Starting phenix.real_space_refine on Fri Mar 6 11:46:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrc_14910/03_2026/7zrc_14910.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrc_14910/03_2026/7zrc_14910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zrc_14910/03_2026/7zrc_14910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrc_14910/03_2026/7zrc_14910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zrc_14910/03_2026/7zrc_14910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrc_14910/03_2026/7zrc_14910.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 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 140 5.16 5 C 19524 2.51 5 N 5064 2.21 5 O 5996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30724 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8272 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 54, 'TRANS': 1004} Chain breaks: 7 Chain: "C" Number of atoms: 8273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8273 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 53, 'TRANS': 1005} Chain breaks: 6 Chain: "A" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8249 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 53, 'TRANS': 1002} Chain breaks: 6 Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "J" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "K" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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 Time building chain proxies: 6.89, per 1000 atoms: 0.22 Number of scatterers: 30724 At special positions: 0 Unit cell: (161.85, 161.02, 213.31, 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 140 16.00 O 5996 8.00 N 5064 7.00 C 19524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 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 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.02 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 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 279 " " NAG B1302 " - " ASN B 328 " " NAG B1303 " - " ASN B 613 " " NAG B1304 " - " ASN B 654 " " NAG B1305 " - " ASN B 706 " " NAG B1306 " - " ASN B1071 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 340 " " NAG B1309 " - " ASN B 61 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 328 " " NAG C1309 " - " ASN C 340 " " NAG D 1 " - " ASN B 798 " " NAG E 1 " - " ASN B 714 " " NAG I 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN C 714 " " NAG O 1 " - " ASN C 798 " " NAG P 1 " - " ASN C1095 " " NAG Q 1 " - " ASN C1131 " " NAG R 1 " - " ASN A 714 " " NAG S 1 " - " ASN A 798 " " NAG T 1 " - " ASN A1095 " " NAG U 1 " - " ASN A1131 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 71 sheets defined 21.5% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.640A pdb=" N TRP B 350 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.233A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.324A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.644A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.139A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.421A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.509A pdb=" N SER B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 380 through 387 removed outlier: 4.164A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 387 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.331A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 756 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: 3.845A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.007A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.555A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 3.536A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.017A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.674A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.210A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.476A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.798A 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 removed outlier: 3.743A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.260A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.549A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.895A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.956A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.120A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.671A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.126A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.676A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 4.102A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.667A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (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 47 through 55 removed outlier: 3.890A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 67 removed outlier: 3.544A pdb=" N ALA B 261 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.803A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.803A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 316 removed outlier: 6.669A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 322 through 325 removed outlier: 5.734A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.568A pdb=" N TRP B 433 " --> pdb=" O ARG B 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.733A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.525A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 698 through 701 removed outlier: 6.264A pdb=" N VAL B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LYS C 787 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.373A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.373A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.413A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.645A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.452A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.136A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 55 removed outlier: 6.371A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.538A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.538A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR C 145 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.630A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 321 through 325 removed outlier: 6.758A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASN C 539 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE C 323 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE C 562 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.602A pdb=" N TRP C 433 " --> pdb=" O ARG C 506 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.809A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AD2, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AD3, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.338A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 699 through 701 removed outlier: 3.628A pdb=" N LYS A 787 " --> pdb=" O ASN C 700 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 708 through 712 removed outlier: 4.442A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 715 through 725 removed outlier: 6.015A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 715 through 725 Processing sheet with id=AD8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.524A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.341A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AE2, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.521A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.922A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.671A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 151 through 162 removed outlier: 5.626A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.636A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.787A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.787A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.541A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.694A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AF4, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.485A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.575A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.058A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.459A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.938A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.938A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY H 100 " --> pdb=" O PHE H 105 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE H 105 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.534A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AG5, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.591A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.925A pdb=" N THR F 112 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.925A pdb=" N THR F 112 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 107 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY F 100 " --> pdb=" O PHE F 105 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE F 105 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.523A pdb=" N VAL G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AH2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.579A pdb=" N TYR G 49 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AH4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.867A pdb=" N THR J 112 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR J 33 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.867A pdb=" N THR J 112 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY J 100 " --> pdb=" O PHE J 105 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE J 105 " --> pdb=" O GLY J 100 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.521A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AH8, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.584A pdb=" N TYR K 49 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 1345 hydrogen bonds defined for protein. 3558 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: 8.49 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9201 1.33 - 1.45: 5905 1.45 - 1.58: 16127 1.58 - 1.70: 0 1.70 - 1.82: 184 Bond restraints: 31417 Sorted by residual: bond pdb=" N ILE C 329 " pdb=" CA ILE C 329 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.82e+00 bond pdb=" N TYR C 263 " pdb=" CA TYR C 263 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.17e-02 7.31e+03 8.16e+00 bond pdb=" N GLN B1033 " pdb=" CA GLN B1033 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.15e+00 bond pdb=" N VAL A 607 " pdb=" CA VAL A 607 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.17e-02 7.31e+03 7.91e+00 bond pdb=" N VAL C 264 " pdb=" CA VAL C 264 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.22e-02 6.72e+03 7.87e+00 ... (remaining 31412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 41179 1.54 - 3.07: 1350 3.07 - 4.61: 179 4.61 - 6.14: 18 6.14 - 7.68: 5 Bond angle restraints: 42731 Sorted by residual: angle pdb=" N GLY C 854 " pdb=" CA GLY C 854 " pdb=" C GLY C 854 " ideal model delta sigma weight residual 114.92 108.42 6.50 1.30e+00 5.92e-01 2.50e+01 angle pdb=" C ASN K 30 " pdb=" CA ASN K 30 " pdb=" CB ASN K 30 " ideal model delta sigma weight residual 117.23 110.84 6.39 1.36e+00 5.41e-01 2.21e+01 angle pdb=" C ALA A 710 " pdb=" N ILE A 711 " pdb=" CA ILE A 711 " ideal model delta sigma weight residual 123.33 119.51 3.82 8.70e-01 1.32e+00 1.92e+01 angle pdb=" N ASN A 603 " pdb=" CA ASN A 603 " pdb=" C ASN A 603 " ideal model delta sigma weight residual 113.30 107.76 5.54 1.34e+00 5.57e-01 1.71e+01 angle pdb=" CA ASN A 61 " pdb=" CB ASN A 61 " pdb=" CG ASN A 61 " ideal model delta sigma weight residual 112.60 116.59 -3.99 1.00e+00 1.00e+00 1.59e+01 ... (remaining 42726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 18373 17.39 - 34.79: 805 34.79 - 52.18: 151 52.18 - 69.58: 30 69.58 - 86.97: 9 Dihedral angle restraints: 19368 sinusoidal: 8188 harmonic: 11180 Sorted by residual: dihedral pdb=" CB CYS C1079 " pdb=" SG CYS C1079 " pdb=" SG CYS C1123 " pdb=" CB CYS C1123 " ideal model delta sinusoidal sigma weight residual -86.00 -133.06 47.06 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS A1079 " pdb=" SG CYS A1079 " pdb=" SG CYS A1123 " pdb=" CB CYS A1123 " ideal model delta sinusoidal sigma weight residual -86.00 -132.11 46.11 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual -86.00 -127.73 41.73 1 1.00e+01 1.00e-02 2.44e+01 ... (remaining 19365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4900 0.122 - 0.244: 66 0.244 - 0.366: 2 0.366 - 0.488: 1 0.488 - 0.610: 1 Chirality restraints: 4970 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 328 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.31e+00 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4967 not shown) Planarity restraints: 5491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " -0.229 2.00e-02 2.50e+03 1.92e-01 4.59e+02 pdb=" C7 NAG A1309 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " 0.317 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.223 2.00e-02 2.50e+03 1.84e-01 4.22e+02 pdb=" C7 NAG B1302 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.299 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " -0.146 2.00e-02 2.50e+03 1.20e-01 1.80e+02 pdb=" C7 NAG A1303 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " 0.191 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.022 2.00e-02 2.50e+03 ... (remaining 5488 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 613 2.68 - 3.23: 28624 3.23 - 3.79: 47491 3.79 - 4.34: 66009 4.34 - 4.90: 110829 Nonbonded interactions: 253566 Sorted by model distance: nonbonded pdb=" O ALA A 876 " pdb=" OG1 THR A 880 " model vdw 2.125 3.040 nonbonded pdb=" O ALA C 876 " pdb=" OG1 THR C 880 " model vdw 2.138 3.040 nonbonded pdb=" OE2 GLU B 915 " pdb=" OG SER A1120 " model vdw 2.161 3.040 nonbonded pdb=" O GLY B 877 " pdb=" OG SER B 881 " model vdw 2.163 3.040 nonbonded pdb=" NH1 ARG A 902 " pdb=" O LEU A1046 " model vdw 2.167 3.120 ... (remaining 253561 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 176 or resid 188 through 617 or resid 638 throu \ gh 1309)) selection = (chain 'B' and (resid 13 through 176 or resid 188 through 617 or resid 638 throu \ gh 1309)) selection = (chain 'C' and (resid 13 through 176 or resid 188 through 617 or resid 638 throu \ gh 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.500 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 37.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.006 0.125 31517 Z= 0.297 Angle : 0.661 21.914 42983 Z= 0.368 Chirality : 0.049 0.610 4970 Planarity : 0.006 0.192 5451 Dihedral : 10.102 86.971 12048 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 0.99 % Allowed : 4.91 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 3797 helix: 1.31 (0.20), residues: 679 sheet: 0.02 (0.16), residues: 1074 loop : -0.44 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1011 TYR 0.020 0.001 TYR B1064 PHE 0.020 0.002 PHE A1118 TRP 0.015 0.001 TRP C1099 HIS 0.006 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00638 (31417) covalent geometry : angle 0.63665 (42731) SS BOND : bond 0.00335 ( 48) SS BOND : angle 1.17684 ( 96) hydrogen bonds : bond 0.13769 ( 1268) hydrogen bonds : angle 7.57905 ( 3558) link_BETA1-4 : bond 0.00196 ( 12) link_BETA1-4 : angle 1.20292 ( 36) link_NAG-ASN : bond 0.02042 ( 40) link_NAG-ASN : angle 3.28956 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 398 time to evaluate : 0.950 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 54 LEU cc_start: 0.9181 (mt) cc_final: 0.8923 (mp) REVERT: B 177 MET cc_start: -0.2768 (ttm) cc_final: -0.4962 (mmt) REVERT: B 581 ILE cc_start: 0.8881 (mm) cc_final: 0.8658 (mp) REVERT: B 737 MET cc_start: 0.8286 (ttt) cc_final: 0.8036 (ttm) REVERT: B 981 LEU cc_start: 0.8926 (mt) cc_final: 0.8617 (mp) REVERT: C 302 SER cc_start: 0.8878 (t) cc_final: 0.8358 (p) REVERT: C 538 PHE cc_start: 0.8280 (p90) cc_final: 0.8021 (p90) REVERT: C 752 GLN cc_start: 0.8491 (mt0) cc_final: 0.8142 (mm-40) REVERT: C 864 ASP cc_start: 0.8365 (m-30) cc_final: 0.8159 (m-30) REVERT: C 1070 LYS cc_start: 0.8062 (mttt) cc_final: 0.7719 (mtpp) REVERT: A 164 ASN cc_start: 0.6444 (OUTLIER) cc_final: 0.5948 (p0) REVERT: A 749 LEU cc_start: 0.8999 (mt) cc_final: 0.8699 (mp) REVERT: A 773 LYS cc_start: 0.8032 (tttt) cc_final: 0.7813 (ttmm) REVERT: A 856 THR cc_start: 0.8834 (p) cc_final: 0.8629 (t) REVERT: A 954 GLN cc_start: 0.7537 (mm110) cc_final: 0.7253 (tp-100) REVERT: A 957 ASN cc_start: 0.8298 (m-40) cc_final: 0.8057 (m-40) REVERT: A 1007 GLN cc_start: 0.7839 (mt0) cc_final: 0.7620 (mp10) REVERT: H 48 MET cc_start: 0.1604 (mtp) cc_final: 0.1037 (ptm) outliers start: 33 outliers final: 15 residues processed: 428 average time/residue: 0.1946 time to fit residues: 133.4471 Evaluate side-chains 265 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 249 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 1078 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.0020 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.2980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN B 196 ASN B 752 GLN B 759 GLN B 904 ASN B 954 GLN B 962 GLN B1007 GLN C 318 GLN C 537 ASN C 561 GLN C 759 GLN C 761 ASN C 946 GLN C 952 ASN C 962 GLN A 311 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 577 GLN A 672 GLN A 910 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN A 966 ASN L 101 GLN G 101 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.208668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.200353 restraints weight = 39623.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.199666 restraints weight = 94932.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.176885 restraints weight = 90708.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.168831 restraints weight = 86001.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.165984 restraints weight = 73030.815| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 31517 Z= 0.118 Angle : 0.547 15.983 42983 Z= 0.280 Chirality : 0.044 0.367 4970 Planarity : 0.004 0.048 5451 Dihedral : 6.090 58.685 5258 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.08 % Rotamer: Outliers : 1.32 % Allowed : 7.36 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.23 (0.14), residues: 3797 helix: 1.83 (0.20), residues: 669 sheet: 0.10 (0.16), residues: 1099 loop : -0.32 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 463 TYR 0.020 0.001 TYR B 262 PHE 0.019 0.001 PHE C 487 TRP 0.021 0.001 TRP J 36 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00258 (31417) covalent geometry : angle 0.52060 (42731) SS BOND : bond 0.00329 ( 48) SS BOND : angle 1.33754 ( 96) hydrogen bonds : bond 0.03871 ( 1268) hydrogen bonds : angle 5.94692 ( 3558) link_BETA1-4 : bond 0.00276 ( 12) link_BETA1-4 : angle 1.01436 ( 36) link_NAG-ASN : bond 0.00494 ( 40) link_NAG-ASN : angle 3.00374 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8929 (mt) cc_final: 0.8714 (mp) REVERT: B 177 MET cc_start: -0.3016 (ttm) cc_final: -0.4816 (mmt) REVERT: B 658 GLU cc_start: 0.7551 (pm20) cc_final: 0.7297 (pm20) REVERT: B 737 MET cc_start: 0.7712 (ttt) cc_final: 0.7504 (ttm) REVERT: B 954 GLN cc_start: 0.7546 (tt0) cc_final: 0.7223 (tp40) REVERT: C 177 MET cc_start: -0.3440 (mtp) cc_final: -0.4018 (mmt) REVERT: C 302 SER cc_start: 0.8354 (t) cc_final: 0.8050 (p) REVERT: C 736 THR cc_start: 0.8822 (m) cc_final: 0.8504 (p) REVERT: C 752 GLN cc_start: 0.8183 (mt0) cc_final: 0.7960 (mm110) REVERT: C 864 ASP cc_start: 0.7787 (m-30) cc_final: 0.7548 (m-30) REVERT: A 773 LYS cc_start: 0.7682 (tttt) cc_final: 0.7351 (ttpp) REVERT: A 856 THR cc_start: 0.8663 (p) cc_final: 0.8388 (t) REVERT: H 48 MET cc_start: 0.2203 (mtp) cc_final: 0.1399 (ptm) outliers start: 44 outliers final: 24 residues processed: 306 average time/residue: 0.1823 time to fit residues: 93.3920 Evaluate side-chains 238 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 368 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 230 optimal weight: 0.0870 chunk 371 optimal weight: 30.0000 chunk 304 optimal weight: 1.9990 chunk 367 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 759 GLN B 952 ASN B1105 ASN C 385 ASN C 932 GLN C 957 ASN C1007 GLN C1085 HIS A 49 HIS A 904 ASN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.205081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.196942 restraints weight = 39606.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.196268 restraints weight = 93514.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.176605 restraints weight = 93342.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.165658 restraints weight = 80204.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.163009 restraints weight = 71961.753| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 31517 Z= 0.263 Angle : 0.602 10.584 42983 Z= 0.311 Chirality : 0.047 0.327 4970 Planarity : 0.004 0.071 5451 Dihedral : 5.819 58.353 5245 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.58 % Rotamer: Outliers : 2.27 % Allowed : 8.56 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.02 (0.14), residues: 3797 helix: 1.31 (0.20), residues: 673 sheet: 0.05 (0.15), residues: 1110 loop : -0.44 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1011 TYR 0.020 0.001 TYR B1064 PHE 0.026 0.002 PHE B 487 TRP 0.013 0.001 TRP A 64 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00633 (31417) covalent geometry : angle 0.58499 (42731) SS BOND : bond 0.00475 ( 48) SS BOND : angle 1.48625 ( 96) hydrogen bonds : bond 0.04615 ( 1268) hydrogen bonds : angle 5.95692 ( 3558) link_BETA1-4 : bond 0.00230 ( 12) link_BETA1-4 : angle 1.18326 ( 36) link_NAG-ASN : bond 0.00460 ( 40) link_NAG-ASN : angle 2.40477 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 226 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2664 (ttm) cc_final: -0.4671 (mmt) REVERT: B 947 ASP cc_start: 0.7667 (m-30) cc_final: 0.7402 (m-30) REVERT: C 302 SER cc_start: 0.8526 (t) cc_final: 0.8111 (p) REVERT: C 752 GLN cc_start: 0.8296 (mt0) cc_final: 0.8085 (mm-40) REVERT: C 864 ASP cc_start: 0.7802 (m-30) cc_final: 0.7589 (m-30) REVERT: C 1042 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.6967 (mtpp) REVERT: A 299 THR cc_start: 0.8766 (m) cc_final: 0.8524 (p) REVERT: A 856 THR cc_start: 0.8604 (p) cc_final: 0.8359 (t) REVERT: H 48 MET cc_start: 0.1989 (mtp) cc_final: 0.1228 (ptm) outliers start: 76 outliers final: 51 residues processed: 289 average time/residue: 0.1791 time to fit residues: 87.6452 Evaluate side-chains 261 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 89 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 30 optimal weight: 50.0000 chunk 285 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 246 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 240 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 GLN C 759 GLN C 957 ASN A 311 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.206882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.198227 restraints weight = 39154.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.197705 restraints weight = 91726.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.178209 restraints weight = 100520.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.167363 restraints weight = 90612.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.163510 restraints weight = 72166.285| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31517 Z= 0.128 Angle : 0.515 7.942 42983 Z= 0.266 Chirality : 0.044 0.306 4970 Planarity : 0.004 0.069 5451 Dihedral : 5.251 58.372 5245 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 1.89 % Allowed : 9.66 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.20 (0.14), residues: 3797 helix: 1.72 (0.20), residues: 666 sheet: 0.11 (0.15), residues: 1108 loop : -0.34 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 158 TYR 0.023 0.001 TYR A1135 PHE 0.018 0.001 PHE B 487 TRP 0.017 0.001 TRP A 104 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00294 (31417) covalent geometry : angle 0.50269 (42731) SS BOND : bond 0.00337 ( 48) SS BOND : angle 1.06153 ( 96) hydrogen bonds : bond 0.03743 ( 1268) hydrogen bonds : angle 5.61469 ( 3558) link_BETA1-4 : bond 0.00311 ( 12) link_BETA1-4 : angle 1.04165 ( 36) link_NAG-ASN : bond 0.00398 ( 40) link_NAG-ASN : angle 1.99331 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.3012 (ttm) cc_final: -0.4559 (mmt) REVERT: B 658 GLU cc_start: 0.7362 (pm20) cc_final: 0.7042 (pm20) REVERT: B 899 MET cc_start: 0.8078 (mmm) cc_final: 0.7768 (mmt) REVERT: B 947 ASP cc_start: 0.7591 (m-30) cc_final: 0.7386 (m-30) REVERT: C 177 MET cc_start: -0.3184 (mmm) cc_final: -0.3921 (mmt) REVERT: C 302 SER cc_start: 0.8650 (t) cc_final: 0.8288 (p) REVERT: C 864 ASP cc_start: 0.7758 (m-30) cc_final: 0.7533 (m-30) REVERT: C 1042 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7031 (mtpp) REVERT: A 299 THR cc_start: 0.8739 (m) cc_final: 0.8451 (p) REVERT: A 856 THR cc_start: 0.8594 (p) cc_final: 0.8339 (t) REVERT: H 48 MET cc_start: 0.1981 (mtp) cc_final: 0.1240 (ptm) outliers start: 63 outliers final: 40 residues processed: 268 average time/residue: 0.1750 time to fit residues: 79.6539 Evaluate side-chains 245 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 61 optimal weight: 0.0980 chunk 376 optimal weight: 8.9990 chunk 353 optimal weight: 50.0000 chunk 33 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 224 optimal weight: 40.0000 chunk 183 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 236 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 752 GLN C 946 GLN A 672 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** 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 = 0.4311 r_free = 0.4311 target = 0.206134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.198499 restraints weight = 39341.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.197337 restraints weight = 79251.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.196103 restraints weight = 89148.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.176757 restraints weight = 99781.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.165619 restraints weight = 88007.511| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31517 Z= 0.160 Angle : 0.517 6.624 42983 Z= 0.268 Chirality : 0.044 0.300 4970 Planarity : 0.004 0.071 5451 Dihedral : 4.968 58.558 5245 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.92 % Rotamer: Outliers : 2.15 % Allowed : 9.46 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3797 helix: 1.77 (0.20), residues: 660 sheet: 0.12 (0.15), residues: 1107 loop : -0.33 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 762 TYR 0.017 0.001 TYR A1064 PHE 0.021 0.001 PHE C 756 TRP 0.019 0.001 TRP A 104 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00376 (31417) covalent geometry : angle 0.50486 (42731) SS BOND : bond 0.00331 ( 48) SS BOND : angle 1.00634 ( 96) hydrogen bonds : bond 0.03875 ( 1268) hydrogen bonds : angle 5.51763 ( 3558) link_BETA1-4 : bond 0.00273 ( 12) link_BETA1-4 : angle 1.05153 ( 36) link_NAG-ASN : bond 0.00278 ( 40) link_NAG-ASN : angle 1.92784 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 217 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.5695 (pt) REVERT: B 177 MET cc_start: -0.3158 (ttm) cc_final: -0.4506 (mmt) REVERT: B 899 MET cc_start: 0.8089 (mmm) cc_final: 0.7733 (mmt) REVERT: B 947 ASP cc_start: 0.7615 (m-30) cc_final: 0.7338 (m-30) REVERT: C 302 SER cc_start: 0.8718 (t) cc_final: 0.8374 (p) REVERT: C 571 ASP cc_start: 0.7591 (t0) cc_final: 0.7374 (t0) REVERT: C 864 ASP cc_start: 0.7832 (m-30) cc_final: 0.7589 (m-30) REVERT: C 1042 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7087 (mtpp) REVERT: A 299 THR cc_start: 0.8761 (m) cc_final: 0.8431 (p) REVERT: A 856 THR cc_start: 0.8609 (p) cc_final: 0.8328 (t) REVERT: A 1007 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6746 (mp10) REVERT: H 48 MET cc_start: 0.1801 (mtp) cc_final: 0.1102 (ptm) outliers start: 72 outliers final: 52 residues processed: 276 average time/residue: 0.1782 time to fit residues: 84.1274 Evaluate side-chains 261 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 180 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 240 optimal weight: 4.9990 chunk 262 optimal weight: 0.0670 chunk 32 optimal weight: 30.0000 chunk 170 optimal weight: 0.8980 chunk 305 optimal weight: 0.6980 chunk 139 optimal weight: 0.0570 chunk 167 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 759 GLN B 954 GLN A 268 GLN A 311 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.207554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.199639 restraints weight = 39196.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.199094 restraints weight = 92596.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.177905 restraints weight = 96097.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.169435 restraints weight = 87026.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.165691 restraints weight = 73314.876| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31517 Z= 0.103 Angle : 0.496 17.935 42983 Z= 0.253 Chirality : 0.043 0.290 4970 Planarity : 0.003 0.069 5451 Dihedral : 4.691 59.463 5245 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 1.59 % Allowed : 9.96 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.38 (0.14), residues: 3797 helix: 2.01 (0.20), residues: 661 sheet: 0.24 (0.16), residues: 1079 loop : -0.27 (0.14), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 762 TYR 0.022 0.001 TYR A1135 PHE 0.020 0.001 PHE B 487 TRP 0.022 0.001 TRP A 104 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00228 (31417) covalent geometry : angle 0.47504 (42731) SS BOND : bond 0.00262 ( 48) SS BOND : angle 0.79538 ( 96) hydrogen bonds : bond 0.03435 ( 1268) hydrogen bonds : angle 5.29562 ( 3558) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 1.00142 ( 36) link_NAG-ASN : bond 0.00464 ( 40) link_NAG-ASN : angle 2.66502 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.5632 (pt) REVERT: B 177 MET cc_start: -0.3451 (ttm) cc_final: -0.4370 (mmt) REVERT: C 302 SER cc_start: 0.8668 (t) cc_final: 0.8326 (p) REVERT: C 571 ASP cc_start: 0.7583 (t0) cc_final: 0.7349 (t0) REVERT: C 864 ASP cc_start: 0.7865 (m-30) cc_final: 0.7635 (m-30) REVERT: C 1011 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7718 (mtt-85) REVERT: C 1042 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7086 (mtpp) REVERT: A 856 THR cc_start: 0.8597 (p) cc_final: 0.8322 (t) REVERT: A 1007 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7345 (pt0) REVERT: H 48 MET cc_start: 0.1779 (mtp) cc_final: 0.1103 (ptm) outliers start: 53 outliers final: 44 residues processed: 262 average time/residue: 0.1822 time to fit residues: 80.9198 Evaluate side-chains 249 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 62 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 293 optimal weight: 2.9990 chunk 302 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 315 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 311 GLN A 759 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.207014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.198820 restraints weight = 39306.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.198113 restraints weight = 87965.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.177217 restraints weight = 88862.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.167984 restraints weight = 82034.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.163658 restraints weight = 69617.398| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31517 Z= 0.129 Angle : 0.507 17.737 42983 Z= 0.258 Chirality : 0.044 0.290 4970 Planarity : 0.004 0.069 5451 Dihedral : 4.601 59.286 5245 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 1.83 % Allowed : 10.56 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.39 (0.14), residues: 3797 helix: 2.01 (0.20), residues: 662 sheet: 0.23 (0.16), residues: 1077 loop : -0.25 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 237 TYR 0.017 0.001 TYR B1064 PHE 0.015 0.001 PHE C 92 TRP 0.022 0.001 TRP A 104 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00298 (31417) covalent geometry : angle 0.48647 (42731) SS BOND : bond 0.00280 ( 48) SS BOND : angle 0.82278 ( 96) hydrogen bonds : bond 0.03591 ( 1268) hydrogen bonds : angle 5.26107 ( 3558) link_BETA1-4 : bond 0.00267 ( 12) link_BETA1-4 : angle 1.00332 ( 36) link_NAG-ASN : bond 0.00519 ( 40) link_NAG-ASN : angle 2.64728 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 1.273 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: B 24 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.5648 (pt) REVERT: B 177 MET cc_start: -0.3485 (ttm) cc_final: -0.4485 (mmt) REVERT: C 302 SER cc_start: 0.8729 (t) cc_final: 0.8408 (p) REVERT: C 571 ASP cc_start: 0.7623 (t0) cc_final: 0.7396 (t0) REVERT: C 864 ASP cc_start: 0.7913 (m-30) cc_final: 0.7683 (m-30) REVERT: C 1042 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7075 (mtpp) REVERT: A 856 THR cc_start: 0.8620 (p) cc_final: 0.8343 (t) REVERT: A 1007 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7390 (pt0) REVERT: H 48 MET cc_start: 0.1843 (mtp) cc_final: 0.1113 (ptm) outliers start: 61 outliers final: 54 residues processed: 261 average time/residue: 0.1805 time to fit residues: 80.1171 Evaluate side-chains 253 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 313 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 chunk 370 optimal weight: 40.0000 chunk 267 optimal weight: 2.9990 chunk 138 optimal weight: 50.0000 chunk 227 optimal weight: 0.9980 chunk 336 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN C 391 ASN C 853 ASN A 268 GLN A 311 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.204141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.195663 restraints weight = 39277.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.194911 restraints weight = 91764.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.174589 restraints weight = 92293.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.162528 restraints weight = 79930.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.159825 restraints weight = 69932.650| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 31517 Z= 0.289 Angle : 0.610 16.076 42983 Z= 0.313 Chirality : 0.048 0.308 4970 Planarity : 0.004 0.074 5451 Dihedral : 5.091 58.616 5245 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 2.36 % Allowed : 10.35 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3797 helix: 1.33 (0.20), residues: 669 sheet: 0.18 (0.16), residues: 1088 loop : -0.37 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.019 0.001 TYR B1064 PHE 0.022 0.002 PHE B1118 TRP 0.021 0.002 TRP A 104 HIS 0.007 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00695 (31417) covalent geometry : angle 0.58901 (42731) SS BOND : bond 0.00513 ( 48) SS BOND : angle 1.55785 ( 96) hydrogen bonds : bond 0.04544 ( 1268) hydrogen bonds : angle 5.62708 ( 3558) link_BETA1-4 : bond 0.00212 ( 12) link_BETA1-4 : angle 1.15350 ( 36) link_NAG-ASN : bond 0.00571 ( 40) link_NAG-ASN : angle 2.69922 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 190 time to evaluate : 1.107 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: B 177 MET cc_start: -0.3226 (ttm) cc_final: -0.4303 (mmt) REVERT: B 658 GLU cc_start: 0.7400 (pm20) cc_final: 0.7120 (pm20) REVERT: C 177 MET cc_start: -0.3720 (mmt) cc_final: -0.4883 (mtt) REVERT: C 233 ILE cc_start: 0.4864 (OUTLIER) cc_final: 0.4637 (pt) REVERT: C 302 SER cc_start: 0.8550 (t) cc_final: 0.8112 (p) REVERT: C 571 ASP cc_start: 0.7583 (t0) cc_final: 0.7344 (t0) REVERT: C 1042 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7024 (mtpp) REVERT: A 856 THR cc_start: 0.8653 (p) cc_final: 0.8357 (t) REVERT: A 1007 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6663 (mp10) REVERT: H 48 MET cc_start: 0.1957 (mtp) cc_final: 0.1126 (ptm) outliers start: 79 outliers final: 66 residues processed: 258 average time/residue: 0.1753 time to fit residues: 77.7795 Evaluate side-chains 253 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 184 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 853 ASN Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain J residue 35 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.6980 chunk 282 optimal weight: 0.4980 chunk 162 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 chunk 195 optimal weight: 0.7980 chunk 238 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 325 optimal weight: 50.0000 chunk 76 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN A 268 GLN A 311 GLN A 759 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN K 89 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.206903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.199144 restraints weight = 39204.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.198096 restraints weight = 85707.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.174049 restraints weight = 91970.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.163753 restraints weight = 75629.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.161265 restraints weight = 69631.425| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 31517 Z= 0.110 Angle : 0.514 15.769 42983 Z= 0.263 Chirality : 0.044 0.287 4970 Planarity : 0.004 0.068 5451 Dihedral : 4.688 58.101 5245 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 1.56 % Allowed : 11.04 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3797 helix: 1.86 (0.20), residues: 661 sheet: 0.25 (0.16), residues: 1075 loop : -0.27 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.027 0.001 TYR A1135 PHE 0.014 0.001 PHE C 92 TRP 0.027 0.001 TRP A 104 HIS 0.002 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00246 (31417) covalent geometry : angle 0.49538 (42731) SS BOND : bond 0.00289 ( 48) SS BOND : angle 1.10875 ( 96) hydrogen bonds : bond 0.03538 ( 1268) hydrogen bonds : angle 5.30594 ( 3558) link_BETA1-4 : bond 0.00354 ( 12) link_BETA1-4 : angle 1.02481 ( 36) link_NAG-ASN : bond 0.00476 ( 40) link_NAG-ASN : angle 2.45278 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 1.148 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 24 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.5675 (pt) REVERT: B 177 MET cc_start: -0.3414 (ttm) cc_final: -0.4336 (mmt) REVERT: C 177 MET cc_start: -0.3824 (mmt) cc_final: -0.4940 (mtt) REVERT: C 302 SER cc_start: 0.8799 (t) cc_final: 0.8452 (p) REVERT: C 571 ASP cc_start: 0.7463 (t0) cc_final: 0.7259 (t0) REVERT: A 856 THR cc_start: 0.8580 (p) cc_final: 0.8306 (t) REVERT: A 1007 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6778 (mp10) REVERT: H 48 MET cc_start: 0.2001 (mtp) cc_final: 0.1142 (ptm) outliers start: 52 outliers final: 44 residues processed: 244 average time/residue: 0.1791 time to fit residues: 74.7115 Evaluate side-chains 234 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain F residue 113 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 114 optimal weight: 0.0000 chunk 26 optimal weight: 0.0770 chunk 119 optimal weight: 0.4980 chunk 363 optimal weight: 0.0070 chunk 290 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 214 optimal weight: 0.0370 chunk 29 optimal weight: 0.0170 chunk 76 optimal weight: 0.0020 chunk 328 optimal weight: 40.0000 overall best weight: 0.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 869 GLN C 853 ASN C1132 ASN A 311 GLN A 932 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.209574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.201201 restraints weight = 39134.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.179244 restraints weight = 107409.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.168751 restraints weight = 96400.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.165967 restraints weight = 75614.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.165066 restraints weight = 64635.314| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31517 Z= 0.087 Angle : 0.494 14.865 42983 Z= 0.252 Chirality : 0.043 0.275 4970 Planarity : 0.004 0.062 5451 Dihedral : 4.180 50.752 5245 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.37 % Rotamer: Outliers : 0.99 % Allowed : 11.76 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.52 (0.14), residues: 3797 helix: 2.04 (0.20), residues: 691 sheet: 0.38 (0.16), residues: 1077 loop : -0.22 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.023 0.001 TYR C 170 PHE 0.013 0.001 PHE B 65 TRP 0.030 0.001 TRP A 104 HIS 0.005 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00183 (31417) covalent geometry : angle 0.47834 (42731) SS BOND : bond 0.00244 ( 48) SS BOND : angle 0.83318 ( 96) hydrogen bonds : bond 0.03129 ( 1268) hydrogen bonds : angle 5.00603 ( 3558) link_BETA1-4 : bond 0.00402 ( 12) link_BETA1-4 : angle 0.97724 ( 36) link_NAG-ASN : bond 0.00433 ( 40) link_NAG-ASN : angle 2.25790 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 1.111 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: B 177 MET cc_start: -0.3761 (ttm) cc_final: -0.4387 (mmt) REVERT: C 177 MET cc_start: -0.3645 (mmt) cc_final: -0.4907 (mtt) REVERT: C 302 SER cc_start: 0.8795 (t) cc_final: 0.8457 (p) REVERT: C 1042 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7164 (mtpp) REVERT: C 1125 VAL cc_start: 0.8424 (t) cc_final: 0.8149 (m) REVERT: A 856 THR cc_start: 0.8593 (p) cc_final: 0.8340 (t) REVERT: A 1007 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: H 48 MET cc_start: 0.1893 (mtp) cc_final: 0.1075 (ptm) REVERT: F 113 MET cc_start: 0.3790 (OUTLIER) cc_final: 0.3402 (tpp) outliers start: 33 outliers final: 27 residues processed: 250 average time/residue: 0.1794 time to fit residues: 76.5279 Evaluate side-chains 230 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 1042 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain F residue 113 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 360 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 180 optimal weight: 0.0070 chunk 339 optimal weight: 40.0000 chunk 271 optimal weight: 0.6980 chunk 355 optimal weight: 20.0000 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 904 ASN C 801 GLN C 932 GLN C 946 GLN A 268 GLN A 311 GLN A 954 GLN K 89 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.207691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.199743 restraints weight = 39372.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.199051 restraints weight = 92114.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178952 restraints weight = 90886.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.170032 restraints weight = 84636.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.166082 restraints weight = 71240.018| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31517 Z= 0.113 Angle : 0.512 14.022 42983 Z= 0.260 Chirality : 0.043 0.280 4970 Planarity : 0.004 0.062 5451 Dihedral : 4.169 45.247 5241 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 1.02 % Allowed : 12.06 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.55 (0.14), residues: 3797 helix: 2.09 (0.20), residues: 673 sheet: 0.43 (0.16), residues: 1085 loop : -0.20 (0.14), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.021 0.001 TYR A1135 PHE 0.018 0.001 PHE C 538 TRP 0.027 0.001 TRP A 104 HIS 0.003 0.001 HIS A 652 Details of bonding type rmsd covalent geometry : bond 0.00256 (31417) covalent geometry : angle 0.49507 (42731) SS BOND : bond 0.00287 ( 48) SS BOND : angle 1.25405 ( 96) hydrogen bonds : bond 0.03397 ( 1268) hydrogen bonds : angle 5.04410 ( 3558) link_BETA1-4 : bond 0.00322 ( 12) link_BETA1-4 : angle 0.98111 ( 36) link_NAG-ASN : bond 0.00391 ( 40) link_NAG-ASN : angle 2.24014 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4780.35 seconds wall clock time: 84 minutes 3.64 seconds (5043.64 seconds total)