Starting phenix.real_space_refine on Mon Jun 16 11:57:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vav_43106/06_2025/8vav_43106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vav_43106/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vav_43106/06_2025/8vav_43106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vav_43106/06_2025/8vav_43106.map" model { file = "/net/cci-nas-00/data/ceres_data/8vav_43106/06_2025/8vav_43106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vav_43106/06_2025/8vav_43106.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 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-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 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-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 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-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 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: 13.13, per 1000 atoms: 0.71 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: 5.47 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.94 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: 4.95 Time building geometry restraints manager: 6.33 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 328 or resid 1101 through 1102 or (resid 1103 a \ nd (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 name 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 name 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 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 name C10 or n \ ame 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 name C32 or n \ ame C35 or name C36 or name 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 O40 or name O42 or name O43 or name O44 or name O54 or n \ ame O77 or name O78 or name O79 or name O82 or name O84)))) selection = (chain 'B' and (resid 12 through 328 or resid 1101 through 1102 or (resid 1103 a \ nd (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 name 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 name 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)) selection = (chain 'C' and (resid 12 through 328 or resid 1101 through 1102 or (resid 1103 a \ nd (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 name 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 name 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)) selection = (chain 'D' and (resid 12 through 328 or resid 1101 or (resid 1102 through 1103 a \ nd (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 name 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 name 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 44.870 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP D 22 HIS 0.002 0.000 HIS A 254 PHE 0.012 0.001 PHE A 252 TYR 0.007 0.001 TYR A 290 ARG 0.002 0.000 ARG A 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 4) link_NAG-ASN : angle 2.86784 ( 12) hydrogen bonds : bond 0.13143 ( 832) hydrogen bonds : angle 4.50767 ( 2424) SS BOND : bond 0.00259 ( 16) SS BOND : angle 0.59640 ( 32) covalent geometry : bond 0.00531 (19156) covalent geometry : angle 0.79891 (26496) *********************** 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 : 1.944 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: 0.3523 time to fit residues: 150.2952 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 : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 188 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 143 ASN C 216 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.110696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.077460 restraints weight = 47815.507| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.84 r_work: 0.3107 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19176 Z= 0.152 Angle : 0.846 8.883 26540 Z= 0.348 Chirality : 0.045 0.277 3436 Planarity : 0.005 0.050 2880 Dihedral : 18.402 117.509 7492 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.57 % Allowed : 7.75 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 2072 helix: 1.96 (0.16), residues: 1048 sheet: -1.87 (0.48), residues: 120 loop : -0.14 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 215 HIS 0.006 0.002 HIS H 80 PHE 0.012 0.001 PHE C 217 TYR 0.012 0.001 TYR D 145 ARG 0.004 0.000 ARG B 167 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 2.53959 ( 12) hydrogen bonds : bond 0.04178 ( 832) hydrogen bonds : angle 3.62018 ( 2424) SS BOND : bond 0.00105 ( 16) SS BOND : angle 0.43966 ( 32) covalent geometry : bond 0.00341 (19156) covalent geometry : angle 0.84466 (26496) *********************** 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 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8516 (t0) cc_final: 0.8176 (t0) REVERT: A 252 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8600 (t80) REVERT: B 173 ASP cc_start: 0.8499 (t0) cc_final: 0.8165 (t0) REVERT: B 252 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8625 (t80) REVERT: C 21 MET cc_start: 0.8556 (mmm) cc_final: 0.8032 (mmm) REVERT: C 173 ASP cc_start: 0.8522 (t0) cc_final: 0.8192 (t0) REVERT: C 252 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8602 (t80) REVERT: D 104 MET cc_start: 0.8522 (tpp) cc_final: 0.8306 (tpp) REVERT: D 173 ASP cc_start: 0.8505 (t0) cc_final: 0.8178 (t0) REVERT: D 252 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8614 (t80) REVERT: E 81 ASN cc_start: 0.8709 (m-40) cc_final: 0.8390 (m-40) REVERT: E 238 THR cc_start: 0.7738 (p) cc_final: 0.7426 (p) REVERT: F 81 ASN cc_start: 0.8751 (m-40) cc_final: 0.8393 (m-40) REVERT: G 81 ASN cc_start: 0.8750 (m-40) cc_final: 0.8418 (m-40) REVERT: G 238 THR cc_start: 0.7706 (p) cc_final: 0.7408 (p) REVERT: H 81 ASN cc_start: 0.8764 (m-40) cc_final: 0.8418 (m-40) REVERT: H 238 THR cc_start: 0.7700 (p) cc_final: 0.7394 (p) outliers start: 27 outliers final: 16 residues processed: 229 average time/residue: 0.3049 time to fit residues: 106.2410 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 : 1.761 ------------------------------------------------------------------------------- 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 200 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 D 143 ASN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.108095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.076363 restraints weight = 47815.799| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.98 r_work: 0.3052 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2538 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= 0.193 Angle : 0.766 9.782 26540 Z= 0.330 Chirality : 0.044 0.309 3436 Planarity : 0.004 0.049 2880 Dihedral : 13.490 115.009 7492 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.86 % Allowed : 10.26 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 2072 helix: 1.96 (0.16), residues: 1044 sheet: -1.94 (0.46), residues: 120 loop : -0.04 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 178 HIS 0.002 0.001 HIS G 252 PHE 0.016 0.001 PHE B 33 TYR 0.011 0.001 TYR A 290 ARG 0.003 0.000 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00120 ( 4) link_NAG-ASN : angle 2.89999 ( 12) hydrogen bonds : bond 0.04910 ( 832) hydrogen bonds : angle 3.71541 ( 2424) SS BOND : bond 0.00092 ( 16) SS BOND : angle 0.28681 ( 32) covalent geometry : bond 0.00450 (19156) covalent geometry : angle 0.76450 (26496) *********************** 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 238 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8611 (t80) REVERT: A 282 MET cc_start: 0.9351 (tpt) cc_final: 0.9008 (tpp) REVERT: A 285 MET cc_start: 0.9139 (mmm) cc_final: 0.8936 (mmt) REVERT: B 180 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8644 (mt-10) REVERT: B 252 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8626 (t80) REVERT: B 282 MET cc_start: 0.9340 (tpt) cc_final: 0.8995 (tpp) REVERT: C 21 MET cc_start: 0.8668 (mmm) cc_final: 0.8144 (mmm) REVERT: C 252 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8635 (t80) REVERT: C 282 MET cc_start: 0.9343 (tpt) cc_final: 0.8999 (tpp) REVERT: D 252 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8626 (t80) REVERT: D 282 MET cc_start: 0.9315 (tpt) cc_final: 0.8965 (tpp) REVERT: E 81 ASN cc_start: 0.8699 (m-40) cc_final: 0.8390 (m-40) REVERT: E 227 GLU cc_start: 0.9655 (tt0) cc_final: 0.9262 (tm-30) REVERT: E 238 THR cc_start: 0.7808 (p) cc_final: 0.7480 (p) REVERT: F 81 ASN cc_start: 0.8744 (m-40) cc_final: 0.8409 (m-40) REVERT: F 227 GLU cc_start: 0.9647 (tt0) cc_final: 0.9245 (tm-30) REVERT: G 81 ASN cc_start: 0.8640 (m-40) cc_final: 0.8337 (m-40) REVERT: G 238 THR cc_start: 0.7729 (p) cc_final: 0.7495 (p) REVERT: H 81 ASN cc_start: 0.8696 (m-40) cc_final: 0.8375 (m-40) REVERT: H 227 GLU cc_start: 0.9659 (tt0) cc_final: 0.9260 (tm-30) REVERT: H 238 THR cc_start: 0.7788 (p) cc_final: 0.7559 (p) outliers start: 32 outliers final: 17 residues processed: 227 average time/residue: 0.2977 time to fit residues: 104.0306 Evaluate side-chains 210 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 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 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 E residue 65 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 216 GLN B 172 ASN C 172 ASN C 216 GLN D 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.108923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.077314 restraints weight = 48120.211| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.03 r_work: 0.3107 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19176 Z= 0.146 Angle : 0.681 9.017 26540 Z= 0.297 Chirality : 0.040 0.296 3436 Planarity : 0.004 0.047 2880 Dihedral : 11.137 118.881 7492 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.81 % Allowed : 12.35 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.19), residues: 2072 helix: 2.15 (0.16), residues: 1044 sheet: -1.86 (0.46), residues: 120 loop : 0.04 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 178 HIS 0.002 0.001 HIS F 80 PHE 0.008 0.001 PHE D 217 TYR 0.011 0.001 TYR D 290 ARG 0.003 0.000 ARG E 157 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 4) link_NAG-ASN : angle 2.75296 ( 12) hydrogen bonds : bond 0.04248 ( 832) hydrogen bonds : angle 3.56259 ( 2424) SS BOND : bond 0.00083 ( 16) SS BOND : angle 0.26169 ( 32) covalent geometry : bond 0.00337 (19156) covalent geometry : angle 0.67850 (26496) *********************** 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 229 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.866 Fit side-chains REVERT: A 173 ASP cc_start: 0.8525 (t0) cc_final: 0.7793 (p0) REVERT: A 180 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8564 (mt-10) REVERT: A 252 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8660 (t80) REVERT: A 282 MET cc_start: 0.9316 (tpt) cc_final: 0.9043 (tpp) REVERT: B 173 ASP cc_start: 0.8493 (t0) cc_final: 0.8277 (t0) REVERT: B 180 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8102 (mt-10) REVERT: B 252 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8692 (t80) REVERT: B 282 MET cc_start: 0.9295 (tpt) cc_final: 0.9023 (tpp) REVERT: C 21 MET cc_start: 0.8634 (mmm) cc_final: 0.8123 (mmm) REVERT: C 173 ASP cc_start: 0.8552 (t0) cc_final: 0.7818 (p0) REVERT: C 180 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8562 (mt-10) REVERT: C 252 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8688 (t80) REVERT: C 282 MET cc_start: 0.9290 (tpt) cc_final: 0.9017 (tpp) REVERT: D 104 MET cc_start: 0.8678 (tpp) cc_final: 0.8216 (tpp) REVERT: D 173 ASP cc_start: 0.8556 (t0) cc_final: 0.7833 (p0) REVERT: D 180 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8562 (mt-10) REVERT: D 252 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (t80) REVERT: D 282 MET cc_start: 0.9277 (tpt) cc_final: 0.9004 (tpp) REVERT: E 81 ASN cc_start: 0.8650 (m-40) cc_final: 0.8382 (m-40) REVERT: E 227 GLU cc_start: 0.9702 (tt0) cc_final: 0.9340 (tm-30) REVERT: E 238 THR cc_start: 0.7735 (p) cc_final: 0.7516 (p) REVERT: F 81 ASN cc_start: 0.8716 (m-40) cc_final: 0.8418 (m-40) REVERT: F 227 GLU cc_start: 0.9706 (tt0) cc_final: 0.9339 (tm-30) REVERT: G 81 ASN cc_start: 0.8645 (m-40) cc_final: 0.8399 (m-40) REVERT: G 227 GLU cc_start: 0.9717 (tt0) cc_final: 0.9329 (tm-30) REVERT: G 238 THR cc_start: 0.7652 (p) cc_final: 0.7438 (p) REVERT: H 81 ASN cc_start: 0.8636 (m-40) cc_final: 0.8366 (m-40) REVERT: H 227 GLU cc_start: 0.9708 (tt0) cc_final: 0.9339 (tm-30) REVERT: H 238 THR cc_start: 0.7704 (p) cc_final: 0.7488 (p) outliers start: 31 outliers final: 16 residues processed: 214 average time/residue: 0.2956 time to fit residues: 97.0829 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 : 1.852 ------------------------------------------------------------------------------- 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 247 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 174 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 170 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 137 optimal weight: 0.0970 chunk 138 optimal weight: 7.9990 chunk 193 optimal weight: 50.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.107806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074079 restraints weight = 48235.250| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.75 r_work: 0.3058 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19176 Z= 0.201 Angle : 0.675 9.760 26540 Z= 0.308 Chirality : 0.041 0.304 3436 Planarity : 0.004 0.047 2880 Dihedral : 10.271 108.958 7492 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.62 % Allowed : 12.70 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 2072 helix: 1.99 (0.16), residues: 1044 sheet: -1.82 (0.47), residues: 120 loop : 0.07 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 178 HIS 0.002 0.001 HIS G 252 PHE 0.013 0.001 PHE C 33 TYR 0.011 0.001 TYR A 290 ARG 0.003 0.000 ARG E 157 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 4) link_NAG-ASN : angle 3.17697 ( 12) hydrogen bonds : bond 0.04866 ( 832) hydrogen bonds : angle 3.70586 ( 2424) SS BOND : bond 0.00108 ( 16) SS BOND : angle 0.30502 ( 32) covalent geometry : bond 0.00473 (19156) covalent geometry : angle 0.67203 (26496) *********************** 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 246 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 2.411 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.9034 (mmt) cc_final: 0.8766 (mmt) REVERT: A 180 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8514 (mt-10) REVERT: A 252 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8719 (t80) REVERT: A 282 MET cc_start: 0.9324 (tpt) cc_final: 0.9039 (tpp) REVERT: B 30 MET cc_start: 0.9045 (mmt) cc_final: 0.8777 (mmt) REVERT: B 180 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8584 (mt-10) REVERT: B 252 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8704 (t80) REVERT: B 282 MET cc_start: 0.9303 (tpt) cc_final: 0.9014 (tpp) REVERT: C 21 MET cc_start: 0.8672 (mmm) cc_final: 0.8147 (mmm) REVERT: C 30 MET cc_start: 0.9013 (mmt) cc_final: 0.8720 (mmt) REVERT: C 180 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8498 (mt-10) REVERT: C 252 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8688 (t80) REVERT: C 282 MET cc_start: 0.9311 (tpt) cc_final: 0.9024 (tpp) REVERT: D 30 MET cc_start: 0.9034 (mmt) cc_final: 0.8772 (mmt) REVERT: D 104 MET cc_start: 0.8621 (tpp) cc_final: 0.8259 (tpp) REVERT: D 252 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8699 (t80) REVERT: D 282 MET cc_start: 0.9305 (tpt) cc_final: 0.9014 (tpp) REVERT: E 81 ASN cc_start: 0.8640 (m-40) cc_final: 0.8337 (m-40) REVERT: E 227 GLU cc_start: 0.9679 (tt0) cc_final: 0.9300 (tm-30) REVERT: E 238 THR cc_start: 0.7831 (p) cc_final: 0.7489 (p) REVERT: F 81 ASN cc_start: 0.8692 (m-40) cc_final: 0.8407 (m-40) REVERT: F 227 GLU cc_start: 0.9681 (tt0) cc_final: 0.9296 (tm-30) REVERT: G 81 ASN cc_start: 0.8664 (m-40) cc_final: 0.8398 (m-40) REVERT: G 227 GLU cc_start: 0.9701 (tt0) cc_final: 0.9279 (tm-30) REVERT: G 238 THR cc_start: 0.7749 (p) cc_final: 0.7512 (p) REVERT: H 81 ASN cc_start: 0.8639 (m-40) cc_final: 0.8342 (m-40) REVERT: H 227 GLU cc_start: 0.9677 (tt0) cc_final: 0.9281 (tm-30) REVERT: H 238 THR cc_start: 0.7795 (p) cc_final: 0.7569 (p) outliers start: 45 outliers final: 30 residues processed: 227 average time/residue: 0.2912 time to fit residues: 102.0672 Evaluate side-chains 220 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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 252 PHE 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 252 PHE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN C 19 GLN D 172 ASN D 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.109343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.075893 restraints weight = 48045.301| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.71 r_work: 0.3102 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3052 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= 0.136 Angle : 0.611 10.245 26540 Z= 0.283 Chirality : 0.037 0.222 3436 Planarity : 0.004 0.048 2880 Dihedral : 9.694 108.578 7492 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.51 % Allowed : 13.81 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 2072 helix: 2.14 (0.16), residues: 1044 sheet: -1.75 (0.47), residues: 120 loop : 0.10 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 178 HIS 0.002 0.001 HIS G 80 PHE 0.008 0.001 PHE B 223 TYR 0.010 0.001 TYR D 290 ARG 0.002 0.000 ARG C 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 4) link_NAG-ASN : angle 3.12918 ( 12) hydrogen bonds : bond 0.04281 ( 832) hydrogen bonds : angle 3.54498 ( 2424) SS BOND : bond 0.00067 ( 16) SS BOND : angle 0.26617 ( 32) covalent geometry : bond 0.00315 (19156) covalent geometry : angle 0.60775 (26496) *********************** 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 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9027 (mmt) cc_final: 0.8709 (mmt) REVERT: A 94 MET cc_start: 0.7584 (mmm) cc_final: 0.7222 (mmp) REVERT: A 173 ASP cc_start: 0.8230 (t0) cc_final: 0.7323 (p0) REVERT: A 180 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8186 (mt-10) REVERT: A 282 MET cc_start: 0.9267 (tpt) cc_final: 0.9010 (tpp) REVERT: B 173 ASP cc_start: 0.8231 (t0) cc_final: 0.7312 (p0) REVERT: B 180 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8164 (mt-10) REVERT: B 282 MET cc_start: 0.9225 (tpt) cc_final: 0.8968 (tpp) REVERT: C 30 MET cc_start: 0.8992 (mmt) cc_final: 0.8683 (mmt) REVERT: C 173 ASP cc_start: 0.8220 (t0) cc_final: 0.7325 (p0) REVERT: C 180 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 282 MET cc_start: 0.9240 (tpt) cc_final: 0.8981 (tpp) REVERT: D 30 MET cc_start: 0.9003 (mmt) cc_final: 0.8692 (mmt) REVERT: D 104 MET cc_start: 0.8695 (tpp) cc_final: 0.8279 (tpp) REVERT: D 173 ASP cc_start: 0.8242 (t0) cc_final: 0.7365 (p0) REVERT: D 282 MET cc_start: 0.9226 (tpt) cc_final: 0.8969 (tpp) REVERT: E 81 ASN cc_start: 0.8684 (m-40) cc_final: 0.8397 (m-40) REVERT: E 227 GLU cc_start: 0.9672 (tt0) cc_final: 0.9283 (tm-30) REVERT: E 238 THR cc_start: 0.7748 (p) cc_final: 0.7533 (p) REVERT: F 81 ASN cc_start: 0.8691 (m-40) cc_final: 0.8392 (m-40) REVERT: F 227 GLU cc_start: 0.9683 (tt0) cc_final: 0.9280 (tm-30) REVERT: G 81 ASN cc_start: 0.8712 (m-40) cc_final: 0.8428 (m-40) REVERT: G 227 GLU cc_start: 0.9703 (tt0) cc_final: 0.9286 (tm-30) REVERT: H 81 ASN cc_start: 0.8674 (m-40) cc_final: 0.8399 (m-40) REVERT: H 227 GLU cc_start: 0.9677 (tt0) cc_final: 0.9286 (tm-30) REVERT: H 238 THR cc_start: 0.7715 (p) cc_final: 0.7506 (p) outliers start: 43 outliers final: 29 residues processed: 221 average time/residue: 0.2885 time to fit residues: 99.8247 Evaluate side-chains 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 2.032 ------------------------------------------------------------------------------- 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 281 LEU 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 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 281 LEU 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 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 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 150 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 174 optimal weight: 0.1980 chunk 162 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.110116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.076666 restraints weight = 47543.645| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.75 r_work: 0.3065 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19176 Z= 0.110 Angle : 0.594 10.456 26540 Z= 0.279 Chirality : 0.036 0.185 3436 Planarity : 0.004 0.047 2880 Dihedral : 9.412 111.008 7492 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.34 % Allowed : 15.56 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 2072 helix: 2.51 (0.16), residues: 1008 sheet: -1.71 (0.47), residues: 120 loop : 0.27 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 178 HIS 0.002 0.001 HIS G 80 PHE 0.013 0.001 PHE D 177 TYR 0.008 0.001 TYR C 163 ARG 0.005 0.000 ARG C 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 4) link_NAG-ASN : angle 3.27756 ( 12) hydrogen bonds : bond 0.03817 ( 832) hydrogen bonds : angle 3.42498 ( 2424) SS BOND : bond 0.00054 ( 16) SS BOND : angle 0.29137 ( 32) covalent geometry : bond 0.00244 (19156) covalent geometry : angle 0.59041 (26496) *********************** 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 205 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 2.345 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7640 (mmm) cc_final: 0.7196 (mmp) REVERT: A 173 ASP cc_start: 0.8189 (t0) cc_final: 0.7174 (p0) REVERT: A 282 MET cc_start: 0.9305 (tpt) cc_final: 0.9053 (tpp) REVERT: B 94 MET cc_start: 0.7480 (mmm) cc_final: 0.7060 (mmp) REVERT: B 173 ASP cc_start: 0.8178 (t0) cc_final: 0.7163 (p0) REVERT: B 282 MET cc_start: 0.9280 (tpt) cc_final: 0.9024 (tpp) REVERT: C 94 MET cc_start: 0.7470 (mmm) cc_final: 0.7053 (mmp) REVERT: C 173 ASP cc_start: 0.8178 (t0) cc_final: 0.7179 (p0) REVERT: C 282 MET cc_start: 0.9284 (tpt) cc_final: 0.9027 (tpp) REVERT: D 94 MET cc_start: 0.7479 (mmm) cc_final: 0.7077 (mmp) REVERT: D 104 MET cc_start: 0.8546 (tpp) cc_final: 0.8158 (tpp) REVERT: D 173 ASP cc_start: 0.8181 (t0) cc_final: 0.7219 (p0) REVERT: D 282 MET cc_start: 0.9263 (tpt) cc_final: 0.9008 (tpp) REVERT: E 81 ASN cc_start: 0.8689 (m-40) cc_final: 0.8395 (m-40) REVERT: E 227 GLU cc_start: 0.9703 (tt0) cc_final: 0.9290 (tm-30) REVERT: E 238 THR cc_start: 0.7718 (p) cc_final: 0.7489 (p) REVERT: F 81 ASN cc_start: 0.8673 (m-40) cc_final: 0.8365 (m-40) REVERT: F 227 GLU cc_start: 0.9707 (tt0) cc_final: 0.9289 (tm-30) REVERT: G 81 ASN cc_start: 0.8734 (m-40) cc_final: 0.8449 (m-40) REVERT: G 132 GLU cc_start: 0.8488 (pm20) cc_final: 0.8241 (mm-30) REVERT: G 159 GLU cc_start: 0.9369 (tp30) cc_final: 0.9128 (tm-30) REVERT: G 227 GLU cc_start: 0.9724 (tt0) cc_final: 0.9291 (tm-30) REVERT: H 81 ASN cc_start: 0.8673 (m-40) cc_final: 0.8389 (m-40) REVERT: H 111 HIS cc_start: 0.9053 (t-90) cc_final: 0.8662 (t-90) REVERT: H 159 GLU cc_start: 0.9369 (tp30) cc_final: 0.9123 (tm-30) REVERT: H 227 GLU cc_start: 0.9705 (tt0) cc_final: 0.9287 (tm-30) REVERT: H 238 THR cc_start: 0.7676 (p) cc_final: 0.7476 (p) outliers start: 23 outliers final: 18 residues processed: 197 average time/residue: 0.3552 time to fit residues: 108.2811 Evaluate side-chains 193 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 234 LYS 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 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 184 optimal weight: 30.0000 chunk 107 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3969 r_free = 0.3969 target = 0.110890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.077808 restraints weight = 47780.541| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.70 r_work: 0.3151 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19176 Z= 0.105 Angle : 0.569 9.016 26540 Z= 0.270 Chirality : 0.035 0.150 3436 Planarity : 0.004 0.047 2880 Dihedral : 9.080 112.938 7492 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.63 % Allowed : 15.68 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.19), residues: 2072 helix: 2.59 (0.16), residues: 1008 sheet: -1.66 (0.47), residues: 120 loop : 0.29 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 178 HIS 0.002 0.000 HIS G 80 PHE 0.008 0.001 PHE D 177 TYR 0.007 0.001 TYR D 290 ARG 0.005 0.000 ARG B 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 4) link_NAG-ASN : angle 3.67326 ( 12) hydrogen bonds : bond 0.03544 ( 832) hydrogen bonds : angle 3.35270 ( 2424) SS BOND : bond 0.00061 ( 16) SS BOND : angle 0.27629 ( 32) covalent geometry : bond 0.00234 (19156) covalent geometry : angle 0.56434 (26496) *********************** 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 211 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7671 (mmm) cc_final: 0.7434 (mmp) REVERT: A 222 GLN cc_start: 0.8458 (tt0) cc_final: 0.8165 (mm-40) REVERT: B 94 MET cc_start: 0.7658 (mmm) cc_final: 0.7365 (mmp) REVERT: C 19 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6979 (pt0) REVERT: C 94 MET cc_start: 0.7641 (mmm) cc_final: 0.7349 (mmp) REVERT: C 222 GLN cc_start: 0.8409 (tt0) cc_final: 0.8075 (mm-40) REVERT: D 94 MET cc_start: 0.7635 (mmm) cc_final: 0.7352 (mmp) REVERT: D 104 MET cc_start: 0.8689 (tpp) cc_final: 0.8283 (tpp) REVERT: D 173 ASP cc_start: 0.8105 (t0) cc_final: 0.7264 (p0) REVERT: D 282 MET cc_start: 0.9211 (tpt) cc_final: 0.9003 (tpp) REVERT: E 81 ASN cc_start: 0.8768 (m-40) cc_final: 0.8440 (m-40) REVERT: E 111 HIS cc_start: 0.9020 (t-90) cc_final: 0.8671 (t-90) REVERT: E 227 GLU cc_start: 0.9673 (tt0) cc_final: 0.9252 (tm-30) REVERT: E 238 THR cc_start: 0.7717 (p) cc_final: 0.7494 (p) REVERT: F 81 ASN cc_start: 0.8749 (m-40) cc_final: 0.8413 (m-40) REVERT: F 111 HIS cc_start: 0.9027 (t-90) cc_final: 0.8691 (t-90) REVERT: F 130 GLN cc_start: 0.8482 (mp10) cc_final: 0.8111 (mp10) REVERT: F 227 GLU cc_start: 0.9695 (tt0) cc_final: 0.9272 (tm-30) REVERT: G 81 ASN cc_start: 0.8764 (m-40) cc_final: 0.8488 (m-40) REVERT: G 111 HIS cc_start: 0.9024 (t-90) cc_final: 0.8669 (t-90) REVERT: G 159 GLU cc_start: 0.9287 (tp30) cc_final: 0.9072 (tm-30) REVERT: G 227 GLU cc_start: 0.9721 (tt0) cc_final: 0.9285 (tm-30) REVERT: H 81 ASN cc_start: 0.8750 (m-40) cc_final: 0.8441 (m-40) REVERT: H 111 HIS cc_start: 0.9005 (t-90) cc_final: 0.8678 (t-90) REVERT: H 159 GLU cc_start: 0.9295 (tp30) cc_final: 0.9074 (tm-30) REVERT: H 227 GLU cc_start: 0.9678 (tt0) cc_final: 0.9257 (tm-30) REVERT: H 238 THR cc_start: 0.7690 (p) cc_final: 0.7471 (p) outliers start: 28 outliers final: 20 residues processed: 201 average time/residue: 0.2757 time to fit residues: 87.7435 Evaluate side-chains 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.933 ------------------------------------------------------------------------------- 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 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 19 GLN 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 E residue 247 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 50 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 45 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 205 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.108430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075099 restraints weight = 47744.519| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.67 r_work: 0.3087 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19176 Z= 0.193 Angle : 0.624 12.196 26540 Z= 0.297 Chirality : 0.037 0.136 3436 Planarity : 0.004 0.046 2880 Dihedral : 9.173 112.041 7492 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.69 % Allowed : 15.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2072 helix: 2.12 (0.16), residues: 1044 sheet: -1.74 (0.46), residues: 120 loop : 0.10 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 178 HIS 0.002 0.001 HIS H 111 PHE 0.012 0.001 PHE C 252 TYR 0.011 0.001 TYR D 279 ARG 0.009 0.000 ARG C 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 4) link_NAG-ASN : angle 4.00392 ( 12) hydrogen bonds : bond 0.04456 ( 832) hydrogen bonds : angle 3.56122 ( 2424) SS BOND : bond 0.00098 ( 16) SS BOND : angle 0.30205 ( 32) covalent geometry : bond 0.00456 (19156) covalent geometry : angle 0.61893 (26496) *********************** 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 221 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9032 (mmt) cc_final: 0.8730 (mmt) REVERT: A 173 ASP cc_start: 0.8117 (t0) cc_final: 0.7360 (p0) REVERT: A 180 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8471 (mt-10) REVERT: A 282 MET cc_start: 0.9266 (tpt) cc_final: 0.9019 (tpp) REVERT: B 30 MET cc_start: 0.9037 (mmt) cc_final: 0.8744 (mmt) REVERT: B 94 MET cc_start: 0.7755 (mmm) cc_final: 0.7505 (mmp) REVERT: B 173 ASP cc_start: 0.8119 (t0) cc_final: 0.7345 (p0) REVERT: B 282 MET cc_start: 0.9249 (tpt) cc_final: 0.9000 (tpp) REVERT: C 94 MET cc_start: 0.7765 (mmm) cc_final: 0.7518 (mmp) REVERT: C 173 ASP cc_start: 0.8100 (t0) cc_final: 0.7347 (p0) REVERT: C 180 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8447 (mt-10) REVERT: C 282 MET cc_start: 0.9231 (tpt) cc_final: 0.8988 (tpp) REVERT: D 30 MET cc_start: 0.9017 (mmt) cc_final: 0.8717 (mmt) REVERT: D 94 MET cc_start: 0.7736 (mmm) cc_final: 0.7496 (mmp) REVERT: D 104 MET cc_start: 0.8702 (tpp) cc_final: 0.8313 (tpp) REVERT: D 173 ASP cc_start: 0.8266 (t0) cc_final: 0.7406 (p0) REVERT: D 282 MET cc_start: 0.9281 (tpt) cc_final: 0.9042 (tpp) REVERT: E 81 ASN cc_start: 0.8722 (m-40) cc_final: 0.8381 (m-40) REVERT: E 227 GLU cc_start: 0.9682 (tt0) cc_final: 0.9268 (tm-30) REVERT: E 238 THR cc_start: 0.7823 (p) cc_final: 0.7488 (p) REVERT: F 81 ASN cc_start: 0.8744 (m-40) cc_final: 0.8392 (m-40) REVERT: F 130 GLN cc_start: 0.8596 (mp10) cc_final: 0.8167 (mp10) REVERT: F 178 GLU cc_start: 0.8257 (mp0) cc_final: 0.7990 (mp0) REVERT: F 227 GLU cc_start: 0.9706 (tt0) cc_final: 0.9283 (tm-30) REVERT: G 81 ASN cc_start: 0.8727 (m-40) cc_final: 0.8442 (m-40) REVERT: G 132 GLU cc_start: 0.8745 (pm20) cc_final: 0.8508 (mm-30) REVERT: G 227 GLU cc_start: 0.9725 (tt0) cc_final: 0.9289 (tm-30) REVERT: H 81 ASN cc_start: 0.8700 (m-40) cc_final: 0.8375 (m-40) REVERT: H 111 HIS cc_start: 0.9035 (t-90) cc_final: 0.8667 (t-90) REVERT: H 178 GLU cc_start: 0.8244 (mp0) cc_final: 0.7910 (mp0) REVERT: H 227 GLU cc_start: 0.9699 (tt0) cc_final: 0.9276 (tm-30) REVERT: H 238 THR cc_start: 0.7791 (p) cc_final: 0.7466 (p) outliers start: 29 outliers final: 23 residues processed: 207 average time/residue: 0.2981 time to fit residues: 95.4941 Evaluate side-chains 204 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 325 LEU 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 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 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 134 optimal weight: 50.0000 chunk 122 optimal weight: 0.0370 chunk 87 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 137 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 184 optimal weight: 40.0000 chunk 164 optimal weight: 20.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN D 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.110860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077443 restraints weight = 47781.668| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.71 r_work: 0.3147 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19176 Z= 0.104 Angle : 0.568 6.849 26540 Z= 0.273 Chirality : 0.034 0.123 3436 Planarity : 0.004 0.046 2880 Dihedral : 8.885 115.027 7492 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.11 % Allowed : 16.03 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.19), residues: 2072 helix: 2.59 (0.16), residues: 1008 sheet: -1.67 (0.47), residues: 120 loop : 0.28 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 275 HIS 0.002 0.001 HIS G 80 PHE 0.009 0.001 PHE A 303 TYR 0.009 0.001 TYR D 290 ARG 0.005 0.000 ARG C 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 4) link_NAG-ASN : angle 3.58251 ( 12) hydrogen bonds : bond 0.03577 ( 832) hydrogen bonds : angle 3.36969 ( 2424) SS BOND : bond 0.00057 ( 16) SS BOND : angle 0.32676 ( 32) covalent geometry : bond 0.00226 (19156) covalent geometry : angle 0.56352 (26496) ********************** 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 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7440 (mmm) cc_final: 0.7033 (mmp) REVERT: A 173 ASP cc_start: 0.8041 (t0) cc_final: 0.7234 (p0) REVERT: A 222 GLN cc_start: 0.8456 (tt0) cc_final: 0.8161 (mm-40) REVERT: A 282 MET cc_start: 0.9226 (tpt) cc_final: 0.8998 (tpp) REVERT: B 94 MET cc_start: 0.7624 (mmm) cc_final: 0.7269 (mmp) REVERT: B 173 ASP cc_start: 0.8033 (t0) cc_final: 0.7266 (p0) REVERT: B 282 MET cc_start: 0.9200 (tpt) cc_final: 0.8975 (tpp) REVERT: C 94 MET cc_start: 0.7642 (mmm) cc_final: 0.7290 (mmp) REVERT: C 173 ASP cc_start: 0.8040 (t0) cc_final: 0.7232 (p0) REVERT: C 222 GLN cc_start: 0.8442 (tt0) cc_final: 0.8151 (mm-40) REVERT: C 282 MET cc_start: 0.9197 (tpt) cc_final: 0.8978 (tpp) REVERT: D 94 MET cc_start: 0.7638 (mmm) cc_final: 0.7302 (mmp) REVERT: D 104 MET cc_start: 0.8690 (tpp) cc_final: 0.8288 (tpp) REVERT: E 81 ASN cc_start: 0.8778 (m-40) cc_final: 0.8445 (m-40) REVERT: E 111 HIS cc_start: 0.9000 (t-90) cc_final: 0.8675 (t-90) REVERT: E 178 GLU cc_start: 0.8243 (mp0) cc_final: 0.7996 (mp0) REVERT: E 227 GLU cc_start: 0.9684 (tt0) cc_final: 0.9267 (tm-30) REVERT: E 238 THR cc_start: 0.7744 (p) cc_final: 0.7531 (p) REVERT: F 81 ASN cc_start: 0.8765 (m-40) cc_final: 0.8424 (m-40) REVERT: F 111 HIS cc_start: 0.9014 (t-90) cc_final: 0.8678 (t-90) REVERT: F 130 GLN cc_start: 0.8480 (mp10) cc_final: 0.8088 (mp10) REVERT: F 178 GLU cc_start: 0.8265 (mp0) cc_final: 0.7849 (mp0) REVERT: F 227 GLU cc_start: 0.9698 (tt0) cc_final: 0.9274 (tm-30) REVERT: F 238 THR cc_start: 0.7945 (p) cc_final: 0.7721 (p) REVERT: G 81 ASN cc_start: 0.8784 (m-40) cc_final: 0.8476 (m-40) REVERT: G 111 HIS cc_start: 0.9017 (t-90) cc_final: 0.8691 (t-90) REVERT: G 132 GLU cc_start: 0.8707 (pm20) cc_final: 0.8485 (mm-30) REVERT: G 178 GLU cc_start: 0.8326 (mp0) cc_final: 0.8031 (mp0) REVERT: G 227 GLU cc_start: 0.9724 (tt0) cc_final: 0.9295 (tm-30) REVERT: H 81 ASN cc_start: 0.8777 (m-40) cc_final: 0.8463 (m-40) REVERT: H 111 HIS cc_start: 0.9025 (t-90) cc_final: 0.8695 (t-90) REVERT: H 178 GLU cc_start: 0.8233 (mp0) cc_final: 0.7794 (mp0) REVERT: H 227 GLU cc_start: 0.9690 (tt0) cc_final: 0.9269 (tm-30) REVERT: H 238 THR cc_start: 0.7728 (p) cc_final: 0.7522 (p) outliers start: 19 outliers final: 17 residues processed: 188 average time/residue: 0.2959 time to fit residues: 88.4787 Evaluate side-chains 193 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 229 THR 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 247 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 247 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 109 optimal weight: 40.0000 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 115 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.109278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075601 restraints weight = 47457.733| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.74 r_work: 0.3051 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3281 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= 0.134 Angle : 0.577 12.421 26540 Z= 0.278 Chirality : 0.035 0.128 3436 Planarity : 0.004 0.046 2880 Dihedral : 8.867 113.534 7492 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.40 % Allowed : 15.79 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2072 helix: 2.52 (0.16), residues: 1008 sheet: -1.70 (0.47), residues: 120 loop : 0.30 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 178 HIS 0.002 0.001 HIS F 252 PHE 0.017 0.001 PHE A 303 TYR 0.009 0.001 TYR D 279 ARG 0.005 0.000 ARG C 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 4) link_NAG-ASN : angle 3.56402 ( 12) hydrogen bonds : bond 0.03952 ( 832) hydrogen bonds : angle 3.42569 ( 2424) SS BOND : bond 0.00085 ( 16) SS BOND : angle 0.31331 ( 32) covalent geometry : bond 0.00318 (19156) covalent geometry : angle 0.57246 (26496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9426.81 seconds wall clock time: 164 minutes 8.24 seconds (9848.24 seconds total)