Starting phenix.real_space_refine on Sat Jul 4 05:19:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vav_43106/07_2026/8vav_43106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vav_43106/07_2026/8vav_43106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vav_43106/07_2026/8vav_43106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vav_43106/07_2026/8vav_43106.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vav_43106/07_2026/8vav_43106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vav_43106/07_2026/8vav_43106.map" } resolution = 3.13 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= 0.004 sd= 0.018 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 S 92 5.16 5 C 12348 2.51 5 N 2744 2.21 5 O 3332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 18532 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2201 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 1 Chain: "B" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2201 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 1 Chain: "C" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2201 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 1 Chain: "D" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2201 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 1 Chain: "E" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1850 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 231} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1850 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 231} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1850 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 231} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1850 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 231} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 567 Ad-hoc single atom residues: {' K': 4} Unusual residues: {'AJP': 8, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 14} Link IDs: {None: 12} Chain breaks: 4 Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 752 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 567 Unusual residues: {'AJP': 8, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 752 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 567 Unusual residues: {'AJP': 8, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 752 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 567 Unusual residues: {'AJP': 8, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 752 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.56, per 1000 atoms: 0.25 Number of scatterers: 18532 At special positions: 0 Unit cell: (132.84, 132.84, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 92 16.00 P 12 15.00 O 3332 8.00 N 2744 7.00 C 12348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 49 " distance=2.03 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS E 57 " distance=2.03 Simple disulfide: pdb=" SG CYS E 205 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 207 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 49 " distance=2.03 Simple disulfide: pdb=" SG CYS F 47 " - pdb=" SG CYS F 57 " distance=2.03 Simple disulfide: pdb=" SG CYS F 205 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 207 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 49 " distance=2.03 Simple disulfide: pdb=" SG CYS G 47 " - pdb=" SG CYS G 57 " distance=2.03 Simple disulfide: pdb=" SG CYS G 205 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 207 " - pdb=" SG CYS G 253 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 49 " distance=2.03 Simple disulfide: pdb=" SG CYS H 47 " - pdb=" SG CYS H 57 " distance=2.03 Simple disulfide: pdb=" SG CYS H 205 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 207 " - pdb=" SG CYS H 253 " 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 NAG-ASN " NAG E 401 " - " ASN E 147 " " NAG F 401 " - " ASN F 147 " " NAG G 401 " - " ASN G 147 " " NAG H 401 " - " ASN H 147 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 797.4 milliseconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 54.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.629A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 200 Proline residue: A 191 - end of helix removed outlier: 3.701A pdb=" N PHE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.940A pdb=" N ARG A 210 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 removed outlier: 3.662A pdb=" N PHE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 260 removed outlier: 3.702A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 327 Proline residue: A 320 - end of helix Processing helix chain 'B' and resid 21 through 46 removed outlier: 3.634A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 148 through 170 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 180 through 200 Proline residue: B 191 - end of helix removed outlier: 3.699A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.998A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 223 removed outlier: 3.687A pdb=" N PHE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 260 removed outlier: 3.699A pdb=" N GLY B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 327 Proline residue: B 320 - end of helix Processing helix chain 'C' and resid 21 through 46 removed outlier: 3.623A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 148 through 170 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix removed outlier: 3.696A pdb=" N PHE C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.970A pdb=" N ARG C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 215 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 removed outlier: 3.652A pdb=" N PHE C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 260 removed outlier: 3.698A pdb=" N GLY C 260 " --> pdb=" O VAL C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 327 Proline residue: C 320 - end of helix Processing helix chain 'D' and resid 21 through 46 removed outlier: 3.629A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 148 through 170 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 200 Proline residue: D 191 - end of helix removed outlier: 3.695A pdb=" N PHE D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 4.003A pdb=" N ARG D 210 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 223 removed outlier: 3.685A pdb=" N PHE D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 260 removed outlier: 3.705A pdb=" N GLY D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 327 Proline residue: D 320 - end of helix Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.681A pdb=" N LEU E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 190 removed outlier: 4.458A pdb=" N LEU E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 209 through 219 Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.611A pdb=" N PHE E 250 " --> pdb=" O SER E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 293 removed outlier: 5.121A pdb=" N GLY E 269 " --> pdb=" O VAL E 265 " (cutoff:3.500A) Proline residue: E 270 - end of helix Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.656A pdb=" N LEU F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 removed outlier: 4.454A pdb=" N LEU F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 209 through 219 Processing helix chain 'F' and resid 222 through 229 Processing helix chain 'F' and resid 246 through 251 removed outlier: 3.608A pdb=" N PHE F 250 " --> pdb=" O SER F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 293 removed outlier: 5.119A pdb=" N GLY F 269 " --> pdb=" O VAL F 265 " (cutoff:3.500A) Proline residue: F 270 - end of helix Processing helix chain 'G' and resid 159 through 164 removed outlier: 3.654A pdb=" N LEU G 163 " --> pdb=" O GLU G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 190 removed outlier: 4.478A pdb=" N LEU G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 209 through 219 Processing helix chain 'G' and resid 222 through 229 Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.578A pdb=" N PHE G 250 " --> pdb=" O SER G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 293 removed outlier: 5.096A pdb=" N GLY G 269 " --> pdb=" O VAL G 265 " (cutoff:3.500A) Proline residue: G 270 - end of helix Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.652A pdb=" N LEU H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 190 removed outlier: 4.482A pdb=" N LEU H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 209 through 219 Processing helix chain 'H' and resid 222 through 229 Processing helix chain 'H' and resid 246 through 251 removed outlier: 3.614A pdb=" N PHE H 250 " --> pdb=" O SER H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 293 removed outlier: 5.135A pdb=" N GLY H 269 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Proline residue: H 270 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AA3, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AA4, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AA5, first strand: chain 'E' and resid 48 through 50 removed outlier: 7.157A pdb=" N LEU E 100 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU E 124 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AA7, first strand: chain 'F' and resid 48 through 50 removed outlier: 7.227A pdb=" N LEU F 100 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU F 124 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'G' and resid 48 through 50 removed outlier: 7.152A pdb=" N LEU G 100 " --> pdb=" O ASP G 125 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU G 124 " --> pdb=" O SER G 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AB2, first strand: chain 'H' and resid 48 through 50 removed outlier: 7.154A pdb=" N LEU H 100 " --> pdb=" O ASP H 125 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU H 124 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 85 through 86 832 hydrogen bonds defined for protein. 2424 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2733 1.33 - 1.45: 5172 1.45 - 1.57: 11099 1.57 - 1.69: 24 1.69 - 1.81: 128 Bond restraints: 19156 Sorted by residual: bond pdb=" C21 POV C1104 " pdb=" O22 POV C1104 " ideal model delta sigma weight residual 1.205 1.331 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C21 POV A1108 " pdb=" O22 POV A1108 " ideal model delta sigma weight residual 1.205 1.331 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C21 POV C1104 " pdb=" O21 POV C1104 " ideal model delta sigma weight residual 1.330 1.204 0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C21 POV A1108 " pdb=" O21 POV A1108 " ideal model delta sigma weight residual 1.330 1.205 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C21 POV B1104 " pdb=" O22 POV B1104 " ideal model delta sigma weight residual 1.205 1.330 -0.125 2.00e-02 2.50e+03 3.91e+01 ... (remaining 19151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 26060 2.89 - 5.78: 421 5.78 - 8.67: 7 8.67 - 11.57: 0 11.57 - 14.46: 8 Bond angle restraints: 26496 Sorted by residual: angle pdb=" C22 POV C1104 " pdb=" C21 POV C1104 " pdb=" O21 POV C1104 " ideal model delta sigma weight residual 111.03 125.49 -14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C22 POV C1104 " pdb=" C21 POV C1104 " pdb=" O22 POV C1104 " ideal model delta sigma weight residual 125.44 110.98 14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C22 POV A1108 " pdb=" C21 POV A1108 " pdb=" O22 POV A1108 " ideal model delta sigma weight residual 125.44 110.99 14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C22 POV B1104 " pdb=" C21 POV B1104 " pdb=" O22 POV B1104 " ideal model delta sigma weight residual 125.44 111.00 14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C22 POV B1104 " pdb=" C21 POV B1104 " pdb=" O21 POV B1104 " ideal model delta sigma weight residual 111.03 125.46 -14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 26491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.63: 13424 25.63 - 51.26: 639 51.26 - 76.89: 398 76.89 - 102.51: 270 102.51 - 128.14: 253 Dihedral angle restraints: 14984 sinusoidal: 8964 harmonic: 6020 Sorted by residual: dihedral pdb=" CB CYS E 43 " pdb=" SG CYS E 43 " pdb=" SG CYS E 49 " pdb=" CB CYS E 49 " ideal model delta sinusoidal sigma weight residual -86.00 -166.45 80.45 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS G 43 " pdb=" SG CYS G 43 " pdb=" SG CYS G 49 " pdb=" CB CYS G 49 " ideal model delta sinusoidal sigma weight residual -86.00 -166.33 80.33 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS F 43 " pdb=" SG CYS F 43 " pdb=" SG CYS F 49 " pdb=" CB CYS F 49 " ideal model delta sinusoidal sigma weight residual -86.00 -166.06 80.06 1 1.00e+01 1.00e-02 7.94e+01 ... (remaining 14981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2535 0.044 - 0.088: 673 0.088 - 0.131: 107 0.131 - 0.175: 55 0.175 - 0.219: 66 Chirality restraints: 3436 Sorted by residual: chirality pdb=" C10 AJP C1108 " pdb=" C08 AJP C1108 " pdb=" C11 AJP C1108 " pdb=" O82 AJP C1108 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C10 AJP B1108 " pdb=" C08 AJP B1108 " pdb=" C11 AJP B1108 " pdb=" O82 AJP B1108 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C10 AJP A1115 " pdb=" C08 AJP A1115 " pdb=" C11 AJP A1115 " pdb=" O82 AJP A1115 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3433 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 191 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 192 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 191 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 192 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 192 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 192 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 191 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 192 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " 0.030 5.00e-02 4.00e+02 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 6227 2.86 - 3.43: 19964 3.43 - 4.00: 33655 4.00 - 4.57: 45475 4.57 - 5.14: 65794 Nonbonded interactions: 171115 Sorted by model distance: nonbonded pdb=" OG SER C 196 " pdb=" O ARG C 201 " model vdw 2.286 3.040 nonbonded pdb=" OG SER A 196 " pdb=" O ARG A 201 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 196 " pdb=" O ARG B 201 " model vdw 2.289 3.040 nonbonded pdb=" OG SER D 196 " pdb=" O ARG D 201 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR A 284 " pdb=" OH TYR B 290 " model vdw 2.290 3.040 ... (remaining 171110 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' and (resid 12 through 1102 or (resid 1103 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name O21)) or (resid 1110 through 1112 and (name C01 or name C02 or name C \ 03 or name C04 or name C05 or name C06 or name C07 or name C08 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or name C \ 24 or name C26 or name C27 or name C28 or name C29 or name C30 or name C32 or na \ me C80 or name C81 or name C83 or name C85 or name O09 or name O25 or name O31 o \ r name O33 or name O34 or name O77 or name O78 or name O79 or name O82 or name O \ 84)) or (resid 1113 and (name C01 or name C02 or name C03 or name C04 or name C0 \ 5 or name C06 or name C07 or name C08 or name C10 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C26 or name C2 \ 7 or name C28 or name C29 or name C30 or name C32 or name C35 or name C36 or nam \ e C37 or name C38 or name C39 or name C41 or name C80 or name C81 or name C83 or \ name C85 or name O09 or name O25 or name O31 or name O33 or name O34 or name O4 \ 0 or name O42 or name O43 or name O44 or name O54 or name O77 or name O78 or nam \ e O79 or name O82 or name O84)))) selection = (chain 'B' and (resid 12 through 1102 or (resid 1103 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name O21)) or (resid 1110 through 1112 and (name C01 or name C02 or name C \ 03 or name C04 or name C05 or name C06 or name C07 or name C08 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or name C \ 24 or name C26 or name C27 or name C28 or name C29 or name C30 or name C32 or na \ me C80 or name C81 or name C83 or name C85 or name O09 or name O25 or name O31 o \ r name O33 or name O34 or name O77 or name O78 or name O79 or name O82 or name O \ 84)) or resid 1113)) selection = (chain 'C' and (resid 12 through 1102 or (resid 1103 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name O21)) or (resid 1110 through 1112 and (name C01 or name C02 or name C \ 03 or name C04 or name C05 or name C06 or name C07 or name C08 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or name C \ 24 or name C26 or name C27 or name C28 or name C29 or name C30 or name C32 or na \ me C80 or name C81 or name C83 or name C85 or name O09 or name O25 or name O31 o \ r name O33 or name O34 or name O77 or name O78 or name O79 or name O82 or name O \ 84)) or resid 1113)) selection = (chain 'D' and (resid 12 through 1101 or (resid 1102 through 1103 and (name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name O21)) or (resid 1110 through 1112 and (name C01 or name \ C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or n \ ame C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24 or name C26 or name C27 or name C28 or name C29 or name C30 or n \ ame C32 or name C80 or name C81 or name C83 or name C85 or name O09 or name O25 \ or name O31 or name O33 or name O34 or name O77 or name O78 or name O79 or name \ O82 or name O84)) or resid 1113)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.850 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 0.126 19176 Z= 0.266 Angle : 0.801 14.458 26540 Z= 0.337 Chirality : 0.051 0.219 3436 Planarity : 0.005 0.053 2880 Dihedral : 27.591 128.142 11040 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 2072 helix: 1.87 (0.16), residues: 1016 sheet: -1.76 (0.49), residues: 120 loop : 0.02 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.007 0.001 TYR A 290 PHE 0.012 0.001 PHE A 252 TRP 0.012 0.001 TRP D 22 HIS 0.002 0.000 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.27 (19156) covalent geometry : angle 0.79891 / 0.34 (26496) SS BOND : bond 0.00259 / 0.15 ( 16) SS BOND : angle 0.59640 / 0.37 ( 32) hydrogen bonds : bond 0.13143 / 8.79 ( 832) hydrogen bonds : angle 4.50767 / 3.23 ( 2424) link_NAG-ASN : bond 0.00364 / 0.17 ( 4) link_NAG-ASN : angle 2.86784 / 1.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8537 (mmm) cc_final: 0.8288 (mmm) REVERT: A 172 ASN cc_start: 0.8779 (p0) cc_final: 0.8562 (m-40) REVERT: B 21 MET cc_start: 0.8497 (mmm) cc_final: 0.8237 (mmm) REVERT: B 172 ASN cc_start: 0.8760 (p0) cc_final: 0.8527 (m-40) REVERT: C 21 MET cc_start: 0.8637 (mmm) cc_final: 0.8109 (mmm) REVERT: C 172 ASN cc_start: 0.8772 (p0) cc_final: 0.8565 (m-40) REVERT: D 21 MET cc_start: 0.8513 (mmm) cc_final: 0.8252 (mmm) REVERT: D 104 MET cc_start: 0.8540 (tpp) cc_final: 0.8317 (tpp) REVERT: D 172 ASN cc_start: 0.8800 (p0) cc_final: 0.8569 (m-40) REVERT: E 81 ASN cc_start: 0.8948 (m-40) cc_final: 0.8559 (m-40) REVERT: E 108 HIS cc_start: 0.8054 (p-80) cc_final: 0.7838 (p-80) REVERT: E 130 GLN cc_start: 0.8963 (mt0) cc_final: 0.8686 (mp10) REVERT: E 238 THR cc_start: 0.7685 (p) cc_final: 0.7388 (p) REVERT: F 81 ASN cc_start: 0.8905 (m-40) cc_final: 0.8479 (m110) REVERT: F 108 HIS cc_start: 0.8084 (p-80) cc_final: 0.7879 (p-80) REVERT: F 130 GLN cc_start: 0.8967 (mt0) cc_final: 0.8742 (mp10) REVERT: F 178 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8080 (tm-30) REVERT: G 81 ASN cc_start: 0.8943 (m-40) cc_final: 0.8490 (m110) REVERT: G 108 HIS cc_start: 0.8108 (p-80) cc_final: 0.7903 (p-80) REVERT: G 130 GLN cc_start: 0.8956 (mt0) cc_final: 0.8680 (mp10) REVERT: G 201 ASN cc_start: 0.8212 (m-40) cc_final: 0.7905 (m-40) REVERT: G 238 THR cc_start: 0.7662 (p) cc_final: 0.7383 (p) REVERT: H 81 ASN cc_start: 0.8912 (m-40) cc_final: 0.8485 (m110) REVERT: H 108 HIS cc_start: 0.8056 (p-80) cc_final: 0.7629 (p90) REVERT: H 130 GLN cc_start: 0.8962 (mt0) cc_final: 0.8684 (mp10) REVERT: H 178 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8115 (tm-30) REVERT: H 238 THR cc_start: 0.7642 (p) cc_final: 0.7337 (p) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1559 time to fit residues: 67.4465 Evaluate side-chains 200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN A 216 GLN B 143 ASN B 216 GLN C 143 ASN C 216 GLN D 143 ASN D 216 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.111254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078151 restraints weight = 47646.429| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.85 r_work: 0.3133 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19176 Z= 0.145 Angle : 0.845 8.738 26540 Z= 0.346 Chirality : 0.046 0.273 3436 Planarity : 0.005 0.050 2880 Dihedral : 19.074 118.197 7492 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.52 % Allowed : 7.81 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 2072 helix: 1.95 (0.16), residues: 1048 sheet: -1.86 (0.48), residues: 120 loop : -0.03 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 17 TYR 0.013 0.001 TYR D 145 PHE 0.011 0.001 PHE C 217 TRP 0.014 0.001 TRP G 215 HIS 0.006 0.002 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (19156) covalent geometry : angle 0.84417 / 0.35 (26496) SS BOND : bond 0.00101 / 0.07 ( 16) SS BOND : angle 0.41792 / 0.31 ( 32) hydrogen bonds : bond 0.03975 / 2.62 ( 832) hydrogen bonds : angle 3.59880 / 2.57 ( 2424) link_NAG-ASN : bond 0.00123 / 0.06 ( 4) link_NAG-ASN : angle 2.50918 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8441 (t0) cc_final: 0.8101 (t0) REVERT: A 252 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8538 (t80) REVERT: B 173 ASP cc_start: 0.8463 (t0) cc_final: 0.8123 (t0) REVERT: B 252 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8577 (t80) REVERT: C 21 MET cc_start: 0.8539 (mmm) cc_final: 0.8013 (mmm) REVERT: C 173 ASP cc_start: 0.8467 (t0) cc_final: 0.8119 (t0) REVERT: C 252 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8583 (t80) REVERT: D 104 MET cc_start: 0.8524 (tpp) cc_final: 0.8290 (tpp) REVERT: D 173 ASP cc_start: 0.8427 (t0) cc_final: 0.8076 (t0) REVERT: D 252 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8584 (t80) REVERT: E 81 ASN cc_start: 0.8743 (m-40) cc_final: 0.8455 (m-40) REVERT: E 238 THR cc_start: 0.7707 (p) cc_final: 0.7396 (p) REVERT: F 81 ASN cc_start: 0.8783 (m-40) cc_final: 0.8472 (m-40) REVERT: G 81 ASN cc_start: 0.8726 (m-40) cc_final: 0.8400 (m-40) REVERT: G 201 ASN cc_start: 0.8387 (m-40) cc_final: 0.8146 (m-40) REVERT: G 238 THR cc_start: 0.7698 (p) cc_final: 0.7411 (p) REVERT: H 81 ASN cc_start: 0.8784 (m-40) cc_final: 0.8480 (m-40) REVERT: H 238 THR cc_start: 0.7681 (p) cc_final: 0.7375 (p) outliers start: 26 outliers final: 16 residues processed: 233 average time/residue: 0.1278 time to fit residues: 45.2302 Evaluate side-chains 196 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 120 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 63 optimal weight: 0.4980 chunk 164 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 169 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 81 optimal weight: 30.0000 chunk 179 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.111573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.080220 restraints weight = 48011.565| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.13 r_work: 0.3146 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19176 Z= 0.117 Angle : 0.717 9.220 26540 Z= 0.300 Chirality : 0.042 0.307 3436 Planarity : 0.004 0.048 2880 Dihedral : 14.018 115.304 7492 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.93 % Allowed : 11.71 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 2072 helix: 2.48 (0.16), residues: 1008 sheet: -1.86 (0.47), residues: 120 loop : 0.22 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 157 TYR 0.007 0.001 TYR C 279 PHE 0.010 0.001 PHE D 223 TRP 0.008 0.001 TRP D 178 HIS 0.004 0.001 HIS G 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (19156) covalent geometry : angle 0.71533 / 0.30 (26496) SS BOND : bond 0.00076 / 0.05 ( 16) SS BOND : angle 0.28634 / 0.21 ( 32) hydrogen bonds : bond 0.03611 / 2.39 ( 832) hydrogen bonds : angle 3.44235 / 2.46 ( 2424) link_NAG-ASN : bond 0.00155 / 0.07 ( 4) link_NAG-ASN : angle 2.52520 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8574 (t80) REVERT: B 222 GLN cc_start: 0.8406 (tt0) cc_final: 0.8113 (mm-40) REVERT: B 252 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8580 (t80) REVERT: C 252 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8582 (t80) REVERT: D 104 MET cc_start: 0.8574 (tpp) cc_final: 0.8292 (tpp) REVERT: D 222 GLN cc_start: 0.8407 (tt0) cc_final: 0.8113 (mm-40) REVERT: D 252 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8588 (t80) REVERT: E 81 ASN cc_start: 0.8727 (m-40) cc_final: 0.8389 (m-40) REVERT: F 81 ASN cc_start: 0.8806 (m-40) cc_final: 0.8452 (m-40) REVERT: G 81 ASN cc_start: 0.8744 (m-40) cc_final: 0.8377 (m-40) REVERT: G 130 GLN cc_start: 0.8509 (mp10) cc_final: 0.8170 (mp10) REVERT: G 201 ASN cc_start: 0.8536 (m-40) cc_final: 0.8326 (m-40) REVERT: H 81 ASN cc_start: 0.8750 (m-40) cc_final: 0.8404 (m-40) outliers start: 16 outliers final: 8 residues processed: 210 average time/residue: 0.1270 time to fit residues: 41.5039 Evaluate side-chains 188 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 6 optimal weight: 0.8980 chunk 185 optimal weight: 0.4980 chunk 164 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 chunk 191 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 204 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 127 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 172 ASN B 172 ASN C 172 ASN D 172 ASN D 216 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.108247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076419 restraints weight = 48415.640| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.04 r_work: 0.3061 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19176 Z= 0.188 Angle : 0.722 9.811 26540 Z= 0.316 Chirality : 0.042 0.292 3436 Planarity : 0.004 0.046 2880 Dihedral : 11.526 118.433 7492 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.10 % Allowed : 11.95 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 2072 helix: 1.99 (0.16), residues: 1044 sheet: -1.88 (0.46), residues: 120 loop : 0.14 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 17 TYR 0.013 0.001 TYR A 290 PHE 0.015 0.001 PHE A 33 TRP 0.014 0.001 TRP D 178 HIS 0.002 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (19156) covalent geometry : angle 0.72047 / 0.32 (26496) SS BOND : bond 0.00073 / 0.05 ( 16) SS BOND : angle 0.27465 / 0.19 ( 32) hydrogen bonds : bond 0.04642 / 3.06 ( 832) hydrogen bonds : angle 3.65710 / 2.61 ( 2424) link_NAG-ASN : bond 0.00085 / 0.04 ( 4) link_NAG-ASN : angle 2.83722 / 1.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8924 (mmm) cc_final: 0.8687 (mmm) REVERT: A 173 ASP cc_start: 0.8563 (t0) cc_final: 0.7883 (p0) REVERT: A 180 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8186 (mt-10) REVERT: A 252 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8690 (t80) REVERT: B 173 ASP cc_start: 0.8530 (t0) cc_final: 0.7807 (p0) REVERT: B 180 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8173 (mt-10) REVERT: B 252 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8685 (t80) REVERT: C 173 ASP cc_start: 0.8561 (t0) cc_final: 0.7886 (p0) REVERT: C 180 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8188 (mt-10) REVERT: C 252 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8687 (t80) REVERT: D 173 ASP cc_start: 0.8564 (t0) cc_final: 0.7891 (p0) REVERT: D 180 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8169 (mt-10) REVERT: D 252 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8683 (t80) REVERT: E 81 ASN cc_start: 0.8671 (m-40) cc_final: 0.8351 (m-40) REVERT: E 227 GLU cc_start: 0.9681 (tt0) cc_final: 0.9309 (tm-30) REVERT: E 238 THR cc_start: 0.7748 (p) cc_final: 0.7398 (p) REVERT: F 81 ASN cc_start: 0.8710 (m-40) cc_final: 0.8393 (m-40) REVERT: F 159 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8963 (tp30) REVERT: F 227 GLU cc_start: 0.9680 (tt0) cc_final: 0.9291 (tm-30) REVERT: G 81 ASN cc_start: 0.8679 (m-40) cc_final: 0.8355 (m-40) REVERT: G 130 GLN cc_start: 0.8369 (mp10) cc_final: 0.8066 (mp10) REVERT: G 201 ASN cc_start: 0.8548 (m-40) cc_final: 0.8329 (m-40) REVERT: G 227 GLU cc_start: 0.9698 (tt0) cc_final: 0.9299 (tm-30) REVERT: G 238 THR cc_start: 0.7752 (p) cc_final: 0.7405 (p) REVERT: H 81 ASN cc_start: 0.8679 (m-40) cc_final: 0.8353 (m-40) REVERT: H 227 GLU cc_start: 0.9667 (tt0) cc_final: 0.9268 (tm-30) REVERT: H 238 THR cc_start: 0.7791 (p) cc_final: 0.7439 (p) outliers start: 36 outliers final: 21 residues processed: 224 average time/residue: 0.1156 time to fit residues: 40.4438 Evaluate side-chains 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 57 optimal weight: 5.9990 chunk 198 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN B 172 ASN B 216 GLN C 172 ASN C 216 GLN D 172 ASN D 216 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.109492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.077986 restraints weight = 47980.761| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.80 r_work: 0.3105 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19176 Z= 0.124 Angle : 0.631 9.746 26540 Z= 0.281 Chirality : 0.039 0.315 3436 Planarity : 0.004 0.046 2880 Dihedral : 10.275 114.104 7492 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.75 % Allowed : 13.11 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.19), residues: 2072 helix: 2.21 (0.16), residues: 1044 sheet: -1.75 (0.47), residues: 120 loop : 0.18 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 17 TYR 0.010 0.001 TYR D 290 PHE 0.007 0.001 PHE A 148 TRP 0.012 0.001 TRP D 100 HIS 0.002 0.001 HIS G 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (19156) covalent geometry : angle 0.62911 / 0.28 (26496) SS BOND : bond 0.00067 / 0.05 ( 16) SS BOND : angle 0.23993 / 0.17 ( 32) hydrogen bonds : bond 0.03938 / 2.60 ( 832) hydrogen bonds : angle 3.45988 / 2.47 ( 2424) link_NAG-ASN : bond 0.00053 / 0.02 ( 4) link_NAG-ASN : angle 2.81153 / 1.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7543 (mmm) cc_final: 0.7156 (mmp) REVERT: A 252 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8671 (t80) REVERT: B 94 MET cc_start: 0.7565 (mmm) cc_final: 0.7176 (mmp) REVERT: D 104 MET cc_start: 0.8702 (tpp) cc_final: 0.8420 (tpp) REVERT: E 81 ASN cc_start: 0.8698 (m-40) cc_final: 0.8367 (m-40) REVERT: E 130 GLN cc_start: 0.8600 (mp10) cc_final: 0.8204 (mp10) REVERT: E 227 GLU cc_start: 0.9693 (tt0) cc_final: 0.9322 (tm-30) REVERT: E 238 THR cc_start: 0.7757 (p) cc_final: 0.7405 (p) REVERT: F 81 ASN cc_start: 0.8768 (m-40) cc_final: 0.8432 (m-40) REVERT: F 227 GLU cc_start: 0.9694 (tt0) cc_final: 0.9314 (tm-30) REVERT: G 81 ASN cc_start: 0.8728 (m-40) cc_final: 0.8375 (m-40) REVERT: G 130 GLN cc_start: 0.8482 (mp10) cc_final: 0.8205 (mp10) REVERT: G 201 ASN cc_start: 0.8474 (m-40) cc_final: 0.8262 (m-40) REVERT: G 227 GLU cc_start: 0.9734 (tt0) cc_final: 0.9341 (tm-30) REVERT: G 238 THR cc_start: 0.7681 (p) cc_final: 0.7321 (p) REVERT: H 81 ASN cc_start: 0.8705 (m-40) cc_final: 0.8375 (m-40) REVERT: H 130 GLN cc_start: 0.8594 (mp10) cc_final: 0.8196 (mp10) REVERT: H 227 GLU cc_start: 0.9678 (tt0) cc_final: 0.9307 (tm-30) REVERT: H 238 THR cc_start: 0.7736 (p) cc_final: 0.7384 (p) outliers start: 30 outliers final: 15 residues processed: 203 average time/residue: 0.1165 time to fit residues: 37.6176 Evaluate side-chains 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 81 optimal weight: 30.0000 chunk 127 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 112 optimal weight: 0.0070 chunk 14 optimal weight: 9.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN B 19 GLN B 216 GLN C 172 ASN D 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.073148 restraints weight = 47791.768| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.74 r_work: 0.3009 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19176 Z= 0.249 Angle : 0.712 10.193 26540 Z= 0.329 Chirality : 0.041 0.223 3436 Planarity : 0.004 0.045 2880 Dihedral : 9.951 103.275 7492 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.56 % Allowed : 12.06 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 2072 helix: 1.86 (0.16), residues: 1044 sheet: -1.80 (0.46), residues: 120 loop : 0.20 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 17 TYR 0.014 0.002 TYR C 290 PHE 0.018 0.002 PHE A 33 TRP 0.013 0.001 TRP B 178 HIS 0.002 0.001 HIS G 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (19156) covalent geometry : angle 0.70842 / 0.33 (26496) SS BOND : bond 0.00147 / 0.09 ( 16) SS BOND : angle 0.32939 / 0.23 ( 32) hydrogen bonds : bond 0.05307 / 3.50 ( 832) hydrogen bonds : angle 3.84801 / 2.75 ( 2424) link_NAG-ASN : bond 0.00260 / 0.13 ( 4) link_NAG-ASN : angle 3.51043 / 1.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9043 (mmt) cc_final: 0.8777 (mmt) REVERT: A 173 ASP cc_start: 0.8355 (t0) cc_final: 0.7558 (p0) REVERT: A 180 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8510 (mt-10) REVERT: A 222 GLN cc_start: 0.8723 (tt0) cc_final: 0.8514 (tt0) REVERT: A 252 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8726 (t80) REVERT: A 282 MET cc_start: 0.9281 (tpt) cc_final: 0.9067 (tpp) REVERT: B 30 MET cc_start: 0.9088 (mmt) cc_final: 0.8835 (mmt) REVERT: B 173 ASP cc_start: 0.8336 (t0) cc_final: 0.7532 (p0) REVERT: B 180 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8549 (mt-10) REVERT: B 282 MET cc_start: 0.9245 (tpt) cc_final: 0.9040 (tpp) REVERT: C 30 MET cc_start: 0.9043 (mmt) cc_final: 0.8793 (mmt) REVERT: C 173 ASP cc_start: 0.8342 (t0) cc_final: 0.7551 (p0) REVERT: C 180 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8509 (mt-10) REVERT: C 222 GLN cc_start: 0.8726 (tt0) cc_final: 0.8517 (tt0) REVERT: C 282 MET cc_start: 0.9276 (tpt) cc_final: 0.9064 (tpp) REVERT: D 30 MET cc_start: 0.9058 (mmt) cc_final: 0.8807 (mmt) REVERT: D 173 ASP cc_start: 0.8352 (t0) cc_final: 0.7543 (p0) REVERT: D 180 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8487 (mt-10) REVERT: E 81 ASN cc_start: 0.8670 (m-40) cc_final: 0.8331 (m-40) REVERT: E 130 GLN cc_start: 0.8680 (mp10) cc_final: 0.8268 (mp10) REVERT: E 227 GLU cc_start: 0.9692 (tt0) cc_final: 0.9305 (tm-30) REVERT: E 238 THR cc_start: 0.7903 (p) cc_final: 0.7537 (p) REVERT: F 81 ASN cc_start: 0.8734 (m-40) cc_final: 0.8408 (m-40) REVERT: F 227 GLU cc_start: 0.9690 (tt0) cc_final: 0.9282 (tm-30) REVERT: G 81 ASN cc_start: 0.8708 (m-40) cc_final: 0.8424 (m-40) REVERT: G 227 GLU cc_start: 0.9710 (tt0) cc_final: 0.9287 (tm-30) REVERT: G 238 THR cc_start: 0.7821 (p) cc_final: 0.7452 (p) REVERT: H 81 ASN cc_start: 0.8720 (m-40) cc_final: 0.8366 (m-40) REVERT: H 130 GLN cc_start: 0.8638 (mp10) cc_final: 0.8206 (mp10) REVERT: H 227 GLU cc_start: 0.9691 (tt0) cc_final: 0.9291 (tm-30) REVERT: H 238 THR cc_start: 0.7839 (p) cc_final: 0.7471 (p) outliers start: 44 outliers final: 30 residues processed: 230 average time/residue: 0.1206 time to fit residues: 43.1706 Evaluate side-chains 220 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 187 optimal weight: 0.1980 chunk 115 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN C 19 GLN C 216 GLN D 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.109042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.075607 restraints weight = 48246.778| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.72 r_work: 0.3104 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19176 Z= 0.131 Angle : 0.624 10.522 26540 Z= 0.290 Chirality : 0.037 0.176 3436 Planarity : 0.004 0.046 2880 Dihedral : 9.538 110.589 7492 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.92 % Allowed : 13.93 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.19), residues: 2072 helix: 2.08 (0.16), residues: 1044 sheet: -1.73 (0.47), residues: 120 loop : 0.20 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.012 0.001 TYR D 290 PHE 0.007 0.001 PHE C 217 TRP 0.010 0.001 TRP D 275 HIS 0.002 0.001 HIS G 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (19156) covalent geometry : angle 0.62002 / 0.29 (26496) SS BOND : bond 0.00093 / 0.07 ( 16) SS BOND : angle 0.30426 / 0.20 ( 32) hydrogen bonds : bond 0.04313 / 2.85 ( 832) hydrogen bonds : angle 3.55571 / 2.54 ( 2424) link_NAG-ASN : bond 0.00103 / 0.05 ( 4) link_NAG-ASN : angle 3.53510 / 2.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9025 (mmt) cc_final: 0.8713 (mmt) REVERT: A 94 MET cc_start: 0.7564 (mmm) cc_final: 0.7159 (mmp) REVERT: A 173 ASP cc_start: 0.8264 (t0) cc_final: 0.7285 (p0) REVERT: A 180 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8482 (mt-10) REVERT: B 30 MET cc_start: 0.9004 (mmt) cc_final: 0.8715 (mmt) REVERT: B 94 MET cc_start: 0.7585 (mmm) cc_final: 0.7188 (mmp) REVERT: B 173 ASP cc_start: 0.8254 (t0) cc_final: 0.7279 (p0) REVERT: B 180 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8466 (mt-10) REVERT: C 21 MET cc_start: 0.8900 (mmm) cc_final: 0.8336 (mmp) REVERT: C 30 MET cc_start: 0.9013 (mmt) cc_final: 0.8712 (mmt) REVERT: C 94 MET cc_start: 0.7621 (mmm) cc_final: 0.7238 (mmp) REVERT: C 173 ASP cc_start: 0.8259 (t0) cc_final: 0.7288 (p0) REVERT: C 180 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8467 (mt-10) REVERT: D 30 MET cc_start: 0.9009 (mmt) cc_final: 0.8705 (mmt) REVERT: D 94 MET cc_start: 0.7563 (mmm) cc_final: 0.7156 (mmp) REVERT: D 173 ASP cc_start: 0.8263 (t0) cc_final: 0.7299 (p0) REVERT: D 180 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8421 (mt-10) REVERT: E 81 ASN cc_start: 0.8730 (m-40) cc_final: 0.8364 (m-40) REVERT: E 130 GLN cc_start: 0.8644 (mp10) cc_final: 0.8273 (mp10) REVERT: E 227 GLU cc_start: 0.9696 (tt0) cc_final: 0.9291 (tm-30) REVERT: E 238 THR cc_start: 0.7786 (p) cc_final: 0.7441 (p) REVERT: F 81 ASN cc_start: 0.8714 (m-40) cc_final: 0.8405 (m-40) REVERT: F 227 GLU cc_start: 0.9704 (tt0) cc_final: 0.9299 (tm-30) REVERT: G 81 ASN cc_start: 0.8749 (m-40) cc_final: 0.8428 (m-40) REVERT: G 201 ASN cc_start: 0.8620 (m-40) cc_final: 0.8191 (m-40) REVERT: G 227 GLU cc_start: 0.9722 (tt0) cc_final: 0.9309 (tm-30) REVERT: G 238 THR cc_start: 0.7705 (p) cc_final: 0.7351 (p) REVERT: H 81 ASN cc_start: 0.8720 (m-40) cc_final: 0.8354 (m-40) REVERT: H 130 GLN cc_start: 0.8645 (mp10) cc_final: 0.8302 (mp10) REVERT: H 227 GLU cc_start: 0.9707 (tt0) cc_final: 0.9329 (tm-30) REVERT: H 238 THR cc_start: 0.7744 (p) cc_final: 0.7393 (p) outliers start: 33 outliers final: 22 residues processed: 214 average time/residue: 0.1236 time to fit residues: 41.3055 Evaluate side-chains 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 14 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.109275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.075913 restraints weight = 47994.895| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.71 r_work: 0.3116 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19176 Z= 0.133 Angle : 0.604 9.482 26540 Z= 0.284 Chirality : 0.036 0.145 3436 Planarity : 0.004 0.046 2880 Dihedral : 9.277 111.382 7492 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.86 % Allowed : 14.45 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 2072 helix: 2.13 (0.16), residues: 1044 sheet: -1.71 (0.47), residues: 120 loop : 0.21 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 157 TYR 0.009 0.001 TYR B 279 PHE 0.010 0.001 PHE A 252 TRP 0.009 0.001 TRP B 178 HIS 0.002 0.001 HIS G 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (19156) covalent geometry : angle 0.59879 / 0.28 (26496) SS BOND : bond 0.00088 / 0.07 ( 16) SS BOND : angle 0.29347 / 0.20 ( 32) hydrogen bonds : bond 0.04093 / 2.70 ( 832) hydrogen bonds : angle 3.50047 / 2.50 ( 2424) link_NAG-ASN : bond 0.00149 / 0.07 ( 4) link_NAG-ASN : angle 3.86472 / 2.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9015 (mmt) cc_final: 0.8697 (mmt) REVERT: A 94 MET cc_start: 0.7722 (mmm) cc_final: 0.7251 (mmp) REVERT: A 173 ASP cc_start: 0.8233 (t0) cc_final: 0.7228 (p0) REVERT: A 180 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8446 (mt-10) REVERT: B 94 MET cc_start: 0.7765 (mmm) cc_final: 0.7307 (mmp) REVERT: B 173 ASP cc_start: 0.8223 (t0) cc_final: 0.7226 (p0) REVERT: B 180 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8398 (mt-10) REVERT: C 30 MET cc_start: 0.9004 (mmt) cc_final: 0.8694 (mmt) REVERT: C 94 MET cc_start: 0.7772 (mmm) cc_final: 0.7316 (mmp) REVERT: C 173 ASP cc_start: 0.8228 (t0) cc_final: 0.7231 (p0) REVERT: D 30 MET cc_start: 0.8997 (mmt) cc_final: 0.8684 (mmt) REVERT: D 94 MET cc_start: 0.7726 (mmm) cc_final: 0.7254 (mmp) REVERT: D 173 ASP cc_start: 0.8230 (t0) cc_final: 0.7235 (p0) REVERT: D 180 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8030 (mt-10) REVERT: E 81 ASN cc_start: 0.8758 (m-40) cc_final: 0.8393 (m-40) REVERT: E 130 GLN cc_start: 0.8625 (mp10) cc_final: 0.8271 (mp10) REVERT: E 227 GLU cc_start: 0.9693 (tt0) cc_final: 0.9284 (tm-30) REVERT: E 238 THR cc_start: 0.7799 (p) cc_final: 0.7443 (p) REVERT: F 81 ASN cc_start: 0.8744 (m-40) cc_final: 0.8430 (m-40) REVERT: F 227 GLU cc_start: 0.9704 (tt0) cc_final: 0.9294 (tm-30) REVERT: G 81 ASN cc_start: 0.8752 (m-40) cc_final: 0.8442 (m-40) REVERT: G 132 GLU cc_start: 0.8514 (pm20) cc_final: 0.8311 (mm-30) REVERT: G 201 ASN cc_start: 0.8552 (m-40) cc_final: 0.8151 (m-40) REVERT: G 227 GLU cc_start: 0.9722 (tt0) cc_final: 0.9295 (tm-30) REVERT: G 238 THR cc_start: 0.7720 (p) cc_final: 0.7473 (p) REVERT: H 81 ASN cc_start: 0.8744 (m-40) cc_final: 0.8375 (m-40) REVERT: H 130 GLN cc_start: 0.8626 (mp10) cc_final: 0.8271 (mp10) REVERT: H 227 GLU cc_start: 0.9703 (tt0) cc_final: 0.9315 (tm-30) REVERT: H 238 THR cc_start: 0.7761 (p) cc_final: 0.7519 (p) outliers start: 32 outliers final: 26 residues processed: 208 average time/residue: 0.1376 time to fit residues: 44.8954 Evaluate side-chains 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 129 optimal weight: 0.0010 chunk 113 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.110667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.077690 restraints weight = 48084.542| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.71 r_work: 0.3156 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19176 Z= 0.104 Angle : 0.574 12.765 26540 Z= 0.272 Chirality : 0.034 0.124 3436 Planarity : 0.004 0.046 2880 Dihedral : 8.967 113.838 7492 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.05 % Allowed : 14.98 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 2072 helix: 2.55 (0.16), residues: 1008 sheet: -1.66 (0.47), residues: 120 loop : 0.36 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 157 TYR 0.008 0.001 TYR B 279 PHE 0.007 0.001 PHE B 223 TRP 0.010 0.001 TRP D 23 HIS 0.002 0.000 HIS F 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (19156) covalent geometry : angle 0.56873 / 0.27 (26496) SS BOND : bond 0.00077 / 0.06 ( 16) SS BOND : angle 0.32982 / 0.23 ( 32) hydrogen bonds : bond 0.03546 / 2.35 ( 832) hydrogen bonds : angle 3.38822 / 2.42 ( 2424) link_NAG-ASN : bond 0.00106 / 0.05 ( 4) link_NAG-ASN : angle 3.66881 / 2.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7635 (mmm) cc_final: 0.7291 (mmp) REVERT: B 94 MET cc_start: 0.7652 (mmm) cc_final: 0.7307 (mmp) REVERT: C 94 MET cc_start: 0.7681 (mmm) cc_final: 0.7354 (mmp) REVERT: D 94 MET cc_start: 0.7631 (mmm) cc_final: 0.7284 (mmp) REVERT: E 81 ASN cc_start: 0.8791 (m-40) cc_final: 0.8451 (m-40) REVERT: E 111 HIS cc_start: 0.9031 (t-90) cc_final: 0.8674 (t-90) REVERT: E 130 GLN cc_start: 0.8576 (mp10) cc_final: 0.8226 (mp10) REVERT: E 227 GLU cc_start: 0.9703 (tt0) cc_final: 0.9292 (tm-30) REVERT: E 238 THR cc_start: 0.7744 (p) cc_final: 0.7486 (p) REVERT: F 81 ASN cc_start: 0.8808 (m-40) cc_final: 0.8478 (m-40) REVERT: F 111 HIS cc_start: 0.9026 (t-90) cc_final: 0.8663 (t-90) REVERT: F 130 GLN cc_start: 0.8528 (mp10) cc_final: 0.7928 (mp10) REVERT: F 178 GLU cc_start: 0.8264 (mp0) cc_final: 0.7940 (mp0) REVERT: F 227 GLU cc_start: 0.9713 (tt0) cc_final: 0.9301 (tm-30) REVERT: G 81 ASN cc_start: 0.8775 (m-40) cc_final: 0.8439 (m-40) REVERT: G 111 HIS cc_start: 0.9032 (t-90) cc_final: 0.8668 (t-90) REVERT: G 201 ASN cc_start: 0.8508 (m-40) cc_final: 0.8088 (m-40) REVERT: G 227 GLU cc_start: 0.9729 (tt0) cc_final: 0.9302 (tm-30) REVERT: G 238 THR cc_start: 0.7665 (p) cc_final: 0.7396 (p) REVERT: H 81 ASN cc_start: 0.8779 (m-40) cc_final: 0.8443 (m-40) REVERT: H 111 HIS cc_start: 0.9020 (t-90) cc_final: 0.8680 (t-90) REVERT: H 130 GLN cc_start: 0.8517 (mp10) cc_final: 0.8164 (mp10) REVERT: H 178 GLU cc_start: 0.8267 (mp0) cc_final: 0.7958 (mp0) REVERT: H 227 GLU cc_start: 0.9715 (tt0) cc_final: 0.9320 (tm-30) REVERT: H 238 THR cc_start: 0.7721 (p) cc_final: 0.7455 (p) outliers start: 18 outliers final: 18 residues processed: 196 average time/residue: 0.1218 time to fit residues: 38.0881 Evaluate side-chains 193 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 180 optimal weight: 3.9990 chunk 151 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 206 optimal weight: 0.0000 chunk 112 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.110128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.076981 restraints weight = 48076.394| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.73 r_work: 0.3145 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19176 Z= 0.112 Angle : 0.572 13.076 26540 Z= 0.273 Chirality : 0.035 0.139 3436 Planarity : 0.004 0.046 2880 Dihedral : 8.885 113.572 7492 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.17 % Allowed : 15.33 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.19), residues: 2072 helix: 2.50 (0.16), residues: 1008 sheet: -1.68 (0.47), residues: 120 loop : 0.37 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 157 TYR 0.009 0.001 TYR B 279 PHE 0.012 0.001 PHE D 303 TRP 0.009 0.001 TRP B 178 HIS 0.002 0.001 HIS F 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (19156) covalent geometry : angle 0.56715 / 0.27 (26496) SS BOND : bond 0.00062 / 0.05 ( 16) SS BOND : angle 0.28984 / 0.20 ( 32) hydrogen bonds : bond 0.03640 / 2.41 ( 832) hydrogen bonds : angle 3.38084 / 2.41 ( 2424) link_NAG-ASN : bond 0.00109 / 0.05 ( 4) link_NAG-ASN : angle 3.54190 / 2.05 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7668 (mmm) cc_final: 0.7315 (mmp) REVERT: A 104 MET cc_start: 0.8459 (ttm) cc_final: 0.8257 (ttm) REVERT: A 173 ASP cc_start: 0.8058 (t0) cc_final: 0.7245 (p0) REVERT: B 94 MET cc_start: 0.7686 (mmm) cc_final: 0.7334 (mmp) REVERT: B 173 ASP cc_start: 0.8050 (t0) cc_final: 0.7229 (p0) REVERT: C 94 MET cc_start: 0.7699 (mmm) cc_final: 0.7363 (mmp) REVERT: C 173 ASP cc_start: 0.8051 (t0) cc_final: 0.7243 (p0) REVERT: D 94 MET cc_start: 0.7666 (mmm) cc_final: 0.7311 (mmp) REVERT: D 173 ASP cc_start: 0.8046 (t0) cc_final: 0.7244 (p0) REVERT: E 81 ASN cc_start: 0.8804 (m-40) cc_final: 0.8459 (m-40) REVERT: E 111 HIS cc_start: 0.9030 (t-90) cc_final: 0.8673 (t-90) REVERT: E 130 GLN cc_start: 0.8602 (mp10) cc_final: 0.8223 (mp10) REVERT: E 178 GLU cc_start: 0.8265 (mp0) cc_final: 0.7954 (mp0) REVERT: E 227 GLU cc_start: 0.9693 (tt0) cc_final: 0.9300 (tm-30) REVERT: E 238 THR cc_start: 0.7774 (p) cc_final: 0.7401 (p) REVERT: F 81 ASN cc_start: 0.8796 (m-40) cc_final: 0.8460 (m-40) REVERT: F 111 HIS cc_start: 0.9029 (t-90) cc_final: 0.8659 (t-90) REVERT: F 130 GLN cc_start: 0.8230 (mp10) cc_final: 0.7839 (mp10) REVERT: F 178 GLU cc_start: 0.8187 (mp0) cc_final: 0.7764 (mp0) REVERT: F 227 GLU cc_start: 0.9719 (tt0) cc_final: 0.9305 (tm-30) REVERT: G 81 ASN cc_start: 0.8759 (m-40) cc_final: 0.8425 (m-40) REVERT: G 111 HIS cc_start: 0.9036 (t-90) cc_final: 0.8669 (t-90) REVERT: G 201 ASN cc_start: 0.8577 (m-40) cc_final: 0.8300 (m-40) REVERT: G 227 GLU cc_start: 0.9734 (tt0) cc_final: 0.9303 (tm-30) REVERT: G 238 THR cc_start: 0.7696 (p) cc_final: 0.7422 (p) REVERT: H 81 ASN cc_start: 0.8778 (m-40) cc_final: 0.8432 (m-40) REVERT: H 111 HIS cc_start: 0.9021 (t-90) cc_final: 0.8667 (t-90) REVERT: H 130 GLN cc_start: 0.8592 (mp10) cc_final: 0.8204 (mp10) REVERT: H 178 GLU cc_start: 0.8208 (mp0) cc_final: 0.7791 (mp0) REVERT: H 227 GLU cc_start: 0.9704 (tt0) cc_final: 0.9308 (tm-30) REVERT: H 238 THR cc_start: 0.7750 (p) cc_final: 0.7479 (p) outliers start: 20 outliers final: 14 residues processed: 185 average time/residue: 0.1288 time to fit residues: 37.8585 Evaluate side-chains 186 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 161 optimal weight: 30.0000 chunk 169 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 120 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 119 optimal weight: 0.2980 chunk 185 optimal weight: 10.0000 chunk 26 optimal weight: 0.0470 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.110757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.077975 restraints weight = 48356.840| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.72 r_work: 0.3169 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19176 Z= 0.103 Angle : 0.554 11.974 26540 Z= 0.268 Chirality : 0.034 0.142 3436 Planarity : 0.004 0.049 2880 Dihedral : 8.723 114.271 7492 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.99 % Allowed : 15.62 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.19), residues: 2072 helix: 2.54 (0.16), residues: 1008 sheet: -1.69 (0.47), residues: 120 loop : 0.34 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 157 TYR 0.009 0.001 TYR B 279 PHE 0.013 0.001 PHE D 303 TRP 0.009 0.001 TRP D 100 HIS 0.002 0.001 HIS F 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (19156) covalent geometry : angle 0.54984 / 0.27 (26496) SS BOND : bond 0.00068 / 0.05 ( 16) SS BOND : angle 0.29186 / 0.21 ( 32) hydrogen bonds : bond 0.03431 / 2.26 ( 832) hydrogen bonds : angle 3.36427 / 2.40 ( 2424) link_NAG-ASN : bond 0.00112 / 0.05 ( 4) link_NAG-ASN : angle 3.30045 / 1.90 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4034.54 seconds wall clock time: 70 minutes 0.37 seconds (4200.37 seconds total)