Starting phenix.real_space_refine on Fri Feb 6 14:18:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6u_62136/02_2026/9k6u_62136_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6u_62136/02_2026/9k6u_62136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6u_62136/02_2026/9k6u_62136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6u_62136/02_2026/9k6u_62136.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6u_62136/02_2026/9k6u_62136_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6u_62136/02_2026/9k6u_62136_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.105 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: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 8184 2.51 5 N 2176 2.21 5 O 2432 1.98 5 H 12424 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25296 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3148 Classifications: {'peptide': 208} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "A" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3148 Classifications: {'peptide': 208} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "D" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3148 Classifications: {'peptide': 208} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "C" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3148 Classifications: {'peptide': 208} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "E" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3148 Classifications: {'peptide': 208} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "H" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3148 Classifications: {'peptide': 208} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "G" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3148 Classifications: {'peptide': 208} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "F" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3148 Classifications: {'peptide': 208} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 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: "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: "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 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: "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 Time building chain proxies: 4.50, per 1000 atoms: 0.18 Number of scatterers: 25296 At special positions: 0 Unit cell: (101.882, 101.04, 90.094, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 2432 8.00 N 2176 7.00 C 8184 6.00 H 12424 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 271 " distance=2.37 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS G 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS G 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 357 " distance=2.04 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 271 " distance=2.19 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS H 318 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS H 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 357 " distance=2.03 Simple disulfide: pdb=" SG CYS D 210 " - pdb=" SG CYS D 271 " distance=1.77 Simple disulfide: pdb=" SG CYS D 317 " - pdb=" SG CYS E 318 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS E 317 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS F 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS F 317 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 357 " distance=2.04 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 357 " distance=2.03 Simple disulfide: pdb=" SG CYS H 210 " - pdb=" SG CYS H 271 " distance=2.04 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 357 " distance=2.04 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 271 " distance=1.94 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 357 " distance=2.04 Simple disulfide: pdb=" SG CYS F 210 " - pdb=" SG CYS F 271 " distance=2.02 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 A1000 " - " ASN A 220 " " NAG B1000 " - " ASN B 220 " " NAG C1000 " - " ASN C 220 " " NAG D1000 " - " ASN D 220 " " NAG E1000 " - " ASN E 220 " " NAG F1000 " - " ASN F 220 " " NAG G1000 " - " ASN G 220 " " NAG H1000 " - " ASN H 220 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 598.5 milliseconds 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 18 sheets defined 5.5% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.657A pdb=" N GLY B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 4.323A pdb=" N GLY A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.654A pdb=" N GLY A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.653A pdb=" N GLY D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.636A pdb=" N GLY C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 removed outlier: 4.327A pdb=" N GLY E 178 " --> pdb=" O LEU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 352 removed outlier: 3.685A pdb=" N GLY E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 352 removed outlier: 3.677A pdb=" N GLY H 352 " --> pdb=" O ILE H 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 179 removed outlier: 4.344A pdb=" N GLY G 178 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 328 Processing helix chain 'G' and resid 344 through 352 Processing helix chain 'F' and resid 344 through 352 removed outlier: 3.685A pdb=" N GLY F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 288 through 293 removed outlier: 6.471A pdb=" N LEU B 283 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR B 292 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR B 281 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 211 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER B 208 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 338 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N CYS B 210 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE B 336 " --> pdb=" O CYS B 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 288 through 293 removed outlier: 6.471A pdb=" N LEU B 283 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR B 292 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR B 281 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER B 208 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 338 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N CYS B 210 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE B 336 " --> pdb=" O CYS B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 255 through 259 removed outlier: 3.527A pdb=" N PHE B 225 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 240 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE B 223 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU B 308 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 370 " --> pdb=" O HIS B 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 293 removed outlier: 6.424A pdb=" N LEU A 283 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR A 292 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 281 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 272 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 209 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP A 212 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY A 335 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LYS A 214 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU A 333 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 255 through 257 removed outlier: 3.527A pdb=" N PHE A 225 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 240 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE A 223 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU A 308 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 195 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 370 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 288 through 293 removed outlier: 6.414A pdb=" N LEU D 283 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR D 292 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR D 281 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER D 208 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE D 338 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS D 210 " --> pdb=" O PHE D 336 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE D 336 " --> pdb=" O CYS D 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 288 through 293 removed outlier: 6.414A pdb=" N LEU D 283 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR D 292 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR D 281 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 273 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER D 208 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE D 338 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS D 210 " --> pdb=" O PHE D 336 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE D 336 " --> pdb=" O CYS D 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 255 through 259 removed outlier: 3.531A pdb=" N PHE D 225 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU D 240 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 223 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU D 308 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER D 195 " --> pdb=" O GLN D 372 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU D 370 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 288 through 293 removed outlier: 6.422A pdb=" N LEU C 283 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR C 292 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR C 281 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER C 208 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE C 338 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS C 210 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE C 336 " --> pdb=" O CYS C 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 255 through 259 removed outlier: 3.502A pdb=" N PHE C 225 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 240 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE C 223 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU C 308 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU C 370 " --> pdb=" O HIS C 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 288 through 293 removed outlier: 6.509A pdb=" N LEU E 283 " --> pdb=" O ALA E 290 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR E 292 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR E 281 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER E 208 " --> pdb=" O ILE E 338 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE E 338 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS E 210 " --> pdb=" O PHE E 336 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE E 336 " --> pdb=" O CYS E 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 255 through 258 removed outlier: 3.537A pdb=" N PHE E 225 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU E 240 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE E 223 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU E 308 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU E 370 " --> pdb=" O HIS E 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 288 through 293 removed outlier: 6.592A pdb=" N LEU H 283 " --> pdb=" O ALA H 290 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR H 292 " --> pdb=" O THR H 281 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR H 281 " --> pdb=" O THR H 292 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP H 212 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLY H 335 " --> pdb=" O TRP H 212 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS H 214 " --> pdb=" O LEU H 333 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU H 333 " --> pdb=" O LYS H 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 255 through 259 removed outlier: 3.529A pdb=" N PHE H 225 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU H 240 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE H 223 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU H 308 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU H 370 " --> pdb=" O HIS H 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 288 through 293 removed outlier: 6.555A pdb=" N LEU G 283 " --> pdb=" O ALA G 290 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR G 292 " --> pdb=" O THR G 281 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR G 281 " --> pdb=" O THR G 292 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE G 211 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY G 272 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G 209 " --> pdb=" O GLY G 272 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP G 212 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLY G 335 " --> pdb=" O TRP G 212 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LYS G 214 " --> pdb=" O LEU G 333 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU G 333 " --> pdb=" O LYS G 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 255 through 258 removed outlier: 3.525A pdb=" N PHE G 225 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU G 240 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE G 223 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU G 308 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU G 370 " --> pdb=" O HIS G 197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 288 through 293 removed outlier: 6.494A pdb=" N LEU F 283 " --> pdb=" O ALA F 290 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR F 292 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N THR F 281 " --> pdb=" O THR F 292 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE F 211 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 272 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA F 209 " --> pdb=" O GLY F 272 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER F 208 " --> pdb=" O ILE F 338 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE F 338 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N CYS F 210 " --> pdb=" O PHE F 336 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE F 336 " --> pdb=" O CYS F 210 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 255 through 257 removed outlier: 3.528A pdb=" N PHE F 225 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU F 240 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE F 223 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU F 308 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU F 370 " --> pdb=" O HIS F 197 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1140 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: 5.21 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 12424 1.03 - 1.23: 1205 1.23 - 1.44: 4612 1.44 - 1.65: 7247 1.65 - 1.86: 112 Bond restraints: 25600 Sorted by residual: bond pdb=" C CYS A 271 " pdb=" O CYS A 271 " ideal model delta sigma weight residual 1.235 1.153 0.082 1.14e-02 7.69e+03 5.19e+01 bond pdb=" C CYS F 271 " pdb=" O CYS F 271 " ideal model delta sigma weight residual 1.235 1.153 0.082 1.23e-02 6.61e+03 4.44e+01 bond pdb=" C LEU A 270 " pdb=" O LEU A 270 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.14e-02 7.69e+03 4.26e+01 bond pdb=" C ILE D 245 " pdb=" O ILE D 245 " ideal model delta sigma weight residual 1.237 1.170 0.067 1.09e-02 8.42e+03 3.77e+01 bond pdb=" C ILE G 245 " pdb=" O ILE G 245 " ideal model delta sigma weight residual 1.238 1.171 0.066 1.10e-02 8.26e+03 3.64e+01 ... (remaining 25595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.26: 46093 7.26 - 14.53: 13 14.53 - 21.79: 0 21.79 - 29.05: 0 29.05 - 36.32: 6 Bond angle restraints: 46112 Sorted by residual: angle pdb=" C VAL B 319 " pdb=" CA VAL B 319 " pdb=" HA VAL B 319 " ideal model delta sigma weight residual 109.00 72.68 36.32 3.00e+00 1.11e-01 1.47e+02 angle pdb=" N VAL B 319 " pdb=" CA VAL B 319 " pdb=" HA VAL B 319 " ideal model delta sigma weight residual 110.00 74.77 35.23 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C VAL D 319 " pdb=" CA VAL D 319 " pdb=" HA VAL D 319 " ideal model delta sigma weight residual 109.00 73.93 35.07 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N VAL D 319 " pdb=" CA VAL D 319 " pdb=" HA VAL D 319 " ideal model delta sigma weight residual 110.00 75.61 34.39 3.00e+00 1.11e-01 1.31e+02 angle pdb=" CB VAL D 319 " pdb=" CA VAL D 319 " pdb=" HA VAL D 319 " ideal model delta sigma weight residual 109.00 75.31 33.69 3.00e+00 1.11e-01 1.26e+02 ... (remaining 46107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.77: 11187 20.77 - 41.54: 696 41.54 - 62.32: 229 62.32 - 83.09: 32 83.09 - 103.86: 24 Dihedral angle restraints: 12168 sinusoidal: 6616 harmonic: 5552 Sorted by residual: dihedral pdb=" CB CYS D 317 " pdb=" SG CYS D 317 " pdb=" SG CYS E 318 " pdb=" CB CYS E 318 " ideal model delta sinusoidal sigma weight residual 93.00 133.37 -40.37 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CB CYS C 318 " pdb=" SG CYS C 318 " pdb=" SG CYS F 317 " pdb=" CB CYS F 317 " ideal model delta sinusoidal sigma weight residual 93.00 129.90 -36.90 1 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" N SER B 244 " pdb=" C SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta harmonic sigma weight residual 122.80 111.86 10.94 0 2.50e+00 1.60e-01 1.91e+01 ... (remaining 12165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1696 0.066 - 0.131: 261 0.131 - 0.197: 28 0.197 - 0.262: 3 0.262 - 0.328: 4 Chirality restraints: 1992 Sorted by residual: chirality pdb=" CA TYR B 242 " pdb=" N TYR B 242 " pdb=" C TYR B 242 " pdb=" CB TYR B 242 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA VAL B 319 " pdb=" N VAL B 319 " pdb=" C VAL B 319 " pdb=" CB VAL B 319 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL D 319 " pdb=" N VAL D 319 " pdb=" C VAL D 319 " pdb=" CB VAL D 319 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1989 not shown) Planarity restraints: 3880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 243 " -0.177 2.00e-02 2.50e+03 4.05e-01 2.46e+03 pdb=" CD GLN E 243 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLN E 243 " 0.169 2.00e-02 2.50e+03 pdb=" NE2 GLN E 243 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN E 243 " -0.684 2.00e-02 2.50e+03 pdb="HE22 GLN E 243 " 0.675 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 243 " 0.208 2.00e-02 2.50e+03 3.90e-01 2.28e+03 pdb=" CD GLN B 243 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN B 243 " -0.200 2.00e-02 2.50e+03 pdb=" NE2 GLN B 243 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 243 " 0.650 2.00e-02 2.50e+03 pdb="HE22 GLN B 243 " -0.638 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 237 " 0.137 2.00e-02 2.50e+03 1.53e-01 3.51e+02 pdb=" CD GLN F 237 " -0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN F 237 " -0.133 2.00e-02 2.50e+03 pdb=" NE2 GLN F 237 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN F 237 " -0.224 2.00e-02 2.50e+03 pdb="HE22 GLN F 237 " 0.231 2.00e-02 2.50e+03 ... (remaining 3877 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 894 2.18 - 2.78: 48899 2.78 - 3.39: 64305 3.39 - 3.99: 92001 3.99 - 4.60: 142142 Nonbonded interactions: 348241 Sorted by model distance: nonbonded pdb=" H VAL D 319 " pdb=" HA VAL D 319 " model vdw 1.570 1.816 nonbonded pdb=" H VAL B 319 " pdb=" HA VAL B 319 " model vdw 1.572 1.816 nonbonded pdb=" HA VAL D 319 " pdb=" HB VAL D 319 " model vdw 1.628 1.952 nonbonded pdb="HE22 GLN H 237 " pdb=" OE2 GLU H 313 " model vdw 1.634 2.450 nonbonded pdb="HE22 GLN C 237 " pdb=" OE2 GLU C 313 " model vdw 1.637 2.450 ... (remaining 348236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = 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=1.00 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: 1.080 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: 0.160 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.880 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 0.007 0.344 13208 Z= 0.379 Angle : 1.000 51.243 17960 Z= 0.532 Chirality : 0.051 0.328 1992 Planarity : 0.004 0.042 2272 Dihedral : 14.971 103.861 4752 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.07 % Allowed : 0.59 % Favored : 99.34 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1648 helix: 1.73 (0.64), residues: 72 sheet: 0.28 (0.21), residues: 616 loop : -1.27 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 231 TYR 0.012 0.002 TYR E 234 PHE 0.009 0.001 PHE B 323 TRP 0.006 0.001 TRP F 212 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00533 (13176) covalent geometry : angle 0.69182 (17888) SS BOND : bond 0.09578 ( 24) SS BOND : angle 13.94509 ( 48) hydrogen bonds : bond 0.24750 ( 442) hydrogen bonds : angle 8.68246 ( 1140) link_NAG-ASN : bond 0.00292 ( 8) link_NAG-ASN : angle 1.47204 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 261 MET cc_start: 0.6671 (mmt) cc_final: 0.6248 (mmt) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 1.7380 time to fit residues: 437.0995 Evaluate side-chains 186 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 309 GLN G 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.156658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122119 restraints weight = 39493.376| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.52 r_work: 0.3479 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13208 Z= 0.136 Angle : 0.577 7.461 17960 Z= 0.314 Chirality : 0.049 0.318 1992 Planarity : 0.004 0.041 2272 Dihedral : 6.255 63.279 1928 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.18 % Allowed : 9.93 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1648 helix: 1.79 (0.62), residues: 72 sheet: 0.29 (0.20), residues: 664 loop : -1.09 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 231 TYR 0.012 0.002 TYR C 239 PHE 0.011 0.002 PHE F 225 TRP 0.009 0.001 TRP D 212 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00321 (13176) covalent geometry : angle 0.56939 (17888) SS BOND : bond 0.00339 ( 24) SS BOND : angle 1.73647 ( 48) hydrogen bonds : bond 0.05229 ( 442) hydrogen bonds : angle 5.39222 ( 1140) link_NAG-ASN : bond 0.00240 ( 8) link_NAG-ASN : angle 1.19365 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 259 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: B 295 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: D 187 MET cc_start: 0.8517 (ptt) cc_final: 0.8258 (ptt) REVERT: D 205 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7571 (tt0) REVERT: D 295 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: C 266 ARG cc_start: 0.7413 (ttt180) cc_final: 0.7211 (ttp-170) REVERT: E 295 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: H 261 MET cc_start: 0.6805 (mmt) cc_final: 0.6431 (mmt) REVERT: G 295 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6791 (mp0) REVERT: F 261 MET cc_start: 0.6472 (mtt) cc_final: 0.6248 (mtt) outliers start: 16 outliers final: 10 residues processed: 203 average time/residue: 1.8153 time to fit residues: 392.0524 Evaluate side-chains 194 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 372 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121185 restraints weight = 39449.486| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.53 r_work: 0.3458 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13208 Z= 0.159 Angle : 0.574 7.082 17960 Z= 0.310 Chirality : 0.049 0.316 1992 Planarity : 0.004 0.036 2272 Dihedral : 5.352 35.127 1928 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.40 % Allowed : 11.32 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1648 helix: 2.48 (0.62), residues: 64 sheet: 0.35 (0.20), residues: 664 loop : -1.19 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 231 TYR 0.010 0.002 TYR C 239 PHE 0.010 0.002 PHE A 225 TRP 0.009 0.001 TRP A 339 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00390 (13176) covalent geometry : angle 0.56270 (17888) SS BOND : bond 0.00342 ( 24) SS BOND : angle 2.02906 ( 48) hydrogen bonds : bond 0.05088 ( 442) hydrogen bonds : angle 5.14997 ( 1140) link_NAG-ASN : bond 0.00251 ( 8) link_NAG-ASN : angle 1.46608 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: D 295 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: C 266 ARG cc_start: 0.7450 (ttt180) cc_final: 0.6978 (ttp80) REVERT: E 295 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: H 261 MET cc_start: 0.6804 (mmt) cc_final: 0.6426 (mmt) REVERT: H 295 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6899 (mp0) REVERT: G 295 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6764 (mp0) outliers start: 19 outliers final: 11 residues processed: 192 average time/residue: 1.8627 time to fit residues: 379.8931 Evaluate side-chains 196 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 104 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121704 restraints weight = 39218.835| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.57 r_work: 0.3478 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13208 Z= 0.129 Angle : 0.552 6.993 17960 Z= 0.297 Chirality : 0.048 0.315 1992 Planarity : 0.003 0.037 2272 Dihedral : 5.057 28.921 1928 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.96 % Allowed : 12.65 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.21), residues: 1648 helix: 1.98 (0.59), residues: 72 sheet: 0.49 (0.20), residues: 648 loop : -1.23 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 231 TYR 0.011 0.001 TYR D 239 PHE 0.009 0.001 PHE G 225 TRP 0.010 0.001 TRP D 212 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00314 (13176) covalent geometry : angle 0.54097 (17888) SS BOND : bond 0.00327 ( 24) SS BOND : angle 1.89626 ( 48) hydrogen bonds : bond 0.04413 ( 442) hydrogen bonds : angle 4.96875 ( 1140) link_NAG-ASN : bond 0.00246 ( 8) link_NAG-ASN : angle 1.60636 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7101 (mp0) cc_final: 0.6781 (mt-10) REVERT: A 304 GLU cc_start: 0.7798 (pm20) cc_final: 0.7596 (pm20) REVERT: D 205 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7558 (tt0) REVERT: D 295 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: C 266 ARG cc_start: 0.7405 (ttt180) cc_final: 0.6958 (ttp80) REVERT: H 261 MET cc_start: 0.6777 (mmt) cc_final: 0.6439 (mmt) REVERT: H 295 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6703 (mp0) REVERT: G 295 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6734 (mp0) REVERT: G 304 GLU cc_start: 0.7815 (pm20) cc_final: 0.7605 (pm20) REVERT: F 191 LYS cc_start: 0.8465 (mtmt) cc_final: 0.7384 (mmtm) REVERT: F 252 GLU cc_start: 0.7055 (mp0) cc_final: 0.6757 (mt-10) outliers start: 13 outliers final: 10 residues processed: 188 average time/residue: 1.7354 time to fit residues: 347.2556 Evaluate side-chains 193 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 157 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.156814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121485 restraints weight = 38923.973| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.54 r_work: 0.3472 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13208 Z= 0.141 Angle : 0.555 8.565 17960 Z= 0.299 Chirality : 0.048 0.315 1992 Planarity : 0.004 0.057 2272 Dihedral : 4.962 25.765 1928 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.25 % Allowed : 12.87 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1648 helix: 2.15 (0.58), residues: 72 sheet: 0.51 (0.20), residues: 648 loop : -1.22 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 231 TYR 0.010 0.002 TYR D 239 PHE 0.010 0.002 PHE G 225 TRP 0.009 0.001 TRP D 212 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00346 (13176) covalent geometry : angle 0.54335 (17888) SS BOND : bond 0.00379 ( 24) SS BOND : angle 1.96687 ( 48) hydrogen bonds : bond 0.04444 ( 442) hydrogen bonds : angle 4.92076 ( 1140) link_NAG-ASN : bond 0.00213 ( 8) link_NAG-ASN : angle 1.66098 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: A 252 GLU cc_start: 0.7045 (mp0) cc_final: 0.6778 (mt-10) REVERT: D 295 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: C 266 ARG cc_start: 0.7450 (ttt180) cc_final: 0.7035 (ttp80) REVERT: H 261 MET cc_start: 0.6833 (mmt) cc_final: 0.6498 (mmt) REVERT: H 295 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6730 (mp0) REVERT: G 295 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6743 (mp0) REVERT: G 304 GLU cc_start: 0.7870 (pm20) cc_final: 0.7656 (pm20) REVERT: F 191 LYS cc_start: 0.8493 (mtmt) cc_final: 0.7420 (mmtm) REVERT: F 252 GLU cc_start: 0.7054 (mp0) cc_final: 0.6769 (mt-10) REVERT: F 304 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7296 (mt-10) outliers start: 17 outliers final: 12 residues processed: 187 average time/residue: 1.7331 time to fit residues: 344.3446 Evaluate side-chains 194 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 304 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 66 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.156528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121217 restraints weight = 39169.335| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.55 r_work: 0.3463 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13208 Z= 0.149 Angle : 0.560 7.916 17960 Z= 0.302 Chirality : 0.048 0.314 1992 Planarity : 0.004 0.046 2272 Dihedral : 4.951 25.622 1928 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.18 % Allowed : 13.82 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1648 helix: 2.15 (0.57), residues: 72 sheet: 0.51 (0.20), residues: 648 loop : -1.24 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 231 TYR 0.011 0.002 TYR A 239 PHE 0.010 0.002 PHE G 225 TRP 0.009 0.001 TRP D 212 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00367 (13176) covalent geometry : angle 0.54864 (17888) SS BOND : bond 0.00365 ( 24) SS BOND : angle 1.99343 ( 48) hydrogen bonds : bond 0.04466 ( 442) hydrogen bonds : angle 4.89281 ( 1140) link_NAG-ASN : bond 0.00215 ( 8) link_NAG-ASN : angle 1.66232 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: A 252 GLU cc_start: 0.7084 (mp0) cc_final: 0.6844 (mt-10) REVERT: D 295 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: C 266 ARG cc_start: 0.7441 (ttt180) cc_final: 0.7007 (ttp80) REVERT: H 261 MET cc_start: 0.6835 (mmt) cc_final: 0.6505 (mmt) REVERT: H 295 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6694 (mp0) REVERT: G 295 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6738 (mp0) REVERT: G 304 GLU cc_start: 0.7826 (pm20) cc_final: 0.7584 (pm20) REVERT: F 252 GLU cc_start: 0.7111 (mp0) cc_final: 0.6858 (mt-10) REVERT: F 304 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7285 (mt-10) outliers start: 16 outliers final: 12 residues processed: 190 average time/residue: 1.7397 time to fit residues: 351.3238 Evaluate side-chains 195 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 304 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.158632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123295 restraints weight = 38883.148| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.57 r_work: 0.3499 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13208 Z= 0.104 Angle : 0.523 6.477 17960 Z= 0.281 Chirality : 0.047 0.313 1992 Planarity : 0.003 0.052 2272 Dihedral : 4.627 22.796 1928 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.18 % Allowed : 14.12 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.21), residues: 1648 helix: 2.39 (0.58), residues: 72 sheet: 0.53 (0.20), residues: 648 loop : -1.16 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 231 TYR 0.009 0.001 TYR D 239 PHE 0.008 0.001 PHE A 225 TRP 0.010 0.001 TRP D 212 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00251 (13176) covalent geometry : angle 0.51355 (17888) SS BOND : bond 0.00248 ( 24) SS BOND : angle 1.60863 ( 48) hydrogen bonds : bond 0.03728 ( 442) hydrogen bonds : angle 4.73399 ( 1140) link_NAG-ASN : bond 0.00251 ( 8) link_NAG-ASN : angle 1.59929 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: D 191 LYS cc_start: 0.8387 (mtmt) cc_final: 0.7632 (mtmm) REVERT: D 280 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6996 (mm) REVERT: D 295 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: C 266 ARG cc_start: 0.7450 (ttt180) cc_final: 0.7009 (ttp80) REVERT: E 280 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6978 (mm) REVERT: H 261 MET cc_start: 0.6818 (mmt) cc_final: 0.6527 (mmt) REVERT: H 295 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6677 (mp0) REVERT: G 295 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6724 (mp0) REVERT: G 304 GLU cc_start: 0.7849 (pm20) cc_final: 0.7602 (pm20) REVERT: F 191 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7354 (mmtm) REVERT: F 252 GLU cc_start: 0.7075 (mp0) cc_final: 0.6825 (mt-10) REVERT: F 304 GLU cc_start: 0.7621 (mp0) cc_final: 0.7245 (mt-10) outliers start: 16 outliers final: 11 residues processed: 193 average time/residue: 1.7015 time to fit residues: 349.2168 Evaluate side-chains 189 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 378 GLN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.158363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123140 restraints weight = 39182.799| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.57 r_work: 0.3523 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13208 Z= 0.117 Angle : 0.546 12.226 17960 Z= 0.292 Chirality : 0.048 0.313 1992 Planarity : 0.004 0.065 2272 Dihedral : 4.602 24.006 1928 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.18 % Allowed : 14.41 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1648 helix: 2.38 (0.58), residues: 72 sheet: 0.56 (0.20), residues: 648 loop : -1.12 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 231 TYR 0.010 0.001 TYR F 239 PHE 0.010 0.001 PHE C 225 TRP 0.009 0.001 TRP D 212 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00288 (13176) covalent geometry : angle 0.53241 (17888) SS BOND : bond 0.00450 ( 24) SS BOND : angle 2.14279 ( 48) hydrogen bonds : bond 0.03937 ( 442) hydrogen bonds : angle 4.75282 ( 1140) link_NAG-ASN : bond 0.00213 ( 8) link_NAG-ASN : angle 1.57948 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: D 191 LYS cc_start: 0.8412 (mtmt) cc_final: 0.7663 (mtmm) REVERT: D 280 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7060 (mm) REVERT: D 295 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: C 266 ARG cc_start: 0.7456 (ttt180) cc_final: 0.7047 (ttp80) REVERT: E 280 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7062 (mm) REVERT: H 261 MET cc_start: 0.6810 (mmt) cc_final: 0.6524 (mmt) REVERT: H 295 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6719 (mp0) REVERT: G 295 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6739 (mp0) REVERT: G 304 GLU cc_start: 0.7831 (pm20) cc_final: 0.7569 (pm20) REVERT: F 191 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7378 (mmtm) REVERT: F 252 GLU cc_start: 0.7072 (mp0) cc_final: 0.6829 (mt-10) REVERT: F 304 GLU cc_start: 0.7744 (mp0) cc_final: 0.7328 (mt-10) outliers start: 16 outliers final: 11 residues processed: 183 average time/residue: 1.8149 time to fit residues: 352.4767 Evaluate side-chains 190 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 378 GLN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.155141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119801 restraints weight = 39092.705| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.56 r_work: 0.3457 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13208 Z= 0.195 Angle : 0.621 16.376 17960 Z= 0.332 Chirality : 0.050 0.314 1992 Planarity : 0.004 0.058 2272 Dihedral : 5.089 24.970 1928 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.25 % Allowed : 14.49 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1648 helix: 2.02 (0.55), residues: 72 sheet: 0.54 (0.20), residues: 648 loop : -1.22 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 231 TYR 0.012 0.002 TYR G 239 PHE 0.011 0.002 PHE C 225 TRP 0.009 0.001 TRP H 339 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00491 (13176) covalent geometry : angle 0.60464 (17888) SS BOND : bond 0.00574 ( 24) SS BOND : angle 2.62951 ( 48) hydrogen bonds : bond 0.04946 ( 442) hydrogen bonds : angle 4.95877 ( 1140) link_NAG-ASN : bond 0.00192 ( 8) link_NAG-ASN : angle 1.63200 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.6375 (mmt) cc_final: 0.5812 (mmt) REVERT: B 295 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: A 295 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: A 304 GLU cc_start: 0.7828 (pm20) cc_final: 0.7606 (pm20) REVERT: D 295 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: C 231 ARG cc_start: 0.8065 (mpp80) cc_final: 0.7758 (tpp80) REVERT: C 266 ARG cc_start: 0.7447 (ttt180) cc_final: 0.6973 (ttp80) REVERT: H 261 MET cc_start: 0.6855 (mmt) cc_final: 0.6525 (mmt) REVERT: H 295 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6713 (mp0) REVERT: G 295 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6741 (mp0) REVERT: G 304 GLU cc_start: 0.7787 (pm20) cc_final: 0.7516 (pm20) REVERT: F 191 LYS cc_start: 0.8509 (mtmt) cc_final: 0.7435 (mmtm) REVERT: F 252 GLU cc_start: 0.7162 (mp0) cc_final: 0.6907 (mt-10) REVERT: F 304 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7355 (mt-10) outliers start: 17 outliers final: 13 residues processed: 187 average time/residue: 1.8063 time to fit residues: 358.6995 Evaluate side-chains 196 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 378 GLN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 304 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.155934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120594 restraints weight = 38972.469| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.56 r_work: 0.3468 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13208 Z= 0.164 Angle : 0.599 15.773 17960 Z= 0.319 Chirality : 0.049 0.313 1992 Planarity : 0.004 0.063 2272 Dihedral : 5.044 27.037 1928 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.18 % Allowed : 14.71 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1648 helix: 1.99 (0.55), residues: 72 sheet: 0.51 (0.20), residues: 648 loop : -1.22 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 231 TYR 0.011 0.002 TYR A 239 PHE 0.011 0.002 PHE C 225 TRP 0.009 0.001 TRP D 212 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00411 (13176) covalent geometry : angle 0.58314 (17888) SS BOND : bond 0.00530 ( 24) SS BOND : angle 2.48027 ( 48) hydrogen bonds : bond 0.04572 ( 442) hydrogen bonds : angle 4.88785 ( 1140) link_NAG-ASN : bond 0.00223 ( 8) link_NAG-ASN : angle 1.62451 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.6375 (mmt) cc_final: 0.5807 (mmt) REVERT: B 295 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: A 295 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: A 304 GLU cc_start: 0.7842 (pm20) cc_final: 0.7610 (pm20) REVERT: D 191 LYS cc_start: 0.8447 (mtmt) cc_final: 0.7689 (mtmm) REVERT: D 295 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: C 231 ARG cc_start: 0.8059 (mpp80) cc_final: 0.7737 (tpp80) REVERT: C 266 ARG cc_start: 0.7474 (ttt180) cc_final: 0.7018 (ttp80) REVERT: H 261 MET cc_start: 0.6851 (mmt) cc_final: 0.6521 (mmt) REVERT: H 295 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6774 (mp0) REVERT: G 295 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6776 (mp0) REVERT: G 304 GLU cc_start: 0.7806 (pm20) cc_final: 0.7530 (pm20) REVERT: F 191 LYS cc_start: 0.8466 (mtmt) cc_final: 0.7393 (mmtm) REVERT: F 304 GLU cc_start: 0.7807 (mp0) cc_final: 0.7372 (mt-10) outliers start: 16 outliers final: 12 residues processed: 184 average time/residue: 1.8955 time to fit residues: 369.7591 Evaluate side-chains 192 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 19 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.157473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122294 restraints weight = 38749.866| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.55 r_work: 0.3489 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 13208 Z= 0.122 Angle : 0.559 15.422 17960 Z= 0.299 Chirality : 0.048 0.313 1992 Planarity : 0.003 0.062 2272 Dihedral : 4.789 22.937 1928 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.25 % Allowed : 14.63 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1648 helix: 2.22 (0.56), residues: 72 sheet: 0.52 (0.20), residues: 648 loop : -1.15 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 231 TYR 0.010 0.001 TYR C 234 PHE 0.009 0.001 PHE A 225 TRP 0.010 0.001 TRP D 212 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00300 (13176) covalent geometry : angle 0.54541 (17888) SS BOND : bond 0.00453 ( 24) SS BOND : angle 2.22296 ( 48) hydrogen bonds : bond 0.04010 ( 442) hydrogen bonds : angle 4.76302 ( 1140) link_NAG-ASN : bond 0.00231 ( 8) link_NAG-ASN : angle 1.59768 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9019.71 seconds wall clock time: 152 minutes 57.57 seconds (9177.57 seconds total)