Starting phenix.real_space_refine on Fri Feb 6 02:42:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdw_60015/02_2026/8zdw_60015.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdw_60015/02_2026/8zdw_60015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zdw_60015/02_2026/8zdw_60015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdw_60015/02_2026/8zdw_60015.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zdw_60015/02_2026/8zdw_60015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdw_60015/02_2026/8zdw_60015.map" } resolution = 3.45 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= 0.009 sd= 0.169 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 114 5.16 5 C 14136 2.51 5 N 3795 2.21 5 O 4557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22602 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2549 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1412 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "R" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1683 Classifications: {'peptide': 217} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 205} Chain: "U" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1682 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 207} Chain: "D" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1412 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "I" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1412 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "F" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1682 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 207} Chain: "L" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1682 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 207} Chain: "E" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1683 Classifications: {'peptide': 217} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 205} Chain: "J" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1683 Classifications: {'peptide': 217} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 205} Chain: "C" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2549 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain: "H" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2549 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N CYS U 22 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS U 22 " occ=0.89 residue: pdb=" N LYS U 65 " occ=0.95 ... (7 atoms not shown) pdb=" NZ LYS U 65 " occ=0.95 residue: pdb=" N CYS U 202 " occ=0.96 ... (4 atoms not shown) pdb=" SG CYS U 202 " occ=0.96 residue: pdb=" N CYS F 22 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS F 22 " occ=0.89 residue: pdb=" N LYS F 65 " occ=0.95 ... (7 atoms not shown) pdb=" NZ LYS F 65 " occ=0.95 residue: pdb=" N CYS F 202 " occ=0.96 ... (4 atoms not shown) pdb=" SG CYS F 202 " occ=0.96 residue: pdb=" N CYS L 22 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS L 22 " occ=0.89 residue: pdb=" N LYS L 65 " occ=0.95 ... (7 atoms not shown) pdb=" NZ LYS L 65 " occ=0.95 residue: pdb=" N CYS L 202 " occ=0.96 ... (4 atoms not shown) pdb=" SG CYS L 202 " occ=0.96 Time building chain proxies: 4.78, per 1000 atoms: 0.21 Number of scatterers: 22602 At special positions: 0 Unit cell: (191.4, 190.08, 155.76, 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 114 16.00 O 4557 8.00 N 3795 7.00 C 14136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 138 " - pdb=" SG CYS R 198 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 147 " - pdb=" SG CYS U 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 147 " - pdb=" SG CYS L 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 277 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 139 " distance=2.03 Simple disulfide: pdb=" SG CYS H 281 " - pdb=" SG CYS H 305 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG V 1 " - " GAL V 2 " " NAG W 1 " - " GAL W 2 " " NAG X 1 " - " GAL X 2 " BETA2-3 " GAL V 2 " - " SIA V 3 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL W 2 " - " SIA W 3 " " GAL X 2 " - " SIA X 3 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 158 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 158 " " NAG D 301 " - " ASN D 154 " " NAG E 301 " - " ASN E 67 " " NAG G 1 " - " ASN A 33 " " NAG H 401 " - " ASN H 21 " " NAG H 402 " - " ASN H 158 " " NAG I 301 " - " ASN I 154 " " NAG J 301 " - " ASN J 67 " " NAG K 1 " - " ASN A 169 " " NAG M 1 " - " ASN A 289 " " NAG N 1 " - " ASN C 33 " " NAG O 1 " - " ASN C 169 " " NAG P 1 " - " ASN C 289 " " NAG Q 1 " - " ASN H 33 " " NAG R 301 " - " ASN R 67 " " NAG S 1 " - " ASN H 169 " " NAG T 1 " - " ASN H 289 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 845.1 milliseconds 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 69 sheets defined 16.3% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.830A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 127 removed outlier: 3.650A pdb=" N GLU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.977A pdb=" N MET B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 removed outlier: 3.630A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU B 165 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 131 removed outlier: 3.750A pdb=" N LEU R 129 " --> pdb=" O SER R 125 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR R 130 " --> pdb=" O SER R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 193 removed outlier: 3.845A pdb=" N ARG R 192 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS R 193 " --> pdb=" O TYR R 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 189 through 193' Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'U' and resid 163 through 165 No H-bonds generated for 'chain 'U' and resid 163 through 165' Processing helix chain 'D' and resid 37 through 59 removed outlier: 3.830A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 127 removed outlier: 3.650A pdb=" N GLU D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.977A pdb=" N MET D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.629A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 59 removed outlier: 3.830A pdb=" N THR I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS I 43 " --> pdb=" O GLU I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 127 removed outlier: 3.650A pdb=" N GLU I 78 " --> pdb=" O GLU I 74 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU I 105 " --> pdb=" O LEU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 130 No H-bonds generated for 'chain 'I' and resid 128 through 130' Processing helix chain 'I' and resid 145 through 154 removed outlier: 3.978A pdb=" N MET I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 173 removed outlier: 3.630A pdb=" N GLU I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU I 165 " --> pdb=" O GLN I 161 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE I 173 " --> pdb=" O LYS I 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 163 through 165 No H-bonds generated for 'chain 'F' and resid 163 through 165' Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 163 through 165 No H-bonds generated for 'chain 'L' and resid 163 through 165' Processing helix chain 'E' and resid 125 through 131 removed outlier: 3.750A pdb=" N LEU E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 130 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 193 removed outlier: 3.845A pdb=" N ARG E 192 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS E 193 " --> pdb=" O TYR E 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 189 through 193' Processing helix chain 'J' and resid 125 through 131 removed outlier: 3.751A pdb=" N LEU J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR J 130 " --> pdb=" O SER J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 193 removed outlier: 3.845A pdb=" N ARG J 192 " --> pdb=" O GLU J 189 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS J 193 " --> pdb=" O TYR J 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 189 through 193' Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 104 through 113 Processing helix chain 'H' and resid 187 through 195 Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 53 removed outlier: 6.391A pdb=" N LEU A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.718A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.824A pdb=" N ASP A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.824A pdb=" N ASP A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 181 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.415A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.536A pdb=" N SER A 247 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.366A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 288 " --> pdb=" O CYS A 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AB3, first strand: chain 'R' and resid 5 through 7 removed outlier: 3.569A pdb=" N SER R 22 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA R 19 " --> pdb=" O ILE R 79 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP R 74 " --> pdb=" O SER R 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.310A pdb=" N LEU R 11 " --> pdb=" O GLU R 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'R' and resid 30 through 31 Processing sheet with id=AB6, first strand: chain 'R' and resid 57 through 58 removed outlier: 5.361A pdb=" N LEU R 50 " --> pdb=" O GLN R 41 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN R 41 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 118 through 121 removed outlier: 3.950A pdb=" N ASN R 141 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE R 139 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR R 177 " --> pdb=" O ASN R 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 157 through 158 removed outlier: 3.673A pdb=" N ASN R 149 " --> pdb=" O THR R 201 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR R 197 " --> pdb=" O LYS R 153 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR R 196 " --> pdb=" O PHE R 213 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS R 198 " --> pdb=" O LYS R 211 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS R 211 " --> pdb=" O CYS R 198 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA R 200 " --> pdb=" O ILE R 209 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE R 209 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLU U 10 " --> pdb=" O THR U 117 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR U 33 " --> pdb=" O ASN U 99 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY U 49 " --> pdb=" O TRP U 36 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TRP U 47 " --> pdb=" O LYS U 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLU U 10 " --> pdb=" O THR U 117 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N CYS U 96 " --> pdb=" O TRP U 110 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP U 110 " --> pdb=" O CYS U 96 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ARG U 98 " --> pdb=" O ASP U 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 18 through 23 Processing sheet with id=AC3, first strand: chain 'U' and resid 127 through 131 removed outlier: 3.574A pdb=" N LEU U 148 " --> pdb=" O TYR U 129 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU U 131 " --> pdb=" O GLY U 146 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY U 146 " --> pdb=" O LEU U 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL U 143 " --> pdb=" O VAL U 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU U 145 " --> pdb=" O VAL U 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER U 186 " --> pdb=" O CYS U 147 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY U 151 " --> pdb=" O TYR U 182 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR U 182 " --> pdb=" O GLY U 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 127 through 131 removed outlier: 3.574A pdb=" N LEU U 148 " --> pdb=" O TYR U 129 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU U 131 " --> pdb=" O GLY U 146 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY U 146 " --> pdb=" O LEU U 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL U 143 " --> pdb=" O VAL U 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU U 145 " --> pdb=" O VAL U 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER U 186 " --> pdb=" O CYS U 147 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY U 151 " --> pdb=" O TYR U 182 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR U 182 " --> pdb=" O GLY U 151 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR U 183 " --> pdb=" O VAL U 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 158 through 161 removed outlier: 3.855A pdb=" N LYS U 215 " --> pdb=" O CYS U 202 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL U 204 " --> pdb=" O VAL U 213 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL U 213 " --> pdb=" O VAL U 204 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 32 through 36 Processing sheet with id=AC7, first strand: chain 'I' and resid 32 through 36 Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLU F 10 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR F 33 " --> pdb=" O ASN F 99 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TRP F 47 " --> pdb=" O LYS F 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLU F 10 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N CYS F 96 " --> pdb=" O TRP F 110 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP F 110 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ARG F 98 " --> pdb=" O ASP F 108 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AD2, first strand: chain 'F' and resid 127 through 131 removed outlier: 3.574A pdb=" N LEU F 148 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 131 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY F 146 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL F 143 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 145 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER F 186 " --> pdb=" O CYS F 147 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY F 151 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR F 182 " --> pdb=" O GLY F 151 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 127 through 131 removed outlier: 3.574A pdb=" N LEU F 148 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 131 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY F 146 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL F 143 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 145 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER F 186 " --> pdb=" O CYS F 147 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY F 151 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR F 182 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR F 183 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.855A pdb=" N LYS F 215 " --> pdb=" O CYS F 202 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL F 204 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL F 213 " --> pdb=" O VAL F 204 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLU L 10 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR L 33 " --> pdb=" O ASN L 99 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TRP L 47 " --> pdb=" O LYS L 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLU L 10 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N CYS L 96 " --> pdb=" O TRP L 110 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP L 110 " --> pdb=" O CYS L 96 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG L 98 " --> pdb=" O ASP L 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'L' and resid 127 through 131 removed outlier: 3.574A pdb=" N LEU L 148 " --> pdb=" O TYR L 129 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU L 131 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY L 146 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL L 143 " --> pdb=" O VAL L 190 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU L 145 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER L 186 " --> pdb=" O CYS L 147 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY L 151 " --> pdb=" O TYR L 182 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR L 182 " --> pdb=" O GLY L 151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 127 through 131 removed outlier: 3.574A pdb=" N LEU L 148 " --> pdb=" O TYR L 129 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU L 131 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY L 146 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL L 143 " --> pdb=" O VAL L 190 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU L 145 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER L 186 " --> pdb=" O CYS L 147 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY L 151 " --> pdb=" O TYR L 182 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR L 182 " --> pdb=" O GLY L 151 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR L 183 " --> pdb=" O VAL L 176 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 158 through 161 removed outlier: 3.856A pdb=" N LYS L 215 " --> pdb=" O CYS L 202 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL L 204 " --> pdb=" O VAL L 213 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL L 213 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.569A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA E 19 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP E 74 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.310A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AE5, first strand: chain 'E' and resid 57 through 58 removed outlier: 5.361A pdb=" N LEU E 50 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN E 41 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 118 through 121 removed outlier: 3.950A pdb=" N ASN E 141 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE E 139 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR E 177 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.673A pdb=" N ASN E 149 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 197 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR E 196 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS E 198 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS E 211 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA E 200 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE E 209 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.569A pdb=" N SER J 22 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA J 19 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP J 74 " --> pdb=" O SER J 71 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.311A pdb=" N LEU J 11 " --> pdb=" O GLU J 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'J' and resid 30 through 31 Processing sheet with id=AF2, first strand: chain 'J' and resid 57 through 58 removed outlier: 5.361A pdb=" N LEU J 50 " --> pdb=" O GLN J 41 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN J 41 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 118 through 121 removed outlier: 3.950A pdb=" N ASN J 141 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE J 139 " --> pdb=" O SER J 120 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR J 177 " --> pdb=" O ASN J 142 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 157 through 158 removed outlier: 3.674A pdb=" N ASN J 149 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR J 197 " --> pdb=" O LYS J 153 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR J 196 " --> pdb=" O PHE J 213 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS J 198 " --> pdb=" O LYS J 211 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS J 211 " --> pdb=" O CYS J 198 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA J 200 " --> pdb=" O ILE J 209 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE J 209 " --> pdb=" O ALA J 200 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AF7, first strand: chain 'C' and resid 51 through 53 removed outlier: 6.391A pdb=" N LEU C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.718A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.824A pdb=" N ASP C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.824A pdb=" N ASP C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 181 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.415A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.535A pdb=" N SER C 247 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 209 " --> pdb=" O THR C 206 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.366A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 288 " --> pdb=" O CYS C 281 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AG6, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AG7, first strand: chain 'H' and resid 39 through 41 Processing sheet with id=AG8, first strand: chain 'H' and resid 51 through 53 removed outlier: 6.391A pdb=" N LEU H 51 " --> pdb=" O GLY H 275 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS H 277 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP H 53 " --> pdb=" O CYS H 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.718A pdb=" N LEU H 59 " --> pdb=" O VAL H 88 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 100 through 102 removed outlier: 6.824A pdb=" N ASP H 101 " --> pdb=" O PHE H 232 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N TRP H 234 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 100 through 102 removed outlier: 6.824A pdb=" N ASP H 101 " --> pdb=" O PHE H 232 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N TRP H 234 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU H 179 " --> pdb=" O PRO H 254 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY H 181 " --> pdb=" O ILE H 252 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 136 through 141 removed outlier: 4.415A pdb=" N CYS H 139 " --> pdb=" O SER H 146 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 164 through 169 removed outlier: 3.536A pdb=" N SER H 247 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU H 209 " --> pdb=" O THR H 206 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 281 through 283 removed outlier: 4.367A pdb=" N CYS H 281 " --> pdb=" O ILE H 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 288 " --> pdb=" O CYS H 281 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 294 through 295 801 hydrogen bonds defined for protein. 2106 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: 3.70 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3962 1.32 - 1.45: 6402 1.45 - 1.58: 12589 1.58 - 1.70: 0 1.70 - 1.83: 165 Bond restraints: 23118 Sorted by residual: bond pdb=" CA SER A 129 " pdb=" CB SER A 129 " ideal model delta sigma weight residual 1.532 1.459 0.073 1.28e-02 6.10e+03 3.25e+01 bond pdb=" CA SER C 129 " pdb=" CB SER C 129 " ideal model delta sigma weight residual 1.532 1.460 0.073 1.28e-02 6.10e+03 3.23e+01 bond pdb=" CA SER H 129 " pdb=" CB SER H 129 " ideal model delta sigma weight residual 1.532 1.460 0.072 1.28e-02 6.10e+03 3.21e+01 bond pdb=" C1 SIA V 3 " pdb=" C2 SIA V 3 " ideal model delta sigma weight residual 1.585 1.510 0.075 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 SIA W 3 " pdb=" C2 SIA W 3 " ideal model delta sigma weight residual 1.585 1.510 0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 23113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 30626 2.24 - 4.47: 644 4.47 - 6.71: 83 6.71 - 8.95: 18 8.95 - 11.18: 6 Bond angle restraints: 31377 Sorted by residual: angle pdb=" CA HIS H 130 " pdb=" C HIS H 130 " pdb=" O HIS H 130 " ideal model delta sigma weight residual 121.87 116.83 5.04 1.16e+00 7.43e-01 1.88e+01 angle pdb=" CA HIS C 130 " pdb=" C HIS C 130 " pdb=" O HIS C 130 " ideal model delta sigma weight residual 121.87 116.84 5.03 1.16e+00 7.43e-01 1.88e+01 angle pdb=" CA HIS A 130 " pdb=" C HIS A 130 " pdb=" O HIS A 130 " ideal model delta sigma weight residual 121.87 116.86 5.01 1.16e+00 7.43e-01 1.87e+01 angle pdb=" CA GLN U 5 " pdb=" C GLN U 5 " pdb=" O GLN U 5 " ideal model delta sigma weight residual 121.55 116.55 5.00 1.26e+00 6.30e-01 1.57e+01 angle pdb=" N ARG D 170 " pdb=" CA ARG D 170 " pdb=" C ARG D 170 " ideal model delta sigma weight residual 113.23 108.32 4.91 1.24e+00 6.50e-01 1.57e+01 ... (remaining 31372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 13468 21.81 - 43.62: 773 43.62 - 65.43: 120 65.43 - 87.24: 72 87.24 - 109.05: 30 Dihedral angle restraints: 14463 sinusoidal: 6342 harmonic: 8121 Sorted by residual: dihedral pdb=" CB CYS C 281 " pdb=" SG CYS C 281 " pdb=" SG CYS C 305 " pdb=" CB CYS C 305 " ideal model delta sinusoidal sigma weight residual 93.00 7.32 85.68 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS H 281 " pdb=" SG CYS H 281 " pdb=" SG CYS H 305 " pdb=" CB CYS H 305 " ideal model delta sinusoidal sigma weight residual 93.00 7.33 85.67 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS A 281 " pdb=" SG CYS A 281 " pdb=" SG CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sinusoidal sigma weight residual 93.00 7.34 85.66 1 1.00e+01 1.00e-02 8.87e+01 ... (remaining 14460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 3522 0.200 - 0.399: 24 0.399 - 0.599: 0 0.599 - 0.799: 0 0.799 - 0.998: 3 Chirality restraints: 3549 Sorted by residual: chirality pdb=" C2 SIA V 3 " pdb=" O3 GAL V 2 " pdb=" C1 SIA V 3 " pdb=" O6 SIA V 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.71 0.21 2.00e-02 2.50e+03 1.14e+02 chirality pdb=" C2 SIA X 3 " pdb=" O3 GAL X 2 " pdb=" C1 SIA X 3 " pdb=" O6 SIA X 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.71 0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C2 SIA W 3 " pdb=" O3 GAL W 2 " pdb=" C1 SIA W 3 " pdb=" O6 SIA W 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.71 0.21 2.00e-02 2.50e+03 1.13e+02 ... (remaining 3546 not shown) Planarity restraints: 4029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " 0.287 2.00e-02 2.50e+03 2.41e-01 7.29e+02 pdb=" C7 NAG X 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " 0.287 2.00e-02 2.50e+03 2.41e-01 7.29e+02 pdb=" C7 NAG V 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " -0.286 2.00e-02 2.50e+03 2.41e-01 7.27e+02 pdb=" C7 NAG W 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " 0.411 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " -0.018 2.00e-02 2.50e+03 ... (remaining 4026 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3733 2.77 - 3.30: 21570 3.30 - 3.83: 36018 3.83 - 4.37: 42707 4.37 - 4.90: 73826 Nonbonded interactions: 177854 Sorted by model distance: nonbonded pdb=" O ILE J 154 " pdb=" OG SER J 157 " model vdw 2.237 3.040 nonbonded pdb=" O ILE E 154 " pdb=" OG SER E 157 " model vdw 2.237 3.040 nonbonded pdb=" O ILE R 154 " pdb=" OG SER R 157 " model vdw 2.237 3.040 nonbonded pdb=" O CYS H 52 " pdb=" OH TYR H 86 " model vdw 2.269 3.040 nonbonded pdb=" O CYS C 52 " pdb=" OH TYR C 86 " model vdw 2.270 3.040 ... (remaining 177849 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'U' } ncs_group { reference = chain 'G' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = (chain 'K' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and (resid 1 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 ))) selection = (chain 'W' and (resid 1 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 ))) selection = (chain 'X' and (resid 1 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 ))) } 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=0.89 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: 0.880 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: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.450 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.005 0.075 23187 Z= 0.267 Angle : 0.789 14.030 31557 Z= 0.410 Chirality : 0.058 0.998 3549 Planarity : 0.009 0.241 4008 Dihedral : 15.375 109.047 9174 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.24 % Allowed : 1.18 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.16), residues: 2778 helix: 0.37 (0.26), residues: 381 sheet: 0.18 (0.18), residues: 882 loop : -0.94 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 127 TYR 0.020 0.001 TYR L 182 PHE 0.008 0.001 PHE D 3 TRP 0.017 0.001 TRP R 152 HIS 0.008 0.001 HIS H 130 Details of bonding type rmsd covalent geometry : bond 0.00456 (23118) covalent geometry : angle 0.74564 (31377) SS BOND : bond 0.00174 ( 27) SS BOND : angle 1.16009 ( 54) hydrogen bonds : bond 0.26824 ( 741) hydrogen bonds : angle 9.34650 ( 2106) link_BETA1-4 : bond 0.00652 ( 18) link_BETA1-4 : angle 3.21429 ( 54) link_BETA2-3 : bond 0.02103 ( 3) link_BETA2-3 : angle 6.72620 ( 9) link_NAG-ASN : bond 0.00790 ( 21) link_NAG-ASN : angle 4.26356 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 378 time to evaluate : 0.871 Fit side-chains REVERT: A 150 ASN cc_start: 0.8181 (m110) cc_final: 0.7900 (m-40) REVERT: A 279 THR cc_start: 0.8535 (p) cc_final: 0.8303 (p) REVERT: U 104 TYR cc_start: 0.8712 (m-80) cc_final: 0.8455 (m-80) REVERT: U 181 LEU cc_start: 0.7892 (mm) cc_final: 0.7596 (mm) REVERT: L 181 LEU cc_start: 0.7962 (mm) cc_final: 0.7615 (mm) REVERT: C 30 MET cc_start: 0.8557 (mmt) cc_final: 0.8274 (mmm) REVERT: C 226 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8093 (mm-40) REVERT: H 114 ARG cc_start: 0.7449 (mpt-90) cc_final: 0.7226 (mtt90) outliers start: 6 outliers final: 0 residues processed: 381 average time/residue: 0.1473 time to fit residues: 86.8152 Evaluate side-chains 289 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN U 3 HIS U 171 HIS D 125 GLN I 125 GLN F 3 HIS L 3 HIS C 186 ASN ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 282 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 = 0.4161 r_free = 0.4161 target = 0.193760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.163339 restraints weight = 29116.794| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.47 r_work: 0.3373 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 23187 Z= 0.164 Angle : 0.669 12.732 31557 Z= 0.332 Chirality : 0.048 0.395 3549 Planarity : 0.005 0.051 4008 Dihedral : 10.618 86.755 3987 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.02 % Allowed : 7.55 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2778 helix: 0.88 (0.25), residues: 387 sheet: 0.26 (0.17), residues: 900 loop : -0.94 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 24 TYR 0.020 0.001 TYR E 53 PHE 0.018 0.001 PHE R 122 TRP 0.011 0.001 TRP U 161 HIS 0.013 0.001 HIS L 206 Details of bonding type rmsd covalent geometry : bond 0.00380 (23118) covalent geometry : angle 0.62997 (31377) SS BOND : bond 0.00465 ( 27) SS BOND : angle 1.20931 ( 54) hydrogen bonds : bond 0.05200 ( 741) hydrogen bonds : angle 6.05806 ( 2106) link_BETA1-4 : bond 0.00855 ( 18) link_BETA1-4 : angle 3.15615 ( 54) link_BETA2-3 : bond 0.00344 ( 3) link_BETA2-3 : angle 4.53288 ( 9) link_NAG-ASN : bond 0.00798 ( 21) link_NAG-ASN : angle 3.70687 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 334 time to evaluate : 0.780 Fit side-chains REVERT: B 109 ASP cc_start: 0.8164 (m-30) cc_final: 0.7919 (m-30) REVERT: U 148 LEU cc_start: 0.8431 (tt) cc_final: 0.7769 (pt) REVERT: U 181 LEU cc_start: 0.7973 (mm) cc_final: 0.7447 (mm) REVERT: D 17 MET cc_start: 0.7097 (tpt) cc_final: 0.6734 (ttt) REVERT: D 109 ASP cc_start: 0.8523 (m-30) cc_final: 0.8130 (m-30) REVERT: I 17 MET cc_start: 0.7102 (tpt) cc_final: 0.6679 (ttt) REVERT: I 142 HIS cc_start: 0.4452 (p90) cc_final: 0.4198 (p90) REVERT: F 148 LEU cc_start: 0.7883 (tt) cc_final: 0.7348 (mp) REVERT: L 148 LEU cc_start: 0.8180 (tt) cc_final: 0.7512 (pp) REVERT: L 181 LEU cc_start: 0.7803 (mm) cc_final: 0.7421 (mm) REVERT: E 71 SER cc_start: 0.7583 (t) cc_final: 0.7351 (m) REVERT: E 85 ASP cc_start: 0.7266 (t0) cc_final: 0.7013 (t0) REVERT: J 30 ASP cc_start: 0.7046 (t0) cc_final: 0.6746 (p0) REVERT: J 85 ASP cc_start: 0.7578 (t0) cc_final: 0.7292 (t0) REVERT: J 86 ASP cc_start: 0.7593 (m-30) cc_final: 0.7161 (m-30) REVERT: H 277 CYS cc_start: 0.7516 (p) cc_final: 0.7108 (p) outliers start: 25 outliers final: 18 residues processed: 347 average time/residue: 0.1591 time to fit residues: 85.1869 Evaluate side-chains 316 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 298 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 320 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 165 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 274 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 258 optimal weight: 0.3980 chunk 244 optimal weight: 9.9990 chunk 263 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 HIS F 3 HIS F 171 HIS L 3 HIS ** C 298 HIS ** 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 = 0.4124 r_free = 0.4124 target = 0.190446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.157074 restraints weight = 29310.098| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.56 r_work: 0.3153 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 23187 Z= 0.168 Angle : 0.627 11.736 31557 Z= 0.308 Chirality : 0.047 0.400 3549 Planarity : 0.004 0.045 4008 Dihedral : 8.541 81.971 3987 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.54 % Allowed : 11.08 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2778 helix: 1.15 (0.26), residues: 387 sheet: 0.20 (0.17), residues: 891 loop : -0.91 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 313 TYR 0.019 0.001 TYR E 53 PHE 0.011 0.001 PHE I 88 TRP 0.016 0.001 TRP F 161 HIS 0.008 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00400 (23118) covalent geometry : angle 0.59031 (31377) SS BOND : bond 0.00399 ( 27) SS BOND : angle 1.32450 ( 54) hydrogen bonds : bond 0.04772 ( 741) hydrogen bonds : angle 5.44486 ( 2106) link_BETA1-4 : bond 0.00799 ( 18) link_BETA1-4 : angle 2.98327 ( 54) link_BETA2-3 : bond 0.00498 ( 3) link_BETA2-3 : angle 3.81634 ( 9) link_NAG-ASN : bond 0.00812 ( 21) link_NAG-ASN : angle 3.44345 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 322 time to evaluate : 0.849 Fit side-chains REVERT: A 14 CYS cc_start: 0.7036 (p) cc_final: 0.6666 (p) REVERT: B 109 ASP cc_start: 0.8143 (m-30) cc_final: 0.7907 (m-30) REVERT: B 120 ASP cc_start: 0.8112 (m-30) cc_final: 0.7726 (t0) REVERT: R 30 ASP cc_start: 0.7368 (t0) cc_final: 0.6835 (p0) REVERT: R 109 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7775 (mm-30) REVERT: R 114 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6389 (t0) REVERT: D 15 GLN cc_start: 0.8198 (mp10) cc_final: 0.7981 (mp10) REVERT: D 17 MET cc_start: 0.7046 (tpt) cc_final: 0.6519 (ttt) REVERT: D 154 ASN cc_start: 0.7778 (m-40) cc_final: 0.7291 (p0) REVERT: I 120 ASP cc_start: 0.8141 (m-30) cc_final: 0.7792 (t0) REVERT: I 142 HIS cc_start: 0.4641 (p90) cc_final: 0.4308 (p90) REVERT: L 84 ARG cc_start: 0.6923 (mtt180) cc_final: 0.6691 (mtm-85) REVERT: L 181 LEU cc_start: 0.7682 (mm) cc_final: 0.7303 (mm) REVERT: E 71 SER cc_start: 0.7418 (t) cc_final: 0.7134 (m) REVERT: E 85 ASP cc_start: 0.7692 (t0) cc_final: 0.7343 (t0) REVERT: E 146 LYS cc_start: 0.8089 (pttt) cc_final: 0.7722 (ptmm) REVERT: J 83 GLU cc_start: 0.7676 (pm20) cc_final: 0.7458 (pm20) REVERT: J 85 ASP cc_start: 0.7968 (t0) cc_final: 0.7566 (t0) REVERT: J 86 ASP cc_start: 0.7855 (m-30) cc_final: 0.7419 (m-30) REVERT: J 114 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.6164 (t0) REVERT: H 277 CYS cc_start: 0.7625 (p) cc_final: 0.7252 (p) outliers start: 38 outliers final: 26 residues processed: 346 average time/residue: 0.1665 time to fit residues: 88.7693 Evaluate side-chains 317 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 289 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 320 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 135 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 105 optimal weight: 0.0170 chunk 37 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 HIS F 3 HIS L 3 HIS L 6 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.194098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.170912 restraints weight = 29229.492| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.24 r_work: 0.3345 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23187 Z= 0.127 Angle : 0.596 11.623 31557 Z= 0.292 Chirality : 0.046 0.375 3549 Planarity : 0.004 0.049 4008 Dihedral : 7.759 79.914 3987 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.79 % Allowed : 12.71 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2778 helix: 1.39 (0.26), residues: 387 sheet: 0.32 (0.17), residues: 882 loop : -0.94 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 24 TYR 0.018 0.001 TYR R 53 PHE 0.008 0.001 PHE U 107 TRP 0.017 0.001 TRP F 161 HIS 0.011 0.001 HIS U 3 Details of bonding type rmsd covalent geometry : bond 0.00295 (23118) covalent geometry : angle 0.55906 (31377) SS BOND : bond 0.00366 ( 27) SS BOND : angle 1.22254 ( 54) hydrogen bonds : bond 0.04081 ( 741) hydrogen bonds : angle 5.19691 ( 2106) link_BETA1-4 : bond 0.00784 ( 18) link_BETA1-4 : angle 3.02425 ( 54) link_BETA2-3 : bond 0.00217 ( 3) link_BETA2-3 : angle 3.01867 ( 9) link_NAG-ASN : bond 0.00776 ( 21) link_NAG-ASN : angle 3.46216 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 321 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 14 CYS cc_start: 0.7174 (p) cc_final: 0.6829 (p) REVERT: A 144 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8295 (mmtm) REVERT: B 142 HIS cc_start: 0.4410 (p90) cc_final: 0.3835 (p90) REVERT: R 85 ASP cc_start: 0.7289 (t0) cc_final: 0.7082 (t0) REVERT: R 109 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8012 (mm-30) REVERT: R 114 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6242 (t0) REVERT: U 148 LEU cc_start: 0.8567 (tt) cc_final: 0.7890 (pt) REVERT: D 15 GLN cc_start: 0.8273 (mp10) cc_final: 0.8008 (mp10) REVERT: D 17 MET cc_start: 0.6912 (tpt) cc_final: 0.5837 (ttt) REVERT: D 154 ASN cc_start: 0.7836 (m-40) cc_final: 0.7399 (p0) REVERT: D 158 ASP cc_start: 0.7451 (p0) cc_final: 0.7237 (p0) REVERT: I 142 HIS cc_start: 0.4924 (p90) cc_final: 0.4529 (p90) REVERT: F 142 MET cc_start: 0.7115 (tpp) cc_final: 0.6685 (ppp) REVERT: F 148 LEU cc_start: 0.8221 (tt) cc_final: 0.7750 (mp) REVERT: L 148 LEU cc_start: 0.8564 (tt) cc_final: 0.7876 (pp) REVERT: L 181 LEU cc_start: 0.7681 (mm) cc_final: 0.7288 (mm) REVERT: E 71 SER cc_start: 0.7473 (t) cc_final: 0.7218 (m) REVERT: E 83 GLU cc_start: 0.7943 (pm20) cc_final: 0.7556 (pm20) REVERT: E 85 ASP cc_start: 0.7539 (t0) cc_final: 0.7139 (t0) REVERT: E 136 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7490 (m) REVERT: J 71 SER cc_start: 0.7570 (t) cc_final: 0.7220 (p) REVERT: J 85 ASP cc_start: 0.7709 (t0) cc_final: 0.7324 (t0) REVERT: J 86 ASP cc_start: 0.7859 (m-30) cc_final: 0.7533 (m-30) REVERT: J 114 ASP cc_start: 0.6234 (OUTLIER) cc_final: 0.5863 (t0) REVERT: C 18 HIS cc_start: 0.8443 (t70) cc_final: 0.8230 (t-170) REVERT: H 114 ARG cc_start: 0.8251 (mpt-90) cc_final: 0.8008 (mtt90) REVERT: H 277 CYS cc_start: 0.7396 (p) cc_final: 0.7089 (p) outliers start: 44 outliers final: 34 residues processed: 352 average time/residue: 0.1602 time to fit residues: 86.6709 Evaluate side-chains 340 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 71 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 320 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 157 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 39 optimal weight: 0.0570 chunk 191 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 181 optimal weight: 0.0770 chunk 31 optimal weight: 5.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 HIS U 6 GLN F 3 HIS L 3 HIS ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN H 186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.189418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150617 restraints weight = 29079.044| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.73 r_work: 0.3126 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23187 Z= 0.137 Angle : 0.582 11.285 31557 Z= 0.289 Chirality : 0.045 0.373 3549 Planarity : 0.004 0.046 4008 Dihedral : 7.473 84.886 3987 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.99 % Allowed : 14.05 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 2778 helix: 1.42 (0.26), residues: 387 sheet: 0.30 (0.17), residues: 885 loop : -0.94 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 313 TYR 0.018 0.001 TYR E 53 PHE 0.012 0.001 PHE F 107 TRP 0.019 0.001 TRP F 161 HIS 0.015 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00324 (23118) covalent geometry : angle 0.54969 (31377) SS BOND : bond 0.00348 ( 27) SS BOND : angle 1.19401 ( 54) hydrogen bonds : bond 0.03987 ( 741) hydrogen bonds : angle 5.05443 ( 2106) link_BETA1-4 : bond 0.00729 ( 18) link_BETA1-4 : angle 2.80377 ( 54) link_BETA2-3 : bond 0.00115 ( 3) link_BETA2-3 : angle 2.74457 ( 9) link_NAG-ASN : bond 0.00769 ( 21) link_NAG-ASN : angle 3.22481 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 324 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8387 (mmtm) REVERT: B 120 ASP cc_start: 0.8116 (m-30) cc_final: 0.7875 (t0) REVERT: R 40 TYR cc_start: 0.8978 (m-10) cc_final: 0.8518 (m-80) REVERT: R 85 ASP cc_start: 0.7614 (t0) cc_final: 0.7391 (t0) REVERT: R 109 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8113 (mm-30) REVERT: R 114 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6228 (t0) REVERT: R 175 SER cc_start: 0.9039 (m) cc_final: 0.8655 (p) REVERT: U 148 LEU cc_start: 0.8665 (tt) cc_final: 0.7937 (pt) REVERT: D 15 GLN cc_start: 0.8245 (mp10) cc_final: 0.7759 (mp10) REVERT: D 17 MET cc_start: 0.6935 (tpt) cc_final: 0.5813 (ttt) REVERT: D 154 ASN cc_start: 0.7828 (m-40) cc_final: 0.7424 (p0) REVERT: D 162 TYR cc_start: 0.7522 (m-80) cc_final: 0.6714 (m-80) REVERT: I 142 HIS cc_start: 0.4894 (p90) cc_final: 0.4463 (p90) REVERT: F 142 MET cc_start: 0.7000 (tpp) cc_final: 0.6660 (ppp) REVERT: L 46 GLU cc_start: 0.8801 (mp0) cc_final: 0.8570 (mt-10) REVERT: L 142 MET cc_start: 0.6592 (tpp) cc_final: 0.6302 (mmm) REVERT: L 181 LEU cc_start: 0.7667 (mm) cc_final: 0.7255 (mm) REVERT: E 71 SER cc_start: 0.7548 (t) cc_final: 0.7256 (m) REVERT: E 85 ASP cc_start: 0.7660 (t0) cc_final: 0.7275 (t0) REVERT: E 136 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7513 (m) REVERT: J 37 MET cc_start: 0.8584 (ttt) cc_final: 0.8358 (ttt) REVERT: J 71 SER cc_start: 0.7717 (t) cc_final: 0.7390 (m) REVERT: J 85 ASP cc_start: 0.7906 (t0) cc_final: 0.7480 (t0) REVERT: J 86 ASP cc_start: 0.8066 (m-30) cc_final: 0.7709 (m-30) REVERT: J 109 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7721 (mm-30) REVERT: J 114 ASP cc_start: 0.6355 (OUTLIER) cc_final: 0.5909 (t0) REVERT: C 18 HIS cc_start: 0.8446 (t70) cc_final: 0.8220 (t-170) REVERT: C 277 CYS cc_start: 0.7609 (p) cc_final: 0.7362 (p) REVERT: H 75 MET cc_start: 0.8266 (mmp) cc_final: 0.8003 (mmm) REVERT: H 114 ARG cc_start: 0.8485 (mpt-90) cc_final: 0.8251 (mtt90) REVERT: H 277 CYS cc_start: 0.7699 (p) cc_final: 0.7388 (p) outliers start: 49 outliers final: 35 residues processed: 360 average time/residue: 0.1645 time to fit residues: 90.5163 Evaluate side-chains 354 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 316 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 71 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 320 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 160 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 107 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN R 93 GLN U 3 HIS D 71 ASN F 3 HIS F 6 GLN L 3 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142437 restraints weight = 29579.375| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.83 r_work: 0.2996 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 23187 Z= 0.290 Angle : 0.700 11.016 31557 Z= 0.348 Chirality : 0.048 0.366 3549 Planarity : 0.005 0.047 4008 Dihedral : 7.756 89.629 3987 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.76 % Allowed : 14.74 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2778 helix: 1.14 (0.25), residues: 387 sheet: 0.31 (0.17), residues: 894 loop : -1.07 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 65 TYR 0.030 0.002 TYR C 105 PHE 0.019 0.002 PHE L 107 TRP 0.022 0.002 TRP F 161 HIS 0.012 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00703 (23118) covalent geometry : angle 0.66868 (31377) SS BOND : bond 0.00594 ( 27) SS BOND : angle 1.80865 ( 54) hydrogen bonds : bond 0.04594 ( 741) hydrogen bonds : angle 5.14738 ( 2106) link_BETA1-4 : bond 0.00764 ( 18) link_BETA1-4 : angle 2.83015 ( 54) link_BETA2-3 : bond 0.00301 ( 3) link_BETA2-3 : angle 3.08150 ( 9) link_NAG-ASN : bond 0.00748 ( 21) link_NAG-ASN : angle 3.39896 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 336 time to evaluate : 0.855 Fit side-chains REVERT: A 280 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8291 (ptmt) REVERT: B 85 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 142 HIS cc_start: 0.4333 (p90) cc_final: 0.3910 (p90) REVERT: B 158 ASP cc_start: 0.7437 (p0) cc_final: 0.7119 (p0) REVERT: R 85 ASP cc_start: 0.7866 (t0) cc_final: 0.7596 (t0) REVERT: R 109 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7842 (mm-30) REVERT: R 114 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6386 (t0) REVERT: R 175 SER cc_start: 0.9062 (m) cc_final: 0.8742 (p) REVERT: D 15 GLN cc_start: 0.8232 (mp10) cc_final: 0.7978 (mp10) REVERT: D 17 MET cc_start: 0.7032 (tpt) cc_final: 0.6144 (tpp) REVERT: D 154 ASN cc_start: 0.7817 (m-40) cc_final: 0.7469 (p0) REVERT: D 162 TYR cc_start: 0.7394 (m-80) cc_final: 0.6708 (m-80) REVERT: I 142 HIS cc_start: 0.4991 (p90) cc_final: 0.4626 (p90) REVERT: F 148 LEU cc_start: 0.8326 (tt) cc_final: 0.7847 (mp) REVERT: L 46 GLU cc_start: 0.8683 (mp0) cc_final: 0.8454 (mt-10) REVERT: L 84 ARG cc_start: 0.7056 (mtt180) cc_final: 0.6614 (mtm-85) REVERT: L 145 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7947 (tt) REVERT: L 181 LEU cc_start: 0.7756 (mm) cc_final: 0.7393 (mm) REVERT: E 71 SER cc_start: 0.7475 (t) cc_final: 0.7166 (m) REVERT: E 85 ASP cc_start: 0.7805 (t0) cc_final: 0.7549 (t0) REVERT: E 109 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7764 (mm-30) REVERT: E 136 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7423 (m) REVERT: J 30 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6994 (p0) REVERT: J 37 MET cc_start: 0.8485 (ttt) cc_final: 0.8279 (ttt) REVERT: J 71 SER cc_start: 0.8240 (t) cc_final: 0.7858 (p) REVERT: J 85 ASP cc_start: 0.8028 (t0) cc_final: 0.7656 (t0) REVERT: J 109 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7696 (mm-30) REVERT: C 18 HIS cc_start: 0.8470 (t70) cc_final: 0.8239 (t-170) outliers start: 68 outliers final: 46 residues processed: 382 average time/residue: 0.1542 time to fit residues: 91.3441 Evaluate side-chains 359 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain U residue 145 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 320 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 215 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 HIS F 3 HIS L 3 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN H 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.189736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.163835 restraints weight = 29085.419| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.35 r_work: 0.3364 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 23187 Z= 0.196 Angle : 0.641 10.957 31557 Z= 0.317 Chirality : 0.046 0.357 3549 Planarity : 0.004 0.046 4008 Dihedral : 7.621 89.771 3987 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.15 % Allowed : 16.48 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2778 helix: 1.31 (0.25), residues: 387 sheet: 0.29 (0.17), residues: 894 loop : -1.05 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 18 TYR 0.021 0.001 TYR B 119 PHE 0.017 0.001 PHE R 122 TRP 0.025 0.001 TRP F 161 HIS 0.013 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00472 (23118) covalent geometry : angle 0.61106 (31377) SS BOND : bond 0.00409 ( 27) SS BOND : angle 1.66166 ( 54) hydrogen bonds : bond 0.04192 ( 741) hydrogen bonds : angle 5.00316 ( 2106) link_BETA1-4 : bond 0.00702 ( 18) link_BETA1-4 : angle 2.71883 ( 54) link_BETA2-3 : bond 0.00265 ( 3) link_BETA2-3 : angle 2.70919 ( 9) link_NAG-ASN : bond 0.00924 ( 21) link_NAG-ASN : angle 3.21695 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 320 time to evaluate : 0.858 Fit side-chains REVERT: A 280 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8168 (ptmt) REVERT: B 142 HIS cc_start: 0.4467 (p90) cc_final: 0.4106 (p90) REVERT: R 85 ASP cc_start: 0.7631 (t0) cc_final: 0.7396 (t0) REVERT: R 109 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7887 (mm-30) REVERT: R 114 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6229 (t0) REVERT: R 175 SER cc_start: 0.8993 (m) cc_final: 0.8782 (p) REVERT: U 148 LEU cc_start: 0.8027 (tt) cc_final: 0.7281 (pt) REVERT: D 15 GLN cc_start: 0.8429 (mp10) cc_final: 0.8218 (mp10) REVERT: D 17 MET cc_start: 0.7269 (tpt) cc_final: 0.6460 (tpp) REVERT: D 109 ASP cc_start: 0.8303 (m-30) cc_final: 0.7956 (m-30) REVERT: D 162 TYR cc_start: 0.7253 (m-80) cc_final: 0.6656 (m-80) REVERT: I 109 ASP cc_start: 0.8198 (m-30) cc_final: 0.7885 (m-30) REVERT: I 113 SER cc_start: 0.8517 (m) cc_final: 0.8309 (t) REVERT: F 148 LEU cc_start: 0.7851 (tt) cc_final: 0.7436 (mp) REVERT: L 84 ARG cc_start: 0.6823 (mtt180) cc_final: 0.6583 (mtm-85) REVERT: L 142 MET cc_start: 0.6415 (tpp) cc_final: 0.5814 (mmm) REVERT: L 145 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7944 (tt) REVERT: E 71 SER cc_start: 0.7797 (t) cc_final: 0.7482 (m) REVERT: E 85 ASP cc_start: 0.7480 (t0) cc_final: 0.7241 (t0) REVERT: E 109 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7437 (mm-30) REVERT: E 136 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7210 (m) REVERT: J 71 SER cc_start: 0.8304 (t) cc_final: 0.7945 (m) REVERT: J 85 ASP cc_start: 0.7747 (t0) cc_final: 0.7430 (t0) REVERT: J 109 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7629 (mm-30) REVERT: C 18 HIS cc_start: 0.8558 (t70) cc_final: 0.8318 (t-170) REVERT: H 277 CYS cc_start: 0.7403 (p) cc_final: 0.7069 (p) outliers start: 53 outliers final: 34 residues processed: 354 average time/residue: 0.1650 time to fit residues: 90.1309 Evaluate side-chains 347 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 309 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 71 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain U residue 145 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 320 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 251 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 197 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 147 optimal weight: 30.0000 chunk 261 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 HIS U 3 HIS F 3 HIS L 3 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS H 150 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.191355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.162223 restraints weight = 28971.086| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.38 r_work: 0.3359 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23187 Z= 0.135 Angle : 0.615 10.722 31557 Z= 0.303 Chirality : 0.045 0.351 3549 Planarity : 0.004 0.045 4008 Dihedral : 7.908 103.334 3987 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.75 % Allowed : 16.57 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.16), residues: 2778 helix: 1.46 (0.26), residues: 387 sheet: 0.30 (0.17), residues: 894 loop : -0.98 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 18 TYR 0.018 0.001 TYR J 53 PHE 0.029 0.001 PHE R 122 TRP 0.027 0.001 TRP F 161 HIS 0.022 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00320 (23118) covalent geometry : angle 0.58864 (31377) SS BOND : bond 0.00361 ( 27) SS BOND : angle 1.51127 ( 54) hydrogen bonds : bond 0.03881 ( 741) hydrogen bonds : angle 4.91119 ( 2106) link_BETA1-4 : bond 0.00694 ( 18) link_BETA1-4 : angle 2.62086 ( 54) link_BETA2-3 : bond 0.00228 ( 3) link_BETA2-3 : angle 2.52303 ( 9) link_NAG-ASN : bond 0.00841 ( 21) link_NAG-ASN : angle 2.85897 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 323 time to evaluate : 0.796 Fit side-chains REVERT: A 18 HIS cc_start: 0.8443 (t70) cc_final: 0.7925 (t-170) REVERT: A 280 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8014 (ptmt) REVERT: B 109 ASP cc_start: 0.8266 (m-30) cc_final: 0.7961 (m-30) REVERT: B 142 HIS cc_start: 0.4392 (p90) cc_final: 0.4108 (p90) REVERT: R 85 ASP cc_start: 0.7681 (t0) cc_final: 0.7357 (t0) REVERT: R 109 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7807 (mm-30) REVERT: R 114 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6099 (t0) REVERT: R 122 PHE cc_start: 0.5008 (m-80) cc_final: 0.4729 (m-80) REVERT: U 148 LEU cc_start: 0.7858 (tt) cc_final: 0.7309 (pt) REVERT: D 15 GLN cc_start: 0.8423 (mp10) cc_final: 0.8211 (mp10) REVERT: D 17 MET cc_start: 0.7292 (tpt) cc_final: 0.6530 (tpp) REVERT: D 109 ASP cc_start: 0.8189 (m-30) cc_final: 0.7936 (m-30) REVERT: D 162 TYR cc_start: 0.7211 (m-80) cc_final: 0.6665 (m-80) REVERT: I 109 ASP cc_start: 0.8299 (m-30) cc_final: 0.7994 (m-30) REVERT: I 113 SER cc_start: 0.8441 (m) cc_final: 0.8240 (t) REVERT: I 142 HIS cc_start: 0.4585 (p90) cc_final: 0.4344 (p90) REVERT: F 142 MET cc_start: 0.7042 (ppp) cc_final: 0.5941 (tpp) REVERT: F 148 LEU cc_start: 0.7816 (tt) cc_final: 0.7409 (mp) REVERT: L 84 ARG cc_start: 0.6791 (mtt180) cc_final: 0.6588 (mtm-85) REVERT: L 145 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7937 (tt) REVERT: L 148 LEU cc_start: 0.8037 (tt) cc_final: 0.7328 (pp) REVERT: E 71 SER cc_start: 0.7602 (t) cc_final: 0.7284 (m) REVERT: E 109 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7489 (mm-30) REVERT: E 136 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7156 (m) REVERT: J 37 MET cc_start: 0.8276 (ttt) cc_final: 0.8036 (ttt) REVERT: J 71 SER cc_start: 0.8249 (t) cc_final: 0.7903 (m) REVERT: J 85 ASP cc_start: 0.7818 (t0) cc_final: 0.7561 (t0) REVERT: J 109 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7512 (mm-30) REVERT: J 114 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.6098 (t0) REVERT: C 18 HIS cc_start: 0.8622 (t70) cc_final: 0.8356 (t-170) REVERT: H 277 CYS cc_start: 0.7321 (p) cc_final: 0.7091 (p) outliers start: 43 outliers final: 31 residues processed: 356 average time/residue: 0.1608 time to fit residues: 87.8394 Evaluate side-chains 346 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 310 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain U residue 145 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 320 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 0.6980 chunk 227 optimal weight: 0.0570 chunk 195 optimal weight: 0.8980 chunk 259 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN U 3 HIS F 3 HIS L 3 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.192971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.167404 restraints weight = 29320.829| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.30 r_work: 0.3421 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23187 Z= 0.118 Angle : 0.593 10.463 31557 Z= 0.296 Chirality : 0.044 0.345 3549 Planarity : 0.004 0.046 4008 Dihedral : 7.701 102.743 3987 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.87 % Allowed : 16.89 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 2778 helix: 1.54 (0.26), residues: 387 sheet: 0.35 (0.17), residues: 888 loop : -0.96 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 18 TYR 0.019 0.001 TYR J 53 PHE 0.024 0.001 PHE R 122 TRP 0.029 0.001 TRP F 161 HIS 0.015 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00275 (23118) covalent geometry : angle 0.56815 (31377) SS BOND : bond 0.00341 ( 27) SS BOND : angle 1.39417 ( 54) hydrogen bonds : bond 0.03706 ( 741) hydrogen bonds : angle 4.78505 ( 2106) link_BETA1-4 : bond 0.00683 ( 18) link_BETA1-4 : angle 2.54477 ( 54) link_BETA2-3 : bond 0.00161 ( 3) link_BETA2-3 : angle 2.38807 ( 9) link_NAG-ASN : bond 0.00693 ( 21) link_NAG-ASN : angle 2.68714 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 0.717 Fit side-chains REVERT: A 18 HIS cc_start: 0.8369 (t-90) cc_final: 0.8075 (t-170) REVERT: A 280 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8164 (ptmt) REVERT: B 109 ASP cc_start: 0.8264 (m-30) cc_final: 0.7999 (m-30) REVERT: B 142 HIS cc_start: 0.4652 (p90) cc_final: 0.4380 (p90) REVERT: R 85 ASP cc_start: 0.7883 (t0) cc_final: 0.7548 (t0) REVERT: R 109 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7969 (mm-30) REVERT: R 114 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.5918 (t0) REVERT: U 148 LEU cc_start: 0.7902 (tt) cc_final: 0.7390 (pt) REVERT: D 17 MET cc_start: 0.7038 (tpt) cc_final: 0.6318 (tpp) REVERT: D 158 ASP cc_start: 0.7229 (p0) cc_final: 0.6901 (p0) REVERT: D 162 TYR cc_start: 0.7244 (m-80) cc_final: 0.6548 (m-80) REVERT: I 109 ASP cc_start: 0.8279 (m-30) cc_final: 0.7909 (m-30) REVERT: I 113 SER cc_start: 0.8410 (m) cc_final: 0.8189 (t) REVERT: I 142 HIS cc_start: 0.5161 (p90) cc_final: 0.4782 (p90) REVERT: F 142 MET cc_start: 0.7065 (ppp) cc_final: 0.6111 (tpp) REVERT: F 148 LEU cc_start: 0.7888 (tt) cc_final: 0.7461 (mp) REVERT: L 84 ARG cc_start: 0.6816 (mtt180) cc_final: 0.6583 (mtm-85) REVERT: L 145 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7926 (tt) REVERT: L 148 LEU cc_start: 0.7943 (tt) cc_final: 0.7281 (pp) REVERT: E 30 ASP cc_start: 0.7457 (t0) cc_final: 0.7056 (p0) REVERT: E 71 SER cc_start: 0.7684 (t) cc_final: 0.7373 (m) REVERT: E 109 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7619 (mm-30) REVERT: E 136 VAL cc_start: 0.7544 (OUTLIER) cc_final: 0.7187 (m) REVERT: J 37 MET cc_start: 0.8240 (ttt) cc_final: 0.8034 (ttt) REVERT: J 71 SER cc_start: 0.8364 (t) cc_final: 0.8044 (m) REVERT: J 109 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7691 (mm-30) REVERT: J 114 ASP cc_start: 0.6421 (OUTLIER) cc_final: 0.6101 (t0) REVERT: C 18 HIS cc_start: 0.8819 (t70) cc_final: 0.8476 (t-170) REVERT: H 18 HIS cc_start: 0.8376 (t70) cc_final: 0.8149 (t-170) outliers start: 46 outliers final: 33 residues processed: 359 average time/residue: 0.1497 time to fit residues: 83.9327 Evaluate side-chains 352 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 314 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 145 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 59 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 231 optimal weight: 0.6980 chunk 252 optimal weight: 0.3980 chunk 270 optimal weight: 0.9990 chunk 265 optimal weight: 0.0170 chunk 134 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 HIS I 26 HIS F 3 HIS L 3 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.192819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.165980 restraints weight = 29162.809| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.34 r_work: 0.3409 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23187 Z= 0.119 Angle : 0.604 10.329 31557 Z= 0.300 Chirality : 0.044 0.341 3549 Planarity : 0.004 0.046 4008 Dihedral : 8.112 103.519 3987 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.62 % Allowed : 17.66 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2778 helix: 1.59 (0.26), residues: 387 sheet: 0.34 (0.17), residues: 870 loop : -0.91 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 24 TYR 0.018 0.001 TYR J 53 PHE 0.024 0.001 PHE R 122 TRP 0.031 0.001 TRP F 161 HIS 0.024 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00280 (23118) covalent geometry : angle 0.58125 (31377) SS BOND : bond 0.00351 ( 27) SS BOND : angle 1.60027 ( 54) hydrogen bonds : bond 0.03629 ( 741) hydrogen bonds : angle 4.75050 ( 2106) link_BETA1-4 : bond 0.00683 ( 18) link_BETA1-4 : angle 2.51247 ( 54) link_BETA2-3 : bond 0.00154 ( 3) link_BETA2-3 : angle 2.34550 ( 9) link_NAG-ASN : bond 0.00604 ( 21) link_NAG-ASN : angle 2.43449 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 326 time to evaluate : 0.860 Fit side-chains REVERT: A 18 HIS cc_start: 0.8317 (t-90) cc_final: 0.8008 (t-170) REVERT: A 236 ILE cc_start: 0.8882 (mm) cc_final: 0.8100 (tt) REVERT: A 280 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8000 (ptmt) REVERT: B 109 ASP cc_start: 0.8184 (m-30) cc_final: 0.7907 (m-30) REVERT: R 85 ASP cc_start: 0.7663 (t0) cc_final: 0.7337 (t0) REVERT: R 109 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7739 (mm-30) REVERT: R 114 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.5941 (t0) REVERT: U 10 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7435 (mt-10) REVERT: U 148 LEU cc_start: 0.7780 (tt) cc_final: 0.7315 (pt) REVERT: D 17 MET cc_start: 0.7099 (tpt) cc_final: 0.6360 (tpp) REVERT: D 158 ASP cc_start: 0.7154 (p0) cc_final: 0.6792 (p0) REVERT: D 162 TYR cc_start: 0.7119 (m-80) cc_final: 0.6502 (m-80) REVERT: I 109 ASP cc_start: 0.8161 (m-30) cc_final: 0.7768 (m-30) REVERT: I 113 SER cc_start: 0.8443 (m) cc_final: 0.8234 (t) REVERT: I 142 HIS cc_start: 0.4885 (p90) cc_final: 0.4565 (p90) REVERT: I 162 TYR cc_start: 0.7214 (m-80) cc_final: 0.7009 (m-80) REVERT: F 142 MET cc_start: 0.6940 (ppp) cc_final: 0.6142 (tpp) REVERT: F 148 LEU cc_start: 0.7732 (tt) cc_final: 0.7325 (mp) REVERT: L 142 MET cc_start: 0.5817 (tpp) cc_final: 0.5455 (mmm) REVERT: L 145 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7828 (tt) REVERT: L 148 LEU cc_start: 0.7779 (tt) cc_final: 0.7173 (pt) REVERT: E 71 SER cc_start: 0.7578 (t) cc_final: 0.7255 (m) REVERT: E 109 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7405 (mm-30) REVERT: E 136 VAL cc_start: 0.7434 (OUTLIER) cc_final: 0.7088 (m) REVERT: J 71 SER cc_start: 0.8260 (t) cc_final: 0.7962 (m) REVERT: J 109 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7454 (mm-30) REVERT: J 114 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.6096 (t0) REVERT: C 18 HIS cc_start: 0.8766 (t70) cc_final: 0.8438 (t-170) REVERT: C 313 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.8094 (mtp-110) outliers start: 40 outliers final: 30 residues processed: 354 average time/residue: 0.1572 time to fit residues: 86.0557 Evaluate side-chains 355 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 320 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain H residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 242 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 chunk 126 optimal weight: 0.0020 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS L 3 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.191686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159950 restraints weight = 29053.267| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.47 r_work: 0.3379 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23187 Z= 0.120 Angle : 0.598 10.105 31557 Z= 0.299 Chirality : 0.044 0.332 3549 Planarity : 0.004 0.045 4008 Dihedral : 8.013 103.682 3987 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.83 % Allowed : 17.86 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2778 helix: 1.62 (0.26), residues: 387 sheet: 0.35 (0.17), residues: 870 loop : -0.90 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 74 TYR 0.018 0.001 TYR E 53 PHE 0.022 0.001 PHE R 122 TRP 0.029 0.001 TRP F 161 HIS 0.012 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00284 (23118) covalent geometry : angle 0.57660 (31377) SS BOND : bond 0.00362 ( 27) SS BOND : angle 1.57031 ( 54) hydrogen bonds : bond 0.03582 ( 741) hydrogen bonds : angle 4.68705 ( 2106) link_BETA1-4 : bond 0.00684 ( 18) link_BETA1-4 : angle 2.46587 ( 54) link_BETA2-3 : bond 0.00303 ( 3) link_BETA2-3 : angle 2.33528 ( 9) link_NAG-ASN : bond 0.00575 ( 21) link_NAG-ASN : angle 2.32220 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7014.87 seconds wall clock time: 120 minutes 42.99 seconds (7242.99 seconds total)