Starting phenix.real_space_refine on Thu Jul 2 20:35:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uwl_26835/07_2026/7uwl_26835.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwl_26835/07_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_26835/07_2026/7uwl_26835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwl_26835/07_2026/7uwl_26835.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwl_26835/07_2026/7uwl_26835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwl_26835/07_2026/7uwl_26835.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uwl_26835/07_2026/7uwl_26835.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uwl_26835/07_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-6108/lib/python3.11/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 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 1.88, per 1000 atoms: 0.19 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: 0.65 Conformation dependent library (CDL) restraints added in 242.9 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: 0.19 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: 0.84 Time building geometry restraints manager: 0.85 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 - 18.02: 5312 18.02 - 36.05: 610 36.05 - 54.07: 172 54.07 - 72.10: 20 72.10 - 90.12: 7 Dihedral angle restraints: 6121 sinusoidal: 2503 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 6118 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.540 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 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 : 16.043 81.265 3683 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/Z covalent geometry : bond 0.00485 / 0.24 (10358) covalent geometry : angle 0.77972 / 0.40 (14093) SS BOND : bond 0.00808 / 0.63 ( 26) SS BOND : angle 2.17910 / 1.33 ( 52) hydrogen bonds : bond 0.29993 / 20.32 ( 255) hydrogen bonds : angle 10.44482 / 7.23 ( 627) link_BETA1-4 : bond 0.00111 / 0.05 ( 4) link_BETA1-4 : angle 1.75307 / 0.92 ( 12) link_NAG-ASN : bond 0.00546 / 0.38 ( 18) link_NAG-ASN : angle 2.88559 / 1.90 ( 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 : 0.298 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: 0.0937 time to fit residues: 34.9208 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 : 0.214 ------------------------------------------------------------------------------- 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... 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 251 HIS ** 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 175 HIS F 176 GLN F 231 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.198470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.154425 restraints weight = 18137.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.159293 restraints weight = 9667.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.162518 restraints weight = 6045.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.164664 restraints weight = 4255.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.165531 restraints weight = 3276.222| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10406 Z= 0.162 Angle : 0.755 9.708 14211 Z= 0.366 Chirality : 0.047 0.260 1631 Planarity : 0.005 0.048 1800 Dihedral : 6.013 58.796 1345 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.15 % Allowed : 21.28 % Favored : 74.57 % 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: -1.46 (0.23), residues: 1216 helix: -1.73 (0.98), residues: 26 sheet: -0.19 (0.23), residues: 540 loop : -1.65 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 46 TYR 0.018 0.002 TYR A 141 PHE 0.011 0.001 PHE C 157 TRP 0.024 0.002 TRP D 70 HIS 0.008 0.001 HIS E 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (10358) covalent geometry : angle 0.73436 / 0.36 (14093) SS BOND : bond 0.00515 / 0.34 ( 26) SS BOND : angle 1.26355 / 0.85 ( 52) hydrogen bonds : bond 0.04827 / 3.28 ( 255) hydrogen bonds : angle 7.78738 / 5.41 ( 627) link_BETA1-4 : bond 0.00341 / 0.17 ( 4) link_BETA1-4 : angle 1.42316 / 0.77 ( 12) link_NAG-ASN : bond 0.00541 / 0.36 ( 18) link_NAG-ASN : angle 2.66933 / 1.75 ( 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 323 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.6297 (p-80) REVERT: A 163 ARG cc_start: 0.7426 (tpp80) cc_final: 0.6980 (ttt90) REVERT: A 166 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6444 (mp) REVERT: B 124 MET cc_start: 0.5434 (ppp) cc_final: 0.5181 (ppp) REVERT: C 111 GLN cc_start: 0.6997 (mt0) cc_final: 0.6742 (mt0) REVERT: C 155 VAL cc_start: 0.7117 (OUTLIER) cc_final: 0.6763 (m) REVERT: C 230 GLN cc_start: 0.5844 (OUTLIER) cc_final: 0.5506 (tm-30) REVERT: D 193 THR cc_start: 0.8391 (m) cc_final: 0.7886 (p) REVERT: D 265 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7642 (mtmt) REVERT: F 79 GLN cc_start: 0.6793 (mm-40) cc_final: 0.6378 (tm-30) REVERT: F 80 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7489 (mt) REVERT: F 142 TRP cc_start: 0.7447 (m100) cc_final: 0.6563 (m100) REVERT: F 147 SER cc_start: 0.8062 (t) cc_final: 0.7852 (t) REVERT: F 212 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5710 (tt) outliers start: 46 outliers final: 25 residues processed: 300 average time/residue: 0.0911 time to fit residues: 36.5203 Evaluate side-chains 303 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 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 22 VAL 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 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: 0.0020 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.197634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152929 restraints weight = 17949.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.157890 restraints weight = 9558.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.161163 restraints weight = 5968.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.163358 restraints weight = 4194.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.164472 restraints weight = 3224.423| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10406 Z= 0.184 Angle : 0.764 10.867 14211 Z= 0.372 Chirality : 0.048 0.267 1631 Planarity : 0.005 0.049 1800 Dihedral : 6.055 59.782 1344 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.14 % Allowed : 22.72 % Favored : 72.14 % 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: -1.64 (0.23), residues: 1216 helix: -1.72 (0.95), residues: 26 sheet: -0.40 (0.23), residues: 533 loop : -1.67 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 34 TYR 0.020 0.003 TYR A 141 PHE 0.012 0.001 PHE E 149 TRP 0.027 0.002 TRP D 70 HIS 0.011 0.001 HIS E 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (10358) covalent geometry : angle 0.74184 / 0.37 (14093) SS BOND : bond 0.00706 / 0.41 ( 26) SS BOND : angle 1.67056 / 1.05 ( 52) hydrogen bonds : bond 0.04620 / 3.18 ( 255) hydrogen bonds : angle 7.44615 / 5.20 ( 627) link_BETA1-4 : bond 0.00328 / 0.17 ( 4) link_BETA1-4 : angle 1.39248 / 0.74 ( 12) link_NAG-ASN : bond 0.00483 / 0.32 ( 18) link_NAG-ASN : angle 2.63233 / 1.77 ( 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 326 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 269 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.6281 (p-80) REVERT: A 163 ARG cc_start: 0.7461 (tpp80) cc_final: 0.7016 (ttt90) REVERT: B 124 MET cc_start: 0.5584 (ppp) cc_final: 0.5161 (ppp) REVERT: C 155 VAL cc_start: 0.7036 (OUTLIER) cc_final: 0.6665 (m) REVERT: C 230 GLN cc_start: 0.5819 (OUTLIER) cc_final: 0.5467 (tm-30) REVERT: C 232 ARG cc_start: 0.5359 (OUTLIER) cc_final: 0.4669 (tpp-160) REVERT: D 100 VAL cc_start: 0.7571 (m) cc_final: 0.7273 (p) REVERT: D 101 ARG cc_start: 0.8084 (tmm-80) cc_final: 0.7417 (ptm160) REVERT: D 193 THR cc_start: 0.8384 (m) cc_final: 0.7854 (p) REVERT: D 250 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7600 (mm) REVERT: F 142 TRP cc_start: 0.7527 (m100) cc_final: 0.6636 (m100) REVERT: F 156 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7313 (mm-30) REVERT: F 212 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5840 (tt) outliers start: 57 outliers final: 34 residues processed: 295 average time/residue: 0.0979 time to fit residues: 38.5810 Evaluate side-chains 309 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 269 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 88 VAL 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 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 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 168 ILE 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 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: 0.1980 chunk 65 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 0.0060 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 175 HIS F 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.198905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.154170 restraints weight = 18051.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.159177 restraints weight = 9622.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162480 restraints weight = 6003.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.164697 restraints weight = 4210.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.165892 restraints weight = 3223.699| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10406 Z= 0.132 Angle : 0.720 10.960 14211 Z= 0.343 Chirality : 0.046 0.276 1631 Planarity : 0.005 0.045 1800 Dihedral : 5.618 57.361 1340 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.50 % Allowed : 22.72 % Favored : 71.78 % 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: -1.59 (0.23), residues: 1216 helix: -1.75 (0.97), residues: 26 sheet: -0.43 (0.23), residues: 525 loop : -1.55 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 34 TYR 0.017 0.002 TYR D 253 PHE 0.011 0.001 PHE C 94 TRP 0.021 0.001 TRP D 70 HIS 0.013 0.001 HIS E 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (10358) covalent geometry : angle 0.70226 / 0.34 (14093) SS BOND : bond 0.00571 / 0.34 ( 26) SS BOND : angle 1.21258 / 0.84 ( 52) hydrogen bonds : bond 0.03772 / 2.59 ( 255) hydrogen bonds : angle 7.03914 / 4.89 ( 627) link_BETA1-4 : bond 0.00299 / 0.15 ( 4) link_BETA1-4 : angle 1.36223 / 0.72 ( 12) link_NAG-ASN : bond 0.00437 / 0.31 ( 18) link_NAG-ASN : angle 2.45540 / 1.65 ( 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 327 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 266 time to evaluate : 0.289 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: 0.6432 (OUTLIER) cc_final: 0.6101 (p-80) REVERT: A 163 ARG cc_start: 0.7435 (tpp80) cc_final: 0.7030 (ttt90) REVERT: A 166 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6417 (mp) REVERT: B 124 MET cc_start: 0.5678 (ppp) cc_final: 0.5187 (ppp) REVERT: C 155 VAL cc_start: 0.6900 (OUTLIER) cc_final: 0.6569 (m) REVERT: C 230 GLN cc_start: 0.5847 (OUTLIER) cc_final: 0.5471 (tm-30) REVERT: D 101 ARG cc_start: 0.8043 (tmm-80) cc_final: 0.7732 (ptm-80) REVERT: D 193 THR cc_start: 0.8354 (m) cc_final: 0.7829 (p) REVERT: D 250 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7693 (mm) REVERT: F 142 TRP cc_start: 0.7512 (m100) cc_final: 0.6716 (m100) REVERT: F 143 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6885 (mpt180) REVERT: F 156 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7251 (mm-30) REVERT: F 217 LEU cc_start: -0.5212 (OUTLIER) cc_final: -0.6224 (tp) outliers start: 61 outliers final: 36 residues processed: 296 average time/residue: 0.0920 time to fit residues: 36.2649 Evaluate side-chains 303 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 122 SER 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 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 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 168 ILE 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 143 ARG Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 281 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 chunk 76 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.198694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.153886 restraints weight = 17833.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.158914 restraints weight = 9527.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.162179 restraints weight = 5943.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.164399 restraints weight = 4170.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.165944 restraints weight = 3195.392| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.1901 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= 0.150 Angle : 0.730 11.904 14211 Z= 0.348 Chirality : 0.046 0.273 1631 Planarity : 0.005 0.044 1800 Dihedral : 5.387 52.132 1338 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 5.95 % Allowed : 23.99 % Favored : 70.06 % 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: -1.58 (0.23), residues: 1216 helix: -1.64 (0.98), residues: 26 sheet: -0.42 (0.23), residues: 517 loop : -1.54 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 136 TYR 0.018 0.002 TYR D 253 PHE 0.011 0.001 PHE E 149 TRP 0.026 0.002 TRP D 70 HIS 0.012 0.001 HIS E 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10358) covalent geometry : angle 0.71203 / 0.34 (14093) SS BOND : bond 0.00553 / 0.34 ( 26) SS BOND : angle 1.21622 / 0.91 ( 52) hydrogen bonds : bond 0.03831 / 2.63 ( 255) hydrogen bonds : angle 6.95413 / 4.83 ( 627) link_BETA1-4 : bond 0.00347 / 0.17 ( 4) link_BETA1-4 : angle 1.29710 / 0.69 ( 12) link_NAG-ASN : bond 0.00452 / 0.31 ( 18) link_NAG-ASN : angle 2.47360 / 1.66 ( 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 332 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6431 (OUTLIER) cc_final: 0.6108 (p-80) REVERT: A 163 ARG cc_start: 0.7511 (tpp80) cc_final: 0.7081 (ttt90) REVERT: A 166 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6428 (mp) REVERT: B 124 MET cc_start: 0.5754 (ppp) cc_final: 0.5254 (ppp) REVERT: C 111 GLN cc_start: 0.7216 (mt0) cc_final: 0.6806 (mt0) REVERT: C 155 VAL cc_start: 0.6921 (OUTLIER) cc_final: 0.6569 (m) REVERT: C 167 MET cc_start: 0.5861 (mmm) cc_final: 0.5623 (mmm) REVERT: C 230 GLN cc_start: 0.5869 (OUTLIER) cc_final: 0.5482 (tm-30) REVERT: D 193 THR cc_start: 0.8336 (m) cc_final: 0.7806 (p) REVERT: D 250 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7684 (mm) REVERT: E 143 ARG cc_start: 0.6509 (mtp85) cc_final: 0.5680 (mmp80) REVERT: F 128 ARG cc_start: 0.6612 (mtt-85) cc_final: 0.6246 (mtt-85) REVERT: F 143 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6838 (mpt180) REVERT: F 156 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7313 (mm-30) REVERT: F 212 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5702 (tt) outliers start: 66 outliers final: 43 residues processed: 301 average time/residue: 0.1038 time to fit residues: 41.6787 Evaluate side-chains 312 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 A residue 176 MET 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 122 SER 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 253 TYR Chi-restraints excluded: chain C residue 262 ILE 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 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 109 LEU Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 168 ILE 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 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 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: 2.9990 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4505 r_free = 0.4505 target = 0.197586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152571 restraints weight = 18081.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157615 restraints weight = 9655.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.160878 restraints weight = 6019.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.163084 restraints weight = 4232.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.164351 restraints weight = 3251.622| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10406 Z= 0.168 Angle : 0.750 11.692 14211 Z= 0.360 Chirality : 0.047 0.272 1631 Planarity : 0.005 0.047 1800 Dihedral : 5.543 54.532 1338 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.68 % Allowed : 24.26 % Favored : 70.06 % 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: -1.54 (1.00), residues: 26 sheet: -0.46 (0.23), residues: 517 loop : -1.55 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 101 TYR 0.016 0.002 TYR D 253 PHE 0.012 0.001 PHE E 149 TRP 0.027 0.002 TRP D 70 HIS 0.013 0.001 HIS E 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (10358) covalent geometry : angle 0.73215 / 0.36 (14093) SS BOND : bond 0.00563 / 0.34 ( 26) SS BOND : angle 1.29809 / 0.98 ( 52) hydrogen bonds : bond 0.03918 / 2.69 ( 255) hydrogen bonds : angle 6.87208 / 4.77 ( 627) link_BETA1-4 : bond 0.00558 / 0.27 ( 4) link_BETA1-4 : angle 1.14218 / 0.63 ( 12) link_NAG-ASN : bond 0.00451 / 0.30 ( 18) link_NAG-ASN : angle 2.51034 / 1.71 ( 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 331 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6426 (OUTLIER) cc_final: 0.6090 (p-80) REVERT: A 163 ARG cc_start: 0.7498 (tpp80) cc_final: 0.7064 (ttt90) REVERT: A 166 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6501 (mp) REVERT: B 124 MET cc_start: 0.5824 (ppp) cc_final: 0.5298 (ppp) REVERT: C 155 VAL cc_start: 0.6951 (OUTLIER) cc_final: 0.6585 (m) REVERT: D 100 VAL cc_start: 0.7616 (m) cc_final: 0.7363 (p) REVERT: D 193 THR cc_start: 0.8350 (m) cc_final: 0.7819 (p) REVERT: D 250 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7693 (mm) REVERT: F 68 LEU cc_start: 0.5286 (OUTLIER) cc_final: 0.4479 (pp) REVERT: F 79 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6697 (mm-40) REVERT: F 128 ARG cc_start: 0.6637 (mtt-85) cc_final: 0.6277 (mtt-85) REVERT: F 143 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6851 (mpt180) REVERT: F 156 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7346 (mm-30) REVERT: F 212 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5706 (tt) REVERT: F 217 LEU cc_start: -0.5230 (OUTLIER) cc_final: -0.6515 (tp) outliers start: 63 outliers final: 45 residues processed: 296 average time/residue: 0.0957 time to fit residues: 37.7686 Evaluate side-chains 320 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 A residue 176 MET 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 122 SER Chi-restraints excluded: chain C residue 146 MET 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 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 109 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 HIS 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 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 143 ARG 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 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: 3.9990 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 0.0000 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.203850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.161469 restraints weight = 21186.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.164544 restraints weight = 12825.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.166510 restraints weight = 8893.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.167819 restraints weight = 6942.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.169237 restraints weight = 5919.139| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.2245 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= 0.140 Angle : 0.745 11.564 14211 Z= 0.353 Chirality : 0.046 0.276 1631 Planarity : 0.005 0.047 1800 Dihedral : 5.464 54.813 1338 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.78 % Allowed : 25.07 % Favored : 70.15 % 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: -1.35 (0.99), residues: 26 sheet: -0.50 (0.23), residues: 526 loop : -1.53 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 34 TYR 0.024 0.002 TYR C 253 PHE 0.015 0.001 PHE C 94 TRP 0.046 0.002 TRP C 180 HIS 0.014 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10358) covalent geometry : angle 0.72718 / 0.35 (14093) SS BOND : bond 0.00559 / 0.34 ( 26) SS BOND : angle 1.35914 / 0.98 ( 52) hydrogen bonds : bond 0.03671 / 2.52 ( 255) hydrogen bonds : angle 6.77095 / 4.71 ( 627) link_BETA1-4 : bond 0.00341 / 0.17 ( 4) link_BETA1-4 : angle 1.21351 / 0.64 ( 12) link_NAG-ASN : bond 0.00461 / 0.31 ( 18) link_NAG-ASN : angle 2.42427 / 1.65 ( 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 316 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 263 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6342 (OUTLIER) cc_final: 0.6023 (p-80) REVERT: A 163 ARG cc_start: 0.7425 (tpp80) cc_final: 0.7026 (ttt90) REVERT: A 166 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6395 (mp) REVERT: B 124 MET cc_start: 0.5796 (ppp) cc_final: 0.5304 (ppp) REVERT: D 101 ARG cc_start: 0.8106 (tmm-80) cc_final: 0.7803 (ptm-80) REVERT: D 193 THR cc_start: 0.8355 (m) cc_final: 0.7809 (p) REVERT: D 250 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7749 (mm) REVERT: E 156 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7763 (mm-30) REVERT: F 68 LEU cc_start: 0.5165 (OUTLIER) cc_final: 0.4390 (pp) REVERT: F 79 GLN cc_start: 0.7157 (mm-40) cc_final: 0.6864 (mm-40) REVERT: F 128 ARG cc_start: 0.6731 (mtt-85) cc_final: 0.6332 (mtt-85) REVERT: F 143 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6853 (mpt180) REVERT: F 156 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7646 (mm-30) REVERT: F 217 LEU cc_start: -0.6026 (OUTLIER) cc_final: -0.6731 (tp) outliers start: 53 outliers final: 42 residues processed: 289 average time/residue: 0.0964 time to fit residues: 37.2487 Evaluate side-chains 311 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 263 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 146 MET 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 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 50 CYS 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 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 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 175 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 281 VAL 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: 1.9990 chunk 98 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 120 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.196782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.151756 restraints weight = 17793.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.156730 restraints weight = 9573.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.159949 restraints weight = 6005.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.161828 restraints weight = 4242.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.163407 restraints weight = 3322.863| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10406 Z= 0.212 Angle : 0.806 11.992 14211 Z= 0.385 Chirality : 0.048 0.265 1631 Planarity : 0.005 0.051 1800 Dihedral : 5.397 26.378 1335 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 5.41 % Allowed : 24.80 % 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: -1.73 (0.23), residues: 1216 helix: -1.16 (1.00), residues: 26 sheet: -0.57 (0.23), residues: 533 loop : -1.64 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 113 TYR 0.032 0.003 TYR D 253 PHE 0.015 0.002 PHE C 94 TRP 0.065 0.003 TRP C 180 HIS 0.020 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (10358) covalent geometry : angle 0.78593 / 0.38 (14093) SS BOND : bond 0.00626 / 0.38 ( 26) SS BOND : angle 1.50715 / 1.10 ( 52) hydrogen bonds : bond 0.04179 / 2.87 ( 255) hydrogen bonds : angle 6.90683 / 4.79 ( 627) link_BETA1-4 : bond 0.00359 / 0.18 ( 4) link_BETA1-4 : angle 1.15051 / 0.60 ( 12) link_NAG-ASN : bond 0.00498 / 0.32 ( 18) link_NAG-ASN : angle 2.66232 / 1.81 ( 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 322 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 262 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6377 (OUTLIER) cc_final: 0.6050 (p-80) REVERT: A 163 ARG cc_start: 0.7504 (tpp80) cc_final: 0.7052 (ttt90) REVERT: A 166 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6359 (mp) REVERT: B 124 MET cc_start: 0.5855 (ppp) cc_final: 0.5314 (ppp) REVERT: C 167 MET cc_start: 0.6403 (mmm) cc_final: 0.5997 (mmm) REVERT: D 100 VAL cc_start: 0.7756 (m) cc_final: 0.7452 (p) REVERT: D 101 ARG cc_start: 0.8172 (tmm-80) cc_final: 0.7642 (ptm160) REVERT: D 193 THR cc_start: 0.8377 (m) cc_final: 0.7806 (p) REVERT: D 250 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7681 (mm) REVERT: E 156 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7393 (mm-30) REVERT: F 68 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.4465 (pp) REVERT: F 79 GLN cc_start: 0.6911 (mm-40) cc_final: 0.6672 (mm-40) REVERT: F 128 ARG cc_start: 0.6735 (mtt-85) cc_final: 0.6353 (mtt-85) REVERT: F 143 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6884 (mpt180) REVERT: F 156 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7437 (mm-30) REVERT: F 217 LEU cc_start: -0.5111 (OUTLIER) cc_final: -0.6427 (tp) outliers start: 60 outliers final: 46 residues processed: 290 average time/residue: 0.1054 time to fit residues: 40.4371 Evaluate side-chains 313 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 A residue 176 MET 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 84 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 146 MET 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 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 50 CYS 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 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 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 143 ARG Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 175 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 0.0020 chunk 71 optimal weight: 0.5980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.198997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154820 restraints weight = 18071.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.159899 restraints weight = 9570.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.163278 restraints weight = 5950.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.165526 restraints weight = 4171.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.166465 restraints weight = 3200.339| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10406 Z= 0.127 Angle : 0.765 11.521 14211 Z= 0.359 Chirality : 0.047 0.280 1631 Planarity : 0.005 0.043 1800 Dihedral : 5.160 25.802 1335 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.42 % Allowed : 25.97 % 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: -1.61 (0.23), residues: 1216 helix: -1.14 (0.98), residues: 26 sheet: -0.57 (0.23), residues: 531 loop : -1.48 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 34 TYR 0.027 0.002 TYR C 253 PHE 0.015 0.001 PHE C 94 TRP 0.059 0.002 TRP C 180 HIS 0.017 0.001 HIS E 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10358) covalent geometry : angle 0.74821 / 0.35 (14093) SS BOND : bond 0.00533 / 0.32 ( 26) SS BOND : angle 1.39697 / 0.97 ( 52) hydrogen bonds : bond 0.03516 / 2.41 ( 255) hydrogen bonds : angle 6.69610 / 4.67 ( 627) link_BETA1-4 : bond 0.00385 / 0.19 ( 4) link_BETA1-4 : angle 1.17491 / 0.63 ( 12) link_NAG-ASN : bond 0.00447 / 0.31 ( 18) link_NAG-ASN : angle 2.39195 / 1.62 ( 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 311 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6534 (tmm-80) REVERT: A 163 ARG cc_start: 0.7494 (tpp80) cc_final: 0.7022 (ttt90) REVERT: A 166 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6232 (mp) REVERT: B 124 MET cc_start: 0.5846 (ppp) cc_final: 0.5224 (ppp) REVERT: D 95 GLN cc_start: 0.7137 (mp10) cc_final: 0.6887 (mp10) REVERT: D 101 ARG cc_start: 0.8051 (tmm-80) cc_final: 0.7767 (ptm-80) REVERT: D 193 THR cc_start: 0.8372 (m) cc_final: 0.7805 (p) REVERT: D 250 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7528 (mm) REVERT: E 156 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7429 (mm-30) REVERT: F 68 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4230 (pp) REVERT: F 79 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6643 (mm-40) REVERT: F 128 ARG cc_start: 0.6739 (mtt-85) cc_final: 0.6322 (mtt-85) REVERT: F 143 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6832 (mpt180) REVERT: F 156 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7400 (mm-30) REVERT: F 217 LEU cc_start: -0.5178 (OUTLIER) cc_final: -0.6485 (tp) outliers start: 49 outliers final: 38 residues processed: 282 average time/residue: 0.0991 time to fit residues: 37.2911 Evaluate side-chains 303 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 160 ARG Chi-restraints excluded: chain A residue 166 LEU 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 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 146 MET 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 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 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 175 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.197817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.153502 restraints weight = 17888.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158482 restraints weight = 9549.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.161806 restraints weight = 5973.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.163986 restraints weight = 4187.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.165133 restraints weight = 3212.754| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10406 Z= 0.171 Angle : 0.799 11.779 14211 Z= 0.377 Chirality : 0.047 0.272 1631 Planarity : 0.005 0.047 1800 Dihedral : 5.298 25.963 1335 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 4.15 % Allowed : 26.24 % 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: -1.70 (0.24), residues: 1216 helix: -1.17 (0.97), residues: 26 sheet: -0.73 (0.22), residues: 558 loop : -1.46 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 34 TYR 0.014 0.002 TYR D 253 PHE 0.014 0.001 PHE C 94 TRP 0.052 0.002 TRP C 180 HIS 0.015 0.001 HIS E 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (10358) covalent geometry : angle 0.78224 / 0.37 (14093) SS BOND : bond 0.00573 / 0.35 ( 26) SS BOND : angle 1.43328 / 1.04 ( 52) hydrogen bonds : bond 0.03790 / 2.60 ( 255) hydrogen bonds : angle 6.70431 / 4.67 ( 627) link_BETA1-4 : bond 0.00307 / 0.15 ( 4) link_BETA1-4 : angle 1.17300 / 0.61 ( 12) link_NAG-ASN : bond 0.00456 / 0.30 ( 18) link_NAG-ASN : angle 2.48541 / 1.68 ( 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 311 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 265 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6541 (tmm-80) REVERT: A 163 ARG cc_start: 0.7517 (tpp80) cc_final: 0.7020 (ttt90) REVERT: B 124 MET cc_start: 0.5872 (ppp) cc_final: 0.5255 (ppp) REVERT: C 167 MET cc_start: 0.5832 (mmm) cc_final: 0.5564 (mmm) REVERT: D 95 GLN cc_start: 0.7103 (mp10) cc_final: 0.6869 (mp10) REVERT: D 100 VAL cc_start: 0.7602 (m) cc_final: 0.7347 (p) REVERT: D 101 ARG cc_start: 0.8129 (tmm-80) cc_final: 0.7531 (ptm160) REVERT: D 193 THR cc_start: 0.8367 (m) cc_final: 0.7794 (p) REVERT: D 208 MET cc_start: 0.6484 (mmm) cc_final: 0.6208 (mtt) REVERT: D 250 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7593 (mm) REVERT: E 98 TRP cc_start: 0.7195 (p90) cc_final: 0.6456 (p90) REVERT: E 156 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7460 (mm-30) REVERT: F 68 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.4592 (pt) REVERT: F 79 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6684 (mm-40) REVERT: F 128 ARG cc_start: 0.6796 (mtt-85) cc_final: 0.6383 (mtt-85) REVERT: F 143 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6911 (mpt180) REVERT: F 156 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7475 (mm-30) REVERT: F 217 LEU cc_start: -0.5081 (OUTLIER) cc_final: -0.6408 (tp) outliers start: 46 outliers final: 39 residues processed: 282 average time/residue: 0.0930 time to fit residues: 35.0499 Evaluate side-chains 308 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 160 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 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 146 MET 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 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 95 HIS 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 175 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 chunk 19 optimal weight: 0.0670 chunk 67 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 chunk 98 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.199251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.155248 restraints weight = 18053.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160383 restraints weight = 9583.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.163791 restraints weight = 5951.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.165898 restraints weight = 4151.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.167055 restraints weight = 3209.627| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.2655 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= 0.118 Angle : 0.764 12.058 14211 Z= 0.354 Chirality : 0.046 0.281 1631 Planarity : 0.005 0.041 1800 Dihedral : 5.070 25.389 1335 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.43 % Allowed : 26.69 % Favored : 69.88 % 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: -1.55 (0.24), residues: 1216 helix: -1.13 (0.99), residues: 26 sheet: -0.60 (0.22), residues: 547 loop : -1.38 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 34 TYR 0.015 0.001 TYR D 253 PHE 0.012 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/Z covalent geometry : bond 0.00281 / 0.12 (10358) covalent geometry : angle 0.74987 / 0.35 (14093) SS BOND : bond 0.00505 / 0.31 ( 26) SS BOND : angle 1.26131 / 0.91 ( 52) hydrogen bonds : bond 0.03299 / 2.23 ( 255) hydrogen bonds : angle 6.49804 / 4.52 ( 627) link_BETA1-4 : bond 0.00323 / 0.16 ( 4) link_BETA1-4 : angle 1.24434 / 0.66 ( 12) link_NAG-ASN : bond 0.00437 / 0.31 ( 18) link_NAG-ASN : angle 2.27048 / 1.52 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.00 seconds wall clock time: 31 minutes 43.83 seconds (1903.83 seconds total)