Starting phenix.real_space_refine on Mon Jul 6 03:23:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7we7_32441/07_2026/7we7_32441.cif Found real_map, /net/cci-nas-00/data/ceres_data/7we7_32441/07_2026/7we7_32441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7we7_32441/07_2026/7we7_32441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7we7_32441/07_2026/7we7_32441.map" model { file = "/net/cci-nas-00/data/ceres_data/7we7_32441/07_2026/7we7_32441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7we7_32441/07_2026/7we7_32441.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7we7_32441/07_2026/7we7_32441.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7we7_32441/07_2026/7we7_32441.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.058 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 135 5.16 5 C 20394 2.51 5 N 5274 2.21 5 O 6292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32095 Number of models: 1 Model: "" Number of chains: 33 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "D" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "E" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "G" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "M" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.10, per 1000 atoms: 0.22 Number of scatterers: 32095 At special positions: 0 Unit cell: (157.29, 141.24, 233.26, 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 135 16.00 O 6292 8.00 N 5274 7.00 C 20394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 134 " distance=2.03 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 288 " - pdb=" SG CYS D 298 " distance=2.03 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 358 " distance=2.03 Simple disulfide: pdb=" SG CYS D 376 " - pdb=" SG CYS D 429 " distance=2.04 Simple disulfide: pdb=" SG CYS D 388 " - pdb=" SG CYS D 522 " distance=2.03 Simple disulfide: pdb=" SG CYS D 477 " - pdb=" SG CYS D 485 " distance=2.03 Simple disulfide: pdb=" SG CYS D 614 " - pdb=" SG CYS D 646 " distance=2.03 Simple disulfide: pdb=" SG CYS D 659 " - pdb=" SG CYS D 668 " distance=2.03 Simple disulfide: pdb=" SG CYS D 735 " - pdb=" SG CYS D 757 " distance=2.03 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 746 " distance=2.03 Simple disulfide: pdb=" SG CYS D1029 " - pdb=" SG CYS D1040 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 134 " distance=2.03 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 298 " distance=2.03 Simple disulfide: pdb=" SG CYS E 333 " - pdb=" SG CYS E 358 " distance=2.03 Simple disulfide: pdb=" SG CYS E 376 " - pdb=" SG CYS E 429 " distance=2.04 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 522 " distance=2.03 Simple disulfide: pdb=" SG CYS E 477 " - pdb=" SG CYS E 485 " distance=2.03 Simple disulfide: pdb=" SG CYS E 614 " - pdb=" SG CYS E 646 " distance=2.03 Simple disulfide: pdb=" SG CYS E 659 " - pdb=" SG CYS E 668 " distance=2.03 Simple disulfide: pdb=" SG CYS E 735 " - pdb=" SG CYS E 757 " distance=2.03 Simple disulfide: pdb=" SG CYS E 740 " - pdb=" SG CYS E 746 " distance=2.03 Simple disulfide: pdb=" SG CYS E1029 " - pdb=" SG CYS E1040 " distance=2.03 Simple disulfide: pdb=" SG CYS E1079 " - pdb=" SG CYS E1123 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 136 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 163 " distance=2.03 Simple disulfide: pdb=" SG CYS G 290 " - pdb=" SG CYS G 300 " distance=2.03 Simple disulfide: pdb=" SG CYS G 335 " - pdb=" SG CYS G 360 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 431 " distance=2.04 Simple disulfide: pdb=" SG CYS G 390 " - pdb=" SG CYS G 524 " distance=2.03 Simple disulfide: pdb=" SG CYS G 479 " - pdb=" SG CYS G 487 " distance=2.03 Simple disulfide: pdb=" SG CYS G 616 " - pdb=" SG CYS G 648 " distance=2.03 Simple disulfide: pdb=" SG CYS G 661 " - pdb=" SG CYS G 670 " distance=2.03 Simple disulfide: pdb=" SG CYS G 737 " - pdb=" SG CYS G 759 " distance=2.03 Simple disulfide: pdb=" SG CYS G 742 " - pdb=" SG CYS G 748 " distance=2.03 Simple disulfide: pdb=" SG CYS G1031 " - pdb=" SG CYS G1042 " distance=2.03 Simple disulfide: pdb=" SG CYS G1081 " - pdb=" SG CYS G1125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=1.94 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.51 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 1 " - " ASN D 231 " " NAG B 1 " - " ASN D 328 " " NAG C 1 " - " ASN D 714 " " NAG D1302 " - " ASN D1155 " " NAG D1303 " - " ASN D 143 " " NAG D1304 " - " ASN D 17 " " NAG D1305 " - " ASN D 61 " " NAG D1306 " - " ASN D 600 " " NAG D1307 " - " ASN D 654 " " NAG D1308 " - " ASN D 613 " " NAG D1309 " - " ASN D 706 " " NAG E1301 " - " ASN E1155 " " NAG E1302 " - " ASN E 123 " " NAG E1303 " - " ASN E 143 " " NAG E1304 " - " ASN E 17 " " NAG E1305 " - " ASN E 61 " " NAG E1306 " - " ASN E 600 " " NAG E1307 " - " ASN E 654 " " NAG E1308 " - " ASN E 613 " " NAG E1309 " - " ASN E 706 " " NAG F 1 " - " ASN D1071 " " NAG G1301 " - " ASN G1157 " " NAG G1302 " - " ASN G 125 " " NAG G1303 " - " ASN G 145 " " NAG G1304 " - " ASN G 17 " " NAG G1305 " - " ASN G 61 " " NAG G1306 " - " ASN G 602 " " NAG G1307 " - " ASN G 656 " " NAG G1308 " - " ASN G 615 " " NAG G1309 " - " ASN G 708 " " NAG I 1 " - " ASN D 798 " " NAG O 1 " - " ASN D1095 " " NAG P 1 " - " ASN D1131 " " NAG S 1 " - " ASN E 714 " " NAG U 1 " - " ASN E 798 " " NAG V 1 " - " ASN E1095 " " NAG W 1 " - " ASN E1131 " " NAG X 1 " - " ASN G 233 " " NAG Z 1 " - " ASN G 716 " " NAG b 1 " - " ASN G 800 " " NAG c 1 " - " ASN G1097 " " NAG d 1 " - " ASN G1133 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7416 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 67 sheets defined 21.2% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.562A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.222A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.823A pdb=" N VAL D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 362 through 367 removed outlier: 3.501A pdb=" N ASN D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 402 through 408 removed outlier: 5.347A pdb=" N ARG D 405 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 616 through 621 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 743 through 752 removed outlier: 3.722A pdb=" N GLN D 752 " --> pdb=" O ASN D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 779 removed outlier: 3.620A pdb=" N LEU D 760 " --> pdb=" O PHE D 756 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 767 " --> pdb=" O ALA D 763 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP D 772 " --> pdb=" O ALA D 768 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS D 773 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN D 776 " --> pdb=" O ASP D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 822 Processing helix chain 'D' and resid 863 through 879 removed outlier: 3.528A pdb=" N ALA D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN D 869 " --> pdb=" O GLU D 865 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 907 removed outlier: 3.664A pdb=" N MET D 899 " --> pdb=" O PHE D 895 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR D 901 " --> pdb=" O MET D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 removed outlier: 3.838A pdb=" N TYR D 914 " --> pdb=" O GLN D 910 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 915 " --> pdb=" O ASN D 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 910 through 915' Processing helix chain 'D' and resid 916 through 938 removed outlier: 3.672A pdb=" N ASN D 922 " --> pdb=" O LYS D 918 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN D 932 " --> pdb=" O ILE D 928 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP D 933 " --> pdb=" O GLY D 929 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 938 " --> pdb=" O SER D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 963 removed outlier: 3.535A pdb=" N ASN D 952 " --> pdb=" O VAL D 948 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN D 957 " --> pdb=" O ALA D 953 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 974 through 979 removed outlier: 4.013A pdb=" N PHE D 978 " --> pdb=" O LEU D 974 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 1029 removed outlier: 4.265A pdb=" N GLU D 987 " --> pdb=" O LYS D 983 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL D 988 " --> pdb=" O VAL D 984 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 993 " --> pdb=" O GLN D 989 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY D 996 " --> pdb=" O ARG D 992 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D1021 " --> pdb=" O ALA D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1113 through 1115 No H-bonds generated for 'chain 'D' and resid 1113 through 1115' Processing helix chain 'D' and resid 1138 through 1158 removed outlier: 3.578A pdb=" N PHE D1145 " --> pdb=" O GLU D1141 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS D1151 " --> pdb=" O GLU D1147 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 380 through 384 removed outlier: 3.582A pdb=" N LEU E 384 " --> pdb=" O PRO E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 419 Processing helix chain 'E' and resid 615 through 620 removed outlier: 3.665A pdb=" N VAL E 619 " --> pdb=" O THR E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 636 removed outlier: 3.558A pdb=" N TYR E 633 " --> pdb=" O TRP E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 741 Processing helix chain 'E' and resid 743 through 751 removed outlier: 3.698A pdb=" N ASN E 748 " --> pdb=" O THR E 744 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU E 749 " --> pdb=" O GLU E 745 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 751 " --> pdb=" O SER E 747 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 756 removed outlier: 6.979A pdb=" N SER E 755 " --> pdb=" O GLN E 752 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 756 " --> pdb=" O TYR E 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 752 through 756' Processing helix chain 'E' and resid 757 through 775 removed outlier: 3.530A pdb=" N LYS E 761 " --> pdb=" O CYS E 757 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 762 " --> pdb=" O THR E 758 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP E 772 " --> pdb=" O ALA E 768 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR E 775 " --> pdb=" O GLN E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 776 through 778 No H-bonds generated for 'chain 'E' and resid 776 through 778' Processing helix chain 'E' and resid 813 through 823 removed outlier: 3.761A pdb=" N LEU E 818 " --> pdb=" O PHE E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 847 through 853 removed outlier: 3.721A pdb=" N LYS E 851 " --> pdb=" O ILE E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 863 through 878 removed outlier: 3.720A pdb=" N THR E 878 " --> pdb=" O LEU E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 883 through 887 Processing helix chain 'E' and resid 894 through 907 removed outlier: 3.852A pdb=" N MET E 899 " --> pdb=" O PHE E 895 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA E 900 " --> pdb=" O ALA E 896 " (cutoff:3.500A) Processing helix chain 'E' and resid 910 through 915 removed outlier: 3.732A pdb=" N TYR E 914 " --> pdb=" O GLN E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 938 removed outlier: 3.524A pdb=" N LYS E 930 " --> pdb=" O SER E 926 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 931 " --> pdb=" O ALA E 927 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN E 932 " --> pdb=" O ILE E 928 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 936 " --> pdb=" O GLN E 932 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR E 938 " --> pdb=" O SER E 934 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 963 removed outlier: 4.450A pdb=" N VAL E 948 " --> pdb=" O LYS E 944 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 963 " --> pdb=" O LEU E 959 " (cutoff:3.500A) Processing helix chain 'E' and resid 973 through 981 removed outlier: 4.050A pdb=" N ILE E 977 " --> pdb=" O VAL E 973 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE E 978 " --> pdb=" O LEU E 974 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 1029 removed outlier: 4.139A pdb=" N GLU E 987 " --> pdb=" O LYS E 983 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL E 988 " --> pdb=" O VAL E 984 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG E 992 " --> pdb=" O VAL E 988 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU E 993 " --> pdb=" O GLN E 989 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE E1010 " --> pdb=" O THR E1006 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER E1018 " --> pdb=" O GLU E1014 " (cutoff:3.500A) Processing helix chain 'E' and resid 1113 through 1115 No H-bonds generated for 'chain 'E' and resid 1113 through 1115' Processing helix chain 'E' and resid 1137 through 1144 removed outlier: 4.038A pdb=" N GLU E1141 " --> pdb=" O PRO E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1145 through 1158 Processing helix chain 'G' and resid 293 through 302 Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'G' and resid 364 through 370 Processing helix chain 'G' and resid 382 through 388 removed outlier: 4.205A pdb=" N LEU G 386 " --> pdb=" O PRO G 383 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASN G 387 " --> pdb=" O THR G 384 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP G 388 " --> pdb=" O LYS G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 410 removed outlier: 4.982A pdb=" N ARG G 407 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA G 410 " --> pdb=" O ARG G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 618 through 623 Processing helix chain 'G' and resid 737 through 743 removed outlier: 3.904A pdb=" N ILE G 741 " --> pdb=" O CYS G 737 " (cutoff:3.500A) Processing helix chain 'G' and resid 745 through 752 removed outlier: 3.564A pdb=" N LEU G 751 " --> pdb=" O GLU G 747 " (cutoff:3.500A) Processing helix chain 'G' and resid 753 through 756 removed outlier: 3.575A pdb=" N GLY G 756 " --> pdb=" O LEU G 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 753 through 756' Processing helix chain 'G' and resid 759 through 781 removed outlier: 3.693A pdb=" N THR G 777 " --> pdb=" O GLN G 773 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 823 removed outlier: 3.735A pdb=" N LEU G 820 " --> pdb=" O PHE G 816 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE G 822 " --> pdb=" O GLU G 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 865 through 880 removed outlier: 4.461A pdb=" N GLN G 871 " --> pdb=" O GLU G 867 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 872 " --> pdb=" O MET G 868 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR G 873 " --> pdb=" O ILE G 869 " (cutoff:3.500A) Processing helix chain 'G' and resid 885 through 889 removed outlier: 3.769A pdb=" N GLY G 888 " --> pdb=" O TRP G 885 " (cutoff:3.500A) Processing helix chain 'G' and resid 896 through 909 removed outlier: 3.695A pdb=" N MET G 901 " --> pdb=" O PHE G 897 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA G 902 " --> pdb=" O ALA G 898 " (cutoff:3.500A) Processing helix chain 'G' and resid 912 through 917 removed outlier: 3.689A pdb=" N TYR G 916 " --> pdb=" O GLN G 912 " (cutoff:3.500A) Processing helix chain 'G' and resid 918 through 940 removed outlier: 3.741A pdb=" N ALA G 929 " --> pdb=" O GLN G 925 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE G 933 " --> pdb=" O ALA G 929 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN G 934 " --> pdb=" O ILE G 930 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP G 935 " --> pdb=" O GLY G 931 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER G 938 " --> pdb=" O GLN G 934 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR G 940 " --> pdb=" O SER G 936 " (cutoff:3.500A) Processing helix chain 'G' and resid 941 through 943 No H-bonds generated for 'chain 'G' and resid 941 through 943' Processing helix chain 'G' and resid 944 through 964 removed outlier: 3.575A pdb=" N ASP G 949 " --> pdb=" O GLY G 945 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL G 950 " --> pdb=" O LYS G 946 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL G 951 " --> pdb=" O LEU G 947 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN G 954 " --> pdb=" O VAL G 950 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN G 959 " --> pdb=" O ALA G 955 " (cutoff:3.500A) Processing helix chain 'G' and resid 965 through 967 No H-bonds generated for 'chain 'G' and resid 965 through 967' Processing helix chain 'G' and resid 975 through 983 removed outlier: 3.623A pdb=" N ILE G 979 " --> pdb=" O VAL G 975 " (cutoff:3.500A) Processing helix chain 'G' and resid 984 through 1031 removed outlier: 4.045A pdb=" N GLU G 989 " --> pdb=" O LYS G 985 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL G 990 " --> pdb=" O VAL G 986 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN G 991 " --> pdb=" O GLU G 987 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 998 " --> pdb=" O ARG G 994 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR G1006 " --> pdb=" O SER G1002 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG G1013 " --> pdb=" O GLN G1009 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA G1019 " --> pdb=" O ALA G1015 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU G1023 " --> pdb=" O ALA G1019 " (cutoff:3.500A) Processing helix chain 'G' and resid 1115 through 1117 No H-bonds generated for 'chain 'G' and resid 1115 through 1117' Processing helix chain 'G' and resid 1141 through 1160 removed outlier: 3.925A pdb=" N SER G1146 " --> pdb=" O PRO G1142 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE G1147 " --> pdb=" O GLU G1143 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU G1149 " --> pdb=" O ASP G1145 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU G1150 " --> pdb=" O SER G1146 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER G1160 " --> pdb=" O LYS G1156 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'M' and resid 80 through 84 removed outlier: 4.066A pdb=" N GLU M 84 " --> pdb=" O SER M 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'N' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.486A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AA3, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.941A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 10 Processing sheet with id=AA6, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 31 removed outlier: 7.851A pdb=" N ASN D 61 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR D 266 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 261 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN D 183 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER D 200 " --> pdb=" O PRO D 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.718A pdb=" N ASP D 284 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.742A pdb=" N GLY D 101 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 128 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE D 163 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 311 removed outlier: 3.779A pdb=" N THR D 596 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR D 609 " --> pdb=" O CYS D 646 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS D 646 " --> pdb=" O TYR D 609 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY D 645 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 351 through 355 removed outlier: 3.628A pdb=" N ASN D 351 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 396 " --> pdb=" O ASN D 351 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 430 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS D 375 " --> pdb=" O VAL D 430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 358 through 359 removed outlier: 7.323A pdb=" N CYS D 358 " --> pdb=" O CYS D 522 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 449 through 451 Processing sheet with id=AB5, first strand: chain 'D' and resid 470 through 471 removed outlier: 3.601A pdb=" N TYR D 470 " --> pdb=" O TYR D 486 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 539 through 540 removed outlier: 3.640A pdb=" N PHE D 540 " --> pdb=" O LEU D 543 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 548 through 551 removed outlier: 3.536A pdb=" N THR D 585 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 661 through 662 removed outlier: 3.734A pdb=" N GLN D 672 " --> pdb=" O SER D 688 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 708 through 712 Processing sheet with id=AC1, first strand: chain 'D' and resid 715 through 725 removed outlier: 3.635A pdb=" N SER D 718 " --> pdb=" O THR D1063 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR D1064 " --> pdb=" O HIS D1045 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N HIS D1045 " --> pdb=" O TYR D1064 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 732 through 733 Processing sheet with id=AC3, first strand: chain 'D' and resid 785 through 787 removed outlier: 5.290A pdb=" N ILE D 785 " --> pdb=" O ASN E 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 1117 through 1122 removed outlier: 3.512A pdb=" N SER D1120 " --> pdb=" O ALA D1084 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA D1084 " --> pdb=" O SER D1120 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 27 through 31 removed outlier: 7.927A pdb=" N ASN E 61 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR E 266 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE E 196 " --> pdb=" O ASP E 225 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP E 225 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE E 198 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS E 202 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N ALA E 219 " --> pdb=" O HIS E 202 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL E 36 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 42 through 44 removed outlier: 6.535A pdb=" N GLY G 565 " --> pdb=" O ASP G 573 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.726A pdb=" N ASP E 284 " --> pdb=" O LYS E 275 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 82 through 83 Processing sheet with id=AC9, first strand: chain 'E' and resid 109 through 114 removed outlier: 6.042A pdb=" N THR E 112 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 131 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 118 " --> pdb=" O VAL E 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 109 through 114 removed outlier: 6.042A pdb=" N THR E 112 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 131 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL E 128 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE E 163 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 308 through 315 removed outlier: 3.670A pdb=" N THR E 596 " --> pdb=" O GLY E 308 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL E 592 " --> pdb=" O THR E 312 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN E 314 " --> pdb=" O GLY E 590 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY E 590 " --> pdb=" O ASN E 314 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY E 591 " --> pdb=" O GLN E 610 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 321 through 325 removed outlier: 4.338A pdb=" N GLU E 321 " --> pdb=" O CYS E 535 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 321 through 325 removed outlier: 4.338A pdb=" N GLU E 321 " --> pdb=" O CYS E 535 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP E 583 " --> pdb=" O THR E 550 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 351 through 355 removed outlier: 4.096A pdb=" N ASN E 351 " --> pdb=" O SER E 396 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER E 396 " --> pdb=" O ASN E 351 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E 392 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS E 429 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA E 432 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 358 through 359 removed outlier: 7.372A pdb=" N CYS E 358 " --> pdb=" O CYS E 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 449 through 451 Processing sheet with id=AD8, first strand: chain 'E' and resid 470 through 471 Processing sheet with id=AD9, first strand: chain 'E' and resid 651 through 657 removed outlier: 6.699A pdb=" N GLU E 651 " --> pdb=" O ALA E 691 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N THR E 693 " --> pdb=" O GLU E 651 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N VAL E 653 " --> pdb=" O THR E 693 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER E 688 " --> pdb=" O GLN E 672 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN E 672 " --> pdb=" O SER E 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR E 692 " --> pdb=" O CYS E 668 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 708 through 712 removed outlier: 3.628A pdb=" N ILE E 711 " --> pdb=" O LYS E1070 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E1073 " --> pdb=" O SER E1094 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E1075 " --> pdb=" O PHE E1092 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE E1092 " --> pdb=" O ALA E1075 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL E1091 " --> pdb=" O THR E1102 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E1102 " --> pdb=" O VAL E1091 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 715 through 725 removed outlier: 7.182A pdb=" N GLY E1056 " --> pdb=" O SER E1052 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER E1052 " --> pdb=" O GLY E1056 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL E1058 " --> pdb=" O PRO E1050 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU E1060 " --> pdb=" O SER E1048 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER E1048 " --> pdb=" O LEU E1060 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL E1062 " --> pdb=" O LEU E1046 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 732 through 733 Processing sheet with id=AE4, first strand: chain 'E' and resid 1117 through 1122 removed outlier: 3.523A pdb=" N PHE E1086 " --> pdb=" O PHE E1118 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E1120 " --> pdb=" O ALA E1084 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA E1084 " --> pdb=" O SER E1120 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 27 through 30 removed outlier: 7.947A pdb=" N ASN G 61 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR G 268 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA G 263 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SER G 202 " --> pdb=" O PRO G 224 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 36 through 37 removed outlier: 6.442A pdb=" N VAL G 36 " --> pdb=" O LEU G 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'G' and resid 48 through 55 removed outlier: 3.634A pdb=" N ASP G 286 " --> pdb=" O LYS G 277 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 103 through 106 removed outlier: 3.861A pdb=" N PHE G 165 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 310 through 313 removed outlier: 3.557A pdb=" N THR G 598 " --> pdb=" O GLY G 310 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS G 648 " --> pdb=" O TYR G 611 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 355 through 357 removed outlier: 4.538A pdb=" N VAL G 432 " --> pdb=" O LYS G 377 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS G 377 " --> pdb=" O VAL G 432 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR G 375 " --> pdb=" O ALA G 434 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 360 through 361 removed outlier: 6.827A pdb=" N CYS G 360 " --> pdb=" O CYS G 524 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 451 through 453 Processing sheet with id=AF4, first strand: chain 'G' and resid 472 through 473 removed outlier: 3.558A pdb=" N TYR G 472 " --> pdb=" O TYR G 488 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 541 through 542 removed outlier: 3.593A pdb=" N PHE G 542 " --> pdb=" O LEU G 545 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 550 through 551 Processing sheet with id=AF7, first strand: chain 'G' and resid 653 through 659 removed outlier: 3.564A pdb=" N ALA G 693 " --> pdb=" O GLU G 653 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR G 695 " --> pdb=" O VAL G 655 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASN G 657 " --> pdb=" O THR G 695 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 710 through 714 removed outlier: 3.680A pdb=" N THR G1075 " --> pdb=" O SER G1096 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 717 through 727 removed outlier: 3.504A pdb=" N MET G1049 " --> pdb=" O VAL G1064 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR G1066 " --> pdb=" O HIS G1047 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N HIS G1047 " --> pdb=" O TYR G1066 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 732 through 734 removed outlier: 4.273A pdb=" N LYS G 732 " --> pdb=" O LEU G 860 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER G 734 " --> pdb=" O THR G 858 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 1119 through 1124 removed outlier: 6.164A pdb=" N VAL G1121 " --> pdb=" O PHE G1088 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE G1088 " --> pdb=" O VAL G1121 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY G1123 " --> pdb=" O ALA G1086 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AG4, first strand: chain 'J' and resid 58 through 60 removed outlier: 3.564A pdb=" N GLY J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL J 93 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AG6, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AG7, first strand: chain 'M' and resid 46 through 49 removed outlier: 6.721A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 46 through 49 removed outlier: 6.721A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.523A pdb=" N ALA K 118 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 19 through 23 removed outlier: 4.185A pdb=" N THR K 78 " --> pdb=" O ASP K 73 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP K 73 " --> pdb=" O THR K 78 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.032A pdb=" N ALA N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.032A pdb=" N ALA N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 18 through 23 1070 hydrogen bonds defined for protein. 2793 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: 7.63 Time building geometry restraints manager: 4.62 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: 8978 1.33 - 1.46: 8197 1.46 - 1.58: 15484 1.58 - 1.71: 0 1.71 - 1.83: 171 Bond restraints: 32830 Sorted by residual: bond pdb=" N ARG M 55 " pdb=" CA ARG M 55 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.87e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" N VAL K 37 " pdb=" CA VAL K 37 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" N ILE N 49 " pdb=" CA ILE N 49 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.29e+01 bond pdb=" N VAL H 93 " pdb=" CA VAL H 93 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.29e+01 ... (remaining 32825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 42251 1.63 - 3.26: 2057 3.26 - 4.89: 278 4.89 - 6.52: 42 6.52 - 8.15: 12 Bond angle restraints: 44640 Sorted by residual: angle pdb=" CA PRO M 56 " pdb=" C PRO M 56 " pdb=" O PRO M 56 " ideal model delta sigma weight residual 121.31 116.63 4.68 7.40e-01 1.83e+00 4.00e+01 angle pdb=" N LEU E 139 " pdb=" CA LEU E 139 " pdb=" C LEU E 139 " ideal model delta sigma weight residual 112.92 105.30 7.62 1.23e+00 6.61e-01 3.84e+01 angle pdb=" CA GLY J 114 " pdb=" C GLY J 114 " pdb=" O GLY J 114 " ideal model delta sigma weight residual 122.23 118.27 3.96 6.90e-01 2.10e+00 3.29e+01 angle pdb=" CA GLY K 114 " pdb=" C GLY K 114 " pdb=" O GLY K 114 " ideal model delta sigma weight residual 122.23 118.37 3.86 6.90e-01 2.10e+00 3.14e+01 angle pdb=" CA GLY H 114 " pdb=" C GLY H 114 " pdb=" O GLY H 114 " ideal model delta sigma weight residual 121.77 117.58 4.19 8.60e-01 1.35e+00 2.37e+01 ... (remaining 44635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 17093 17.77 - 35.55: 1529 35.55 - 53.32: 251 53.32 - 71.10: 52 71.10 - 88.87: 20 Dihedral angle restraints: 18945 sinusoidal: 7392 harmonic: 11553 Sorted by residual: dihedral pdb=" CB CYS G 479 " pdb=" SG CYS G 479 " pdb=" SG CYS G 487 " pdb=" CB CYS G 487 " ideal model delta sinusoidal sigma weight residual 93.00 37.84 55.16 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CB CYS E 477 " pdb=" SG CYS E 477 " pdb=" SG CYS E 485 " pdb=" CB CYS E 485 " ideal model delta sinusoidal sigma weight residual 93.00 147.89 -54.89 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS E 740 " pdb=" SG CYS E 740 " pdb=" SG CYS E 746 " pdb=" CB CYS E 746 " ideal model delta sinusoidal sigma weight residual -86.00 -32.69 -53.31 1 1.00e+01 1.00e-02 3.86e+01 ... (remaining 18942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 5004 0.116 - 0.232: 185 0.232 - 0.347: 24 0.347 - 0.463: 1 0.463 - 0.579: 1 Chirality restraints: 5215 Sorted by residual: chirality pdb=" C1 NAG E1302 " pdb=" ND2 ASN E 123 " pdb=" C2 NAG E1302 " pdb=" O5 NAG E1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" CA ASN G 146 " pdb=" N ASN G 146 " pdb=" C ASN G 146 " pdb=" CB ASN G 146 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C1 NAG E1304 " pdb=" ND2 ASN E 17 " pdb=" C2 NAG E1304 " pdb=" O5 NAG E1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 5212 not shown) Planarity restraints: 5709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1303 " -0.151 2.00e-02 2.50e+03 1.25e-01 1.96e+02 pdb=" C7 NAG E1303 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG E1303 " -0.113 2.00e-02 2.50e+03 pdb=" N2 NAG E1303 " 0.202 2.00e-02 2.50e+03 pdb=" O7 NAG E1303 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1302 " 0.137 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" C7 NAG E1302 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG E1302 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG E1302 " -0.183 2.00e-02 2.50e+03 pdb=" O7 NAG E1302 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1304 " 0.100 2.00e-02 2.50e+03 8.26e-02 8.53e+01 pdb=" C7 NAG E1304 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG E1304 " 0.076 2.00e-02 2.50e+03 pdb=" N2 NAG E1304 " -0.131 2.00e-02 2.50e+03 pdb=" O7 NAG E1304 " -0.016 2.00e-02 2.50e+03 ... (remaining 5706 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 7 2.08 - 2.79: 7433 2.79 - 3.49: 44358 3.49 - 4.20: 75749 4.20 - 4.90: 128630 Nonbonded interactions: 256177 Sorted by model distance: nonbonded pdb=" CG PHE H 106 " pdb=" OG SER D 443 " model vdw 1.378 3.260 nonbonded pdb=" CD1 PHE H 106 " pdb=" OG SER D 443 " model vdw 1.453 3.340 nonbonded pdb=" OG SER E 443 " pdb=" CB PHE J 106 " model vdw 1.710 3.440 nonbonded pdb=" OG SER E 443 " pdb=" CG PHE J 106 " model vdw 1.939 3.260 nonbonded pdb=" CB PHE H 106 " pdb=" OG SER D 443 " model vdw 1.976 3.440 ... (remaining 256172 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'W' selection = chain 'c' selection = chain 'd' } 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.650 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 0.483 32949 Z= 0.366 Angle : 0.787 31.534 44934 Z= 0.471 Chirality : 0.055 0.579 5215 Planarity : 0.004 0.125 5667 Dihedral : 13.636 88.874 11394 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.95 % Favored : 94.92 % Rotamer: Outliers : 0.87 % Allowed : 1.45 % Favored : 97.69 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 3939 helix: -0.98 (0.19), residues: 725 sheet: -0.36 (0.17), residues: 903 loop : -1.00 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 155 TYR 0.014 0.001 TYR H 94 PHE 0.017 0.001 PHE G 198 TRP 0.028 0.002 TRP G 632 HIS 0.003 0.001 HIS D1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.34 (32830) covalent geometry : angle 0.75902 / 0.46 (44640) SS BOND : bond 0.07330 / 5.31 ( 45) SS BOND : angle 3.81970 / 3.37 ( 90) hydrogen bonds : bond 0.25237 / 16.60 ( 1046) hydrogen bonds : angle 9.42946 / 6.59 ( 2793) Misc. bond : bond 0.00267 / 0.13 ( 6) link_BETA1-4 : bond 0.00481 / 0.31 ( 26) link_BETA1-4 : angle 1.21823 / 0.83 ( 78) link_NAG-ASN : bond 0.00590 / 0.43 ( 42) link_NAG-ASN : angle 2.37354 / 1.71 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 SER cc_start: 0.3548 (OUTLIER) cc_final: 0.3150 (m) REVERT: H 45 LEU cc_start: 0.7475 (mm) cc_final: 0.7191 (mm) REVERT: D 132 GLN cc_start: 0.8656 (mm110) cc_final: 0.8038 (tm-30) REVERT: E 172 MET cc_start: 0.2658 (mtt) cc_final: 0.1514 (mtt) REVERT: E 559 PHE cc_start: 0.7833 (p90) cc_final: 0.7581 (p90) REVERT: E 1147 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8039 (mp0) REVERT: J 111 TRP cc_start: 0.1699 (m-90) cc_final: 0.0926 (m-90) outliers start: 30 outliers final: 9 residues processed: 212 average time/residue: 0.2004 time to fit residues: 70.4657 Evaluate side-chains 128 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain M residue 16 GLN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 110 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1033 GLN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 954 GLN ** E1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 852 GLN G 925 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 113 GLN M 39 GLN N 38 GLN N 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.111931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.075789 restraints weight = 122385.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.075194 restraints weight = 76830.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.075062 restraints weight = 61207.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.075523 restraints weight = 63229.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.075895 restraints weight = 51490.680| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32949 Z= 0.163 Angle : 0.636 13.296 44934 Z= 0.323 Chirality : 0.046 0.360 5215 Planarity : 0.004 0.049 5667 Dihedral : 4.951 59.102 4294 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 0.64 % Allowed : 6.31 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 3939 helix: -0.73 (0.18), residues: 769 sheet: -0.30 (0.17), residues: 934 loop : -0.98 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 98 TYR 0.028 0.001 TYR N 50 PHE 0.018 0.001 PHE N 63 TRP 0.020 0.001 TRP G 632 HIS 0.005 0.001 HIS G 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (32830) covalent geometry : angle 0.62520 / 0.32 (44640) SS BOND : bond 0.00302 / 0.19 ( 45) SS BOND : angle 1.08618 / 0.74 ( 90) hydrogen bonds : bond 0.05328 / 3.53 ( 1046) hydrogen bonds : angle 6.74275 / 4.78 ( 2793) Misc. bond : bond 0.00213 / 0.10 ( 6) link_BETA1-4 : bond 0.00491 / 0.29 ( 26) link_BETA1-4 : angle 1.40455 / 1.03 ( 78) link_NAG-ASN : bond 0.00370 / 0.26 ( 42) link_NAG-ASN : angle 1.89533 / 1.43 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8083 (t0) cc_final: 0.7729 (t0) REVERT: H 76 THR cc_start: 0.8539 (p) cc_final: 0.8229 (p) REVERT: L 16 GLN cc_start: 0.6519 (pt0) cc_final: 0.6176 (pm20) REVERT: D 999 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7878 (tm-30) REVERT: E 172 MET cc_start: 0.3422 (mtt) cc_final: 0.2158 (mtt) REVERT: E 217 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: G 368 TYR cc_start: 0.8046 (t80) cc_final: 0.7651 (t80) REVERT: J 111 TRP cc_start: 0.2828 (m-90) cc_final: 0.1759 (m-90) outliers start: 22 outliers final: 14 residues processed: 162 average time/residue: 0.1711 time to fit residues: 48.2408 Evaluate side-chains 138 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 382 optimal weight: 1.9990 chunk 319 optimal weight: 0.0980 chunk 365 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 329 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 231 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 386 optimal weight: 40.0000 chunk 300 optimal weight: 6.9990 chunk 283 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 750 ASN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN M 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.111683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.074895 restraints weight = 122628.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.074580 restraints weight = 75241.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.074488 restraints weight = 58394.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.074818 restraints weight = 62894.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.075027 restraints weight = 52170.890| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32949 Z= 0.162 Angle : 0.592 10.536 44934 Z= 0.300 Chirality : 0.045 0.365 5215 Planarity : 0.004 0.050 5667 Dihedral : 4.757 58.883 4289 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.67 % Rotamer: Outliers : 0.84 % Allowed : 10.10 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 3939 helix: -0.54 (0.19), residues: 768 sheet: -0.24 (0.17), residues: 914 loop : -0.97 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 902 TYR 0.024 0.001 TYR D 393 PHE 0.018 0.001 PHE N 63 TRP 0.023 0.001 TRP G 104 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (32830) covalent geometry : angle 0.58191 / 0.30 (44640) SS BOND : bond 0.00246 / 0.15 ( 45) SS BOND : angle 0.90427 / 0.62 ( 90) hydrogen bonds : bond 0.04530 / 3.03 ( 1046) hydrogen bonds : angle 6.22749 / 4.43 ( 2793) Misc. bond : bond 0.00209 / 0.10 ( 6) link_BETA1-4 : bond 0.00448 / 0.28 ( 26) link_BETA1-4 : angle 1.32652 / 0.93 ( 78) link_NAG-ASN : bond 0.00349 / 0.25 ( 42) link_NAG-ASN : angle 1.82874 / 1.40 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 GLN cc_start: 0.6965 (tm-30) cc_final: 0.6743 (tm-30) REVERT: H 73 ASP cc_start: 0.7950 (t0) cc_final: 0.7543 (t0) REVERT: L 16 GLN cc_start: 0.6661 (pt0) cc_final: 0.6369 (pm20) REVERT: L 74 LEU cc_start: 0.8536 (tt) cc_final: 0.8017 (tt) REVERT: D 999 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7763 (tm-30) REVERT: E 172 MET cc_start: 0.3250 (mtt) cc_final: 0.1942 (mtt) REVERT: E 217 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.5972 (m-80) REVERT: G 368 TYR cc_start: 0.7958 (t80) cc_final: 0.7469 (t80) REVERT: J 6 GLN cc_start: 0.6295 (OUTLIER) cc_final: 0.5049 (mm-40) REVERT: K 48 MET cc_start: 0.2390 (tmm) cc_final: 0.0250 (mtm) outliers start: 29 outliers final: 16 residues processed: 160 average time/residue: 0.1918 time to fit residues: 52.5262 Evaluate side-chains 137 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 119 optimal weight: 0.4980 chunk 234 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 351 optimal weight: 20.0000 chunk 321 optimal weight: 0.4980 chunk 305 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 384 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN M 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.111442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.073344 restraints weight = 122158.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.073670 restraints weight = 76118.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.073856 restraints weight = 58948.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.074247 restraints weight = 51357.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.074339 restraints weight = 47326.832| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32949 Z= 0.173 Angle : 0.599 9.634 44934 Z= 0.300 Chirality : 0.045 0.357 5215 Planarity : 0.004 0.050 5667 Dihedral : 4.757 59.784 4288 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 1.42 % Allowed : 12.01 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.13), residues: 3939 helix: -0.41 (0.19), residues: 770 sheet: -0.20 (0.17), residues: 933 loop : -0.97 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 902 TYR 0.030 0.001 TYR H 108 PHE 0.019 0.001 PHE G 92 TRP 0.041 0.002 TRP J 111 HIS 0.005 0.001 HIS J 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (32830) covalent geometry : angle 0.58833 / 0.30 (44640) SS BOND : bond 0.00417 / 0.31 ( 45) SS BOND : angle 1.10795 / 0.77 ( 90) hydrogen bonds : bond 0.04130 / 2.77 ( 1046) hydrogen bonds : angle 6.02309 / 4.28 ( 2793) Misc. bond : bond 0.00207 / 0.10 ( 6) link_BETA1-4 : bond 0.00510 / 0.32 ( 26) link_BETA1-4 : angle 1.29438 / 0.91 ( 78) link_NAG-ASN : bond 0.00351 / 0.25 ( 42) link_NAG-ASN : angle 1.83137 / 1.40 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 GLN cc_start: 0.6939 (tm-30) cc_final: 0.6688 (tm-30) REVERT: H 73 ASP cc_start: 0.7897 (t0) cc_final: 0.7625 (t0) REVERT: L 74 LEU cc_start: 0.8620 (tt) cc_final: 0.8360 (tt) REVERT: D 737 MET cc_start: 0.7837 (tmm) cc_final: 0.7574 (ttt) REVERT: D 999 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7653 (tm-30) REVERT: E 172 MET cc_start: 0.3619 (mtt) cc_final: 0.2370 (mtt) REVERT: E 217 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: E 899 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8513 (tpt) REVERT: G 368 TYR cc_start: 0.7920 (t80) cc_final: 0.7324 (t80) REVERT: K 48 MET cc_start: 0.2087 (tmm) cc_final: 0.0201 (mtm) outliers start: 49 outliers final: 28 residues processed: 166 average time/residue: 0.1729 time to fit residues: 49.8499 Evaluate side-chains 146 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 899 MET Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 948 VAL Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 769 ILE Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 288 optimal weight: 20.0000 chunk 200 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 384 optimal weight: 40.0000 chunk 139 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 361 optimal weight: 40.0000 chunk 24 optimal weight: 0.6980 chunk 347 optimal weight: 4.9990 chunk 388 optimal weight: 40.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.111198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.072769 restraints weight = 122467.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.073201 restraints weight = 76429.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.073396 restraints weight = 55412.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.073939 restraints weight = 51653.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.074064 restraints weight = 45718.786| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32949 Z= 0.180 Angle : 0.597 9.547 44934 Z= 0.300 Chirality : 0.045 0.358 5215 Planarity : 0.004 0.050 5667 Dihedral : 4.739 59.623 4288 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 1.62 % Allowed : 13.57 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3939 helix: -0.32 (0.19), residues: 770 sheet: -0.24 (0.17), residues: 929 loop : -0.96 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 814 TYR 0.024 0.001 TYR D 393 PHE 0.026 0.001 PHE G 374 TRP 0.053 0.002 TRP J 111 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (32830) covalent geometry : angle 0.58704 / 0.30 (44640) SS BOND : bond 0.00339 / 0.24 ( 45) SS BOND : angle 1.04363 / 0.71 ( 90) hydrogen bonds : bond 0.04001 / 2.68 ( 1046) hydrogen bonds : angle 5.88405 / 4.17 ( 2793) Misc. bond : bond 0.00207 / 0.10 ( 6) link_BETA1-4 : bond 0.00468 / 0.29 ( 26) link_BETA1-4 : angle 1.27479 / 0.89 ( 78) link_NAG-ASN : bond 0.00350 / 0.25 ( 42) link_NAG-ASN : angle 1.82956 / 1.40 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 132 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 39 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6935 (tm-30) REVERT: H 73 ASP cc_start: 0.7743 (t0) cc_final: 0.7438 (t0) REVERT: D 756 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6557 (t80) REVERT: D 782 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8497 (p) REVERT: D 999 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7695 (tm-30) REVERT: E 172 MET cc_start: 0.3701 (mtt) cc_final: 0.2829 (mtt) REVERT: E 217 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.5938 (m-80) REVERT: E 899 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8538 (tpt) REVERT: G 610 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9090 (tt) REVERT: K 48 MET cc_start: 0.2081 (tmm) cc_final: 0.0305 (mtm) outliers start: 56 outliers final: 36 residues processed: 177 average time/residue: 0.1811 time to fit residues: 55.8396 Evaluate side-chains 157 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 782 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1101 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 570 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 899 MET Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 948 VAL Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 769 ILE Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 2 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 372 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 274 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 GLN ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 852 GLN G1105 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN M 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.111350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.073115 restraints weight = 121411.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.073632 restraints weight = 78675.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.073748 restraints weight = 58440.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.074355 restraints weight = 53338.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.074375 restraints weight = 45898.650| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32949 Z= 0.163 Angle : 0.589 9.475 44934 Z= 0.296 Chirality : 0.045 0.350 5215 Planarity : 0.004 0.050 5667 Dihedral : 4.739 59.367 4288 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 1.74 % Allowed : 14.61 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.96 (0.13), residues: 3939 helix: -0.26 (0.19), residues: 770 sheet: -0.16 (0.17), residues: 917 loop : -0.95 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 902 TYR 0.037 0.001 TYR H 108 PHE 0.022 0.001 PHE G 92 TRP 0.070 0.002 TRP J 111 HIS 0.011 0.001 HIS E 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (32830) covalent geometry : angle 0.57970 / 0.29 (44640) SS BOND : bond 0.00287 / 0.19 ( 45) SS BOND : angle 0.95038 / 0.66 ( 90) hydrogen bonds : bond 0.03823 / 2.57 ( 1046) hydrogen bonds : angle 5.78497 / 4.11 ( 2793) Misc. bond : bond 0.00203 / 0.10 ( 6) link_BETA1-4 : bond 0.00467 / 0.29 ( 26) link_BETA1-4 : angle 1.25584 / 0.88 ( 78) link_NAG-ASN : bond 0.00339 / 0.24 ( 42) link_NAG-ASN : angle 1.79852 / 1.38 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6919 (tm-30) REVERT: H 48 MET cc_start: 0.8216 (mmm) cc_final: 0.7717 (mmm) REVERT: H 73 ASP cc_start: 0.7762 (t0) cc_final: 0.7384 (t0) REVERT: D 737 MET cc_start: 0.7855 (tmm) cc_final: 0.7537 (ttt) REVERT: D 756 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6571 (t80) REVERT: D 999 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7713 (tm-30) REVERT: E 172 MET cc_start: 0.3743 (mtt) cc_final: 0.2896 (mtt) REVERT: E 217 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.5987 (m-80) REVERT: K 48 MET cc_start: 0.2232 (tmm) cc_final: 0.0536 (mtm) outliers start: 60 outliers final: 39 residues processed: 181 average time/residue: 0.1830 time to fit residues: 57.5291 Evaluate side-chains 156 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 906 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 948 VAL Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 561 PHE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain G residue 1007 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 59 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 236 optimal weight: 0.1980 chunk 33 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 916 ASN D1116 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 543 ASN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.110153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.073242 restraints weight = 122316.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.072443 restraints weight = 78793.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.072326 restraints weight = 64796.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.072590 restraints weight = 61906.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.072735 restraints weight = 56887.770| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 32949 Z= 0.253 Angle : 0.659 9.423 44934 Z= 0.331 Chirality : 0.046 0.365 5215 Planarity : 0.004 0.049 5667 Dihedral : 4.941 58.209 4288 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 1.74 % Allowed : 15.42 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 3939 helix: -0.31 (0.19), residues: 762 sheet: -0.29 (0.17), residues: 938 loop : -1.02 (0.13), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 814 TYR 0.033 0.002 TYR H 108 PHE 0.028 0.002 PHE G 374 TRP 0.026 0.002 TRP G 104 HIS 0.005 0.001 HIS E1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.25 (32830) covalent geometry : angle 0.64840 / 0.33 (44640) SS BOND : bond 0.00448 / 0.30 ( 45) SS BOND : angle 1.22888 / 0.94 ( 90) hydrogen bonds : bond 0.04182 / 2.81 ( 1046) hydrogen bonds : angle 5.92957 / 4.19 ( 2793) Misc. bond : bond 0.00217 / 0.11 ( 6) link_BETA1-4 : bond 0.00503 / 0.32 ( 26) link_BETA1-4 : angle 1.29741 / 0.90 ( 78) link_NAG-ASN : bond 0.00451 / 0.29 ( 42) link_NAG-ASN : angle 1.95037 / 1.46 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 129 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7760 (t0) cc_final: 0.7395 (t0) REVERT: L 28 ASN cc_start: 0.7155 (t0) cc_final: 0.6626 (m-40) REVERT: D 756 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6575 (t80) REVERT: D 782 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8509 (p) REVERT: D 999 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7735 (tm-30) REVERT: E 132 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8479 (tp-100) REVERT: E 172 MET cc_start: 0.4091 (mtt) cc_final: 0.3205 (mtt) REVERT: E 217 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.5962 (m-80) REVERT: G 610 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9100 (tt) REVERT: K 48 MET cc_start: 0.2347 (tmm) cc_final: 0.0612 (mtm) outliers start: 60 outliers final: 42 residues processed: 179 average time/residue: 0.1747 time to fit residues: 53.7186 Evaluate side-chains 164 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 782 VAL Chi-restraints excluded: chain D residue 788 THR Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1101 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 875 LEU Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 948 VAL Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain G residue 1007 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 3 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 358 optimal weight: 40.0000 chunk 295 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 0.2980 chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 112 optimal weight: 0.0270 overall best weight: 1.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 HIS E 687 GLN ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 627 GLN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.111490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.074198 restraints weight = 122263.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.074636 restraints weight = 75731.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.074014 restraints weight = 57579.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074436 restraints weight = 63354.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.074724 restraints weight = 52509.357| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32949 Z= 0.150 Angle : 0.615 17.230 44934 Z= 0.306 Chirality : 0.045 0.340 5215 Planarity : 0.004 0.140 5667 Dihedral : 4.833 56.538 4288 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.53 % Favored : 94.41 % Rotamer: Outliers : 1.68 % Allowed : 15.77 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 3939 helix: -0.13 (0.19), residues: 763 sheet: -0.29 (0.17), residues: 886 loop : -0.99 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 38 TYR 0.032 0.001 TYR H 108 PHE 0.022 0.001 PHE G 92 TRP 0.079 0.002 TRP J 111 HIS 0.005 0.001 HIS J 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (32830) covalent geometry : angle 0.60590 / 0.30 (44640) SS BOND : bond 0.00293 / 0.19 ( 45) SS BOND : angle 1.00813 / 0.76 ( 90) hydrogen bonds : bond 0.03735 / 2.50 ( 1046) hydrogen bonds : angle 5.67150 / 4.03 ( 2793) Misc. bond : bond 0.00608 / 0.30 ( 6) link_BETA1-4 : bond 0.00483 / 0.30 ( 26) link_BETA1-4 : angle 1.27482 / 0.88 ( 78) link_NAG-ASN : bond 0.00322 / 0.24 ( 42) link_NAG-ASN : angle 1.80559 / 1.39 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 127 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 MET cc_start: 0.8152 (mmm) cc_final: 0.7915 (mpp) REVERT: H 73 ASP cc_start: 0.7631 (t0) cc_final: 0.7257 (t0) REVERT: H 94 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7141 (m-10) REVERT: L 28 ASN cc_start: 0.6764 (t0) cc_final: 0.6208 (m-40) REVERT: D 756 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6513 (t80) REVERT: D 782 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8468 (p) REVERT: D 901 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7599 (m-10) REVERT: D 999 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7626 (tm-30) REVERT: E 132 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8532 (tp-100) REVERT: E 172 MET cc_start: 0.4087 (mtt) cc_final: 0.3176 (mtt) REVERT: E 217 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: G 610 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9030 (tt) REVERT: K 48 MET cc_start: 0.1893 (tmm) cc_final: 0.0489 (mtm) outliers start: 58 outliers final: 39 residues processed: 176 average time/residue: 0.1820 time to fit residues: 55.1392 Evaluate side-chains 168 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 782 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 901 TYR Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1101 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 870 TYR Chi-restraints excluded: chain E residue 906 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 948 VAL Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 361 optimal weight: 20.0000 chunk 307 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 349 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 338 optimal weight: 0.9980 chunk 175 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 chunk 54 optimal weight: 9.9990 chunk 256 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.110830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.072501 restraints weight = 121124.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.072779 restraints weight = 80041.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.073245 restraints weight = 55840.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.073424 restraints weight = 55634.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.073604 restraints weight = 47469.001| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 32949 Z= 0.198 Angle : 0.641 14.423 44934 Z= 0.319 Chirality : 0.045 0.351 5215 Planarity : 0.004 0.071 5667 Dihedral : 4.875 57.304 4288 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 1.85 % Allowed : 16.00 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 3939 helix: -0.11 (0.19), residues: 760 sheet: -0.29 (0.17), residues: 909 loop : -1.01 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 98 TYR 0.033 0.001 TYR H 108 PHE 0.030 0.001 PHE G 374 TRP 0.094 0.002 TRP J 111 HIS 0.004 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (32830) covalent geometry : angle 0.63116 / 0.32 (44640) SS BOND : bond 0.00306 / 0.20 ( 45) SS BOND : angle 1.05758 / 0.79 ( 90) hydrogen bonds : bond 0.03850 / 2.59 ( 1046) hydrogen bonds : angle 5.72923 / 4.06 ( 2793) Misc. bond : bond 0.00495 / 0.25 ( 6) link_BETA1-4 : bond 0.00489 / 0.32 ( 26) link_BETA1-4 : angle 1.27202 / 0.88 ( 78) link_NAG-ASN : bond 0.00364 / 0.25 ( 42) link_NAG-ASN : angle 1.85745 / 1.41 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7716 (t0) cc_final: 0.7354 (t0) REVERT: H 94 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7070 (m-10) REVERT: L 28 ASN cc_start: 0.6755 (t0) cc_final: 0.6255 (m-40) REVERT: D 132 GLN cc_start: 0.8824 (mm110) cc_final: 0.8606 (mm110) REVERT: D 756 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6609 (t80) REVERT: D 782 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8475 (p) REVERT: D 901 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: D 999 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7665 (tm-30) REVERT: E 172 MET cc_start: 0.4172 (mtt) cc_final: 0.3291 (mtt) REVERT: E 217 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6235 (m-80) REVERT: G 610 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9054 (tt) REVERT: K 48 MET cc_start: 0.1915 (tmm) cc_final: 0.1235 (tmm) outliers start: 64 outliers final: 46 residues processed: 179 average time/residue: 0.1811 time to fit residues: 55.9385 Evaluate side-chains 173 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 121 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 782 VAL Chi-restraints excluded: chain D residue 788 THR Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 901 TYR Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1101 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 870 TYR Chi-restraints excluded: chain E residue 906 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 948 VAL Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 63 optimal weight: 8.9990 chunk 355 optimal weight: 40.0000 chunk 296 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 378 optimal weight: 30.0000 chunk 347 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 314 optimal weight: 0.4980 chunk 337 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 326 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.111756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.074022 restraints weight = 121723.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.074252 restraints weight = 76151.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.073903 restraints weight = 56159.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.074174 restraints weight = 62569.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074406 restraints weight = 53417.847| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32949 Z= 0.158 Angle : 0.624 14.199 44934 Z= 0.310 Chirality : 0.045 0.339 5215 Planarity : 0.004 0.050 5667 Dihedral : 4.855 58.926 4288 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 1.68 % Allowed : 16.41 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.99 (0.13), residues: 3939 helix: -0.05 (0.19), residues: 766 sheet: -0.28 (0.17), residues: 892 loop : -1.02 (0.13), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.029 0.001 TYR H 108 PHE 0.028 0.001 PHE N 63 TRP 0.071 0.002 TRP J 111 HIS 0.005 0.001 HIS J 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (32830) covalent geometry : angle 0.61483 / 0.31 (44640) SS BOND : bond 0.00322 / 0.21 ( 45) SS BOND : angle 1.04779 / 0.80 ( 90) hydrogen bonds : bond 0.03674 / 2.48 ( 1046) hydrogen bonds : angle 5.63341 / 3.98 ( 2793) Misc. bond : bond 0.00430 / 0.21 ( 6) link_BETA1-4 : bond 0.00490 / 0.31 ( 26) link_BETA1-4 : angle 1.26714 / 0.88 ( 78) link_NAG-ASN : bond 0.00323 / 0.23 ( 42) link_NAG-ASN : angle 1.78530 / 1.38 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7721 (t0) cc_final: 0.7340 (t0) REVERT: L 28 ASN cc_start: 0.6667 (t0) cc_final: 0.6254 (m-40) REVERT: D 132 GLN cc_start: 0.8799 (mm110) cc_final: 0.8129 (tm-30) REVERT: D 756 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6620 (t80) REVERT: D 782 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8446 (p) REVERT: D 901 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: D 999 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7636 (tm-30) REVERT: E 172 MET cc_start: 0.4199 (mtt) cc_final: 0.3311 (mtt) REVERT: E 217 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: G 610 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9020 (tt) outliers start: 58 outliers final: 46 residues processed: 178 average time/residue: 0.1804 time to fit residues: 55.3865 Evaluate side-chains 174 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 782 VAL Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 901 TYR Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1101 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 870 TYR Chi-restraints excluded: chain E residue 875 LEU Chi-restraints excluded: chain E residue 906 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 948 VAL Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain G residue 1007 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 216 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 286 optimal weight: 30.0000 chunk 119 optimal weight: 0.0270 chunk 59 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 287 optimal weight: 20.0000 chunk 193 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.120941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.082976 restraints weight = 129622.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.079685 restraints weight = 92250.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.079944 restraints weight = 79967.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.080250 restraints weight = 75107.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.080273 restraints weight = 70569.400| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32949 Z= 0.146 Angle : 0.623 13.974 44934 Z= 0.310 Chirality : 0.045 0.339 5215 Planarity : 0.004 0.065 5667 Dihedral : 4.818 58.952 4287 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 1.59 % Allowed : 16.61 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.97 (0.13), residues: 3939 helix: -0.03 (0.19), residues: 766 sheet: -0.28 (0.17), residues: 903 loop : -1.00 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.026 0.001 TYR H 108 PHE 0.028 0.001 PHE G 198 TRP 0.066 0.002 TRP J 111 HIS 0.004 0.001 HIS J 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (32830) covalent geometry : angle 0.61438 / 0.31 (44640) SS BOND : bond 0.00313 / 0.20 ( 45) SS BOND : angle 1.02323 / 0.78 ( 90) hydrogen bonds : bond 0.03615 / 2.42 ( 1046) hydrogen bonds : angle 5.56830 / 3.94 ( 2793) Misc. bond : bond 0.00413 / 0.20 ( 6) link_BETA1-4 : bond 0.00490 / 0.31 ( 26) link_BETA1-4 : angle 1.25565 / 0.87 ( 78) link_NAG-ASN : bond 0.00321 / 0.24 ( 42) link_NAG-ASN : angle 1.76202 / 1.37 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5435.21 seconds wall clock time: 95 minutes 19.89 seconds (5719.89 seconds total)