Starting phenix.real_space_refine on Wed Mar 4 02:27:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwl_26835/03_2026/7uwl_26835.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwl_26835/03_2026/7uwl_26835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uwl_26835/03_2026/7uwl_26835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwl_26835/03_2026/7uwl_26835.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwl_26835/03_2026/7uwl_26835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwl_26835/03_2026/7uwl_26835.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 80 5.16 5 C 6326 2.51 5 N 1792 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10100 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 232} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1947 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 234} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2180 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 252} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2186 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 252} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 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: "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 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 2.39, per 1000 atoms: 0.24 Number of scatterers: 10100 At special positions: 0 Unit cell: (201.948, 95.4352, 100.548, 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 80 16.00 O 1902 8.00 N 1792 7.00 C 6326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 99 " distance=2.05 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 187 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 257 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 102 " distance=2.04 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 99 " distance=2.05 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 187 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 261 " distance=2.06 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 245 " - pdb=" SG CYS E 276 " distance=2.03 Simple disulfide: pdb=" SG CYS E 290 " - pdb=" SG CYS E 294 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 50 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 245 " - pdb=" SG CYS F 276 " distance=2.03 Simple disulfide: pdb=" SG CYS F 290 " - pdb=" SG CYS F 294 " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 301 " - " ASN A 136 " " NAG B 301 " - " ASN B 136 " " NAG C 401 " - " ASN C 156 " " NAG C 402 " - " ASN C 67 " " NAG C 403 " - " ASN C 103 " " NAG D 401 " - " ASN D 103 " " NAG D 402 " - " ASN D 156 " " NAG D 403 " - " ASN D 67 " " NAG E 401 " - " ASN E 225 " " NAG E 402 " - " ASN E 265 " " NAG E 403 " - " ASN E 67 " " NAG F 401 " - " ASN F 67 " " NAG F 402 " - " ASN F 225 " " NAG F 403 " - " ASN F 265 " " NAG G 1 " - " ASN C 197 " " NAG H 1 " - " ASN C 183 " " NAG I 1 " - " ASN D 197 " " NAG J 1 " - " ASN D 183 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 418.3 milliseconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 25 sheets defined 7.5% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.510A pdb=" N SER A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'C' and resid 31 through 36 removed outlier: 4.327A pdb=" N MET C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 36 " --> pdb=" O PRO C 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 36' Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.543A pdb=" N CYS C 257 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 36 removed outlier: 4.305A pdb=" N MET D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU D 36 " --> pdb=" O PRO D 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 36' Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.822A pdb=" N LYS D 168 " --> pdb=" O HIS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.748A pdb=" N LYS D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 109 removed outlier: 3.525A pdb=" N LEU E 109 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.725A pdb=" N VAL E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 256 through 260 Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.590A pdb=" N ILE F 106 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 109 " --> pdb=" O ILE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 4.206A pdb=" N VAL F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 Processing helix chain 'F' and resid 256 through 260 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.790A pdb=" N CYS A 115 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 143 removed outlier: 3.615A pdb=" N VAL A 164 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.462A pdb=" N MET A 176 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N THR D 267 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS D 264 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE D 211 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE D 217 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.462A pdb=" N MET A 176 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N THR D 267 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE D 184 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N VAL D 269 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA D 186 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.631A pdb=" N ARG B 91 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 141 removed outlier: 4.151A pdb=" N ALA B 167 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS B 135 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 165 " --> pdb=" O HIS B 135 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN B 137 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG B 163 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 139 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU B 161 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TYR B 141 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG B 159 " --> pdb=" O TYR B 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.690A pdb=" N LYS C 265 " --> pdb=" O MET B 176 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 207 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA C 209 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER C 220 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE C 211 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY C 218 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.690A pdb=" N LYS C 265 " --> pdb=" O MET B 176 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE C 184 " --> pdb=" O LYS C 265 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N THR C 267 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA C 186 " --> pdb=" O THR C 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.520A pdb=" N GLN C 23 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER C 98 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 88 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 100 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 86 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA C 83 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 138 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET C 153 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.951A pdb=" N THR C 55 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER C 63 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 68 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 123 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.864A pdb=" N SER D 98 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL D 88 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS D 102 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 133 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 138 " --> pdb=" O MET D 153 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET D 153 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 47 through 54 removed outlier: 3.677A pdb=" N GLY D 125 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 68 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 123 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP D 70 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 206 through 207 removed outlier: 3.641A pdb=" N TYR D 207 " --> pdb=" O VAL D 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 74 through 83 removed outlier: 5.245A pdb=" N ASP E 75 " --> pdb=" O THR E 99 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 125 through 128 removed outlier: 3.821A pdb=" N VAL E 159 " --> pdb=" O LYS E 178 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS E 178 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN E 176 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 208 through 210 removed outlier: 3.694A pdb=" N ARG E 218 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 246 through 252 removed outlier: 3.768A pdb=" N PHE E 246 " --> pdb=" O SER E 236 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 83 removed outlier: 5.117A pdb=" N ASP F 75 " --> pdb=" O THR F 99 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.684A pdb=" N GLY F 111 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 159 " --> pdb=" O LYS F 178 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN F 176 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 208 through 210 Processing sheet with id=AC7, first strand: chain 'F' and resid 246 through 252 removed outlier: 3.734A pdb=" N PHE F 246 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN F 231 " --> pdb=" O GLN F 284 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN F 284 " --> pdb=" O GLN F 231 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 627 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: 1.19 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1601 1.32 - 1.44: 2926 1.44 - 1.57: 5727 1.57 - 1.70: 0 1.70 - 1.83: 104 Bond restraints: 10358 Sorted by residual: bond pdb=" CD GLN E 231 " pdb=" NE2 GLN E 231 " ideal model delta sigma weight residual 1.328 1.230 0.098 2.10e-02 2.27e+03 2.16e+01 bond pdb=" C1 NAG F 402 " pdb=" O5 NAG F 402 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 NAG E 401 " pdb=" O5 NAG E 401 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" N THR F 69 " pdb=" CA THR F 69 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.60e-02 3.91e+03 7.79e+00 bond pdb=" N CYS D 102 " pdb=" CA CYS D 102 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.23e-02 6.61e+03 7.39e+00 ... (remaining 10353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 13597 1.96 - 3.92: 434 3.92 - 5.87: 47 5.87 - 7.83: 10 7.83 - 9.79: 5 Bond angle restraints: 14093 Sorted by residual: angle pdb=" C SER C 98 " pdb=" N CYS C 99 " pdb=" CA CYS C 99 " ideal model delta sigma weight residual 121.87 115.24 6.63 1.64e+00 3.72e-01 1.64e+01 angle pdb=" C LEU F 212 " pdb=" CA LEU F 212 " pdb=" CB LEU F 212 " ideal model delta sigma weight residual 116.34 110.90 5.44 1.40e+00 5.10e-01 1.51e+01 angle pdb=" C CYS D 102 " pdb=" CA CYS D 102 " pdb=" CB CYS D 102 " ideal model delta sigma weight residual 109.37 102.55 6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" CA CYS C 102 " pdb=" C CYS C 102 " pdb=" O CYS C 102 " ideal model delta sigma weight residual 121.11 117.38 3.73 1.13e+00 7.83e-01 1.09e+01 angle pdb=" N CYS C 99 " pdb=" CA CYS C 99 " pdb=" C CYS C 99 " ideal model delta sigma weight residual 108.96 113.67 -4.71 1.49e+00 4.50e-01 9.99e+00 ... (remaining 14088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 5959 23.62 - 47.24: 528 47.24 - 70.87: 81 70.87 - 94.49: 9 94.49 - 118.11: 6 Dihedral angle restraints: 6583 sinusoidal: 2965 harmonic: 3618 Sorted by residual: dihedral pdb=" CB CYS C 162 " pdb=" SG CYS C 162 " pdb=" SG CYS C 173 " pdb=" CB CYS C 173 " ideal model delta sinusoidal sigma weight residual -86.00 -176.12 90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS D 87 " pdb=" SG CYS D 87 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 14.71 78.29 1 1.00e+01 1.00e-02 7.65e+01 dihedral pdb=" CB CYS C 87 " pdb=" SG CYS C 87 " pdb=" SG CYS C 99 " pdb=" CB CYS C 99 " ideal model delta sinusoidal sigma weight residual 93.00 38.21 54.79 1 1.00e+01 1.00e-02 4.06e+01 ... (remaining 6580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1223 0.048 - 0.097: 291 0.097 - 0.145: 99 0.145 - 0.193: 10 0.193 - 0.241: 8 Chirality restraints: 1631 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.24e+00 chirality pdb=" CA CYS D 102 " pdb=" N CYS D 102 " pdb=" C CYS D 102 " pdb=" CB CYS D 102 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA CYS D 87 " pdb=" N CYS D 87 " pdb=" C CYS D 87 " pdb=" CB CYS D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1628 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 231 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" CD GLN E 231 " -0.063 2.00e-02 2.50e+03 pdb=" OE1 GLN E 231 " 0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN E 231 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.023 2.00e-02 2.50e+03 2.82e-02 9.95e+00 pdb=" CG ASN C 156 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " -0.004 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" CG ASN C 156 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " -0.017 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 296 2.69 - 3.24: 9298 3.24 - 3.79: 14646 3.79 - 4.35: 18403 4.35 - 4.90: 30313 Nonbonded interactions: 72956 Sorted by model distance: nonbonded pdb=" OG1 THR F 85 " pdb=" O ASP F 89 " model vdw 2.137 3.040 nonbonded pdb=" OD1 ASP F 89 " pdb=" OG1 THR F 194 " model vdw 2.164 3.040 nonbonded pdb=" OD1 ASP A 97 " pdb=" N LEU A 98 " model vdw 2.166 3.120 nonbonded pdb=" NE2 GLN E 231 " pdb=" OE1 GLN E 284 " model vdw 2.169 3.120 nonbonded pdb=" O SER B 88 " pdb=" OG SER B 88 " model vdw 2.217 3.040 ... (remaining 72951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 19 through 272 or resid 401 through 403)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 33 through 123 or (resid 124 and (name N or name CA or nam \ e C or name O or name CB )) or resid 125 through 403)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.710 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 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 0.098 10406 Z= 0.243 Angle : 0.809 12.741 14211 Z= 0.404 Chirality : 0.049 0.241 1631 Planarity : 0.005 0.042 1800 Dihedral : 16.739 118.111 4145 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.63 % Allowed : 23.99 % Favored : 75.38 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.23), residues: 1216 helix: -1.68 (0.99), residues: 26 sheet: -0.13 (0.24), residues: 487 loop : -1.52 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 66 TYR 0.027 0.003 TYR C 253 PHE 0.010 0.001 PHE F 180 TRP 0.019 0.002 TRP D 70 HIS 0.021 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00485 (10358) covalent geometry : angle 0.77972 (14093) SS BOND : bond 0.00808 ( 26) SS BOND : angle 2.17910 ( 52) hydrogen bonds : bond 0.29993 ( 255) hydrogen bonds : angle 10.44482 ( 627) link_BETA1-4 : bond 0.00111 ( 4) link_BETA1-4 : angle 1.75307 ( 12) link_NAG-ASN : bond 0.00546 ( 18) link_NAG-ASN : angle 2.88559 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 276 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.7193 (p-80) cc_final: 0.6919 (p-80) REVERT: D 265 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7853 (mtmt) REVERT: F 142 TRP cc_start: 0.7501 (m100) cc_final: 0.6586 (m100) REVERT: F 154 ASP cc_start: 0.7543 (t0) cc_final: 0.7318 (m-30) outliers start: 7 outliers final: 4 residues processed: 279 average time/residue: 0.1192 time to fit residues: 44.1149 Evaluate side-chains 271 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 267 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 143 ASN D 93 ASN D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN F 231 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.198975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.154367 restraints weight = 18059.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159369 restraints weight = 9563.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.162669 restraints weight = 5955.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.164832 restraints weight = 4174.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.166162 restraints weight = 3216.527| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10406 Z= 0.164 Angle : 0.763 9.844 14211 Z= 0.370 Chirality : 0.047 0.265 1631 Planarity : 0.005 0.046 1800 Dihedral : 10.828 97.770 1807 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.97 % Allowed : 21.64 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.23), residues: 1216 helix: -1.78 (0.96), residues: 26 sheet: -0.13 (0.23), residues: 524 loop : -1.65 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 46 TYR 0.021 0.002 TYR F 157 PHE 0.011 0.001 PHE E 149 TRP 0.022 0.002 TRP D 70 HIS 0.007 0.001 HIS E 148 Details of bonding type rmsd covalent geometry : bond 0.00372 (10358) covalent geometry : angle 0.74081 (14093) SS BOND : bond 0.00511 ( 26) SS BOND : angle 1.22313 ( 52) hydrogen bonds : bond 0.04964 ( 255) hydrogen bonds : angle 7.87230 ( 627) link_BETA1-4 : bond 0.00278 ( 4) link_BETA1-4 : angle 1.53567 ( 12) link_NAG-ASN : bond 0.00547 ( 18) link_NAG-ASN : angle 2.82053 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 275 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6741 (OUTLIER) cc_final: 0.6473 (p-80) REVERT: C 111 GLN cc_start: 0.6993 (mt0) cc_final: 0.6735 (mt0) REVERT: C 155 VAL cc_start: 0.7141 (OUTLIER) cc_final: 0.6772 (m) REVERT: C 230 GLN cc_start: 0.5846 (OUTLIER) cc_final: 0.5501 (tm-30) REVERT: D 193 THR cc_start: 0.8383 (m) cc_final: 0.7871 (p) REVERT: D 265 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7674 (mtmt) REVERT: F 79 GLN cc_start: 0.6778 (mm-40) cc_final: 0.6344 (tm-30) REVERT: F 80 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7463 (mt) REVERT: F 142 TRP cc_start: 0.7469 (m100) cc_final: 0.6567 (m100) REVERT: F 147 SER cc_start: 0.8084 (t) cc_final: 0.7854 (t) REVERT: F 212 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5726 (tt) outliers start: 44 outliers final: 26 residues processed: 297 average time/residue: 0.1217 time to fit residues: 48.1080 Evaluate side-chains 299 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.196643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.152686 restraints weight = 17901.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.157526 restraints weight = 9622.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.160722 restraints weight = 6037.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.162796 restraints weight = 4257.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163895 restraints weight = 3284.989| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10406 Z= 0.208 Angle : 0.794 11.135 14211 Z= 0.387 Chirality : 0.049 0.264 1631 Planarity : 0.005 0.051 1800 Dihedral : 10.596 93.418 1806 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 5.95 % Allowed : 21.82 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.23), residues: 1216 helix: -1.86 (0.91), residues: 26 sheet: -0.43 (0.23), residues: 537 loop : -1.70 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 34 TYR 0.025 0.003 TYR A 141 PHE 0.012 0.002 PHE E 149 TRP 0.031 0.002 TRP D 70 HIS 0.012 0.001 HIS E 148 Details of bonding type rmsd covalent geometry : bond 0.00473 (10358) covalent geometry : angle 0.77054 (14093) SS BOND : bond 0.00587 ( 26) SS BOND : angle 1.53500 ( 52) hydrogen bonds : bond 0.04771 ( 255) hydrogen bonds : angle 7.51828 ( 627) link_BETA1-4 : bond 0.00416 ( 4) link_BETA1-4 : angle 1.41927 ( 12) link_NAG-ASN : bond 0.00521 ( 18) link_NAG-ASN : angle 2.87739 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 271 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.7806 (mm) cc_final: 0.7592 (mt) REVERT: A 135 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.6146 (p-80) REVERT: A 163 ARG cc_start: 0.7508 (tpp80) cc_final: 0.7048 (ttt90) REVERT: A 166 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6473 (mp) REVERT: B 124 MET cc_start: 0.5487 (ppp) cc_final: 0.5213 (ppp) REVERT: C 155 VAL cc_start: 0.7035 (OUTLIER) cc_final: 0.6668 (m) REVERT: C 230 GLN cc_start: 0.5840 (OUTLIER) cc_final: 0.5472 (tm-30) REVERT: D 101 ARG cc_start: 0.8104 (tmm-80) cc_final: 0.7467 (ptm160) REVERT: D 193 THR cc_start: 0.8370 (m) cc_final: 0.7806 (p) REVERT: D 250 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7588 (mm) REVERT: F 142 TRP cc_start: 0.7560 (m100) cc_final: 0.6709 (m100) REVERT: F 212 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5841 (tt) outliers start: 66 outliers final: 40 residues processed: 298 average time/residue: 0.1200 time to fit residues: 47.4542 Evaluate side-chains 315 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 269 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 281 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.0270 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN D 131 ASN E 79 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.197517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152953 restraints weight = 18026.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.157809 restraints weight = 9700.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.161063 restraints weight = 6108.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.163174 restraints weight = 4301.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.164392 restraints weight = 3321.111| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10406 Z= 0.155 Angle : 0.753 11.276 14211 Z= 0.359 Chirality : 0.047 0.268 1631 Planarity : 0.005 0.048 1800 Dihedral : 10.068 90.462 1802 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.32 % Allowed : 23.35 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.23), residues: 1216 helix: -1.53 (0.95), residues: 26 sheet: -0.48 (0.23), residues: 534 loop : -1.63 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 34 TYR 0.018 0.002 TYR D 253 PHE 0.012 0.001 PHE E 149 TRP 0.024 0.002 TRP D 70 HIS 0.012 0.001 HIS E 148 Details of bonding type rmsd covalent geometry : bond 0.00356 (10358) covalent geometry : angle 0.73151 (14093) SS BOND : bond 0.00581 ( 26) SS BOND : angle 1.26074 ( 52) hydrogen bonds : bond 0.03978 ( 255) hydrogen bonds : angle 7.14475 ( 627) link_BETA1-4 : bond 0.00364 ( 4) link_BETA1-4 : angle 1.33302 ( 12) link_NAG-ASN : bond 0.00421 ( 18) link_NAG-ASN : angle 2.75638 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 272 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6420 (OUTLIER) cc_final: 0.6105 (p-80) REVERT: A 163 ARG cc_start: 0.7479 (tpp80) cc_final: 0.7055 (ttt90) REVERT: A 166 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6498 (mp) REVERT: B 124 MET cc_start: 0.5599 (ppp) cc_final: 0.5252 (ppp) REVERT: C 111 GLN cc_start: 0.7149 (mt0) cc_final: 0.6807 (mt0) REVERT: C 155 VAL cc_start: 0.6973 (OUTLIER) cc_final: 0.6731 (p) REVERT: C 230 GLN cc_start: 0.5858 (OUTLIER) cc_final: 0.5483 (tm-30) REVERT: D 101 ARG cc_start: 0.8053 (tmm-80) cc_final: 0.7783 (ptm-80) REVERT: D 193 THR cc_start: 0.8344 (m) cc_final: 0.7800 (p) REVERT: D 250 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7696 (mm) REVERT: F 142 TRP cc_start: 0.7561 (m100) cc_final: 0.6623 (m100) REVERT: F 156 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7276 (mm-30) REVERT: F 217 LEU cc_start: -0.5171 (OUTLIER) cc_final: -0.6189 (tp) outliers start: 59 outliers final: 33 residues processed: 299 average time/residue: 0.1198 time to fit residues: 46.8941 Evaluate side-chains 307 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 chunk 114 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN D 93 ASN D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.198224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153133 restraints weight = 17804.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.158132 restraints weight = 9570.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.161421 restraints weight = 5990.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.163398 restraints weight = 4212.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.164965 restraints weight = 3287.056| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10406 Z= 0.151 Angle : 0.752 11.537 14211 Z= 0.357 Chirality : 0.047 0.271 1631 Planarity : 0.005 0.045 1800 Dihedral : 9.809 88.743 1800 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.77 % Allowed : 23.90 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.23), residues: 1216 helix: -1.49 (0.96), residues: 26 sheet: -0.53 (0.23), residues: 540 loop : -1.51 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 136 TYR 0.020 0.002 TYR D 253 PHE 0.013 0.001 PHE C 94 TRP 0.029 0.002 TRP D 70 HIS 0.017 0.001 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00348 (10358) covalent geometry : angle 0.73208 (14093) SS BOND : bond 0.00563 ( 26) SS BOND : angle 1.22822 ( 52) hydrogen bonds : bond 0.03859 ( 255) hydrogen bonds : angle 7.02337 ( 627) link_BETA1-4 : bond 0.00406 ( 4) link_BETA1-4 : angle 1.23387 ( 12) link_NAG-ASN : bond 0.00452 ( 18) link_NAG-ASN : angle 2.67394 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 266 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6413 (OUTLIER) cc_final: 0.6099 (p-80) REVERT: A 163 ARG cc_start: 0.7509 (tpp80) cc_final: 0.7041 (ttt90) REVERT: A 166 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6432 (mp) REVERT: B 124 MET cc_start: 0.5703 (ppp) cc_final: 0.5295 (ppp) REVERT: C 101 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6656 (ttt90) REVERT: C 155 VAL cc_start: 0.6920 (OUTLIER) cc_final: 0.6697 (p) REVERT: D 193 THR cc_start: 0.8351 (m) cc_final: 0.7813 (p) REVERT: D 250 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7695 (mm) REVERT: E 143 ARG cc_start: 0.6581 (mtp85) cc_final: 0.5778 (mmp80) REVERT: F 128 ARG cc_start: 0.6602 (mtt-85) cc_final: 0.6238 (mtt-85) REVERT: F 156 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7294 (mm-30) REVERT: F 212 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5669 (tt) REVERT: F 217 LEU cc_start: -0.5233 (OUTLIER) cc_final: -0.6197 (tp) REVERT: F 270 LEU cc_start: -0.5775 (OUTLIER) cc_final: -0.6103 (mp) outliers start: 64 outliers final: 44 residues processed: 297 average time/residue: 0.1244 time to fit residues: 48.4375 Evaluate side-chains 315 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 281 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 40 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 HIS C 111 GLN D 93 ASN D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.198499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153496 restraints weight = 18048.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.158502 restraints weight = 9636.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161758 restraints weight = 6025.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.163960 restraints weight = 4231.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.165132 restraints weight = 3264.787| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10406 Z= 0.144 Angle : 0.756 11.384 14211 Z= 0.356 Chirality : 0.046 0.272 1631 Planarity : 0.005 0.048 1800 Dihedral : 9.639 86.591 1800 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.59 % Allowed : 24.62 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.23), residues: 1216 helix: -1.51 (1.01), residues: 26 sheet: -0.53 (0.23), residues: 539 loop : -1.51 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 34 TYR 0.018 0.002 TYR D 253 PHE 0.014 0.001 PHE C 94 TRP 0.040 0.002 TRP C 180 HIS 0.013 0.001 HIS E 148 Details of bonding type rmsd covalent geometry : bond 0.00335 (10358) covalent geometry : angle 0.73703 (14093) SS BOND : bond 0.00541 ( 26) SS BOND : angle 1.18062 ( 52) hydrogen bonds : bond 0.03714 ( 255) hydrogen bonds : angle 6.90721 ( 627) link_BETA1-4 : bond 0.00388 ( 4) link_BETA1-4 : angle 1.24513 ( 12) link_NAG-ASN : bond 0.00440 ( 18) link_NAG-ASN : angle 2.63338 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 266 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6760 (mtp85) REVERT: A 135 HIS cc_start: 0.6372 (OUTLIER) cc_final: 0.6082 (p-80) REVERT: A 163 ARG cc_start: 0.7488 (tpp80) cc_final: 0.7052 (ttt90) REVERT: A 166 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6379 (mp) REVERT: B 124 MET cc_start: 0.5732 (ppp) cc_final: 0.5299 (ppp) REVERT: C 101 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6619 (ttt90) REVERT: D 101 ARG cc_start: 0.8069 (tmm-80) cc_final: 0.7801 (ptm-80) REVERT: D 193 THR cc_start: 0.8346 (m) cc_final: 0.7805 (p) REVERT: D 250 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7704 (mm) REVERT: E 143 ARG cc_start: 0.6653 (mtp85) cc_final: 0.5916 (mmp80) REVERT: F 68 LEU cc_start: 0.5216 (OUTLIER) cc_final: 0.4474 (pp) REVERT: F 79 GLN cc_start: 0.6910 (mm-40) cc_final: 0.6669 (mm-40) REVERT: F 128 ARG cc_start: 0.6601 (mtt-85) cc_final: 0.6246 (mtt-85) REVERT: F 156 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7323 (mm-30) REVERT: F 212 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5674 (tt) outliers start: 62 outliers final: 45 residues processed: 295 average time/residue: 0.1212 time to fit residues: 47.1250 Evaluate side-chains 319 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 86 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.195505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.149966 restraints weight = 17835.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.154905 restraints weight = 9618.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.158131 restraints weight = 6066.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.160176 restraints weight = 4291.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.161315 restraints weight = 3343.147| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10406 Z= 0.275 Angle : 0.869 12.236 14211 Z= 0.422 Chirality : 0.050 0.256 1631 Planarity : 0.006 0.054 1800 Dihedral : 9.855 83.360 1797 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 5.77 % Allowed : 24.62 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.23), residues: 1216 helix: -1.52 (1.05), residues: 26 sheet: -0.67 (0.23), residues: 541 loop : -1.73 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 113 TYR 0.031 0.003 TYR D 253 PHE 0.018 0.002 PHE E 149 TRP 0.062 0.004 TRP C 180 HIS 0.014 0.002 HIS E 148 Details of bonding type rmsd covalent geometry : bond 0.00614 (10358) covalent geometry : angle 0.84290 (14093) SS BOND : bond 0.00691 ( 26) SS BOND : angle 1.68532 ( 52) hydrogen bonds : bond 0.04802 ( 255) hydrogen bonds : angle 7.20554 ( 627) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 1.12272 ( 12) link_NAG-ASN : bond 0.00613 ( 18) link_NAG-ASN : angle 3.23086 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7567 (tpp80) cc_final: 0.7040 (ttt90) REVERT: A 174 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6903 (mtm180) REVERT: B 124 MET cc_start: 0.5868 (ppp) cc_final: 0.5374 (ppp) REVERT: C 101 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6693 (ttt90) REVERT: C 167 MET cc_start: 0.6343 (mmm) cc_final: 0.6019 (mmm) REVERT: D 100 VAL cc_start: 0.7850 (m) cc_final: 0.7524 (p) REVERT: D 193 THR cc_start: 0.8384 (m) cc_final: 0.7827 (p) REVERT: E 143 ARG cc_start: 0.6871 (mtp85) cc_final: 0.6649 (mmp80) REVERT: E 156 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7475 (mm-30) REVERT: F 68 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.5019 (pt) REVERT: F 79 GLN cc_start: 0.7053 (mm-40) cc_final: 0.6793 (mm-40) REVERT: F 81 HIS cc_start: 0.7878 (t70) cc_final: 0.7633 (t70) REVERT: F 128 ARG cc_start: 0.6787 (mtt-85) cc_final: 0.6374 (mtt-85) REVERT: F 142 TRP cc_start: 0.7622 (m100) cc_final: 0.6896 (m100) REVERT: F 156 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7460 (mm-30) REVERT: F 212 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5643 (tt) REVERT: F 217 LEU cc_start: -0.4911 (OUTLIER) cc_final: -0.5937 (tp) outliers start: 64 outliers final: 46 residues processed: 296 average time/residue: 0.1225 time to fit residues: 47.5870 Evaluate side-chains 318 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.207819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.159788 restraints weight = 17411.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164667 restraints weight = 9489.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.167931 restraints weight = 6130.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.170094 restraints weight = 4458.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.171416 restraints weight = 3540.010| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10406 Z= 0.147 Angle : 0.804 11.856 14211 Z= 0.376 Chirality : 0.047 0.272 1631 Planarity : 0.005 0.047 1800 Dihedral : 9.379 80.747 1797 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.87 % Allowed : 25.88 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.23), residues: 1216 helix: -1.57 (1.02), residues: 26 sheet: -0.75 (0.22), residues: 554 loop : -1.60 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 109 TYR 0.025 0.002 TYR D 253 PHE 0.012 0.001 PHE C 94 TRP 0.050 0.002 TRP C 180 HIS 0.018 0.001 HIS E 148 Details of bonding type rmsd covalent geometry : bond 0.00344 (10358) covalent geometry : angle 0.78287 (14093) SS BOND : bond 0.00563 ( 26) SS BOND : angle 1.39150 ( 52) hydrogen bonds : bond 0.03768 ( 255) hydrogen bonds : angle 6.93843 ( 627) link_BETA1-4 : bond 0.00306 ( 4) link_BETA1-4 : angle 1.26893 ( 12) link_NAG-ASN : bond 0.00439 ( 18) link_NAG-ASN : angle 2.80128 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6374 (OUTLIER) cc_final: 0.6134 (p-80) REVERT: A 160 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6542 (tmm-80) REVERT: A 163 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7026 (ttt90) REVERT: B 124 MET cc_start: 0.5869 (ppp) cc_final: 0.5377 (ppp) REVERT: C 101 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6563 (ttt90) REVERT: C 167 MET cc_start: 0.6216 (mmm) cc_final: 0.5980 (mmm) REVERT: D 100 VAL cc_start: 0.7617 (m) cc_final: 0.7347 (p) REVERT: D 193 THR cc_start: 0.8424 (m) cc_final: 0.7891 (p) REVERT: D 250 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7700 (mm) REVERT: E 156 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7435 (mm-30) REVERT: F 68 LEU cc_start: 0.5097 (OUTLIER) cc_final: 0.4699 (pt) REVERT: F 79 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6642 (mm-40) REVERT: F 81 HIS cc_start: 0.7854 (t70) cc_final: 0.7610 (t70) REVERT: F 128 ARG cc_start: 0.6686 (mtt-85) cc_final: 0.6301 (mtt-85) REVERT: F 142 TRP cc_start: 0.7533 (m100) cc_final: 0.6858 (m100) REVERT: F 156 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7325 (mm-30) REVERT: F 176 GLN cc_start: 0.7477 (mt0) cc_final: 0.7273 (mt0) REVERT: F 212 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5685 (tt) REVERT: F 217 LEU cc_start: -0.5163 (OUTLIER) cc_final: -0.6160 (tp) outliers start: 54 outliers final: 40 residues processed: 287 average time/residue: 0.1197 time to fit residues: 45.3103 Evaluate side-chains 309 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 41 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 0.0370 chunk 71 optimal weight: 0.5980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.199294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.155179 restraints weight = 18217.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.160166 restraints weight = 9714.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.163400 restraints weight = 6081.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165556 restraints weight = 4279.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.167026 restraints weight = 3283.498| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10406 Z= 0.119 Angle : 0.761 11.346 14211 Z= 0.353 Chirality : 0.046 0.277 1631 Planarity : 0.005 0.046 1800 Dihedral : 8.875 76.027 1797 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.33 % Allowed : 26.24 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.23), residues: 1216 helix: -1.56 (1.00), residues: 26 sheet: -0.55 (0.22), residues: 533 loop : -1.51 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 34 TYR 0.031 0.001 TYR D 253 PHE 0.011 0.001 PHE C 94 TRP 0.041 0.002 TRP C 180 HIS 0.019 0.001 HIS E 148 Details of bonding type rmsd covalent geometry : bond 0.00281 (10358) covalent geometry : angle 0.74348 (14093) SS BOND : bond 0.00500 ( 26) SS BOND : angle 1.20607 ( 52) hydrogen bonds : bond 0.03390 ( 255) hydrogen bonds : angle 6.64939 ( 627) link_BETA1-4 : bond 0.00432 ( 4) link_BETA1-4 : angle 1.32856 ( 12) link_NAG-ASN : bond 0.00413 ( 18) link_NAG-ASN : angle 2.51403 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6474 (OUTLIER) cc_final: 0.6202 (p-80) REVERT: A 160 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.6444 (tmm-80) REVERT: A 163 ARG cc_start: 0.7393 (tpp80) cc_final: 0.7049 (ttt90) REVERT: B 124 MET cc_start: 0.5794 (ppp) cc_final: 0.5303 (ppp) REVERT: C 101 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6641 (ttt90) REVERT: C 232 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.3762 (tpm170) REVERT: D 101 ARG cc_start: 0.8069 (tmm-80) cc_final: 0.7754 (ptm-80) REVERT: D 193 THR cc_start: 0.8390 (m) cc_final: 0.7842 (p) REVERT: E 156 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7390 (mm-30) REVERT: F 79 GLN cc_start: 0.6737 (mm-40) cc_final: 0.6516 (mm-40) REVERT: F 81 HIS cc_start: 0.7847 (t70) cc_final: 0.7623 (t70) REVERT: F 128 ARG cc_start: 0.6581 (mtt-85) cc_final: 0.6229 (mtt-85) REVERT: F 142 TRP cc_start: 0.7508 (m100) cc_final: 0.6858 (m100) REVERT: F 156 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7261 (mm-30) REVERT: F 212 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5711 (tt) REVERT: F 217 LEU cc_start: -0.5212 (OUTLIER) cc_final: -0.6257 (tp) outliers start: 48 outliers final: 34 residues processed: 282 average time/residue: 0.1176 time to fit residues: 43.7805 Evaluate side-chains 293 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.198698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.154544 restraints weight = 17881.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.159500 restraints weight = 9546.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.162828 restraints weight = 5972.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.165044 restraints weight = 4190.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.166565 restraints weight = 3211.473| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10406 Z= 0.142 Angle : 0.776 11.447 14211 Z= 0.363 Chirality : 0.047 0.271 1631 Planarity : 0.005 0.047 1800 Dihedral : 8.844 72.988 1797 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.88 % Allowed : 26.69 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.23), residues: 1216 helix: -1.53 (1.00), residues: 26 sheet: -0.53 (0.22), residues: 542 loop : -1.53 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 34 TYR 0.031 0.002 TYR D 253 PHE 0.011 0.001 PHE E 287 TRP 0.033 0.002 TRP C 180 HIS 0.008 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00333 (10358) covalent geometry : angle 0.75699 (14093) SS BOND : bond 0.00529 ( 26) SS BOND : angle 1.38311 ( 52) hydrogen bonds : bond 0.03622 ( 255) hydrogen bonds : angle 6.67928 ( 627) link_BETA1-4 : bond 0.00361 ( 4) link_BETA1-4 : angle 1.32725 ( 12) link_NAG-ASN : bond 0.00408 ( 18) link_NAG-ASN : angle 2.56522 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6479 (OUTLIER) cc_final: 0.6217 (p-80) REVERT: A 160 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6506 (tmm-80) REVERT: A 163 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7091 (ttt90) REVERT: B 124 MET cc_start: 0.5805 (ppp) cc_final: 0.5255 (ppp) REVERT: C 101 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6611 (ttt90) REVERT: C 232 ARG cc_start: 0.5391 (OUTLIER) cc_final: 0.3764 (tpm170) REVERT: D 101 ARG cc_start: 0.8075 (tmm-80) cc_final: 0.7750 (ptm-80) REVERT: D 193 THR cc_start: 0.8395 (m) cc_final: 0.7826 (p) REVERT: E 156 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7482 (mm-30) REVERT: F 79 GLN cc_start: 0.6921 (mm-40) cc_final: 0.6662 (mm-40) REVERT: F 81 HIS cc_start: 0.7878 (t70) cc_final: 0.7645 (t70) REVERT: F 128 ARG cc_start: 0.6735 (mtt-85) cc_final: 0.6311 (mtt-85) REVERT: F 156 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7411 (mm-30) REVERT: F 212 LEU cc_start: 0.5885 (OUTLIER) cc_final: 0.5679 (tt) REVERT: F 217 LEU cc_start: -0.5113 (OUTLIER) cc_final: -0.6164 (tp) outliers start: 43 outliers final: 34 residues processed: 273 average time/residue: 0.1186 time to fit residues: 42.9982 Evaluate side-chains 293 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.0270 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.198616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153978 restraints weight = 18031.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.158980 restraints weight = 9657.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.162237 restraints weight = 6049.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.164456 restraints weight = 4270.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165960 restraints weight = 3279.081| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10406 Z= 0.163 Angle : 0.798 11.663 14211 Z= 0.375 Chirality : 0.047 0.267 1631 Planarity : 0.005 0.049 1800 Dihedral : 8.833 69.781 1797 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.06 % Allowed : 26.51 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.23), residues: 1216 helix: -1.55 (1.00), residues: 26 sheet: -0.51 (0.22), residues: 537 loop : -1.59 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 109 TYR 0.028 0.002 TYR D 253 PHE 0.012 0.001 PHE E 149 TRP 0.028 0.002 TRP C 180 HIS 0.016 0.001 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00377 (10358) covalent geometry : angle 0.77819 (14093) SS BOND : bond 0.00552 ( 26) SS BOND : angle 1.43318 ( 52) hydrogen bonds : bond 0.03792 ( 255) hydrogen bonds : angle 6.70090 ( 627) link_BETA1-4 : bond 0.00303 ( 4) link_BETA1-4 : angle 1.29893 ( 12) link_NAG-ASN : bond 0.00409 ( 18) link_NAG-ASN : angle 2.67007 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2229.42 seconds wall clock time: 38 minutes 57.00 seconds (2337.00 seconds total)