Starting phenix.real_space_refine on Mon Jul 6 02:43:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wtf_32784/07_2026/7wtf_32784.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtf_32784/07_2026/7wtf_32784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wtf_32784/07_2026/7wtf_32784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtf_32784/07_2026/7wtf_32784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wtf_32784/07_2026/7wtf_32784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtf_32784/07_2026/7wtf_32784.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wtf_32784/07_2026/7wtf_32784.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wtf_32784/07_2026/7wtf_32784.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.100 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 144 5.16 5 C 20372 2.51 5 N 5254 2.21 5 O 6279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32049 Number of models: 1 Model: "" Number of chains: 32 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "D" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "J" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" 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: "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: 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: "W" 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: "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: 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: "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: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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 Time building chain proxies: 6.95, per 1000 atoms: 0.22 Number of scatterers: 32049 At special positions: 0 Unit cell: (150.8, 145.6, 251.68, 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 144 16.00 O 6279 8.00 N 5254 7.00 C 20372 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 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 434 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 651 " distance=2.02 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS B 673 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 751 " distance=2.03 Simple disulfide: pdb=" SG CYS B1034 " - pdb=" SG CYS B1045 " distance=2.03 Simple disulfide: pdb=" SG CYS B1084 " - pdb=" SG CYS B1128 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 338 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 381 " - pdb=" SG CYS C 434 " distance=2.03 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 527 " distance=2.03 Simple disulfide: pdb=" SG CYS C 482 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 651 " distance=2.02 Simple disulfide: pdb=" SG CYS C 664 " - pdb=" SG CYS C 673 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 751 " distance=2.03 Simple disulfide: pdb=" SG CYS C1034 " - pdb=" SG CYS C1045 " distance=2.03 Simple disulfide: pdb=" SG CYS C1084 " - pdb=" SG CYS C1128 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 163 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 303 " distance=2.03 Simple disulfide: pdb=" SG CYS D 338 " - pdb=" SG CYS D 363 " distance=2.04 Simple disulfide: pdb=" SG CYS D 381 " - pdb=" SG CYS D 434 " distance=2.04 Simple disulfide: pdb=" SG CYS D 393 " - pdb=" SG CYS D 527 " distance=2.03 Simple disulfide: pdb=" SG CYS D 482 " - pdb=" SG CYS D 490 " distance=2.03 Simple disulfide: pdb=" SG CYS D 619 " - pdb=" SG CYS D 651 " distance=2.03 Simple disulfide: pdb=" SG CYS D 664 " - pdb=" SG CYS D 673 " distance=2.03 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 762 " distance=2.04 Simple disulfide: pdb=" SG CYS D 745 " - pdb=" SG CYS D 751 " distance=2.03 Simple disulfide: pdb=" SG CYS D1034 " - pdb=" SG CYS D1045 " distance=2.03 Simple disulfide: pdb=" SG CYS D1084 " - pdb=" SG CYS D1128 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A 1 " - " ASN B 719 " " NAG B1201 " - " ASN B1160 " " NAG B1202 " - " ASN B 17 " " NAG B1203 " - " ASN B 61 " " NAG B1204 " - " ASN B 605 " " NAG B1205 " - " ASN B 659 " " NAG B1206 " - " ASN B 618 " " NAG B1207 " - " ASN B 711 " " NAG B1208 " - " ASN B 122 " " NAG B1209 " - " ASN B 149 " " NAG B1210 " - " ASN B 333 " " NAG B1211 " - " ASN B 284 " " NAG C1201 " - " ASN C1160 " " NAG C1202 " - " ASN C 125 " " NAG C1203 " - " ASN C 17 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 605 " " NAG C1206 " - " ASN C 659 " " NAG C1207 " - " ASN C 711 " " NAG C1208 " - " ASN C 146 " " NAG C1209 " - " ASN C 162 " " NAG C1210 " - " ASN C 618 " " NAG D1201 " - " ASN D1160 " " NAG D1202 " - " ASN D 17 " " NAG D1203 " - " ASN D 61 " " NAG D1204 " - " ASN D 605 " " NAG D1205 " - " ASN D 659 " " NAG D1206 " - " ASN D 711 " " NAG D1207 " - " ASN D 146 " " NAG D1208 " - " ASN D 284 " " NAG D1209 " - " ASN D 618 " " NAG E 1 " - " ASN B 803 " " NAG F 1 " - " ASN B1100 " " NAG M 1 " - " ASN B1136 " " NAG N 1 " - " ASN B1076 " " NAG P 1 " - " ASN C 719 " " NAG Q 1 " - " ASN C 803 " " NAG R 1 " - " ASN C1100 " " NAG S 1 " - " ASN C1136 " " NAG T 1 " - " ASN C 284 " " NAG U 1 " - " ASN C1076 " " NAG V 1 " - " ASN C 333 " " NAG W 1 " - " ASN D 233 " " NAG X 1 " - " ASN D 719 " " NAG Y 1 " - " ASN D1076 " " NAG Z 1 " - " ASN D 803 " " NAG a 1 " - " ASN D1100 " " NAG b 1 " - " ASN D1136 " " NAG c 1 " - " ASN D 333 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.5 seconds 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7398 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 61 sheets defined 20.0% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'B' and resid 296 through 306 Processing helix chain 'B' and resid 339 through 345 removed outlier: 4.041A pdb=" N VAL B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.575A pdb=" N LEU B 389 " --> pdb=" O PRO B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.666A pdb=" N ALA B 413 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 545 through 548 Processing helix chain 'B' and resid 635 through 640 removed outlier: 4.090A pdb=" N THR B 640 " --> pdb=" O VAL B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 748 through 755 Processing helix chain 'B' and resid 756 through 759 removed outlier: 3.713A pdb=" N GLY B 759 " --> pdb=" O LEU B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 759' Processing helix chain 'B' and resid 760 through 785 removed outlier: 3.843A pdb=" N ASP B 777 " --> pdb=" O ALA B 773 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 783 " --> pdb=" O ASN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.532A pdb=" N ALA B 854 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN B 855 " --> pdb=" O ILE B 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 851 through 855' Processing helix chain 'B' and resid 868 through 886 removed outlier: 3.886A pdb=" N GLN B 874 " --> pdb=" O GLU B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 892 Processing helix chain 'B' and resid 899 through 912 removed outlier: 3.751A pdb=" N ALA B 905 " --> pdb=" O PRO B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 removed outlier: 3.915A pdb=" N TYR B 919 " --> pdb=" O GLN B 915 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 915 through 920' Processing helix chain 'B' and resid 921 through 942 removed outlier: 3.628A pdb=" N LYS B 935 " --> pdb=" O SER B 931 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN B 937 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 938 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 941 " --> pdb=" O GLN B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 967 removed outlier: 3.794A pdb=" N ASP B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 953 " --> pdb=" O LYS B 949 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 970 No H-bonds generated for 'chain 'B' and resid 968 through 970' Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 987 through 995 removed outlier: 3.540A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 993 " --> pdb=" O PRO B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1000 removed outlier: 3.512A pdb=" N THR B1000 " --> pdb=" O ASP B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1034 removed outlier: 3.515A pdb=" N THR B1008 " --> pdb=" O GLN B1004 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B1009 " --> pdb=" O SER B1005 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B1023 " --> pdb=" O GLU B1019 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1149 removed outlier: 4.180A pdb=" N GLU B1146 " --> pdb=" O PRO B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1163 removed outlier: 3.592A pdb=" N ASP B1155 " --> pdb=" O LYS B1151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B1156 " --> pdb=" O GLU B1152 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS B1161 " --> pdb=" O TYR B1157 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B1162 " --> pdb=" O PHE B1158 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 340 through 345 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.029A pdb=" N ASN C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.524A pdb=" N ILE C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 408 through 413' Processing helix chain 'C' and resid 419 through 424 removed outlier: 3.598A pdb=" N TYR C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 419 through 424' Processing helix chain 'C' and resid 440 through 445 removed outlier: 3.788A pdb=" N SER C 445 " --> pdb=" O ASN C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 746 removed outlier: 3.952A pdb=" N ILE C 744 " --> pdb=" O CYS C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 756 removed outlier: 3.697A pdb=" N SER C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN C 753 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C 754 " --> pdb=" O GLU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 759 No H-bonds generated for 'chain 'C' and resid 757 through 759' Processing helix chain 'C' and resid 762 through 784 removed outlier: 3.553A pdb=" N ASP C 777 " --> pdb=" O ALA C 773 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 780 " --> pdb=" O GLN C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 825 removed outlier: 3.569A pdb=" N LEU C 823 " --> pdb=" O PRO C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 886 removed outlier: 3.544A pdb=" N ALA C 873 " --> pdb=" O ASP C 869 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 874 " --> pdb=" O GLU C 870 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 884 " --> pdb=" O LEU C 880 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 912 removed outlier: 3.956A pdb=" N ALA C 905 " --> pdb=" O PRO C 901 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 911 " --> pdb=" O ARG C 907 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 912 " --> pdb=" O PHE C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 920 removed outlier: 3.697A pdb=" N TYR C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 940 removed outlier: 3.569A pdb=" N LYS C 935 " --> pdb=" O SER C 931 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 936 " --> pdb=" O ALA C 932 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN C 937 " --> pdb=" O ILE C 933 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 938 " --> pdb=" O GLY C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 946 removed outlier: 3.911A pdb=" N ALA C 946 " --> pdb=" O THR C 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 943 through 946' Processing helix chain 'C' and resid 947 through 966 removed outlier: 4.151A pdb=" N VAL C 953 " --> pdb=" O LYS C 949 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN C 957 " --> pdb=" O VAL C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 985 removed outlier: 3.615A pdb=" N PHE C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 995 removed outlier: 3.646A pdb=" N GLU C 992 " --> pdb=" O PRO C 988 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 993 " --> pdb=" O PRO C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1034 removed outlier: 3.806A pdb=" N ARG C1002 " --> pdb=" O LEU C 998 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C1003 " --> pdb=" O ILE C 999 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1149 removed outlier: 3.917A pdb=" N GLU C1146 " --> pdb=" O PRO C1142 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C1149 " --> pdb=" O PRO C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1150 through 1159 removed outlier: 3.701A pdb=" N ASP C1155 " --> pdb=" O LYS C1151 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C1156 " --> pdb=" O GLU C1152 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 340 through 345 removed outlier: 3.930A pdb=" N PHE D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 407 through 413 removed outlier: 4.120A pdb=" N GLN D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 626 removed outlier: 3.947A pdb=" N ILE D 626 " --> pdb=" O PRO D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 746 removed outlier: 3.520A pdb=" N TYR D 743 " --> pdb=" O ASP D 739 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D 745 " --> pdb=" O THR D 741 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D 746 " --> pdb=" O MET D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 removed outlier: 4.096A pdb=" N ASN D 753 " --> pdb=" O THR D 749 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 754 " --> pdb=" O GLU D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 759 No H-bonds generated for 'chain 'D' and resid 757 through 759' Processing helix chain 'D' and resid 760 through 785 removed outlier: 3.650A pdb=" N GLN D 764 " --> pdb=" O SER D 760 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 765 " --> pdb=" O PHE D 761 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 766 " --> pdb=" O CYS D 762 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN D 776 " --> pdb=" O ILE D 772 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP D 777 " --> pdb=" O ALA D 773 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 780 " --> pdb=" O GLN D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 828 removed outlier: 3.523A pdb=" N ASN D 826 " --> pdb=" O ASP D 822 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 886 removed outlier: 3.814A pdb=" N THR D 885 " --> pdb=" O ALA D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 892 removed outlier: 3.535A pdb=" N GLY D 891 " --> pdb=" O TRP D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 912 removed outlier: 3.709A pdb=" N ALA D 905 " --> pdb=" O PRO D 901 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 906 " --> pdb=" O MET D 902 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 911 " --> pdb=" O ARG D 907 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 912 " --> pdb=" O PHE D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 920 removed outlier: 3.696A pdb=" N TYR D 919 " --> pdb=" O GLN D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 943 removed outlier: 3.550A pdb=" N ILE D 936 " --> pdb=" O ALA D 932 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN D 937 " --> pdb=" O ILE D 933 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 938 " --> pdb=" O GLY D 934 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 946 No H-bonds generated for 'chain 'D' and resid 944 through 946' Processing helix chain 'D' and resid 947 through 967 removed outlier: 3.828A pdb=" N VAL D 953 " --> pdb=" O LYS D 949 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 963 " --> pdb=" O GLN D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 970 No H-bonds generated for 'chain 'D' and resid 968 through 970' Processing helix chain 'D' and resid 980 through 985 removed outlier: 3.750A pdb=" N SER D 984 " --> pdb=" O ASN D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1000 removed outlier: 3.657A pdb=" N LEU D 998 " --> pdb=" O GLN D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1034 removed outlier: 3.536A pdb=" N LEU D1026 " --> pdb=" O ALA D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1162 removed outlier: 4.259A pdb=" N GLU D1146 " --> pdb=" O PRO D1142 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.426A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 46 through 49 removed outlier: 5.903A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.657A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 44 through 46 Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.023A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASN B 61 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR B 271 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.248A pdb=" N ASP B 289 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 168 through 172 removed outlier: 4.089A pdb=" N ILE B 105 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 241 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 313 through 320 removed outlier: 5.769A pdb=" N ILE B 314 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR B 601 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN B 316 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 599 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 318 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 360 Processing sheet with id=AB2, first strand: chain 'B' and resid 358 through 360 Processing sheet with id=AB3, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AB4, first strand: chain 'B' and resid 475 through 476 Processing sheet with id=AB5, first strand: chain 'B' and resid 567 through 569 Processing sheet with id=AB6, first strand: chain 'B' and resid 656 through 657 removed outlier: 5.972A pdb=" N GLU B 656 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 698 " --> pdb=" O GLU B 656 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 697 " --> pdb=" O CYS B 673 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 672 " --> pdb=" O ILE B 668 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 703 through 706 Processing sheet with id=AB8, first strand: chain 'B' and resid 713 through 721 removed outlier: 6.521A pdb=" N SER B 713 " --> pdb=" O THR B1078 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B1078 " --> pdb=" O SER B 713 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 715 " --> pdb=" O ASN B1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN B1076 " --> pdb=" O ALA B 715 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU B1074 " --> pdb=" O PRO B 717 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN B 719 " --> pdb=" O ALA B1072 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B1078 " --> pdb=" O SER B1099 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B1080 " --> pdb=" O PHE B1097 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE B1097 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 724 through 730 Processing sheet with id=AC1, first strand: chain 'B' and resid 736 through 738 removed outlier: 3.550A pdb=" N THR B 861 " --> pdb=" O SER B 737 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 790 through 792 removed outlier: 5.406A pdb=" N ILE B 790 " --> pdb=" O ASN C 705 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id=AC4, first strand: chain 'C' and resid 27 through 31 removed outlier: 7.830A pdb=" N ASN C 61 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR C 271 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 96 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN C 185 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE C 198 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP C 227 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE C 200 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 225 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.573A pdb=" N ALA D 577 " --> pdb=" O GLY D 568 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 590 " --> pdb=" O VAL D 553 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.805A pdb=" N ASP C 289 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC8, first strand: chain 'C' and resid 165 through 169 removed outlier: 5.701A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 313 through 321 removed outlier: 5.283A pdb=" N ILE C 314 " --> pdb=" O THR C 601 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 601 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN C 316 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C 599 " --> pdb=" O GLN C 316 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER C 318 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 597 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 652 " --> pdb=" O PHE C 645 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 645 " --> pdb=" O LEU C 652 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 326 through 330 removed outlier: 7.454A pdb=" N GLU C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASN C 544 " --> pdb=" O GLU C 326 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE C 328 " --> pdb=" O ASN C 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 358 through 360 removed outlier: 3.952A pdb=" N ILE C 360 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 397 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 511 " --> pdb=" O TRP C 438 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP C 438 " --> pdb=" O ARG C 511 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 475 through 476 removed outlier: 3.630A pdb=" N TYR C 475 " --> pdb=" O TYR C 491 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 553 through 556 removed outlier: 3.656A pdb=" N THR C 590 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 577 " --> pdb=" O GLY C 568 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 656 through 657 removed outlier: 6.118A pdb=" N GLU C 656 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR C 698 " --> pdb=" O GLU C 656 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE C 672 " --> pdb=" O ILE C 668 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 713 through 730 removed outlier: 6.548A pdb=" N SER C 713 " --> pdb=" O THR C1078 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C1078 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 715 " --> pdb=" O ASN C1076 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C1076 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU C1074 " --> pdb=" O PRO C 717 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY C1061 " --> pdb=" O SER C1057 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER C1057 " --> pdb=" O GLY C1061 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C1063 " --> pdb=" O PRO C1055 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU C1065 " --> pdb=" O SER C1053 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER C1053 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL C1067 " --> pdb=" O LEU C1051 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 713 through 730 removed outlier: 6.548A pdb=" N SER C 713 " --> pdb=" O THR C1078 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C1078 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 715 " --> pdb=" O ASN C1076 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C1076 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU C1074 " --> pdb=" O PRO C 717 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C1080 " --> pdb=" O PHE C1097 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C1097 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 737 through 738 Processing sheet with id=AD9, first strand: chain 'C' and resid 789 through 792 removed outlier: 6.033A pdb=" N ILE C 790 " --> pdb=" O ASN D 705 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 1122 through 1124 Processing sheet with id=AE2, first strand: chain 'D' and resid 27 through 31 removed outlier: 7.993A pdb=" N ASN D 61 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR D 271 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA D 266 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER D 202 " --> pdb=" O PRO D 224 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N HIS D 204 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N LEU D 222 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL D 36 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.722A pdb=" N ASP D 289 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'D' and resid 168 through 169 Processing sheet with id=AE6, first strand: chain 'D' and resid 313 through 321 removed outlier: 5.214A pdb=" N ILE D 314 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D 601 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN D 316 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL D 599 " --> pdb=" O GLN D 316 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER D 318 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL D 597 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS D 651 " --> pdb=" O TYR D 614 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY D 650 " --> pdb=" O THR D 647 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 358 through 360 removed outlier: 3.982A pdb=" N ALA D 399 " --> pdb=" O LYS D 358 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 360 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 363 through 364 removed outlier: 6.832A pdb=" N CYS D 363 " --> pdb=" O CYS D 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 402 through 404 removed outlier: 3.878A pdb=" N ILE D 404 " --> pdb=" O TYR D 510 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 511 " --> pdb=" O TRP D 438 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP D 438 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 513 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 436 " --> pdb=" O VAL D 513 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 454 through 456 Processing sheet with id=AF2, first strand: chain 'D' and resid 475 through 476 Processing sheet with id=AF3, first strand: chain 'D' and resid 544 through 545 Processing sheet with id=AF4, first strand: chain 'D' and resid 656 through 657 removed outlier: 6.142A pdb=" N GLU D 656 " --> pdb=" O ALA D 696 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR D 698 " --> pdb=" O GLU D 656 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR D 697 " --> pdb=" O CYS D 673 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE D 672 " --> pdb=" O ILE D 668 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 713 through 721 removed outlier: 6.536A pdb=" N SER D 713 " --> pdb=" O THR D1078 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR D1078 " --> pdb=" O SER D 713 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA D 715 " --> pdb=" O ASN D1076 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN D1076 " --> pdb=" O ALA D 715 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU D1074 " --> pdb=" O PRO D 717 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR D1069 " --> pdb=" O HIS D1050 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS D1050 " --> pdb=" O TYR D1069 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 724 through 730 removed outlier: 3.627A pdb=" N ALA D1080 " --> pdb=" O PHE D1097 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE D1097 " --> pdb=" O ALA D1080 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 737 through 738 Processing sheet with id=AF8, first strand: chain 'D' and resid 1122 through 1127 removed outlier: 3.603A pdb=" N SER D1125 " --> pdb=" O ALA D1089 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA D1089 " --> pdb=" O SER D1125 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.898A pdb=" N SER G 77 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.096A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 19 through 24 removed outlier: 3.786A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE J 75 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 45 through 46 Processing sheet with id=AG4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'I' and resid 47 through 51 removed outlier: 7.171A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 21 through 24 Processing sheet with id=AG7, first strand: chain 'K' and resid 44 through 48 removed outlier: 6.572A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.31 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5146 1.28 - 1.41: 8250 1.41 - 1.55: 19155 1.55 - 1.69: 56 1.69 - 1.82: 186 Bond restraints: 32793 Sorted by residual: bond pdb=" C PRO C 899 " pdb=" O PRO C 899 " ideal model delta sigma weight residual 1.233 1.140 0.093 1.13e-02 7.83e+03 6.82e+01 bond pdb=" C PRO B 899 " pdb=" O PRO B 899 " ideal model delta sigma weight residual 1.233 1.144 0.089 1.13e-02 7.83e+03 6.19e+01 bond pdb=" C PRO D 899 " pdb=" O PRO D 899 " ideal model delta sigma weight residual 1.233 1.150 0.084 1.10e-02 8.26e+03 5.79e+01 bond pdb=" C PRO C 901 " pdb=" O PRO C 901 " ideal model delta sigma weight residual 1.237 1.142 0.096 1.32e-02 5.74e+03 5.25e+01 bond pdb=" C PRO D 901 " pdb=" O PRO D 901 " ideal model delta sigma weight residual 1.238 1.154 0.083 1.24e-02 6.50e+03 4.51e+01 ... (remaining 32788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 43032 2.58 - 5.16: 1324 5.16 - 7.73: 185 7.73 - 10.31: 40 10.31 - 12.89: 9 Bond angle restraints: 44590 Sorted by residual: angle pdb=" N PRO D 988 " pdb=" CA PRO D 988 " pdb=" C PRO D 988 " ideal model delta sigma weight residual 110.70 123.15 -12.45 1.22e+00 6.72e-01 1.04e+02 angle pdb=" C ASN C 544 " pdb=" CA ASN C 544 " pdb=" CB ASN C 544 " ideal model delta sigma weight residual 111.82 101.11 10.71 1.38e+00 5.25e-01 6.02e+01 angle pdb=" N SER B 942 " pdb=" CA SER B 942 " pdb=" C SER B 942 " ideal model delta sigma weight residual 113.20 103.92 9.28 1.21e+00 6.83e-01 5.88e+01 angle pdb=" N ALA B 946 " pdb=" CA ALA B 946 " pdb=" C ALA B 946 " ideal model delta sigma weight residual 111.82 103.44 8.38 1.16e+00 7.43e-01 5.21e+01 angle pdb=" C THR B 943 " pdb=" CA THR B 943 " pdb=" CB THR B 943 " ideal model delta sigma weight residual 110.71 121.56 -10.85 1.53e+00 4.27e-01 5.03e+01 ... (remaining 44585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 17592 21.97 - 43.94: 1184 43.94 - 65.91: 134 65.91 - 87.88: 51 87.88 - 109.85: 5 Dihedral angle restraints: 18966 sinusoidal: 7443 harmonic: 11523 Sorted by residual: dihedral pdb=" CA ASN D 145 " pdb=" C ASN D 145 " pdb=" N ASN D 146 " pdb=" CA ASN D 146 " ideal model delta harmonic sigma weight residual -180.00 -70.15 -109.85 0 5.00e+00 4.00e-02 4.83e+02 dihedral pdb=" CA ASP C 142 " pdb=" C ASP C 142 " pdb=" N HIS C 143 " pdb=" CA HIS C 143 " ideal model delta harmonic sigma weight residual 180.00 70.18 109.82 0 5.00e+00 4.00e-02 4.82e+02 dihedral pdb=" CB CYS D 740 " pdb=" SG CYS D 740 " pdb=" SG CYS D 762 " pdb=" CB CYS D 762 " ideal model delta sinusoidal sigma weight residual 93.00 3.84 89.16 1 1.00e+01 1.00e-02 9.46e+01 ... (remaining 18963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 5051 0.155 - 0.309: 141 0.309 - 0.464: 6 0.464 - 0.618: 2 0.618 - 0.773: 1 Chirality restraints: 5201 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN D 333 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" C1 NAG C1208 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C1208 " pdb=" O5 NAG C1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CA PRO D 988 " pdb=" N PRO D 988 " pdb=" C PRO D 988 " pdb=" CB PRO D 988 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 5198 not shown) Planarity restraints: 5717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 147 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C LYS D 147 " -0.063 2.00e-02 2.50e+03 pdb=" O LYS D 147 " 0.023 2.00e-02 2.50e+03 pdb=" N SER D 148 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 941 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C SER B 941 " -0.060 2.00e-02 2.50e+03 pdb=" O SER B 941 " 0.022 2.00e-02 2.50e+03 pdb=" N SER B 942 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 762 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C CYS D 762 " -0.056 2.00e-02 2.50e+03 pdb=" O CYS D 762 " 0.020 2.00e-02 2.50e+03 pdb=" N THR D 763 " 0.019 2.00e-02 2.50e+03 ... (remaining 5714 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 8677 2.80 - 3.33: 26820 3.33 - 3.85: 52153 3.85 - 4.38: 58528 4.38 - 4.90: 101123 Nonbonded interactions: 247301 Sorted by model distance: nonbonded pdb=" O GLY C 882 " pdb=" OG SER C 886 " model vdw 2.278 3.040 nonbonded pdb=" O VAL D 610 " pdb=" OH TYR D 638 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR B 647 " pdb=" O GLY B 650 " model vdw 2.286 3.040 nonbonded pdb=" O ASP H 112 " pdb=" OH TYR L 49 " model vdw 2.290 3.040 nonbonded pdb=" OG SER H 21 " pdb=" OG1 THR H 78 " model vdw 2.298 3.040 ... (remaining 247296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'B' and resid 14 through 1209) selection = (chain 'C' and resid 14 through 1209) selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'M' selection = chain 'R' selection = chain 'S' selection = chain 'a' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.720 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 0.103 32913 Z= 0.391 Angle : 1.026 15.177 44902 Z= 0.579 Chirality : 0.065 0.773 5201 Planarity : 0.007 0.082 5668 Dihedral : 14.512 109.850 11433 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 0.52 % Allowed : 1.16 % Favored : 98.32 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.03 (0.12), residues: 3924 helix: -3.29 (0.12), residues: 669 sheet: -0.40 (0.19), residues: 783 loop : -2.30 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 187 TYR 0.045 0.002 TYR B 455 PHE 0.030 0.002 PHE C 106 TRP 0.037 0.002 TRP C 260 HIS 0.013 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.39 (32793) covalent geometry : angle 1.00946 / 0.58 (44590) SS BOND : bond 0.00360 / 0.21 ( 45) SS BOND : angle 1.52739 / 0.98 ( 90) hydrogen bonds : bond 0.23343 / 15.43 ( 932) hydrogen bonds : angle 9.01661 / 6.15 ( 2535) Misc. bond : bond 0.00059 / 0.03 ( 1) link_BETA1-4 : bond 0.00851 / 0.52 ( 25) link_BETA1-4 : angle 2.19906 / 1.47 ( 75) link_NAG-ASN : bond 0.00713 / 0.44 ( 49) link_NAG-ASN : angle 2.94654 / 1.90 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 436 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 MET cc_start: 0.1742 (tpt) cc_final: 0.1148 (mtm) REVERT: B 360 ILE cc_start: 0.7982 (mt) cc_final: 0.7722 (mm) REVERT: B 367 TYR cc_start: 0.7255 (m-80) cc_final: 0.6924 (m-80) REVERT: B 983 PHE cc_start: 0.6700 (m-10) cc_final: 0.6393 (m-10) REVERT: C 117 LEU cc_start: 0.6081 (mt) cc_final: 0.5562 (tt) REVERT: C 142 ASP cc_start: 0.1998 (OUTLIER) cc_final: 0.1052 (t0) REVERT: C 823 LEU cc_start: 0.8218 (mt) cc_final: 0.7937 (mp) REVERT: D 1074 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7225 (pt0) outliers start: 18 outliers final: 8 residues processed: 449 average time/residue: 0.5925 time to fit residues: 322.6508 Evaluate side-chains 221 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 1074 GLU 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: 0.0030 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 91 GLN B 49 HIS B 362 ASN B 615 GLN B 677 GLN B 753 ASN B 757 GLN B 764 GLN B 903 GLN B 909 ASN B1121 ASN C 99 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN C 546 ASN C 582 GLN C 903 GLN C 927 ASN C 967 GLN C1012 GLN C1115 GLN D 14 GLN D 273 GLN D 424 ASN D 582 GLN D 615 GLN D 786 GLN D1004 GLN D1121 ASN I 31 ASN K 31 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.215852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.162955 restraints weight = 48954.628| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.75 r_work: 0.3575 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32913 Z= 0.133 Angle : 0.666 12.360 44902 Z= 0.329 Chirality : 0.047 0.608 5201 Planarity : 0.005 0.059 5668 Dihedral : 5.279 57.429 4286 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 1.94 % Allowed : 9.79 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.12), residues: 3924 helix: -1.03 (0.18), residues: 689 sheet: -0.15 (0.19), residues: 801 loop : -2.13 (0.11), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.018 0.001 TYR B 170 PHE 0.026 0.001 PHE B 983 TRP 0.024 0.001 TRP C 260 HIS 0.013 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (32793) covalent geometry : angle 0.64099 / 0.32 (44590) SS BOND : bond 0.00343 / 0.23 ( 45) SS BOND : angle 1.56094 / 0.97 ( 90) hydrogen bonds : bond 0.05048 / 3.31 ( 932) hydrogen bonds : angle 6.31941 / 4.31 ( 2535) Misc. bond : bond 0.00005 / 0.00 ( 1) link_BETA1-4 : bond 0.00536 / 0.33 ( 25) link_BETA1-4 : angle 1.71482 / 1.17 ( 75) link_NAG-ASN : bond 0.00696 / 0.49 ( 49) link_NAG-ASN : angle 2.77060 / 1.92 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 207 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 MET cc_start: 0.1358 (tpt) cc_final: 0.1156 (mtm) REVERT: B 360 ILE cc_start: 0.8192 (mt) cc_final: 0.7964 (mm) REVERT: B 367 TYR cc_start: 0.7698 (m-80) cc_final: 0.7424 (m-80) REVERT: C 167 TYR cc_start: 0.7579 (t80) cc_final: 0.7339 (t80) REVERT: C 174 MET cc_start: 0.2723 (mtt) cc_final: 0.0926 (mmt) REVERT: C 316 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: C 570 ASP cc_start: 0.7943 (p0) cc_final: 0.7626 (p0) REVERT: C 677 GLN cc_start: 0.7669 (mm110) cc_final: 0.7316 (mm-40) REVERT: D 128 ILE cc_start: 0.3931 (OUTLIER) cc_final: 0.3180 (pt) REVERT: D 241 LEU cc_start: 0.6837 (mp) cc_final: 0.6565 (mp) REVERT: D 271 TYR cc_start: 0.7694 (m-10) cc_final: 0.7481 (m-10) REVERT: D 1121 ASN cc_start: 0.6974 (m-40) cc_final: 0.6609 (m110) REVERT: G 81 MET cc_start: 0.1970 (tpt) cc_final: 0.0831 (ptm) outliers start: 67 outliers final: 25 residues processed: 252 average time/residue: 0.5089 time to fit residues: 161.5754 Evaluate side-chains 196 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 363 CYS Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain G residue 114 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 40 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 351 optimal weight: 40.0000 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 91 GLN B 49 HIS B 753 ASN B 921 ASN C 441 ASN C 789 GLN D 14 GLN D 99 ASN D 273 GLN D 903 GLN J 37 GLN J 55 GLN I 31 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.209249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.146267 restraints weight = 47904.281| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.68 r_work: 0.3388 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 32913 Z= 0.282 Angle : 0.758 11.062 44902 Z= 0.378 Chirality : 0.052 0.384 5201 Planarity : 0.005 0.055 5668 Dihedral : 5.288 53.199 4274 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.78 % Favored : 93.17 % Rotamer: Outliers : 2.92 % Allowed : 13.12 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.12), residues: 3924 helix: -0.62 (0.19), residues: 704 sheet: -0.19 (0.18), residues: 819 loop : -2.14 (0.11), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 44 TYR 0.028 0.002 TYR C 906 PHE 0.034 0.002 PHE C 106 TRP 0.022 0.002 TRP C 260 HIS 0.008 0.002 HIS C1050 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.28 (32793) covalent geometry : angle 0.73333 / 0.37 (44590) SS BOND : bond 0.00529 / 0.32 ( 45) SS BOND : angle 2.09529 / 1.34 ( 90) hydrogen bonds : bond 0.05193 / 3.36 ( 932) hydrogen bonds : angle 6.13452 / 4.22 ( 2535) Misc. bond : bond 0.00070 / 0.04 ( 1) link_BETA1-4 : bond 0.00536 / 0.31 ( 25) link_BETA1-4 : angle 1.77423 / 1.19 ( 75) link_NAG-ASN : bond 0.00621 / 0.42 ( 49) link_NAG-ASN : angle 2.81263 / 1.94 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 184 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.8303 (mt) cc_final: 0.8021 (mm) REVERT: B 367 TYR cc_start: 0.7791 (m-80) cc_final: 0.7547 (m-80) REVERT: B 995 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7782 (mp) REVERT: B 1043 ASP cc_start: 0.8559 (t0) cc_final: 0.8342 (m-30) REVERT: B 1094 GLU cc_start: 0.8640 (tt0) cc_final: 0.8265 (pt0) REVERT: C 174 MET cc_start: 0.3676 (mtt) cc_final: 0.2876 (mmp) REVERT: C 197 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7308 (t80) REVERT: C 560 LYS cc_start: 0.8285 (ttpt) cc_final: 0.8063 (mtmp) REVERT: C 570 ASP cc_start: 0.8126 (p0) cc_final: 0.7782 (p0) REVERT: C 677 GLN cc_start: 0.7814 (mm110) cc_final: 0.7422 (mm-40) REVERT: C 978 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8397 (m) REVERT: D 54 LEU cc_start: 0.8861 (mt) cc_final: 0.8570 (mp) REVERT: D 1121 ASN cc_start: 0.8076 (m-40) cc_final: 0.7794 (m110) REVERT: G 81 MET cc_start: 0.1524 (tpt) cc_final: 0.0990 (ptm) REVERT: K 4 MET cc_start: 0.0993 (ptp) cc_final: -0.0456 (ptt) outliers start: 101 outliers final: 47 residues processed: 265 average time/residue: 0.5058 time to fit residues: 167.8171 Evaluate side-chains 203 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1143 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 363 CYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 148 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 327 optimal weight: 0.0050 chunk 90 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 HIS B 362 ASN B 489 ASN B1073 GLN C 238 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 994 GLN J 37 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.211942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.155683 restraints weight = 47793.158| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.70 r_work: 0.3473 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32913 Z= 0.115 Angle : 0.608 11.754 44902 Z= 0.299 Chirality : 0.046 0.377 5201 Planarity : 0.004 0.068 5668 Dihedral : 4.732 45.759 4273 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.06 % Rotamer: Outliers : 2.00 % Allowed : 15.93 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.13), residues: 3924 helix: 0.03 (0.20), residues: 700 sheet: -0.17 (0.18), residues: 822 loop : -1.98 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.018 0.001 TYR B 170 PHE 0.018 0.001 PHE C 219 TRP 0.024 0.001 TRP C 104 HIS 0.009 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (32793) covalent geometry : angle 0.58993 / 0.29 (44590) SS BOND : bond 0.00352 / 0.18 ( 45) SS BOND : angle 1.37796 / 0.87 ( 90) hydrogen bonds : bond 0.03776 / 2.47 ( 932) hydrogen bonds : angle 5.73164 / 3.92 ( 2535) Misc. bond : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : bond 0.00535 / 0.33 ( 25) link_BETA1-4 : angle 1.53471 / 1.04 ( 75) link_NAG-ASN : bond 0.00475 / 0.31 ( 49) link_NAG-ASN : angle 2.23551 / 1.52 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 178 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.8291 (mt) cc_final: 0.8048 (mm) REVERT: B 367 TYR cc_start: 0.7719 (m-80) cc_final: 0.7481 (m-80) REVERT: B 857 PHE cc_start: 0.7013 (m-80) cc_final: 0.6622 (m-80) REVERT: C 197 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7328 (t80) REVERT: C 570 ASP cc_start: 0.8022 (p0) cc_final: 0.7568 (p0) REVERT: C 677 GLN cc_start: 0.7790 (mm110) cc_final: 0.7415 (mm-40) REVERT: C 788 LYS cc_start: 0.7411 (pmtt) cc_final: 0.7124 (mmtm) REVERT: C 1121 ASN cc_start: 0.8143 (m-40) cc_final: 0.7941 (m110) REVERT: D 549 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7334 (mmmt) outliers start: 69 outliers final: 30 residues processed: 232 average time/residue: 0.4872 time to fit residues: 142.3923 Evaluate side-chains 179 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1113 GLU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 363 CYS Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 258 optimal weight: 0.7980 chunk 349 optimal weight: 40.0000 chunk 173 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 276 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 386 optimal weight: 30.0000 chunk 214 optimal weight: 0.7980 chunk 259 optimal weight: 0.0570 chunk 205 optimal weight: 1.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 HIS B 362 ASN B1073 GLN B1103 HIS B1121 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D 903 GLN D 994 GLN G 31 ASN J 37 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.211410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.155081 restraints weight = 47943.078| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.79 r_work: 0.3452 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32913 Z= 0.126 Angle : 0.598 10.296 44902 Z= 0.294 Chirality : 0.046 0.358 5201 Planarity : 0.004 0.054 5668 Dihedral : 4.567 44.049 4273 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 2.66 % Allowed : 16.51 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.13), residues: 3924 helix: 0.30 (0.20), residues: 700 sheet: -0.10 (0.18), residues: 810 loop : -1.92 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.016 0.001 TYR B 267 PHE 0.019 0.001 PHE C 219 TRP 0.037 0.001 TRP C 104 HIS 0.008 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (32793) covalent geometry : angle 0.58101 / 0.29 (44590) SS BOND : bond 0.00287 / 0.17 ( 45) SS BOND : angle 1.31629 / 0.85 ( 90) hydrogen bonds : bond 0.03676 / 2.39 ( 932) hydrogen bonds : angle 5.55136 / 3.79 ( 2535) Misc. bond : bond 0.00003 / 0.00 ( 1) link_BETA1-4 : bond 0.00493 / 0.30 ( 25) link_BETA1-4 : angle 1.45928 / 0.98 ( 75) link_NAG-ASN : bond 0.00425 / 0.27 ( 49) link_NAG-ASN : angle 2.16672 / 1.49 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 170 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.8315 (mt) cc_final: 0.8035 (mm) REVERT: B 588 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6941 (p0) REVERT: B 857 PHE cc_start: 0.7045 (m-80) cc_final: 0.6690 (m-80) REVERT: B 877 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.9097 (p) REVERT: C 117 LEU cc_start: 0.7340 (mt) cc_final: 0.6890 (tp) REVERT: C 197 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7490 (t80) REVERT: C 570 ASP cc_start: 0.8040 (p0) cc_final: 0.7690 (p0) REVERT: C 677 GLN cc_start: 0.7810 (mm110) cc_final: 0.7417 (mm-40) REVERT: C 978 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8293 (m) REVERT: C 1121 ASN cc_start: 0.8177 (m-40) cc_final: 0.7943 (m110) REVERT: D 549 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7316 (mmmt) REVERT: I 48 MET cc_start: 0.2164 (mpt) cc_final: 0.1669 (mmm) outliers start: 92 outliers final: 41 residues processed: 247 average time/residue: 0.4528 time to fit residues: 142.2598 Evaluate side-chains 197 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 370 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 344 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 250 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 317 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 HIS B 362 ASN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 994 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.210301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.153259 restraints weight = 47667.367| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.73 r_work: 0.3422 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 32913 Z= 0.171 Angle : 0.639 12.061 44902 Z= 0.312 Chirality : 0.047 0.424 5201 Planarity : 0.004 0.130 5668 Dihedral : 4.639 50.362 4271 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 2.75 % Allowed : 17.20 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 3924 helix: 0.32 (0.20), residues: 699 sheet: -0.07 (0.18), residues: 800 loop : -1.91 (0.12), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG C 997 TYR 0.020 0.001 TYR L 49 PHE 0.026 0.001 PHE C 106 TRP 0.040 0.002 TRP C 104 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (32793) covalent geometry : angle 0.61999 / 0.31 (44590) SS BOND : bond 0.00548 / 0.38 ( 45) SS BOND : angle 1.85016 / 1.23 ( 90) hydrogen bonds : bond 0.03913 / 2.54 ( 932) hydrogen bonds : angle 5.59317 / 3.83 ( 2535) Misc. bond : bond 0.00013 / 0.01 ( 1) link_BETA1-4 : bond 0.00455 / 0.28 ( 25) link_BETA1-4 : angle 1.45921 / 0.98 ( 75) link_NAG-ASN : bond 0.00386 / 0.24 ( 49) link_NAG-ASN : angle 2.19383 / 1.52 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 161 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TRP cc_start: 0.6230 (m-90) cc_final: 0.5992 (t-100) REVERT: B 360 ILE cc_start: 0.8327 (mt) cc_final: 0.8061 (mm) REVERT: B 857 PHE cc_start: 0.7094 (m-80) cc_final: 0.6759 (m-80) REVERT: B 1103 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7040 (p90) REVERT: C 117 LEU cc_start: 0.7407 (mt) cc_final: 0.6916 (tp) REVERT: C 197 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7482 (t80) REVERT: C 570 ASP cc_start: 0.8068 (p0) cc_final: 0.7674 (p0) REVERT: C 677 GLN cc_start: 0.7855 (mm110) cc_final: 0.7460 (mm-40) REVERT: C 978 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8258 (m) REVERT: C 1121 ASN cc_start: 0.8292 (m-40) cc_final: 0.8055 (m110) REVERT: D 54 LEU cc_start: 0.8894 (mt) cc_final: 0.8554 (mp) REVERT: D 549 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7374 (mmmt) REVERT: I 48 MET cc_start: 0.2231 (mpt) cc_final: 0.1253 (mmm) outliers start: 95 outliers final: 55 residues processed: 242 average time/residue: 0.4519 time to fit residues: 141.6161 Evaluate side-chains 215 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1103 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 255 optimal weight: 10.0000 chunk 109 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 386 optimal weight: 30.0000 chunk 209 optimal weight: 0.0170 chunk 124 optimal weight: 0.5980 chunk 327 optimal weight: 0.9990 chunk 295 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 306 optimal weight: 1.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 HIS B 362 ASN B1073 GLN B1103 HIS B1137 ASN ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.211366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.155990 restraints weight = 47713.208| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.69 r_work: 0.3475 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 32913 Z= 0.113 Angle : 0.598 14.018 44902 Z= 0.291 Chirality : 0.045 0.479 5201 Planarity : 0.004 0.073 5668 Dihedral : 4.442 43.831 4271 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 2.20 % Allowed : 18.07 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.13), residues: 3924 helix: 0.53 (0.21), residues: 693 sheet: 0.01 (0.18), residues: 813 loop : -1.85 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 997 TYR 0.015 0.001 TYR C1069 PHE 0.020 0.001 PHE C 92 TRP 0.033 0.001 TRP C 104 HIS 0.003 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (32793) covalent geometry : angle 0.58228 / 0.29 (44590) SS BOND : bond 0.00274 / 0.18 ( 45) SS BOND : angle 1.38551 / 0.91 ( 90) hydrogen bonds : bond 0.03421 / 2.24 ( 932) hydrogen bonds : angle 5.42338 / 3.70 ( 2535) Misc. bond : bond 0.00001 / 0.00 ( 1) link_BETA1-4 : bond 0.00478 / 0.29 ( 25) link_BETA1-4 : angle 1.40640 / 0.95 ( 75) link_NAG-ASN : bond 0.00407 / 0.26 ( 49) link_NAG-ASN : angle 2.07005 / 1.46 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 174 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.8375 (mt) cc_final: 0.8106 (mm) REVERT: B 520 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.4470 (tp) REVERT: B 857 PHE cc_start: 0.7025 (m-80) cc_final: 0.6801 (m-80) REVERT: C 197 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7555 (t80) REVERT: C 570 ASP cc_start: 0.8003 (p0) cc_final: 0.7645 (p0) REVERT: C 677 GLN cc_start: 0.7848 (mm110) cc_final: 0.7484 (mm-40) REVERT: C 978 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8279 (m) REVERT: D 193 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8062 (m-40) REVERT: D 549 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7217 (mmmt) REVERT: G 48 MET cc_start: 0.3588 (ppp) cc_final: 0.0175 (mpp) REVERT: I 48 MET cc_start: 0.1839 (mpt) cc_final: 0.1038 (mmm) outliers start: 76 outliers final: 41 residues processed: 239 average time/residue: 0.5404 time to fit residues: 161.3444 Evaluate side-chains 201 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 983 PHE Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 327 optimal weight: 0.0370 chunk 182 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 363 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 358 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 ASN B1073 GLN B1103 HIS B1121 ASN C 145 ASN C1121 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 994 GLN I 31 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.211625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.157695 restraints weight = 47595.551| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.65 r_work: 0.3503 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32913 Z= 0.111 Angle : 0.593 11.726 44902 Z= 0.290 Chirality : 0.045 0.354 5201 Planarity : 0.004 0.058 5668 Dihedral : 4.304 37.065 4271 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 2.14 % Allowed : 18.82 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 3924 helix: 0.70 (0.21), residues: 690 sheet: 0.08 (0.18), residues: 813 loop : -1.81 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 997 TYR 0.025 0.001 TYR B 170 PHE 0.015 0.001 PHE C 106 TRP 0.036 0.001 TRP C 104 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (32793) covalent geometry : angle 0.58053 / 0.29 (44590) SS BOND : bond 0.00247 / 0.15 ( 45) SS BOND : angle 1.23566 / 0.81 ( 90) hydrogen bonds : bond 0.03310 / 2.17 ( 932) hydrogen bonds : angle 5.30771 / 3.61 ( 2535) Misc. bond : bond 0.00001 / 0.00 ( 1) link_BETA1-4 : bond 0.00490 / 0.32 ( 25) link_BETA1-4 : angle 1.36163 / 0.91 ( 75) link_NAG-ASN : bond 0.00402 / 0.26 ( 49) link_NAG-ASN : angle 1.85698 / 1.27 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 162 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.8378 (mt) cc_final: 0.8110 (mm) REVERT: B 520 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4381 (tp) REVERT: B 588 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6892 (p0) REVERT: B 857 PHE cc_start: 0.6899 (m-80) cc_final: 0.6659 (m-80) REVERT: B 877 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.9016 (p) REVERT: C 197 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7618 (t80) REVERT: C 570 ASP cc_start: 0.7957 (p0) cc_final: 0.7526 (p0) REVERT: C 677 GLN cc_start: 0.7865 (mm110) cc_final: 0.7511 (mm-40) REVERT: C 978 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8295 (m) REVERT: D 549 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7213 (mmmt) REVERT: D 573 ASP cc_start: 0.7630 (p0) cc_final: 0.7426 (p0) REVERT: G 48 MET cc_start: 0.3299 (ppp) cc_final: 0.0210 (mpp) REVERT: I 48 MET cc_start: 0.1835 (mpt) cc_final: 0.1054 (mmm) outliers start: 74 outliers final: 43 residues processed: 224 average time/residue: 0.4739 time to fit residues: 136.7607 Evaluate side-chains 200 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 345 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 179 optimal weight: 30.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 196 ASN B 362 ASN B1103 HIS B1121 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.210233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.157862 restraints weight = 47598.386| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.70 r_work: 0.3430 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 32913 Z= 0.159 Angle : 0.630 12.848 44902 Z= 0.309 Chirality : 0.047 0.438 5201 Planarity : 0.004 0.060 5668 Dihedral : 4.449 44.461 4271 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 2.11 % Allowed : 18.85 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 3924 helix: 0.66 (0.21), residues: 690 sheet: 0.08 (0.18), residues: 823 loop : -1.84 (0.12), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 997 TYR 0.017 0.001 TYR C1069 PHE 0.025 0.001 PHE C 106 TRP 0.033 0.002 TRP D 149 HIS 0.005 0.001 HIS C1050 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (32793) covalent geometry : angle 0.61440 / 0.31 (44590) SS BOND : bond 0.00342 / 0.21 ( 45) SS BOND : angle 1.49464 / 0.99 ( 90) hydrogen bonds : bond 0.03736 / 2.44 ( 932) hydrogen bonds : angle 5.41660 / 3.69 ( 2535) Misc. bond : bond 0.00022 / 0.01 ( 1) link_BETA1-4 : bond 0.00443 / 0.28 ( 25) link_BETA1-4 : angle 1.38324 / 0.92 ( 75) link_NAG-ASN : bond 0.00337 / 0.19 ( 49) link_NAG-ASN : angle 2.12135 / 1.52 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 157 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TRP cc_start: 0.6230 (t-100) cc_final: 0.5394 (t-100) REVERT: B 196 ASN cc_start: -0.0065 (OUTLIER) cc_final: -0.0409 (p0) REVERT: B 360 ILE cc_start: 0.8394 (mt) cc_final: 0.8121 (mm) REVERT: B 520 LEU cc_start: 0.5395 (OUTLIER) cc_final: 0.4527 (tp) REVERT: B 756 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9097 (mp) REVERT: B 857 PHE cc_start: 0.7002 (m-80) cc_final: 0.6725 (m-80) REVERT: C 117 LEU cc_start: 0.7394 (mt) cc_final: 0.6945 (tp) REVERT: C 197 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7475 (t80) REVERT: C 570 ASP cc_start: 0.8034 (p0) cc_final: 0.7667 (p0) REVERT: C 677 GLN cc_start: 0.7911 (mm110) cc_final: 0.7585 (mm-40) REVERT: C 978 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8274 (m) REVERT: D 54 LEU cc_start: 0.8847 (mt) cc_final: 0.8505 (mp) REVERT: D 549 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7241 (mmmt) REVERT: G 48 MET cc_start: 0.3436 (ppp) cc_final: 0.0449 (mpp) REVERT: I 48 MET cc_start: 0.1777 (mpt) cc_final: 0.0951 (mmm) REVERT: I 114 MET cc_start: -0.2428 (ttm) cc_final: -0.2659 (ptp) outliers start: 73 outliers final: 51 residues processed: 222 average time/residue: 0.4649 time to fit residues: 132.8550 Evaluate side-chains 205 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 983 PHE Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1108 GLN Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1120 ASP Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 93 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 51 optimal weight: 0.0870 chunk 363 optimal weight: 0.0570 chunk 80 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 332 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 272 optimal weight: 3.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN B 196 ASN B 362 ASN B1073 GLN B1103 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 994 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.211610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.157135 restraints weight = 48019.038| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.68 r_work: 0.3465 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 32913 Z= 0.107 Angle : 0.600 12.972 44902 Z= 0.292 Chirality : 0.045 0.456 5201 Planarity : 0.004 0.055 5668 Dihedral : 4.299 37.770 4271 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.89 % Favored : 95.06 % Rotamer: Outliers : 1.56 % Allowed : 19.66 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 3924 helix: 0.80 (0.21), residues: 691 sheet: 0.12 (0.18), residues: 801 loop : -1.77 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 997 TYR 0.034 0.001 TYR B 170 PHE 0.026 0.001 PHE C 140 TRP 0.037 0.001 TRP D 149 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (32793) covalent geometry : angle 0.58659 / 0.29 (44590) SS BOND : bond 0.00228 / 0.14 ( 45) SS BOND : angle 1.19033 / 0.78 ( 90) hydrogen bonds : bond 0.03297 / 2.17 ( 932) hydrogen bonds : angle 5.28477 / 3.59 ( 2535) Misc. bond : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : bond 0.00478 / 0.30 ( 25) link_BETA1-4 : angle 1.34319 / 0.90 ( 75) link_NAG-ASN : bond 0.00393 / 0.25 ( 49) link_NAG-ASN : angle 1.91163 / 1.33 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TRP cc_start: 0.6230 (t-100) cc_final: 0.5305 (t-100) REVERT: B 128 ILE cc_start: 0.6519 (mp) cc_final: 0.6195 (pp) REVERT: B 360 ILE cc_start: 0.8380 (mt) cc_final: 0.8108 (mm) REVERT: B 520 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.4613 (tp) REVERT: B 857 PHE cc_start: 0.6908 (m-80) cc_final: 0.6678 (m-80) REVERT: B 877 SER cc_start: 0.9274 (OUTLIER) cc_final: 0.9035 (p) REVERT: B 1121 ASN cc_start: 0.7991 (m-40) cc_final: 0.7782 (m110) REVERT: C 117 LEU cc_start: 0.7283 (mt) cc_final: 0.6815 (tp) REVERT: C 197 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7590 (t80) REVERT: C 570 ASP cc_start: 0.7928 (p0) cc_final: 0.7521 (p0) REVERT: C 677 GLN cc_start: 0.7910 (mm110) cc_final: 0.7526 (mm-40) REVERT: C 978 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8294 (m) REVERT: D 549 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7213 (mmmt) REVERT: G 48 MET cc_start: 0.3147 (ppp) cc_final: 0.0280 (mpp) REVERT: I 48 MET cc_start: 0.1727 (mpt) cc_final: 0.0943 (mmm) outliers start: 54 outliers final: 39 residues processed: 208 average time/residue: 0.4598 time to fit residues: 124.2402 Evaluate side-chains 197 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 44 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 351 optimal weight: 30.0000 chunk 97 optimal weight: 0.0570 chunk 177 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 49 optimal weight: 0.0870 chunk 367 optimal weight: 20.0000 chunk 375 optimal weight: 30.0000 overall best weight: 1.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 ASN B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 897 GLN D 994 GLN I 31 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.209166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.153618 restraints weight = 47383.214| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.63 r_work: 0.3438 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 32913 Z= 0.193 Angle : 0.660 12.723 44902 Z= 0.323 Chirality : 0.048 0.378 5201 Planarity : 0.004 0.055 5668 Dihedral : 4.542 49.229 4271 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.40 % Favored : 93.53 % Rotamer: Outliers : 2.06 % Allowed : 19.43 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.13), residues: 3924 helix: 0.67 (0.21), residues: 684 sheet: 0.06 (0.18), residues: 814 loop : -1.84 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 997 TYR 0.020 0.001 TYR B 267 PHE 0.031 0.002 PHE C 106 TRP 0.031 0.002 TRP D 149 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (32793) covalent geometry : angle 0.64474 / 0.32 (44590) SS BOND : bond 0.00409 / 0.26 ( 45) SS BOND : angle 1.65861 / 1.11 ( 90) hydrogen bonds : bond 0.04031 / 2.64 ( 932) hydrogen bonds : angle 5.49653 / 3.74 ( 2535) Misc. bond : bond 0.00038 / 0.02 ( 1) link_BETA1-4 : bond 0.00434 / 0.26 ( 25) link_BETA1-4 : angle 1.40670 / 0.93 ( 75) link_NAG-ASN : bond 0.00385 / 0.24 ( 49) link_NAG-ASN : angle 2.03318 / 1.42 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12813.93 seconds wall clock time: 218 minutes 51.29 seconds (13131.29 seconds total)