Starting phenix.real_space_refine on Thu Sep 18 17:09:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vav_43106/09_2025/8vav_43106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vav_43106/09_2025/8vav_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_43106/09_2025/8vav_43106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vav_43106/09_2025/8vav_43106.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vav_43106/09_2025/8vav_43106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vav_43106/09_2025/8vav_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-2.0-5805/lib/python3.9/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, 571 Unusual residues: {' K': 4, 'AJP': 8, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 18} Link IDs: {None: 17} 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: 5.39, per 1000 atoms: 0.29 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: 1.90 Conformation dependent library (CDL) restraints added in 754.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.58 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: 3.04 Time building geometry restraints manager: 2.43 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.870 Find NCS groups from input model: 0.420 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: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 aren 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 covalent geometry : bond 0.00531 (19156) covalent geometry : angle 0.79891 (26496) SS BOND : bond 0.00259 ( 16) SS BOND : angle 0.59640 ( 32) hydrogen bonds : bond 0.13143 ( 832) hydrogen bonds : angle 4.50767 ( 2424) link_NAG-ASN : bond 0.00364 ( 4) link_NAG-ASN : angle 2.86784 ( 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 : 0.677 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: 0.1729 time to fit residues: 74.0387 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 : 0.769 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 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 = 0.3974 r_free = 0.3974 target = 0.111284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.078073 restraints weight = 47716.603| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.82 r_work: 0.3125 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19176 Z= 0.145 Angle : 0.835 8.756 26540 Z= 0.343 Chirality : 0.045 0.286 3436 Planarity : 0.005 0.051 2880 Dihedral : 18.580 117.728 7492 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.52 % Allowed : 7.69 % Favored : 90.79 % 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 aren not related in a simple way. whole: 1.22 (0.19), residues: 2072 helix: 1.97 (0.16), residues: 1048 sheet: -1.86 (0.48), residues: 120 loop : -0.14 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 17 TYR 0.011 0.001 TYR B 145 PHE 0.010 0.001 PHE C 217 TRP 0.018 0.001 TRP G 215 HIS 0.007 0.002 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00317 (19156) covalent geometry : angle 0.83397 (26496) SS BOND : bond 0.00093 ( 16) SS BOND : angle 0.44099 ( 32) hydrogen bonds : bond 0.04072 ( 832) hydrogen bonds : angle 3.59146 ( 2424) link_NAG-ASN : bond 0.00145 ( 4) link_NAG-ASN : angle 2.48374 ( 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 : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8490 (t0) cc_final: 0.8150 (t0) REVERT: A 252 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8576 (t80) REVERT: B 173 ASP cc_start: 0.8480 (t0) cc_final: 0.8140 (t0) REVERT: B 252 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8601 (t80) REVERT: C 173 ASP cc_start: 0.8490 (t0) cc_final: 0.8148 (t0) REVERT: C 252 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8573 (t80) REVERT: D 104 MET cc_start: 0.8515 (tpp) cc_final: 0.8292 (tpp) REVERT: D 173 ASP cc_start: 0.8490 (t0) cc_final: 0.8152 (t0) REVERT: D 252 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8582 (t80) REVERT: E 81 ASN cc_start: 0.8858 (m-40) cc_final: 0.8491 (m-40) REVERT: E 238 THR cc_start: 0.7713 (p) cc_final: 0.7401 (p) REVERT: F 81 ASN cc_start: 0.8766 (m-40) cc_final: 0.8419 (m-40) REVERT: G 81 ASN cc_start: 0.8760 (m-40) cc_final: 0.8431 (m-40) REVERT: G 201 ASN cc_start: 0.8390 (m-40) cc_final: 0.8147 (m-40) REVERT: G 238 THR cc_start: 0.7665 (p) cc_final: 0.7364 (p) REVERT: H 81 ASN cc_start: 0.8765 (m-40) cc_final: 0.8426 (m-40) REVERT: H 238 THR cc_start: 0.7681 (p) cc_final: 0.7374 (p) outliers start: 26 outliers final: 16 residues processed: 233 average time/residue: 0.1575 time to fit residues: 55.0002 Evaluate side-chains 194 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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: 40.0000 chunk 136 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 169 optimal weight: 0.0020 chunk 15 optimal weight: 0.7980 chunk 81 optimal weight: 30.0000 chunk 179 optimal weight: 20.0000 overall best weight: 2.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN B 143 ASN B 216 GLN C 143 ASN D 143 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 = 0.3931 r_free = 0.3931 target = 0.108508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076824 restraints weight = 48155.358| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.00 r_work: 0.3064 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19176 Z= 0.186 Angle : 0.764 9.601 26540 Z= 0.327 Chirality : 0.044 0.315 3436 Planarity : 0.004 0.048 2880 Dihedral : 13.767 114.719 7492 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.75 % Allowed : 10.61 % Favored : 87.65 % 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 aren not related in a simple way. whole: 1.29 (0.19), residues: 2072 helix: 2.01 (0.16), residues: 1044 sheet: -1.92 (0.46), residues: 120 loop : -0.04 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 170 TYR 0.010 0.001 TYR D 290 PHE 0.016 0.001 PHE A 33 TRP 0.012 0.001 TRP B 178 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00431 (19156) covalent geometry : angle 0.76212 (26496) SS BOND : bond 0.00087 ( 16) SS BOND : angle 0.30375 ( 32) hydrogen bonds : bond 0.04771 ( 832) hydrogen bonds : angle 3.67304 ( 2424) link_NAG-ASN : bond 0.00101 ( 4) link_NAG-ASN : angle 2.83974 ( 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 244 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8610 (t80) REVERT: A 282 MET cc_start: 0.9351 (tpt) cc_final: 0.9000 (tpp) REVERT: B 252 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8674 (t80) REVERT: B 282 MET cc_start: 0.9342 (tpt) cc_final: 0.8989 (tpp) REVERT: C 252 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8666 (t80) REVERT: C 282 MET cc_start: 0.9345 (tpt) cc_final: 0.8991 (tpp) REVERT: D 252 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8656 (t80) REVERT: D 282 MET cc_start: 0.9329 (tpt) cc_final: 0.8974 (tpp) REVERT: E 81 ASN cc_start: 0.8614 (m-40) cc_final: 0.8320 (m-40) REVERT: E 227 GLU cc_start: 0.9682 (tt0) cc_final: 0.9285 (tm-30) REVERT: E 238 THR cc_start: 0.7798 (p) cc_final: 0.7472 (p) REVERT: F 81 ASN cc_start: 0.8692 (m-40) cc_final: 0.8364 (m-40) REVERT: F 159 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8929 (tp30) REVERT: G 81 ASN cc_start: 0.8623 (m-40) cc_final: 0.8337 (m-40) REVERT: G 201 ASN cc_start: 0.8568 (m-40) cc_final: 0.8302 (m-40) REVERT: G 238 THR cc_start: 0.7719 (p) cc_final: 0.7484 (p) REVERT: H 81 ASN cc_start: 0.8650 (m-40) cc_final: 0.8337 (m-40) REVERT: H 238 THR cc_start: 0.7756 (p) cc_final: 0.7526 (p) outliers start: 30 outliers final: 15 residues processed: 231 average time/residue: 0.1488 time to fit residues: 52.7879 Evaluate side-chains 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 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 109 THR Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 109 THR 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 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 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: 8.9990 chunk 164 optimal weight: 20.0000 chunk 109 optimal weight: 50.0000 chunk 191 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 204 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 171 optimal weight: 0.4980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 172 ASN A 216 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.108814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075529 restraints weight = 48443.104| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.78 r_work: 0.3075 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19176 Z= 0.155 Angle : 0.692 9.714 26540 Z= 0.301 Chirality : 0.041 0.290 3436 Planarity : 0.004 0.047 2880 Dihedral : 11.471 118.600 7492 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.98 % Allowed : 12.24 % Favored : 85.78 % 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 aren not related in a simple way. whole: 1.44 (0.19), residues: 2072 helix: 2.14 (0.16), residues: 1044 sheet: -1.85 (0.47), residues: 120 loop : 0.01 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 17 TYR 0.011 0.001 TYR D 290 PHE 0.009 0.001 PHE D 33 TRP 0.013 0.001 TRP B 178 HIS 0.002 0.001 HIS F 80 Details of bonding type rmsd covalent geometry : bond 0.00361 (19156) covalent geometry : angle 0.68989 (26496) SS BOND : bond 0.00076 ( 16) SS BOND : angle 0.28177 ( 32) hydrogen bonds : bond 0.04297 ( 832) hydrogen bonds : angle 3.57923 ( 2424) link_NAG-ASN : bond 0.00046 ( 4) link_NAG-ASN : angle 2.76601 ( 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 240 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8499 (mmm) cc_final: 0.8205 (mmp) REVERT: A 180 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8506 (mt-10) REVERT: A 252 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8704 (t80) REVERT: A 282 MET cc_start: 0.9309 (tpt) cc_final: 0.9022 (tpp) REVERT: B 21 MET cc_start: 0.8489 (mmm) cc_final: 0.8174 (mmp) REVERT: B 180 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8501 (mt-10) REVERT: B 252 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8679 (t80) REVERT: B 282 MET cc_start: 0.9291 (tpt) cc_final: 0.9002 (tpp) REVERT: C 180 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8471 (mt-10) REVERT: C 252 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8672 (t80) REVERT: C 282 MET cc_start: 0.9299 (tpt) cc_final: 0.9012 (tpp) REVERT: D 104 MET cc_start: 0.8591 (tpp) cc_final: 0.8177 (tpp) REVERT: D 180 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8490 (mt-10) REVERT: D 252 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8677 (t80) REVERT: D 282 MET cc_start: 0.9277 (tpt) cc_final: 0.8989 (tpp) REVERT: E 81 ASN cc_start: 0.8640 (m-40) cc_final: 0.8371 (m-40) REVERT: E 227 GLU cc_start: 0.9689 (tt0) cc_final: 0.9317 (tm-30) REVERT: E 238 THR cc_start: 0.7751 (p) cc_final: 0.7531 (p) REVERT: F 81 ASN cc_start: 0.8715 (m-40) cc_final: 0.8426 (m-40) REVERT: F 227 GLU cc_start: 0.9695 (tt0) cc_final: 0.9312 (tm-30) REVERT: G 81 ASN cc_start: 0.8634 (m-40) cc_final: 0.8376 (m-40) REVERT: G 201 ASN cc_start: 0.8534 (m-40) cc_final: 0.8327 (m-40) REVERT: G 227 GLU cc_start: 0.9705 (tt0) cc_final: 0.9307 (tm-30) REVERT: G 238 THR cc_start: 0.7665 (p) cc_final: 0.7442 (p) REVERT: H 81 ASN cc_start: 0.8672 (m-40) cc_final: 0.8376 (m-40) REVERT: H 227 GLU cc_start: 0.9694 (tt0) cc_final: 0.9314 (tm-30) REVERT: H 238 THR cc_start: 0.7720 (p) cc_final: 0.7507 (p) outliers start: 34 outliers final: 19 residues processed: 222 average time/residue: 0.1441 time to fit residues: 49.4809 Evaluate side-chains 207 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 252 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 103 VAL 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 57 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3937 r_free = 0.3937 target = 0.109263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.077700 restraints weight = 48082.115| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.80 r_work: 0.3095 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2819 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= 0.123 Angle : 0.623 9.756 26540 Z= 0.280 Chirality : 0.039 0.316 3436 Planarity : 0.004 0.047 2880 Dihedral : 10.150 112.796 7492 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.92 % Allowed : 12.70 % 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 aren not related in a simple way. whole: 1.86 (0.19), residues: 2072 helix: 2.59 (0.16), residues: 1004 sheet: -1.77 (0.47), residues: 120 loop : 0.22 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 17 TYR 0.009 0.001 TYR A 290 PHE 0.006 0.001 PHE B 242 TRP 0.009 0.001 TRP B 178 HIS 0.002 0.001 HIS E 252 Details of bonding type rmsd covalent geometry : bond 0.00280 (19156) covalent geometry : angle 0.62034 (26496) SS BOND : bond 0.00069 ( 16) SS BOND : angle 0.28656 ( 32) hydrogen bonds : bond 0.03923 ( 832) hydrogen bonds : angle 3.42560 ( 2424) link_NAG-ASN : bond 0.00063 ( 4) link_NAG-ASN : angle 2.82795 ( 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 228 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7607 (mmm) cc_final: 0.7219 (mmp) REVERT: A 173 ASP cc_start: 0.8196 (t0) cc_final: 0.7278 (p0) REVERT: A 282 MET cc_start: 0.9247 (tpt) cc_final: 0.8999 (tpp) REVERT: B 94 MET cc_start: 0.7628 (mmm) cc_final: 0.7247 (mmp) REVERT: B 173 ASP cc_start: 0.8204 (t0) cc_final: 0.7271 (p0) REVERT: B 282 MET cc_start: 0.9226 (tpt) cc_final: 0.8976 (tpp) REVERT: C 94 MET cc_start: 0.7630 (mmm) cc_final: 0.7243 (mmp) REVERT: C 173 ASP cc_start: 0.8190 (t0) cc_final: 0.7289 (p0) REVERT: C 282 MET cc_start: 0.9240 (tpt) cc_final: 0.8991 (tpp) REVERT: D 94 MET cc_start: 0.7597 (mmm) cc_final: 0.7150 (mmp) REVERT: D 104 MET cc_start: 0.8634 (tpp) cc_final: 0.8328 (tpp) REVERT: D 173 ASP cc_start: 0.8200 (t0) cc_final: 0.7289 (p0) REVERT: D 282 MET cc_start: 0.9227 (tpt) cc_final: 0.8979 (tpp) REVERT: E 81 ASN cc_start: 0.8696 (m-40) cc_final: 0.8413 (m-40) REVERT: E 159 GLU cc_start: 0.9253 (tp30) cc_final: 0.9026 (tm-30) REVERT: E 227 GLU cc_start: 0.9695 (tt0) cc_final: 0.9321 (tm-30) REVERT: E 238 THR cc_start: 0.7733 (p) cc_final: 0.7522 (p) REVERT: F 81 ASN cc_start: 0.8732 (m-40) cc_final: 0.8429 (m-40) REVERT: F 130 GLN cc_start: 0.8671 (mp10) cc_final: 0.8264 (mp10) REVERT: F 227 GLU cc_start: 0.9695 (tt0) cc_final: 0.9315 (tm-30) REVERT: G 81 ASN cc_start: 0.8701 (m-40) cc_final: 0.8453 (m-40) REVERT: G 201 ASN cc_start: 0.8513 (m-40) cc_final: 0.8286 (m-40) REVERT: G 227 GLU cc_start: 0.9726 (tt0) cc_final: 0.9314 (tm-30) REVERT: H 81 ASN cc_start: 0.8704 (m-40) cc_final: 0.8389 (m-40) REVERT: H 227 GLU cc_start: 0.9696 (tt0) cc_final: 0.9318 (tm-30) REVERT: H 238 THR cc_start: 0.7695 (p) cc_final: 0.7489 (p) outliers start: 33 outliers final: 20 residues processed: 220 average time/residue: 0.1377 time to fit residues: 47.5062 Evaluate side-chains 202 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 234 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 81 optimal weight: 30.0000 chunk 127 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 202 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN C 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.107978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074486 restraints weight = 47833.271| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.73 r_work: 0.3008 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19176 Z= 0.204 Angle : 0.661 10.182 26540 Z= 0.306 Chirality : 0.039 0.225 3436 Planarity : 0.004 0.047 2880 Dihedral : 9.808 105.947 7492 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.91 % Allowed : 12.24 % Favored : 84.85 % 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 aren not related in a simple way. whole: 1.37 (0.19), residues: 2072 helix: 2.03 (0.16), residues: 1044 sheet: -1.82 (0.46), residues: 120 loop : 0.05 (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 B 279 PHE 0.013 0.001 PHE D 33 TRP 0.011 0.001 TRP B 178 HIS 0.002 0.001 HIS G 111 Details of bonding type rmsd covalent geometry : bond 0.00477 (19156) covalent geometry : angle 0.65748 (26496) SS BOND : bond 0.00111 ( 16) SS BOND : angle 0.29926 ( 32) hydrogen bonds : bond 0.04759 ( 832) hydrogen bonds : angle 3.66812 ( 2424) link_NAG-ASN : bond 0.00189 ( 4) link_NAG-ASN : angle 3.30437 ( 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 249 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8995 (mmt) cc_final: 0.8716 (mmt) REVERT: A 173 ASP cc_start: 0.8307 (t0) cc_final: 0.7315 (p0) REVERT: A 180 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8567 (mt-10) REVERT: A 282 MET cc_start: 0.9341 (tpt) cc_final: 0.9057 (tpp) REVERT: B 30 MET cc_start: 0.9015 (mmt) cc_final: 0.8748 (mmt) REVERT: B 173 ASP cc_start: 0.8308 (t0) cc_final: 0.7302 (p0) REVERT: B 180 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8570 (mt-10) REVERT: B 282 MET cc_start: 0.9328 (tpt) cc_final: 0.9042 (tpp) REVERT: C 30 MET cc_start: 0.8988 (mmt) cc_final: 0.8689 (mmt) REVERT: C 173 ASP cc_start: 0.8301 (t0) cc_final: 0.7318 (p0) REVERT: C 180 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8541 (mt-10) REVERT: C 282 MET cc_start: 0.9338 (tpt) cc_final: 0.9052 (tpp) REVERT: D 30 MET cc_start: 0.8989 (mmt) cc_final: 0.8692 (mmt) REVERT: D 104 MET cc_start: 0.8646 (tpp) cc_final: 0.8319 (tpp) REVERT: D 173 ASP cc_start: 0.8309 (t0) cc_final: 0.7319 (p0) REVERT: D 180 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8541 (mt-10) REVERT: D 282 MET cc_start: 0.9331 (tpt) cc_final: 0.9035 (tpp) REVERT: E 81 ASN cc_start: 0.8651 (m-40) cc_final: 0.8394 (m-40) REVERT: E 227 GLU cc_start: 0.9688 (tt0) cc_final: 0.9280 (tm-30) REVERT: E 238 THR cc_start: 0.7833 (p) cc_final: 0.7604 (p) REVERT: F 81 ASN cc_start: 0.8705 (m-40) cc_final: 0.8438 (m-40) REVERT: F 130 GLN cc_start: 0.8510 (mp10) cc_final: 0.8068 (mp10) REVERT: F 227 GLU cc_start: 0.9692 (tt0) cc_final: 0.9276 (tm-30) REVERT: G 81 ASN cc_start: 0.8677 (m-40) cc_final: 0.8428 (m-40) REVERT: G 132 GLU cc_start: 0.8819 (pm20) cc_final: 0.8511 (mm-30) REVERT: G 227 GLU cc_start: 0.9714 (tt0) cc_final: 0.9287 (tm-30) REVERT: H 81 ASN cc_start: 0.8649 (m-40) cc_final: 0.8327 (m-40) REVERT: H 227 GLU cc_start: 0.9685 (tt0) cc_final: 0.9272 (tm-30) REVERT: H 238 THR cc_start: 0.7791 (p) cc_final: 0.7565 (p) outliers start: 50 outliers final: 32 residues processed: 223 average time/residue: 0.1429 time to fit residues: 49.1670 Evaluate side-chains 218 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 234 LYS 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 229 THR Chi-restraints excluded: chain D residue 234 LYS 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 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: 0.0020 chunk 115 optimal weight: 30.0000 chunk 170 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 154 optimal weight: 30.0000 chunk 8 optimal weight: 0.0970 chunk 114 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.108975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.075658 restraints weight = 47890.263| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.72 r_work: 0.3036 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19176 Z= 0.145 Angle : 0.620 10.485 26540 Z= 0.289 Chirality : 0.037 0.183 3436 Planarity : 0.004 0.047 2880 Dihedral : 9.538 110.328 7492 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.51 % Allowed : 13.93 % Favored : 83.57 % 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 aren not related in a simple way. whole: 1.45 (0.19), residues: 2072 helix: 2.12 (0.16), residues: 1044 sheet: -1.73 (0.47), residues: 120 loop : 0.05 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 17 TYR 0.010 0.001 TYR A 290 PHE 0.008 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 covalent geometry : bond 0.00343 (19156) covalent geometry : angle 0.61575 (26496) SS BOND : bond 0.00083 ( 16) SS BOND : angle 0.30999 ( 32) hydrogen bonds : bond 0.04312 ( 832) hydrogen bonds : angle 3.54166 ( 2424) link_NAG-ASN : bond 0.00115 ( 4) link_NAG-ASN : angle 3.45909 ( 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 234 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7538 (mmm) cc_final: 0.7319 (mmp) REVERT: A 173 ASP cc_start: 0.8276 (t0) cc_final: 0.7278 (p0) REVERT: A 180 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8520 (mt-10) REVERT: A 282 MET cc_start: 0.9307 (tpt) cc_final: 0.9043 (tpp) REVERT: B 30 MET cc_start: 0.9004 (mmt) cc_final: 0.8721 (mmt) REVERT: B 94 MET cc_start: 0.7551 (mmm) cc_final: 0.7332 (mmp) REVERT: B 173 ASP cc_start: 0.8268 (t0) cc_final: 0.7262 (p0) REVERT: B 180 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8529 (mt-10) REVERT: B 282 MET cc_start: 0.9280 (tpt) cc_final: 0.9012 (tpp) REVERT: C 30 MET cc_start: 0.8990 (mmt) cc_final: 0.8685 (mmt) REVERT: C 94 MET cc_start: 0.7587 (mmm) cc_final: 0.7375 (mmp) REVERT: C 173 ASP cc_start: 0.8269 (t0) cc_final: 0.7279 (p0) REVERT: C 180 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8487 (mt-10) REVERT: C 282 MET cc_start: 0.9292 (tpt) cc_final: 0.9024 (tpp) REVERT: D 30 MET cc_start: 0.8995 (mmt) cc_final: 0.8685 (mmt) REVERT: D 94 MET cc_start: 0.7562 (mmm) cc_final: 0.7166 (mmp) REVERT: D 104 MET cc_start: 0.8698 (tpp) cc_final: 0.8347 (tpp) REVERT: D 173 ASP cc_start: 0.8272 (t0) cc_final: 0.7277 (p0) REVERT: D 180 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8487 (mt-10) REVERT: D 282 MET cc_start: 0.9285 (tpt) cc_final: 0.9012 (tpp) REVERT: E 81 ASN cc_start: 0.8683 (m-40) cc_final: 0.8418 (m-40) REVERT: E 227 GLU cc_start: 0.9676 (tt0) cc_final: 0.9260 (tm-30) REVERT: E 238 THR cc_start: 0.7768 (p) cc_final: 0.7444 (p) REVERT: F 81 ASN cc_start: 0.8679 (m-40) cc_final: 0.8405 (m-40) REVERT: F 130 GLN cc_start: 0.8550 (mp10) cc_final: 0.8186 (mp10) REVERT: F 227 GLU cc_start: 0.9682 (tt0) cc_final: 0.9260 (tm-30) REVERT: G 81 ASN cc_start: 0.8702 (m-40) cc_final: 0.8441 (m-40) REVERT: G 227 GLU cc_start: 0.9717 (tt0) cc_final: 0.9290 (tm-30) REVERT: H 81 ASN cc_start: 0.8667 (m-40) cc_final: 0.8336 (m-40) REVERT: H 227 GLU cc_start: 0.9676 (tt0) cc_final: 0.9259 (tm-30) REVERT: H 238 THR cc_start: 0.7722 (p) cc_final: 0.7514 (p) outliers start: 43 outliers final: 33 residues processed: 216 average time/residue: 0.1426 time to fit residues: 47.9057 Evaluate side-chains 217 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 234 LYS 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 103 VAL Chi-restraints excluded: chain C residue 229 THR 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 109 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 234 LYS 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 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: 7.9990 chunk 94 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.110390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.076771 restraints weight = 47919.687| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.78 r_work: 0.3072 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19176 Z= 0.114 Angle : 0.585 9.229 26540 Z= 0.275 Chirality : 0.035 0.146 3436 Planarity : 0.004 0.047 2880 Dihedral : 9.177 112.337 7492 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.92 % Allowed : 15.50 % Favored : 82.58 % 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 aren not related in a simple way. whole: 1.83 (0.19), residues: 2072 helix: 2.52 (0.16), residues: 1008 sheet: -1.69 (0.47), residues: 120 loop : 0.23 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 17 TYR 0.008 0.001 TYR D 290 PHE 0.007 0.001 PHE D 223 TRP 0.009 0.001 TRP A 178 HIS 0.002 0.001 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00261 (19156) covalent geometry : angle 0.57957 (26496) SS BOND : bond 0.00067 ( 16) SS BOND : angle 0.28142 ( 32) hydrogen bonds : bond 0.03778 ( 832) hydrogen bonds : angle 3.41586 ( 2424) link_NAG-ASN : bond 0.00128 ( 4) link_NAG-ASN : angle 3.75153 ( 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 221 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7625 (mmm) cc_final: 0.7360 (mmp) REVERT: A 222 GLN cc_start: 0.8408 (tt0) cc_final: 0.8101 (mm-40) REVERT: A 282 MET cc_start: 0.9289 (tpt) cc_final: 0.9036 (tpp) REVERT: B 94 MET cc_start: 0.7650 (mmm) cc_final: 0.7387 (mmp) REVERT: B 282 MET cc_start: 0.9283 (tpt) cc_final: 0.9026 (tpp) REVERT: C 94 MET cc_start: 0.7697 (mmm) cc_final: 0.7231 (mmp) REVERT: C 282 MET cc_start: 0.9288 (tpt) cc_final: 0.9030 (tpp) REVERT: D 94 MET cc_start: 0.7635 (mmm) cc_final: 0.6991 (mmp) REVERT: D 104 MET cc_start: 0.8640 (tpp) cc_final: 0.8318 (tpp) REVERT: D 282 MET cc_start: 0.9259 (tpt) cc_final: 0.8997 (tpp) REVERT: E 81 ASN cc_start: 0.8701 (m-40) cc_final: 0.8425 (m-40) REVERT: E 111 HIS cc_start: 0.9046 (t-90) cc_final: 0.8649 (t-90) REVERT: E 132 GLU cc_start: 0.8708 (pm20) cc_final: 0.8460 (mm-30) REVERT: E 227 GLU cc_start: 0.9708 (tt0) cc_final: 0.9295 (tm-30) REVERT: E 238 THR cc_start: 0.7725 (p) cc_final: 0.7497 (p) REVERT: F 81 ASN cc_start: 0.8693 (m-40) cc_final: 0.8405 (m-40) REVERT: F 111 HIS cc_start: 0.9067 (t-90) cc_final: 0.8667 (t-90) REVERT: F 130 GLN cc_start: 0.8521 (mp10) cc_final: 0.8181 (mp10) REVERT: F 227 GLU cc_start: 0.9717 (tt0) cc_final: 0.9297 (tm-30) REVERT: G 81 ASN cc_start: 0.8729 (m-40) cc_final: 0.8496 (m-40) REVERT: G 111 HIS cc_start: 0.9053 (t-90) cc_final: 0.8651 (t-90) REVERT: G 201 ASN cc_start: 0.8481 (m-40) cc_final: 0.8053 (m-40) REVERT: G 227 GLU cc_start: 0.9732 (tt0) cc_final: 0.9292 (tm-30) REVERT: H 81 ASN cc_start: 0.8705 (m-40) cc_final: 0.8404 (m-40) REVERT: H 111 HIS cc_start: 0.9048 (t-90) cc_final: 0.8665 (t-90) REVERT: H 227 GLU cc_start: 0.9711 (tt0) cc_final: 0.9292 (tm-30) REVERT: H 238 THR cc_start: 0.7719 (p) cc_final: 0.7505 (p) outliers start: 33 outliers final: 24 residues processed: 213 average time/residue: 0.1414 time to fit residues: 47.2067 Evaluate side-chains 203 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 229 THR 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 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: 0.9980 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.110202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.076969 restraints weight = 47874.525| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.71 r_work: 0.3130 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19176 Z= 0.113 Angle : 0.565 7.562 26540 Z= 0.270 Chirality : 0.035 0.124 3436 Planarity : 0.004 0.047 2880 Dihedral : 9.002 113.259 7492 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.52 % Allowed : 15.03 % Favored : 83.45 % 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 aren not related in a simple way. whole: 1.85 (0.19), residues: 2072 helix: 2.54 (0.16), residues: 1008 sheet: -1.66 (0.47), residues: 120 loop : 0.24 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 17 TYR 0.008 0.001 TYR D 290 PHE 0.008 0.001 PHE B 223 TRP 0.009 0.001 TRP B 178 HIS 0.002 0.001 HIS G 252 Details of bonding type rmsd covalent geometry : bond 0.00262 (19156) covalent geometry : angle 0.55963 (26496) SS BOND : bond 0.00063 ( 16) SS BOND : angle 0.32483 ( 32) hydrogen bonds : bond 0.03768 ( 832) hydrogen bonds : angle 3.38521 ( 2424) link_NAG-ASN : bond 0.00109 ( 4) link_NAG-ASN : angle 3.77489 ( 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 207 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7665 (mmm) cc_final: 0.7413 (mmp) REVERT: A 173 ASP cc_start: 0.8068 (t0) cc_final: 0.7293 (p0) REVERT: A 222 GLN cc_start: 0.8487 (tt0) cc_final: 0.8184 (mm-40) REVERT: A 282 MET cc_start: 0.9264 (tpt) cc_final: 0.9008 (tpp) REVERT: B 94 MET cc_start: 0.7678 (mmm) cc_final: 0.7426 (mmp) REVERT: B 173 ASP cc_start: 0.8078 (t0) cc_final: 0.7284 (p0) REVERT: B 282 MET cc_start: 0.9232 (tpt) cc_final: 0.8975 (tpp) REVERT: C 94 MET cc_start: 0.7691 (mmm) cc_final: 0.7452 (mmp) REVERT: C 173 ASP cc_start: 0.8064 (t0) cc_final: 0.7287 (p0) REVERT: C 282 MET cc_start: 0.9249 (tpt) cc_final: 0.8992 (tpp) REVERT: D 94 MET cc_start: 0.7705 (mmm) cc_final: 0.7058 (mmp) REVERT: D 104 MET cc_start: 0.8742 (tpp) cc_final: 0.8419 (tpp) REVERT: D 173 ASP cc_start: 0.8063 (t0) cc_final: 0.7285 (p0) REVERT: E 81 ASN cc_start: 0.8756 (m-40) cc_final: 0.8460 (m-40) REVERT: E 111 HIS cc_start: 0.9027 (t-90) cc_final: 0.8681 (t-90) REVERT: E 132 GLU cc_start: 0.8717 (pm20) cc_final: 0.8515 (mm-30) REVERT: E 227 GLU cc_start: 0.9685 (tt0) cc_final: 0.9266 (tm-30) REVERT: E 238 THR cc_start: 0.7748 (p) cc_final: 0.7515 (p) REVERT: F 81 ASN cc_start: 0.8758 (m-40) cc_final: 0.8460 (m-40) REVERT: F 111 HIS cc_start: 0.9032 (t-90) cc_final: 0.8675 (t-90) REVERT: F 130 GLN cc_start: 0.8564 (mp10) cc_final: 0.8203 (mp10) REVERT: F 178 GLU cc_start: 0.8226 (mp0) cc_final: 0.7906 (mp0) REVERT: F 227 GLU cc_start: 0.9700 (tt0) cc_final: 0.9276 (tm-30) REVERT: G 81 ASN cc_start: 0.8761 (m-40) cc_final: 0.8472 (m-40) REVERT: G 111 HIS cc_start: 0.9029 (t-90) cc_final: 0.8674 (t-90) REVERT: G 201 ASN cc_start: 0.8540 (m-40) cc_final: 0.8061 (m-40) REVERT: G 227 GLU cc_start: 0.9726 (tt0) cc_final: 0.9290 (tm-30) REVERT: H 81 ASN cc_start: 0.8751 (m-40) cc_final: 0.8429 (m-40) REVERT: H 111 HIS cc_start: 0.9041 (t-90) cc_final: 0.8688 (t-90) REVERT: H 178 GLU cc_start: 0.8228 (mp0) cc_final: 0.7980 (mp0) REVERT: H 227 GLU cc_start: 0.9698 (tt0) cc_final: 0.9277 (tm-30) REVERT: H 238 THR cc_start: 0.7720 (p) cc_final: 0.7503 (p) outliers start: 26 outliers final: 23 residues processed: 199 average time/residue: 0.1316 time to fit residues: 42.3963 Evaluate side-chains 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 229 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 180 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 206 optimal weight: 4.9990 chunk 112 optimal weight: 0.0370 chunk 64 optimal weight: 3.9990 overall best weight: 2.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.108593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075416 restraints weight = 47250.861| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.66 r_work: 0.3092 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19176 Z= 0.174 Angle : 0.607 12.767 26540 Z= 0.290 Chirality : 0.036 0.134 3436 Planarity : 0.004 0.047 2880 Dihedral : 9.069 112.719 7492 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.57 % Allowed : 15.27 % Favored : 83.16 % 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 aren not related in a simple way. whole: 1.44 (0.19), residues: 2072 helix: 2.08 (0.16), residues: 1044 sheet: -1.74 (0.46), residues: 120 loop : 0.08 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 17 TYR 0.010 0.001 TYR A 279 PHE 0.015 0.001 PHE D 303 TRP 0.009 0.001 TRP B 178 HIS 0.002 0.001 HIS G 252 Details of bonding type rmsd covalent geometry : bond 0.00414 (19156) covalent geometry : angle 0.60172 (26496) SS BOND : bond 0.00094 ( 16) SS BOND : angle 0.32398 ( 32) hydrogen bonds : bond 0.04455 ( 832) hydrogen bonds : angle 3.55668 ( 2424) link_NAG-ASN : bond 0.00206 ( 4) link_NAG-ASN : angle 3.79844 ( 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 220 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9037 (mmt) cc_final: 0.8742 (mmt) REVERT: A 94 MET cc_start: 0.7742 (mmm) cc_final: 0.7497 (mmp) REVERT: A 173 ASP cc_start: 0.8191 (t0) cc_final: 0.7361 (p0) REVERT: A 180 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8474 (mt-10) REVERT: A 222 GLN cc_start: 0.8573 (tt0) cc_final: 0.8256 (mm-40) REVERT: A 282 MET cc_start: 0.9302 (tpt) cc_final: 0.9028 (tpp) REVERT: B 30 MET cc_start: 0.9036 (mmt) cc_final: 0.8744 (mmt) REVERT: B 94 MET cc_start: 0.7745 (mmm) cc_final: 0.7501 (mmp) REVERT: B 180 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8191 (mt-10) REVERT: B 282 MET cc_start: 0.9271 (tpt) cc_final: 0.8995 (tpp) REVERT: C 30 MET cc_start: 0.8995 (mmt) cc_final: 0.8672 (mmt) REVERT: C 94 MET cc_start: 0.7779 (mmm) cc_final: 0.7549 (mmp) REVERT: C 173 ASP cc_start: 0.8159 (t0) cc_final: 0.7342 (p0) REVERT: C 180 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8450 (mt-10) REVERT: C 282 MET cc_start: 0.9296 (tpt) cc_final: 0.9019 (tpp) REVERT: D 30 MET cc_start: 0.9027 (mmt) cc_final: 0.8739 (mmt) REVERT: D 94 MET cc_start: 0.7851 (mmm) cc_final: 0.7632 (mmp) REVERT: D 104 MET cc_start: 0.8720 (tpp) cc_final: 0.8387 (tpp) REVERT: D 173 ASP cc_start: 0.8178 (t0) cc_final: 0.7338 (p0) REVERT: D 180 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8164 (mt-10) REVERT: D 282 MET cc_start: 0.9240 (tpt) cc_final: 0.8995 (tpp) REVERT: E 81 ASN cc_start: 0.8714 (m-40) cc_final: 0.8405 (m-40) REVERT: E 178 GLU cc_start: 0.8254 (mp0) cc_final: 0.7999 (mp0) REVERT: E 227 GLU cc_start: 0.9681 (tt0) cc_final: 0.9263 (tm-30) REVERT: E 238 THR cc_start: 0.7827 (p) cc_final: 0.7485 (p) REVERT: F 81 ASN cc_start: 0.8745 (m-40) cc_final: 0.8426 (m-40) REVERT: F 130 GLN cc_start: 0.8587 (mp10) cc_final: 0.8244 (mp10) REVERT: F 178 GLU cc_start: 0.8251 (mp0) cc_final: 0.7813 (mp0) REVERT: F 227 GLU cc_start: 0.9705 (tt0) cc_final: 0.9282 (tm-30) REVERT: G 81 ASN cc_start: 0.8744 (m-40) cc_final: 0.8482 (m-40) REVERT: G 227 GLU cc_start: 0.9724 (tt0) cc_final: 0.9286 (tm-30) REVERT: H 81 ASN cc_start: 0.8728 (m-40) cc_final: 0.8385 (m-40) REVERT: H 111 HIS cc_start: 0.9050 (t-90) cc_final: 0.8684 (t-90) REVERT: H 178 GLU cc_start: 0.8225 (mp0) cc_final: 0.7799 (mp0) REVERT: H 227 GLU cc_start: 0.9697 (tt0) cc_final: 0.9276 (tm-30) REVERT: H 238 THR cc_start: 0.7791 (p) cc_final: 0.7565 (p) outliers start: 27 outliers final: 25 residues processed: 212 average time/residue: 0.1402 time to fit residues: 46.5429 Evaluate side-chains 214 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 229 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 325 LEU 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 161 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 139 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 26 optimal weight: 0.0170 overall best weight: 1.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.108752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075185 restraints weight = 47889.457| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.76 r_work: 0.3043 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3284 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= 0.135 Angle : 0.574 6.747 26540 Z= 0.277 Chirality : 0.035 0.128 3436 Planarity : 0.004 0.047 2880 Dihedral : 8.970 113.926 7492 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.40 % Allowed : 15.85 % Favored : 82.75 % 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 aren not related in a simple way. whole: 1.49 (0.19), residues: 2072 helix: 2.13 (0.16), residues: 1044 sheet: -1.71 (0.47), residues: 120 loop : 0.10 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 17 TYR 0.009 0.001 TYR D 290 PHE 0.021 0.001 PHE D 303 TRP 0.008 0.001 TRP B 178 HIS 0.002 0.001 HIS G 252 Details of bonding type rmsd covalent geometry : bond 0.00318 (19156) covalent geometry : angle 0.56958 (26496) SS BOND : bond 0.00089 ( 16) SS BOND : angle 0.33722 ( 32) hydrogen bonds : bond 0.04136 ( 832) hydrogen bonds : angle 3.47014 ( 2424) link_NAG-ASN : bond 0.00131 ( 4) link_NAG-ASN : angle 3.61511 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5008.25 seconds wall clock time: 86 minutes 31.82 seconds (5191.82 seconds total)