Starting phenix.real_space_refine on Fri Mar 6 13:14:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zr9_14887/03_2026/7zr9_14887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr9_14887/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zr9_14887/03_2026/7zr9_14887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr9_14887/03_2026/7zr9_14887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zr9_14887/03_2026/7zr9_14887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr9_14887/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.39, per 1000 atoms: 0.24 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: 3.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.60 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: 8.12 Time building geometry restraints manager: 4.08 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: 18518 17.85 - 35.71: 810 35.71 - 53.56: 162 53.56 - 71.41: 42 71.41 - 89.26: 18 Dihedral angle restraints: 19550 sinusoidal: 8264 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 19547 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: 2.730 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.570 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 10.861 89.264 12163 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 covalent geometry : bond 0.00636 (31731) covalent geometry : angle 0.86437 (43180) SS BOND : bond 0.06648 ( 51) SS BOND : angle 5.51113 ( 102) hydrogen bonds : bond 0.13466 ( 1272) hydrogen bonds : angle 7.13014 ( 3480) link_BETA1-4 : bond 0.00305 ( 12) link_BETA1-4 : angle 1.00810 ( 36) link_NAG-ASN : bond 0.00343 ( 42) link_NAG-ASN : angle 1.87812 ( 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 : 0.952 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: 0.1948 time to fit residues: 130.2700 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 : 0.848 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 C 962 GLN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 91 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.122184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.089896 restraints weight = 167362.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.087989 restraints weight = 134158.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088459 restraints weight = 109579.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.088521 restraints weight = 86573.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.088711 restraints weight = 78167.253| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31836 Z= 0.204 Angle : 0.627 9.221 43444 Z= 0.324 Chirality : 0.045 0.214 5015 Planarity : 0.004 0.075 5513 Dihedral : 6.707 59.798 5360 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 2.03 % Allowed : 8.99 % Favored : 88.99 % 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: 0.05 (0.13), residues: 3845 helix: 1.45 (0.19), residues: 704 sheet: 0.09 (0.15), residues: 1040 loop : -0.43 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 574 TYR 0.041 0.002 TYR A 266 PHE 0.023 0.002 PHE A 135 TRP 0.016 0.001 TRP A 883 HIS 0.006 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00441 (31731) covalent geometry : angle 0.61420 (43180) SS BOND : bond 0.00524 ( 51) SS BOND : angle 1.28935 ( 102) hydrogen bonds : bond 0.04276 ( 1272) hydrogen bonds : angle 5.87083 ( 3480) link_BETA1-4 : bond 0.00293 ( 12) link_BETA1-4 : angle 1.15505 ( 36) link_NAG-ASN : bond 0.00442 ( 42) link_NAG-ASN : angle 2.08237 ( 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 254 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 186 time to evaluate : 1.210 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: B 135 PHE cc_start: 0.5331 (m-80) cc_final: 0.5050 (m-10) REVERT: B 177 MET cc_start: 0.1864 (ttm) cc_final: 0.1601 (ttp) REVERT: B 267 LEU cc_start: 0.9140 (mt) cc_final: 0.8814 (mp) REVERT: B 384 LEU cc_start: 0.8251 (mt) cc_final: 0.7752 (mt) REVERT: B 420 TYR cc_start: 0.4976 (t80) cc_final: 0.4383 (t80) REVERT: B 612 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8353 (p) REVERT: B 696 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7767 (mt) REVERT: B 760 LEU cc_start: 0.9620 (mt) cc_final: 0.9388 (mt) REVERT: B 855 LEU cc_start: 0.8647 (mp) cc_final: 0.8292 (pp) REVERT: A 65 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: A 87 ASN cc_start: 0.8890 (t0) cc_final: 0.8573 (t0) REVERT: A 177 MET cc_start: 0.4288 (ttm) cc_final: 0.3414 (mtp) REVERT: A 799 PHE cc_start: 0.8367 (m-10) cc_final: 0.8118 (m-10) REVERT: C 87 ASN cc_start: 0.8646 (m-40) cc_final: 0.7537 (m110) REVERT: C 118 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8153 (mt) REVERT: C 177 MET cc_start: 0.1819 (ttm) cc_final: -0.1268 (tpp) REVERT: C 203 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8768 (pt) REVERT: C 263 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.5890 (m-80) REVERT: C 266 TYR cc_start: 0.7557 (m-80) cc_final: 0.7308 (m-10) REVERT: C 899 MET cc_start: 0.9093 (tpp) cc_final: 0.8797 (tpp) REVERT: C 959 LEU cc_start: 0.9492 (tp) cc_final: 0.9286 (tp) REVERT: H 39 GLN cc_start: 0.6095 (tt0) cc_final: 0.5845 (tp40) REVERT: H 46 GLU cc_start: 0.3945 (OUTLIER) cc_final: 0.3522 (pt0) REVERT: H 63 LYS cc_start: 0.1393 (tttt) cc_final: 0.1154 (ptmt) REVERT: H 81 MET cc_start: 0.4463 (tmm) cc_final: 0.4002 (tmm) REVERT: D 48 MET cc_start: 0.2236 (OUTLIER) cc_final: 0.0501 (ptm) REVERT: E 4 MET cc_start: 0.4734 (mmt) cc_final: 0.4093 (mmt) REVERT: G 4 MET cc_start: 0.3763 (mmm) cc_final: 0.3370 (mtt) outliers start: 68 outliers final: 33 residues processed: 241 average time/residue: 0.1763 time to fit residues: 70.6814 Evaluate side-chains 172 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 769 VAL Chi-restraints excluded: chain B residue 881 SER 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 373 THR Chi-restraints excluded: chain A residue 760 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: 4.9990 chunk 11 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN ** 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 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 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 = 0.4303 r_free = 0.4303 target = 0.120962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.088484 restraints weight = 166831.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.086643 restraints weight = 134673.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.087106 restraints weight = 111185.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.086931 restraints weight = 91492.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.087081 restraints weight = 84352.805| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31836 Z= 0.216 Angle : 0.616 12.585 43444 Z= 0.316 Chirality : 0.044 0.307 5015 Planarity : 0.004 0.054 5513 Dihedral : 6.194 59.934 5350 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.87 % Allowed : 9.94 % Favored : 87.19 % 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: 0.08 (0.13), residues: 3845 helix: 1.62 (0.20), residues: 711 sheet: 0.08 (0.15), residues: 1061 loop : -0.47 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 214 TYR 0.019 0.002 TYR B1064 PHE 0.023 0.002 PHE A 140 TRP 0.023 0.002 TRP A 104 HIS 0.007 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00471 (31731) covalent geometry : angle 0.60111 (43180) SS BOND : bond 0.00507 ( 51) SS BOND : angle 1.65764 ( 102) hydrogen bonds : bond 0.04233 ( 1272) hydrogen bonds : angle 5.74576 ( 3480) link_BETA1-4 : bond 0.00284 ( 12) link_BETA1-4 : angle 1.17145 ( 36) link_NAG-ASN : bond 0.00443 ( 42) link_NAG-ASN : angle 2.08437 ( 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 239 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 143 time to evaluate : 1.049 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: 0.2214 (ttm) cc_final: 0.1960 (ttt) REVERT: B 267 LEU cc_start: 0.9080 (mt) cc_final: 0.8769 (mp) REVERT: B 284 ASP cc_start: 0.7812 (t0) cc_final: 0.7280 (t0) REVERT: B 420 TYR cc_start: 0.5065 (t80) cc_final: 0.4419 (t80) REVERT: B 612 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8414 (p) REVERT: B 696 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7766 (mt) REVERT: B 805 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8769 (p0) REVERT: A 65 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: A 177 MET cc_start: 0.4643 (ttm) cc_final: 0.4061 (mtp) REVERT: C 24 LEU cc_start: 0.1384 (OUTLIER) cc_final: 0.0891 (tp) REVERT: C 87 ASN cc_start: 0.8630 (m-40) cc_final: 0.8403 (m110) REVERT: C 118 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7992 (mt) REVERT: C 177 MET cc_start: 0.1985 (ttm) cc_final: -0.1425 (tpp) REVERT: C 263 TYR cc_start: 0.6616 (OUTLIER) cc_final: 0.5814 (m-80) REVERT: C 311 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: C 899 MET cc_start: 0.9084 (tpp) cc_final: 0.8774 (tpp) REVERT: C 976 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8124 (t70) REVERT: D 48 MET cc_start: 0.1405 (mtm) cc_final: 0.0989 (ptm) REVERT: E 4 MET cc_start: 0.4208 (mmt) cc_final: 0.3404 (tpp) REVERT: G 4 MET cc_start: 0.4515 (mmm) cc_final: 0.4088 (mtt) outliers start: 96 outliers final: 57 residues processed: 229 average time/residue: 0.1629 time to fit residues: 64.2347 Evaluate side-chains 190 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 124 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 7.9990 chunk 305 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 334 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 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** C 952 ASN ** 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 = 0.4320 r_free = 0.4320 target = 0.121823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.089344 restraints weight = 165490.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.088062 restraints weight = 142381.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.088203 restraints weight = 108420.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.088273 restraints weight = 85031.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.088322 restraints weight = 80000.067| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31836 Z= 0.133 Angle : 0.536 10.572 43444 Z= 0.273 Chirality : 0.043 0.237 5015 Planarity : 0.004 0.055 5513 Dihedral : 5.692 59.832 5350 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.51 % Allowed : 10.78 % Favored : 86.72 % 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: 0.26 (0.14), residues: 3845 helix: 1.93 (0.20), residues: 703 sheet: 0.18 (0.15), residues: 1034 loop : -0.40 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.015 0.001 TYR A 366 PHE 0.017 0.001 PHE A 799 TRP 0.027 0.001 TRP A 104 HIS 0.006 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00292 (31731) covalent geometry : angle 0.52533 (43180) SS BOND : bond 0.00386 ( 51) SS BOND : angle 0.95978 ( 102) hydrogen bonds : bond 0.03667 ( 1272) hydrogen bonds : angle 5.38486 ( 3480) link_BETA1-4 : bond 0.00248 ( 12) link_BETA1-4 : angle 1.01030 ( 36) link_NAG-ASN : bond 0.00268 ( 42) link_NAG-ASN : angle 1.86240 ( 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 227 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 143 time to evaluate : 1.171 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: 0.1383 (ttm) cc_final: 0.0992 (ttt) REVERT: B 267 LEU cc_start: 0.9093 (mt) cc_final: 0.8797 (mp) REVERT: B 420 TYR cc_start: 0.4938 (t80) cc_final: 0.4236 (t80) REVERT: B 612 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8414 (p) REVERT: B 696 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7791 (mt) REVERT: B 855 LEU cc_start: 0.8626 (mp) cc_final: 0.8262 (pp) REVERT: A 65 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: A 177 MET cc_start: 0.4556 (ttm) cc_final: 0.3852 (mtp) REVERT: A 704 TYR cc_start: 0.8894 (t80) cc_final: 0.8444 (t80) REVERT: A 985 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8227 (tp30) REVERT: C 24 LEU cc_start: 0.1165 (OUTLIER) cc_final: 0.0699 (tp) REVERT: C 87 ASN cc_start: 0.8591 (m-40) cc_final: 0.8374 (m110) REVERT: C 118 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7923 (mt) REVERT: C 120 VAL cc_start: 0.8009 (m) cc_final: 0.7714 (p) REVERT: C 177 MET cc_start: 0.1651 (ttm) cc_final: -0.1649 (tpp) REVERT: C 263 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5691 (m-80) REVERT: C 311 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: C 893 ILE cc_start: 0.9558 (OUTLIER) cc_final: 0.9259 (mt) REVERT: C 899 MET cc_start: 0.9146 (tpp) cc_final: 0.8805 (tpp) REVERT: C 976 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8157 (t0) REVERT: H 81 MET cc_start: 0.3939 (tmm) cc_final: 0.2757 (tmm) REVERT: D 32 TYR cc_start: 0.1960 (t80) cc_final: 0.1757 (t80) REVERT: D 48 MET cc_start: 0.1597 (mtm) cc_final: 0.1139 (ptm) REVERT: G 4 MET cc_start: 0.4606 (mmm) cc_final: 0.4064 (mtt) outliers start: 84 outliers final: 49 residues processed: 212 average time/residue: 0.1735 time to fit residues: 62.5077 Evaluate side-chains 184 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 125 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 880 THR 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 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 985 GLU 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 311 GLN 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 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 893 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 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: 0.7980 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: 9.9990 chunk 178 optimal weight: 6.9990 chunk 132 optimal weight: 0.1980 chunk 48 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN A 125 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.119628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.087263 restraints weight = 167346.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.084993 restraints weight = 134395.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.085087 restraints weight = 125965.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.085022 restraints weight = 103521.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.085084 restraints weight = 86912.478| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 31836 Z= 0.239 Angle : 0.625 10.665 43444 Z= 0.319 Chirality : 0.044 0.236 5015 Planarity : 0.004 0.055 5513 Dihedral : 5.895 59.382 5350 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.31 % Allowed : 11.13 % Favored : 85.55 % 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: 0.05 (0.14), residues: 3845 helix: 1.68 (0.20), residues: 704 sheet: 0.03 (0.15), residues: 1037 loop : -0.50 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 997 TYR 0.019 0.002 TYR C 263 PHE 0.026 0.002 PHE C1086 TRP 0.026 0.002 TRP A 104 HIS 0.009 0.001 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00524 (31731) covalent geometry : angle 0.61158 (43180) SS BOND : bond 0.00521 ( 51) SS BOND : angle 1.08734 ( 102) hydrogen bonds : bond 0.04136 ( 1272) hydrogen bonds : angle 5.69658 ( 3480) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 1.27659 ( 36) link_NAG-ASN : bond 0.00556 ( 42) link_NAG-ASN : angle 2.28157 ( 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 238 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 127 time to evaluate : 1.100 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: B 177 MET cc_start: 0.2190 (ttm) cc_final: 0.1927 (ttt) REVERT: B 267 LEU cc_start: 0.9072 (mt) cc_final: 0.8777 (mp) REVERT: B 284 ASP cc_start: 0.7818 (t0) cc_final: 0.7302 (t0) REVERT: B 420 TYR cc_start: 0.5178 (t80) cc_final: 0.4433 (t80) REVERT: B 612 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8488 (p) REVERT: B 696 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8014 (mt) REVERT: B 805 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8800 (p0) REVERT: B 855 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8216 (pp) REVERT: A 65 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: A 696 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8691 (mt) REVERT: A 985 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: C 24 LEU cc_start: 0.2103 (OUTLIER) cc_final: 0.1787 (tp) REVERT: C 62 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8544 (p) REVERT: C 118 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7940 (mt) REVERT: C 177 MET cc_start: 0.1281 (ttm) cc_final: -0.1810 (mmp) REVERT: C 263 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: C 311 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8202 (mm110) REVERT: C 976 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8223 (t0) REVERT: C 1031 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8902 (mt) REVERT: H 81 MET cc_start: 0.3320 (tmm) cc_final: 0.2342 (tmm) REVERT: D 32 TYR cc_start: 0.2017 (t80) cc_final: 0.1810 (t80) REVERT: D 48 MET cc_start: 0.1090 (mtm) cc_final: 0.0775 (ptm) REVERT: G 4 MET cc_start: 0.5141 (mmm) cc_final: 0.4528 (mtt) outliers start: 111 outliers final: 71 residues processed: 221 average time/residue: 0.1681 time to fit residues: 64.1834 Evaluate side-chains 198 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 113 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL 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 198 ASP 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 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 731 THR Chi-restraints excluded: chain B residue 737 MET 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 931 ILE 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 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 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 568 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 696 LEU 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 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 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 311 GLN 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 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 193 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 343 optimal weight: 20.0000 chunk 376 optimal weight: 9.9990 chunk 194 optimal weight: 0.4980 chunk 122 optimal weight: 10.0000 chunk 329 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN B 904 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.119813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.087269 restraints weight = 165515.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.084633 restraints weight = 133151.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.084989 restraints weight = 121768.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.085221 restraints weight = 86946.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.085260 restraints weight = 78534.373| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31836 Z= 0.192 Angle : 0.575 10.317 43444 Z= 0.293 Chirality : 0.043 0.234 5015 Planarity : 0.004 0.053 5513 Dihedral : 5.716 59.567 5350 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.19 % Allowed : 12.36 % Favored : 84.45 % 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: 1.84 (0.20), residues: 698 sheet: 0.02 (0.15), residues: 1015 loop : -0.52 (0.14), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 997 TYR 0.020 0.001 TYR C 486 PHE 0.018 0.002 PHE C1086 TRP 0.020 0.001 TRP A 104 HIS 0.007 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00419 (31731) covalent geometry : angle 0.56255 (43180) SS BOND : bond 0.00445 ( 51) SS BOND : angle 0.99832 ( 102) hydrogen bonds : bond 0.03859 ( 1272) hydrogen bonds : angle 5.55839 ( 3480) link_BETA1-4 : bond 0.00265 ( 12) link_BETA1-4 : angle 1.10254 ( 36) link_NAG-ASN : bond 0.00401 ( 42) link_NAG-ASN : angle 2.09125 ( 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 234 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 127 time to evaluate : 1.129 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: B 177 MET cc_start: 0.2267 (ttm) cc_final: 0.1852 (ttt) REVERT: B 267 LEU cc_start: 0.9075 (mt) cc_final: 0.8777 (mp) REVERT: B 284 ASP cc_start: 0.7707 (t0) cc_final: 0.7210 (t0) REVERT: B 420 TYR cc_start: 0.5150 (t80) cc_final: 0.4380 (t80) REVERT: B 612 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8490 (p) REVERT: B 696 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8003 (mt) REVERT: B 855 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8205 (pp) REVERT: A 65 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: A 177 MET cc_start: 0.5181 (mtp) cc_final: 0.4930 (mtp) REVERT: A 696 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8685 (mt) REVERT: C 24 LEU cc_start: 0.2229 (OUTLIER) cc_final: 0.1794 (tt) REVERT: C 62 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8565 (p) REVERT: C 118 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7908 (mt) REVERT: C 177 MET cc_start: 0.2002 (ttm) cc_final: -0.0993 (mmp) REVERT: C 263 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: C 311 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8149 (mm110) REVERT: C 562 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8170 (p90) REVERT: C 899 MET cc_start: 0.8984 (tpp) cc_final: 0.8775 (tpp) REVERT: C 976 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8194 (t0) REVERT: H 81 MET cc_start: 0.3280 (tmm) cc_final: 0.2223 (tmm) REVERT: D 48 MET cc_start: 0.0828 (mtm) cc_final: 0.0615 (ptm) REVERT: G 4 MET cc_start: 0.5441 (mmm) cc_final: 0.5003 (mtt) outliers start: 107 outliers final: 71 residues processed: 216 average time/residue: 0.1720 time to fit residues: 63.4262 Evaluate side-chains 197 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 114 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL 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 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 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 778 VAL Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 855 LEU 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 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 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 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 696 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 897 MET 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 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 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 663 ILE 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 1005 VAL 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: 6.9990 chunk 304 optimal weight: 0.8980 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: 0.9990 chunk 138 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.119618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.088271 restraints weight = 166412.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.085469 restraints weight = 139508.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.086241 restraints weight = 121452.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.086422 restraints weight = 84410.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.086465 restraints weight = 75731.380| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31836 Z= 0.185 Angle : 0.578 10.004 43444 Z= 0.294 Chirality : 0.043 0.231 5015 Planarity : 0.004 0.055 5513 Dihedral : 5.599 57.005 5350 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.34 % Allowed : 12.51 % Favored : 84.15 % 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: 0.03 (0.14), residues: 3845 helix: 1.82 (0.20), residues: 704 sheet: -0.03 (0.15), residues: 1028 loop : -0.53 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 354 TYR 0.024 0.001 TYR A 870 PHE 0.018 0.002 PHE B1086 TRP 0.017 0.001 TRP A 104 HIS 0.007 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00406 (31731) covalent geometry : angle 0.56511 (43180) SS BOND : bond 0.00475 ( 51) SS BOND : angle 1.17375 ( 102) hydrogen bonds : bond 0.03819 ( 1272) hydrogen bonds : angle 5.51578 ( 3480) link_BETA1-4 : bond 0.00244 ( 12) link_BETA1-4 : angle 1.08736 ( 36) link_NAG-ASN : bond 0.00384 ( 42) link_NAG-ASN : angle 2.07116 ( 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 237 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 125 time to evaluate : 0.999 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 177 MET cc_start: 0.0174 (ttm) cc_final: -0.0157 (ttt) REVERT: B 267 LEU cc_start: 0.9069 (mt) cc_final: 0.8770 (mp) REVERT: B 284 ASP cc_start: 0.7753 (t0) cc_final: 0.7288 (t0) REVERT: B 420 TYR cc_start: 0.4902 (t80) cc_final: 0.4263 (t80) REVERT: B 579 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8449 (pt) REVERT: B 612 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8484 (p) REVERT: B 696 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8029 (mt) REVERT: B 855 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8246 (pp) REVERT: A 65 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: C 24 LEU cc_start: 0.2300 (OUTLIER) cc_final: 0.2084 (tt) REVERT: C 62 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8361 (p) REVERT: C 118 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7908 (mt) REVERT: C 120 VAL cc_start: 0.8143 (m) cc_final: 0.7901 (p) REVERT: C 177 MET cc_start: -0.0357 (ttm) cc_final: -0.3167 (mmp) REVERT: C 263 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: C 311 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8248 (mm110) REVERT: C 976 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8080 (t0) REVERT: C 1031 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9043 (mt) REVERT: H 81 MET cc_start: 0.3323 (tmm) cc_final: 0.2101 (tmm) REVERT: G 4 MET cc_start: 0.4127 (mmm) cc_final: 0.3458 (mtt) outliers start: 112 outliers final: 83 residues processed: 220 average time/residue: 0.1668 time to fit residues: 63.2675 Evaluate side-chains 208 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 113 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 120 VAL 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 263 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 447 ASN 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 855 LEU Chi-restraints excluded: chain B residue 885 PHE 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 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 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 617 VAL 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 778 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 897 MET 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 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 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 486 TYR 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 717 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 1005 VAL Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1129 ILE 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: 2.9990 chunk 145 optimal weight: 0.1980 chunk 204 optimal weight: 0.8980 chunk 226 optimal weight: 8.9990 chunk 325 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 34 optimal weight: 20.0000 chunk 180 optimal weight: 0.7980 chunk 234 optimal weight: 9.9990 chunk 125 optimal weight: 0.0470 chunk 257 optimal weight: 8.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN A 434 ASN A 898 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.121253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.090001 restraints weight = 166157.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.087459 restraints weight = 129089.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.087932 restraints weight = 112787.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.087599 restraints weight = 87497.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.087815 restraints weight = 79259.309| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3527 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= 0.097 Angle : 0.531 14.843 43444 Z= 0.266 Chirality : 0.042 0.192 5015 Planarity : 0.004 0.073 5513 Dihedral : 5.018 51.936 5348 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.97 % Allowed : 14.00 % Favored : 84.03 % 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: 0.22 (0.14), residues: 3845 helix: 1.99 (0.20), residues: 705 sheet: 0.16 (0.16), residues: 1010 loop : -0.46 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.021 0.001 TYR C 486 PHE 0.014 0.001 PHE B 140 TRP 0.018 0.001 TRP A 104 HIS 0.006 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00209 (31731) covalent geometry : angle 0.52146 (43180) SS BOND : bond 0.00343 ( 51) SS BOND : angle 0.93331 ( 102) hydrogen bonds : bond 0.03359 ( 1272) hydrogen bonds : angle 5.18727 ( 3480) link_BETA1-4 : bond 0.00292 ( 12) link_BETA1-4 : angle 0.92496 ( 36) link_NAG-ASN : bond 0.00244 ( 42) link_NAG-ASN : angle 1.74622 ( 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 213 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 147 time to evaluate : 1.134 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 177 MET cc_start: 0.1902 (ttm) cc_final: 0.1483 (ttt) REVERT: B 267 LEU cc_start: 0.9034 (mt) cc_final: 0.8691 (mp) REVERT: B 420 TYR cc_start: 0.4852 (t80) cc_final: 0.4095 (t80) REVERT: B 579 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8580 (pt) REVERT: B 612 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8465 (p) REVERT: B 855 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8218 (pp) REVERT: A 866 MET cc_start: 0.9020 (mtt) cc_final: 0.8790 (ptp) REVERT: C 62 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8398 (p) REVERT: C 118 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7854 (mt) REVERT: C 120 VAL cc_start: 0.8042 (m) cc_final: 0.7821 (p) REVERT: C 177 MET cc_start: 0.1831 (ttm) cc_final: -0.1151 (mmp) REVERT: C 266 TYR cc_start: 0.7518 (m-80) cc_final: 0.7225 (m-10) REVERT: C 562 PHE cc_start: 0.8561 (p90) cc_final: 0.8007 (p90) REVERT: C 976 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8046 (t0) REVERT: C 1026 MET cc_start: 0.9076 (tpp) cc_final: 0.8804 (tpp) REVERT: H 81 MET cc_start: 0.3427 (tmm) cc_final: 0.2321 (tmm) REVERT: D 48 MET cc_start: -0.0269 (ptm) cc_final: -0.0657 (ptm) REVERT: G 4 MET cc_start: 0.5068 (mmm) cc_final: 0.4630 (mtt) outliers start: 66 outliers final: 43 residues processed: 196 average time/residue: 0.1735 time to fit residues: 58.1181 Evaluate side-chains 180 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR 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 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 274 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 897 MET 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 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 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER 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: 0.0870 chunk 48 optimal weight: 20.0000 chunk 353 optimal weight: 20.0000 chunk 158 optimal weight: 0.0020 chunk 226 optimal weight: 10.0000 chunk 237 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.0368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 904 ASN A 537 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 = 0.4306 r_free = 0.4306 target = 0.120819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.089896 restraints weight = 165680.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.088135 restraints weight = 131835.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.087959 restraints weight = 110538.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.087985 restraints weight = 105050.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088043 restraints weight = 89991.433| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31836 Z= 0.114 Angle : 0.543 13.091 43444 Z= 0.271 Chirality : 0.042 0.193 5015 Planarity : 0.004 0.076 5513 Dihedral : 4.821 47.599 5343 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.73 % Allowed : 14.54 % Favored : 83.73 % 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: 0.26 (0.14), residues: 3845 helix: 1.98 (0.20), residues: 705 sheet: 0.20 (0.15), residues: 1038 loop : -0.43 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.044 0.001 TYR C 486 PHE 0.027 0.001 PHE C 453 TRP 0.016 0.001 TRP E 36 HIS 0.006 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00251 (31731) covalent geometry : angle 0.53380 (43180) SS BOND : bond 0.00359 ( 51) SS BOND : angle 0.89433 ( 102) hydrogen bonds : bond 0.03379 ( 1272) hydrogen bonds : angle 5.13426 ( 3480) link_BETA1-4 : bond 0.00260 ( 12) link_BETA1-4 : angle 0.99139 ( 36) link_NAG-ASN : bond 0.00215 ( 42) link_NAG-ASN : angle 1.78239 ( 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 194 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 136 time to evaluate : 1.168 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: B 177 MET cc_start: 0.0433 (ttm) cc_final: 0.0090 (ttt) REVERT: B 267 LEU cc_start: 0.9005 (mt) cc_final: 0.8674 (mp) REVERT: B 284 ASP cc_start: 0.7519 (t0) cc_final: 0.7080 (t0) REVERT: B 420 TYR cc_start: 0.4697 (t80) cc_final: 0.4056 (t80) REVERT: B 579 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8437 (pt) REVERT: B 612 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8456 (p) REVERT: B 855 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8188 (pp) REVERT: A 65 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: A 866 MET cc_start: 0.9081 (mtt) cc_final: 0.8835 (ptp) REVERT: C 62 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8389 (p) REVERT: C 118 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7882 (mt) REVERT: C 120 VAL cc_start: 0.8141 (m) cc_final: 0.7931 (p) REVERT: C 177 MET cc_start: 0.0067 (ttm) cc_final: -0.2867 (mmp) REVERT: C 562 PHE cc_start: 0.8504 (p90) cc_final: 0.8020 (p90) REVERT: C 976 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.7946 (t0) REVERT: C 1026 MET cc_start: 0.9154 (tpp) cc_final: 0.8876 (tpp) REVERT: H 81 MET cc_start: 0.3341 (tmm) cc_final: 0.2125 (tmm) REVERT: D 48 MET cc_start: 0.0042 (ptm) cc_final: -0.0780 (ptm) REVERT: G 4 MET cc_start: 0.3587 (mmm) cc_final: 0.3183 (mtt) outliers start: 58 outliers final: 43 residues processed: 183 average time/residue: 0.1731 time to fit residues: 53.6724 Evaluate side-chains 177 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 125 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR 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 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 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 855 LEU Chi-restraints excluded: chain A residue 1003 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 118 LEU Chi-restraints excluded: chain C residue 143 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 392 VAL 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 717 ILE Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER 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: 0.9990 chunk 282 optimal weight: 6.9990 chunk 384 optimal weight: 40.0000 chunk 199 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 249 optimal weight: 20.0000 chunk 351 optimal weight: 40.0000 chunk 191 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN A 125 ASN A 537 ASN A 781 GLN A 801 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 ASN C1139 GLN D 35 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.112765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.083666 restraints weight = 148170.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.080907 restraints weight = 104067.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.081348 restraints weight = 93063.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.081599 restraints weight = 73224.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.081681 restraints weight = 66916.944| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 31836 Z= 0.315 Angle : 0.726 10.455 43444 Z= 0.369 Chirality : 0.046 0.283 5015 Planarity : 0.005 0.086 5513 Dihedral : 5.664 46.767 5343 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.03 % Allowed : 14.51 % Favored : 83.46 % 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: -0.18 (0.14), residues: 3845 helix: 1.51 (0.20), residues: 697 sheet: -0.13 (0.15), residues: 1041 loop : -0.63 (0.14), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.036 0.002 TYR C 486 PHE 0.034 0.002 PHE A 538 TRP 0.029 0.002 TRP H 116 HIS 0.007 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00687 (31731) covalent geometry : angle 0.71188 (43180) SS BOND : bond 0.00573 ( 51) SS BOND : angle 1.23360 ( 102) hydrogen bonds : bond 0.04483 ( 1272) hydrogen bonds : angle 5.80181 ( 3480) link_BETA1-4 : bond 0.00389 ( 12) link_BETA1-4 : angle 1.37408 ( 36) link_NAG-ASN : bond 0.00721 ( 42) link_NAG-ASN : angle 2.53622 ( 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 189 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 121 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: B 117 LEU cc_start: 0.8800 (tt) cc_final: 0.8499 (tp) REVERT: B 267 LEU cc_start: 0.8981 (mt) cc_final: 0.8713 (mp) REVERT: B 284 ASP cc_start: 0.7685 (t0) cc_final: 0.7280 (t0) REVERT: B 420 TYR cc_start: 0.4648 (t80) cc_final: 0.4359 (t80) REVERT: B 579 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8260 (pt) REVERT: B 612 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8469 (p) REVERT: B 855 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8175 (pp) REVERT: A 65 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: C 118 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7838 (mt) REVERT: C 120 VAL cc_start: 0.8155 (m) cc_final: 0.7907 (p) REVERT: C 976 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7901 (t0) REVERT: H 81 MET cc_start: 0.3091 (tmm) cc_final: 0.2424 (tmm) REVERT: D 48 MET cc_start: 0.0488 (ptm) cc_final: -0.0262 (ptm) REVERT: G 4 MET cc_start: 0.2560 (mmm) cc_final: 0.2189 (mtt) outliers start: 68 outliers final: 52 residues processed: 179 average time/residue: 0.1722 time to fit residues: 52.4576 Evaluate side-chains 172 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 114 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 125 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 612 VAL 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 885 PHE Chi-restraints excluded: chain B residue 973 VAL 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 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 592 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 931 ILE 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 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 549 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 788 THR Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1113 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 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: 4.9990 chunk 246 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 300 optimal weight: 0.4980 chunk 274 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 292 optimal weight: 2.9990 chunk 382 optimal weight: 40.0000 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 759 GLN A 537 ASN A 801 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1045 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 = 0.4288 r_free = 0.4288 target = 0.119952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.085560 restraints weight = 166097.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.086062 restraints weight = 122438.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.086248 restraints weight = 84064.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.086083 restraints weight = 67629.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.086284 restraints weight = 74581.332| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31836 Z= 0.123 Angle : 0.576 10.712 43444 Z= 0.287 Chirality : 0.043 0.234 5015 Planarity : 0.004 0.082 5513 Dihedral : 5.151 43.164 5343 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.79 % Allowed : 14.90 % Favored : 83.31 % 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: 0.10 (0.14), residues: 3845 helix: 1.90 (0.20), residues: 697 sheet: 0.01 (0.16), residues: 1029 loop : -0.49 (0.14), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 405 TYR 0.023 0.001 TYR C 486 PHE 0.021 0.001 PHE A 559 TRP 0.019 0.001 TRP F 116 HIS 0.006 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00273 (31731) covalent geometry : angle 0.56552 (43180) SS BOND : bond 0.00374 ( 51) SS BOND : angle 1.04075 ( 102) hydrogen bonds : bond 0.03569 ( 1272) hydrogen bonds : angle 5.32989 ( 3480) link_BETA1-4 : bond 0.00272 ( 12) link_BETA1-4 : angle 1.00206 ( 36) link_NAG-ASN : bond 0.00255 ( 42) link_NAG-ASN : angle 1.90486 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5611.07 seconds wall clock time: 97 minutes 51.46 seconds (5871.46 seconds total)