422.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.085835 restraints weight = 88266.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.085833 restraints weight = 71876.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.085906 restraints weight = 70510.790| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31836 Z= 0.136 Angle : 0.581 12.420 43444 Z= 0.290 Chirality : 0.043 0.211 5015 Planarity : 0.004 0.074 5513 Dihedral : 4.676 43.669 4210 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.73 % Allowed : 16.69 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3845 helix: 1.96 (0.20), residues: 691 sheet: -0.05 (0.16), residues: 1009 loop : -0.58 (0.14), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1016 TYR 0.031 0.001 TYR C 486 PHE 0.017 0.001 PHE B 140 TRP 0.020 0.001 TRP H 116 HIS 0.005 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (31731) covalent geometry : angle 0.57020 / 0.29 (43180) SS BOND : bond 0.00405 / 0.22 ( 51) SS BOND : angle 1.18389 / 0.75 ( 102) hydrogen bonds : bond 0.03578 / 2.40 ( 1272) hydrogen bonds : angle 5.37607 / 3.79 ( 3480) link_BETA1-4 : bond 0.00254 / 0.17 ( 12) link_BETA1-4 : angle 0.93118 / 0.58 ( 36) link_NAG-ASN : bond 0.00274 / 0.19 ( 42) link_NAG-ASN : angle 1.89385 / 1.36 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 122 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.8899 (tt) cc_final: 0.8527 (tp) REVERT: B 158 ARG cc_start: 0.6972 (mtt-85) cc_final: 0.6757 (mpp80) REVERT: B 267 LEU cc_start: 0.8932 (mt) cc_final: 0.8530 (mp) REVERT: B 284 ASP cc_start: 0.7498 (t0) cc_final: 0.7054 (t0) REVERT: B 420 TYR cc_start: 0.5093 (t80) cc_final: 0.4382 (t80) REVERT: B 579 LEU cc_start: 0.8808 (mm) cc_final: 0.8406 (pt) REVERT: B 612 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8530 (p) REVERT: B 855 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8162 (pp) REVERT: A 177 MET cc_start: 0.1451 (mtt) cc_final: 0.0560 (mtp) REVERT: C 177 MET cc_start: 0.0135 (ttt) cc_final: -0.0071 (ttt) REVERT: C 694 MET cc_start: 0.8168 (tpp) cc_final: 0.7882 (mmm) REVERT: C 893 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9208 (mt) REVERT: C 1047 MET cc_start: 0.8233 (ptp) cc_final: 0.7936 (ptp) REVERT: H 81 MET cc_start: 0.3165 (tmm) cc_final: 0.1559 (tmm) REVERT: D 48 MET cc_start: 0.0438 (ptm) cc_final: -0.0418 (ptm) REVERT: E 4 MET cc_start: 0.3029 (tpt) cc_final: 0.2564 (tpp) REVERT: G 4 MET cc_start: 0.4214 (mmm) cc_final: 0.3849 (mtt) outliers start: 58 outliers final: 49 residues processed: 169 average time/residue: 0.1721 time to fit residues: 49.8552 Evaluate side-chains 170 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 132 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 300 optimal weight: 8.9990 chunk 274 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 382 optimal weight: 50.0000 chunk 138 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.113556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.084903 restraints weight = 149366.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.082772 restraints weight = 100483.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.082782 restraints weight = 91066.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.082992 restraints weight = 72340.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.083202 restraints weight = 63502.961| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31836 Z= 0.200 Angle : 0.623 15.591 43444 Z= 0.311 Chirality : 0.044 0.226 5015 Planarity : 0.004 0.073 5513 Dihedral : 4.755 43.821 4210 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.94 % Allowed : 16.54 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.08 (0.14), residues: 3845 helix: 1.78 (0.20), residues: 698 sheet: -0.10 (0.16), residues: 1025 loop : -0.63 (0.14), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.031 0.002 TYR C 486 PHE 0.037 0.002 PHE C 453 TRP 0.018 0.001 TRP C 152 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (31731) covalent geometry : angle 0.61088 / 0.31 (43180) SS BOND : bond 0.00453 / 0.25 ( 51) SS BOND : angle 1.31809 / 0.83 ( 102) hydrogen bonds : bond 0.03807 / 2.56 ( 1272) hydrogen bonds : angle 5.48481 / 3.88 ( 3480) link_BETA1-4 : bond 0.00248 / 0.17 ( 12) link_BETA1-4 : angle 0.99446 / 0.62 ( 36) link_NAG-ASN : bond 0.00404 / 0.29 ( 42) link_NAG-ASN : angle 2.07857 / 1.50 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5227.51 seconds wall clock time: 91 minutes 27.01 seconds (5487.01 seconds total)