Starting phenix.real_space_refine on Thu Feb 5 14:54:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hf0_52103/02_2026/9hf0_52103.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hf0_52103/02_2026/9hf0_52103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hf0_52103/02_2026/9hf0_52103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hf0_52103/02_2026/9hf0_52103.map" model { file = "/net/cci-nas-00/data/ceres_data/9hf0_52103/02_2026/9hf0_52103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hf0_52103/02_2026/9hf0_52103.cif" } resolution = 2.86 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 11977 2.51 5 N 2730 2.21 5 O 3129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17934 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2562 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.53, per 1000 atoms: 0.14 Number of scatterers: 17934 At special positions: 0 Unit cell: (114.675, 112.2, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 3129 8.00 N 2730 7.00 C 11977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 264 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 264 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 264 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 245 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 245 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 245 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 786.7 milliseconds 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4354 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 74.3% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 4.271A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 7 " --> pdb=" O ILE A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 100 through 131 removed outlier: 3.723A pdb=" N TRP A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 156 removed outlier: 3.699A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 206 through 236 removed outlier: 3.665A pdb=" N MET A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 249 through 255 removed outlier: 3.795A pdb=" N ASN A 254 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 294 removed outlier: 3.583A pdb=" N LEU A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 3.823A pdb=" N PHE A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.802A pdb=" N TYR A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.682A pdb=" N LEU A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.725A pdb=" N LEU A 369 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 4.270A pdb=" N LEU B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 7 " --> pdb=" O ILE B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.501A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 100 through 131 removed outlier: 3.723A pdb=" N TRP B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 156 removed outlier: 3.698A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 203 Processing helix chain 'B' and resid 206 through 236 removed outlier: 3.665A pdb=" N MET B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.795A pdb=" N ASN B 254 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 294 removed outlier: 3.584A pdb=" N LEU B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Proline residue: B 288 - end of helix removed outlier: 3.824A pdb=" N PHE B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.802A pdb=" N TYR B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.682A pdb=" N LEU B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 355 Processing helix chain 'B' and resid 362 through 369 removed outlier: 3.726A pdb=" N LEU B 369 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 4.271A pdb=" N LEU C 6 " --> pdb=" O ALA C 2 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 7 " --> pdb=" O ILE C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.500A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 100 through 131 removed outlier: 3.722A pdb=" N TRP C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 156 removed outlier: 3.699A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 203 Processing helix chain 'C' and resid 206 through 236 removed outlier: 3.664A pdb=" N MET C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 249 through 255 removed outlier: 3.794A pdb=" N ASN C 254 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 294 removed outlier: 3.582A pdb=" N LEU C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.824A pdb=" N PHE C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.803A pdb=" N TYR C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.682A pdb=" N LEU C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 355 Processing helix chain 'C' and resid 362 through 369 removed outlier: 3.725A pdb=" N LEU C 369 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 4.272A pdb=" N LEU D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 7 " --> pdb=" O ILE D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.500A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 100 through 131 removed outlier: 3.723A pdb=" N TRP D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 156 removed outlier: 3.699A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 203 Processing helix chain 'D' and resid 206 through 236 removed outlier: 3.665A pdb=" N MET D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 249 through 255 removed outlier: 3.795A pdb=" N ASN D 254 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 294 removed outlier: 3.583A pdb=" N LEU D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Proline residue: D 288 - end of helix removed outlier: 3.823A pdb=" N PHE D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.802A pdb=" N TYR D 308 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.682A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 355 Processing helix chain 'D' and resid 362 through 369 removed outlier: 3.726A pdb=" N LEU D 369 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 4.272A pdb=" N LEU E 6 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 7 " --> pdb=" O ILE E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.500A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 100 through 131 removed outlier: 3.723A pdb=" N TRP E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 156 removed outlier: 3.699A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 Processing helix chain 'E' and resid 206 through 236 removed outlier: 3.664A pdb=" N MET E 210 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 240 Processing helix chain 'E' and resid 249 through 255 removed outlier: 3.796A pdb=" N ASN E 254 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 294 removed outlier: 3.583A pdb=" N LEU E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.823A pdb=" N PHE E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 Processing helix chain 'E' and resid 304 through 309 removed outlier: 3.803A pdb=" N TYR E 308 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 338 removed outlier: 3.682A pdb=" N LEU E 329 " --> pdb=" O ASN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 355 Processing helix chain 'E' and resid 362 through 369 removed outlier: 3.727A pdb=" N LEU E 369 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 removed outlier: 4.271A pdb=" N LEU F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 7 " --> pdb=" O ILE F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.500A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 100 through 131 removed outlier: 3.723A pdb=" N TRP F 104 " --> pdb=" O ASN F 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 156 removed outlier: 3.699A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 203 Processing helix chain 'F' and resid 206 through 236 removed outlier: 3.665A pdb=" N MET F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.795A pdb=" N ASN F 254 " --> pdb=" O VAL F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 294 removed outlier: 3.582A pdb=" N LEU F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Proline residue: F 288 - end of helix removed outlier: 3.822A pdb=" N PHE F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 304 through 309 removed outlier: 3.802A pdb=" N TYR F 308 " --> pdb=" O ILE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 338 removed outlier: 3.682A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 355 Processing helix chain 'F' and resid 362 through 369 removed outlier: 3.726A pdb=" N LEU F 369 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 11 removed outlier: 4.271A pdb=" N LEU G 6 " --> pdb=" O ALA G 2 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA G 7 " --> pdb=" O ILE G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.500A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 100 through 131 removed outlier: 3.722A pdb=" N TRP G 104 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 156 removed outlier: 3.699A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 203 Processing helix chain 'G' and resid 206 through 236 removed outlier: 3.664A pdb=" N MET G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 240 Processing helix chain 'G' and resid 249 through 255 removed outlier: 3.794A pdb=" N ASN G 254 " --> pdb=" O VAL G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 294 removed outlier: 3.583A pdb=" N LEU G 274 " --> pdb=" O GLY G 270 " (cutoff:3.500A) Proline residue: G 288 - end of helix removed outlier: 3.823A pdb=" N PHE G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 304 through 309 removed outlier: 3.803A pdb=" N TYR G 308 " --> pdb=" O ILE G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.682A pdb=" N LEU G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 355 Processing helix chain 'G' and resid 362 through 369 removed outlier: 3.726A pdb=" N LEU G 369 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 1129 hydrogen bonds defined for protein. 3198 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: 2.85 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5243 1.35 - 1.46: 4503 1.46 - 1.58: 8482 1.58 - 1.70: 0 1.70 - 1.81: 133 Bond restraints: 18361 Sorted by residual: bond pdb=" CB CYS F 245 " pdb=" SG CYS F 245 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.97e-01 bond pdb=" CB CYS C 245 " pdb=" SG CYS C 245 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.90e-01 bond pdb=" CB CYS G 245 " pdb=" SG CYS G 245 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.75e-01 bond pdb=" CB CYS E 245 " pdb=" SG CYS E 245 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.73e-01 bond pdb=" CB CYS B 245 " pdb=" SG CYS B 245 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.69e-01 ... (remaining 18356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 23408 1.03 - 2.07: 1221 2.07 - 3.10: 130 3.10 - 4.14: 70 4.14 - 5.17: 70 Bond angle restraints: 24899 Sorted by residual: angle pdb=" C ILE D 287 " pdb=" CA ILE D 287 " pdb=" CB ILE D 287 " ideal model delta sigma weight residual 113.70 111.07 2.63 9.50e-01 1.11e+00 7.65e+00 angle pdb=" C ILE E 287 " pdb=" CA ILE E 287 " pdb=" CB ILE E 287 " ideal model delta sigma weight residual 113.70 111.10 2.60 9.50e-01 1.11e+00 7.48e+00 angle pdb=" C ILE G 287 " pdb=" CA ILE G 287 " pdb=" CB ILE G 287 " ideal model delta sigma weight residual 113.70 111.15 2.55 9.50e-01 1.11e+00 7.19e+00 angle pdb=" C LEU G 286 " pdb=" N ILE G 287 " pdb=" CA ILE G 287 " ideal model delta sigma weight residual 120.43 122.88 -2.45 9.60e-01 1.09e+00 6.50e+00 angle pdb=" C LEU E 286 " pdb=" N ILE E 287 " pdb=" CA ILE E 287 " ideal model delta sigma weight residual 120.43 122.86 -2.43 9.60e-01 1.09e+00 6.43e+00 ... (remaining 24894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 10239 15.84 - 31.68: 562 31.68 - 47.52: 77 47.52 - 63.36: 56 63.36 - 79.20: 35 Dihedral angle restraints: 10969 sinusoidal: 4298 harmonic: 6671 Sorted by residual: dihedral pdb=" CA LEU E 94 " pdb=" C LEU E 94 " pdb=" N GLN E 95 " pdb=" CA GLN E 95 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU A 94 " pdb=" C LEU A 94 " pdb=" N GLN A 95 " pdb=" CA GLN A 95 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA LEU B 94 " pdb=" C LEU B 94 " pdb=" N GLN B 95 " pdb=" CA GLN B 95 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 10966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1723 0.029 - 0.057: 901 0.057 - 0.086: 202 0.086 - 0.115: 116 0.115 - 0.144: 19 Chirality restraints: 2961 Sorted by residual: chirality pdb=" CA ILE F 258 " pdb=" N ILE F 258 " pdb=" C ILE F 258 " pdb=" CB ILE F 258 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE G 258 " pdb=" N ILE G 258 " pdb=" C ILE G 258 " pdb=" CB ILE G 258 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE E 258 " pdb=" N ILE E 258 " pdb=" C ILE E 258 " pdb=" CB ILE E 258 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2958 not shown) Planarity restraints: 2975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 10 " -0.004 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR F 10 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR F 10 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR F 10 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 10 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR F 10 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 10 " 0.036 2.00e-02 2.50e+03 pdb=" OH TYR F 10 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 10 " -0.005 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR B 10 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 10 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR B 10 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 10 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR B 10 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 10 " 0.036 2.00e-02 2.50e+03 pdb=" OH TYR B 10 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 10 " -0.004 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR E 10 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR E 10 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR E 10 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 10 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR E 10 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 10 " 0.036 2.00e-02 2.50e+03 pdb=" OH TYR E 10 " -0.037 2.00e-02 2.50e+03 ... (remaining 2972 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 14 2.21 - 2.88: 6775 2.88 - 3.55: 25628 3.55 - 4.23: 40152 4.23 - 4.90: 72177 Nonbonded interactions: 144746 Sorted by model distance: nonbonded pdb=" O LEU A 369 " pdb=" NZ LYS G 148 " model vdw 1.536 3.120 nonbonded pdb=" NZ LYS F 148 " pdb=" O LEU G 369 " model vdw 1.538 3.120 nonbonded pdb=" NZ LYS B 148 " pdb=" O LEU C 369 " model vdw 1.544 3.120 nonbonded pdb=" NZ LYS D 148 " pdb=" O LEU E 369 " model vdw 1.547 3.120 nonbonded pdb=" NZ LYS C 148 " pdb=" O LEU D 369 " model vdw 1.547 3.120 ... (remaining 144741 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: 0.06 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' } 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.310 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.002 0.025 18375 Z= 0.116 Angle : 0.597 5.173 24927 Z= 0.345 Chirality : 0.038 0.144 2961 Planarity : 0.004 0.040 2975 Dihedral : 12.286 79.205 6573 Min Nonbonded Distance : 1.536 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.19 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: -0.36 (0.17), residues: 2170 helix: -0.15 (0.12), residues: 1484 sheet: None (None), residues: 0 loop : -0.06 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.003 ARG F 216 TYR 0.037 0.004 TYR F 10 PHE 0.008 0.001 PHE D 126 TRP 0.016 0.002 TRP D 104 HIS 0.006 0.001 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00245 (18361) covalent geometry : angle 0.59423 (24899) SS BOND : bond 0.00133 ( 14) SS BOND : angle 1.91981 ( 28) hydrogen bonds : bond 0.18150 ( 1129) hydrogen bonds : angle 6.69864 ( 3198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.700 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: symmetry clash revert: symmetry clash REVERT: A 5 HIS cc_start: 0.8300 (t-170) cc_final: 0.7978 (t-90) REVERT: A 36 LYS cc_start: 0.8828 (tttt) cc_final: 0.8616 (tppp) REVERT: A 56 GLN cc_start: 0.8786 (pp30) cc_final: 0.8406 (pp30) REVERT: A 134 HIS cc_start: 0.8775 (t70) cc_final: 0.8435 (t-170) REVERT: A 143 MET cc_start: 0.9339 (mtm) cc_final: 0.9061 (pp-130) REVERT: A 255 ASP cc_start: 0.8993 (t0) cc_final: 0.8683 (t0) REVERT: A 261 ARG cc_start: 0.8900 (mmt-90) cc_final: 0.8490 (mmm160) REVERT: A 334 LEU cc_start: 0.9724 (mt) cc_final: 0.9454 (pp) REVERT: B 5 HIS cc_start: 0.8260 (t-170) cc_final: 0.7943 (t-90) REVERT: B 56 GLN cc_start: 0.8833 (pp30) cc_final: 0.8631 (pp30) REVERT: B 134 HIS cc_start: 0.8692 (t70) cc_final: 0.8345 (t-170) REVERT: B 143 MET cc_start: 0.9357 (mtm) cc_final: 0.9057 (pp-130) REVERT: B 255 ASP cc_start: 0.8964 (t0) cc_final: 0.8680 (t0) REVERT: B 334 LEU cc_start: 0.9739 (mt) cc_final: 0.9450 (pp) REVERT: C 5 HIS cc_start: 0.8211 (t-170) cc_final: 0.7893 (t-90) REVERT: C 56 GLN cc_start: 0.8848 (pp30) cc_final: 0.8485 (pp30) REVERT: C 134 HIS cc_start: 0.8763 (t70) cc_final: 0.8407 (t-170) REVERT: C 143 MET cc_start: 0.9326 (mtm) cc_final: 0.9065 (pp-130) REVERT: C 255 ASP cc_start: 0.8987 (t0) cc_final: 0.8708 (t0) REVERT: C 334 LEU cc_start: 0.9720 (mt) cc_final: 0.9422 (pp) REVERT: D 56 GLN cc_start: 0.8816 (pp30) cc_final: 0.8519 (pp30) REVERT: D 134 HIS cc_start: 0.8773 (t70) cc_final: 0.8391 (t-170) REVERT: D 143 MET cc_start: 0.9377 (mtm) cc_final: 0.9088 (pp-130) REVERT: D 255 ASP cc_start: 0.8968 (t0) cc_final: 0.8677 (t0) REVERT: D 334 LEU cc_start: 0.9720 (mt) cc_final: 0.9418 (pp) REVERT: E 56 GLN cc_start: 0.8820 (pp30) cc_final: 0.8512 (pp30) REVERT: E 134 HIS cc_start: 0.8734 (t70) cc_final: 0.8311 (t-170) REVERT: E 143 MET cc_start: 0.9328 (mtm) cc_final: 0.9076 (pp-130) REVERT: E 255 ASP cc_start: 0.8997 (t0) cc_final: 0.8728 (t0) REVERT: E 334 LEU cc_start: 0.9727 (mt) cc_final: 0.9449 (pp) REVERT: F 5 HIS cc_start: 0.8267 (t-170) cc_final: 0.8059 (t-90) REVERT: F 56 GLN cc_start: 0.8780 (pp30) cc_final: 0.8321 (pp30) REVERT: F 134 HIS cc_start: 0.8751 (t70) cc_final: 0.8353 (t-170) REVERT: F 143 MET cc_start: 0.9363 (mtm) cc_final: 0.9071 (pp-130) REVERT: F 210 MET cc_start: 0.8452 (ttp) cc_final: 0.8241 (mmt) REVERT: F 255 ASP cc_start: 0.8923 (t0) cc_final: 0.8618 (t0) REVERT: F 334 LEU cc_start: 0.9726 (mt) cc_final: 0.9451 (pp) REVERT: G 56 GLN cc_start: 0.8801 (pp30) cc_final: 0.8392 (pp30) REVERT: G 134 HIS cc_start: 0.8724 (t70) cc_final: 0.8302 (t-170) REVERT: G 143 MET cc_start: 0.9367 (mtm) cc_final: 0.9077 (pp-130) REVERT: G 255 ASP cc_start: 0.8958 (t0) cc_final: 0.8685 (t0) REVERT: G 334 LEU cc_start: 0.9710 (mt) cc_final: 0.9433 (pp) outliers start: 0 outliers final: 3 residues processed: 434 average time/residue: 0.5555 time to fit residues: 272.8877 Evaluate side-chains 171 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain G residue 41 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.094087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062020 restraints weight = 45184.351| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.42 r_work: 0.2829 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18375 Z= 0.221 Angle : 0.713 8.489 24927 Z= 0.351 Chirality : 0.041 0.141 2961 Planarity : 0.004 0.033 2975 Dihedral : 4.694 16.510 2365 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.60 % Allowed : 11.18 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 2170 helix: 1.31 (0.13), residues: 1491 sheet: None (None), residues: 0 loop : 0.24 (0.26), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 216 TYR 0.014 0.001 TYR B 150 PHE 0.010 0.001 PHE F 272 TRP 0.009 0.001 TRP A 74 HIS 0.005 0.002 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00515 (18361) covalent geometry : angle 0.71150 (24899) SS BOND : bond 0.00450 ( 14) SS BOND : angle 1.74374 ( 28) hydrogen bonds : bond 0.05680 ( 1129) hydrogen bonds : angle 4.92669 ( 3198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 235 time to evaluate : 0.772 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 30 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8394 (tp) REVERT: A 56 GLN cc_start: 0.8887 (pp30) cc_final: 0.8540 (pp30) REVERT: A 57 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8696 (mp0) REVERT: A 134 HIS cc_start: 0.8760 (t70) cc_final: 0.8416 (t-170) REVERT: A 255 ASP cc_start: 0.9022 (t0) cc_final: 0.8408 (t0) REVERT: A 261 ARG cc_start: 0.8927 (mmt-90) cc_final: 0.8624 (mmm-85) REVERT: A 334 LEU cc_start: 0.9706 (mt) cc_final: 0.9400 (pp) REVERT: B 30 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8419 (tp) REVERT: B 35 ASP cc_start: 0.8406 (m-30) cc_final: 0.8109 (t70) REVERT: B 56 GLN cc_start: 0.8894 (pp30) cc_final: 0.8476 (pp30) REVERT: B 134 HIS cc_start: 0.8686 (t70) cc_final: 0.8332 (t-170) REVERT: B 255 ASP cc_start: 0.9020 (t0) cc_final: 0.8471 (t0) REVERT: B 278 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8851 (mp) REVERT: B 334 LEU cc_start: 0.9688 (mt) cc_final: 0.9375 (pp) REVERT: C 30 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8393 (tp) REVERT: C 56 GLN cc_start: 0.8952 (pp30) cc_final: 0.8486 (pp30) REVERT: C 95 GLN cc_start: 0.7655 (mp10) cc_final: 0.7314 (mp10) REVERT: C 134 HIS cc_start: 0.8781 (t70) cc_final: 0.8424 (t-170) REVERT: C 334 LEU cc_start: 0.9663 (mt) cc_final: 0.9367 (pp) REVERT: D 29 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7861 (mtm110) REVERT: D 30 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8456 (tp) REVERT: D 56 GLN cc_start: 0.8908 (pp30) cc_final: 0.8477 (pp30) REVERT: D 95 GLN cc_start: 0.7497 (mp10) cc_final: 0.7261 (mp10) REVERT: D 134 HIS cc_start: 0.8774 (t70) cc_final: 0.8343 (t-170) REVERT: D 227 CYS cc_start: 0.9114 (m) cc_final: 0.8639 (t) REVERT: D 255 ASP cc_start: 0.9030 (t0) cc_final: 0.8469 (t0) REVERT: D 334 LEU cc_start: 0.9687 (mt) cc_final: 0.9398 (pp) REVERT: E 29 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7878 (mtm110) REVERT: E 30 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8275 (tp) REVERT: E 56 GLN cc_start: 0.8925 (pp30) cc_final: 0.8494 (pp30) REVERT: E 134 HIS cc_start: 0.8726 (t70) cc_final: 0.8309 (t-170) REVERT: E 255 ASP cc_start: 0.9035 (t0) cc_final: 0.8453 (t0) REVERT: E 278 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8936 (mp) REVERT: E 334 LEU cc_start: 0.9689 (mt) cc_final: 0.9389 (pp) REVERT: F 30 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8413 (tp) REVERT: F 35 ASP cc_start: 0.8288 (m-30) cc_final: 0.7980 (t70) REVERT: F 56 GLN cc_start: 0.8875 (pp30) cc_final: 0.8457 (pp30) REVERT: F 57 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8609 (mp0) REVERT: F 134 HIS cc_start: 0.8754 (t70) cc_final: 0.8304 (t-170) REVERT: F 255 ASP cc_start: 0.9076 (t0) cc_final: 0.8501 (t0) REVERT: F 334 LEU cc_start: 0.9691 (mt) cc_final: 0.9395 (pp) REVERT: G 29 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7921 (mtm110) REVERT: G 30 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8382 (tp) REVERT: G 35 ASP cc_start: 0.8308 (m-30) cc_final: 0.8065 (m-30) REVERT: G 56 GLN cc_start: 0.8874 (pp30) cc_final: 0.8408 (pp30) REVERT: G 95 GLN cc_start: 0.7543 (mp10) cc_final: 0.7300 (mp10) REVERT: G 134 HIS cc_start: 0.8693 (t70) cc_final: 0.8222 (t-170) REVERT: G 334 LEU cc_start: 0.9687 (mt) cc_final: 0.9382 (pp) outliers start: 73 outliers final: 26 residues processed: 288 average time/residue: 0.4949 time to fit residues: 162.9155 Evaluate side-chains 235 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 224 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 5 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN C 5 HIS C 207 HIS C 279 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN E 5 HIS ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 5 HIS ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN G 5 HIS ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.095523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063287 restraints weight = 45056.065| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.51 r_work: 0.2862 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18375 Z= 0.142 Angle : 0.640 9.064 24927 Z= 0.317 Chirality : 0.039 0.143 2961 Planarity : 0.004 0.045 2975 Dihedral : 4.364 17.647 2359 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.81 % Allowed : 14.04 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 2170 helix: 1.71 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : 0.47 (0.27), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 216 TYR 0.012 0.001 TYR C 150 PHE 0.009 0.001 PHE E 333 TRP 0.008 0.001 TRP G 104 HIS 0.005 0.001 HIS E 5 Details of bonding type rmsd covalent geometry : bond 0.00310 (18361) covalent geometry : angle 0.63880 (24899) SS BOND : bond 0.00204 ( 14) SS BOND : angle 1.39021 ( 28) hydrogen bonds : bond 0.04859 ( 1129) hydrogen bonds : angle 4.50317 ( 3198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 0.771 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 30 LEU cc_start: 0.8829 (pt) cc_final: 0.8507 (tp) REVERT: A 56 GLN cc_start: 0.8930 (pp30) cc_final: 0.8706 (pp30) REVERT: A 134 HIS cc_start: 0.8748 (t70) cc_final: 0.8365 (t-170) REVERT: A 261 ARG cc_start: 0.8928 (mmt-90) cc_final: 0.8644 (mmm-85) REVERT: A 334 LEU cc_start: 0.9679 (mt) cc_final: 0.9380 (pp) REVERT: A 352 ASN cc_start: 0.9227 (m110) cc_final: 0.8928 (p0) REVERT: B 30 LEU cc_start: 0.8740 (pt) cc_final: 0.8500 (tp) REVERT: B 35 ASP cc_start: 0.8300 (m-30) cc_final: 0.7962 (t70) REVERT: B 56 GLN cc_start: 0.8894 (pp30) cc_final: 0.8492 (pp30) REVERT: B 134 HIS cc_start: 0.8663 (t70) cc_final: 0.8221 (t-170) REVERT: B 255 ASP cc_start: 0.9012 (t0) cc_final: 0.8412 (t0) REVERT: B 331 ASN cc_start: 0.9231 (m-40) cc_final: 0.9009 (m-40) REVERT: B 334 LEU cc_start: 0.9685 (mt) cc_final: 0.9410 (pp) REVERT: B 352 ASN cc_start: 0.9228 (m110) cc_final: 0.8969 (p0) REVERT: C 30 LEU cc_start: 0.8747 (pt) cc_final: 0.8485 (tp) REVERT: C 56 GLN cc_start: 0.8915 (pp30) cc_final: 0.8445 (pp30) REVERT: C 95 GLN cc_start: 0.7533 (mp10) cc_final: 0.7215 (mp10) REVERT: C 134 HIS cc_start: 0.8784 (t70) cc_final: 0.8373 (t-170) REVERT: C 255 ASP cc_start: 0.8989 (t0) cc_final: 0.8414 (t0) REVERT: C 334 LEU cc_start: 0.9656 (mt) cc_final: 0.9356 (pp) REVERT: C 352 ASN cc_start: 0.9225 (m110) cc_final: 0.8916 (p0) REVERT: D 29 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7880 (mtm110) REVERT: D 30 LEU cc_start: 0.8781 (pt) cc_final: 0.8475 (tp) REVERT: D 56 GLN cc_start: 0.8903 (pp30) cc_final: 0.8464 (pp30) REVERT: D 134 HIS cc_start: 0.8706 (t70) cc_final: 0.8257 (t-170) REVERT: D 227 CYS cc_start: 0.9189 (m) cc_final: 0.8707 (t) REVERT: D 334 LEU cc_start: 0.9662 (mt) cc_final: 0.9367 (pp) REVERT: D 352 ASN cc_start: 0.9278 (m110) cc_final: 0.8979 (p0) REVERT: E 29 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7914 (mtm110) REVERT: E 30 LEU cc_start: 0.8775 (pt) cc_final: 0.8431 (tp) REVERT: E 56 GLN cc_start: 0.8925 (pp30) cc_final: 0.8469 (pp30) REVERT: E 134 HIS cc_start: 0.8708 (t70) cc_final: 0.8195 (t-170) REVERT: E 331 ASN cc_start: 0.9217 (m-40) cc_final: 0.8987 (m-40) REVERT: E 334 LEU cc_start: 0.9671 (mt) cc_final: 0.9369 (pp) REVERT: E 352 ASN cc_start: 0.9252 (m110) cc_final: 0.8947 (p0) REVERT: F 30 LEU cc_start: 0.8792 (pt) cc_final: 0.8444 (tp) REVERT: F 35 ASP cc_start: 0.8194 (m-30) cc_final: 0.7801 (t70) REVERT: F 56 GLN cc_start: 0.8834 (pp30) cc_final: 0.8427 (pp30) REVERT: F 57 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8556 (mp0) REVERT: F 134 HIS cc_start: 0.8736 (t70) cc_final: 0.8295 (t-170) REVERT: F 227 CYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8827 (t) REVERT: F 255 ASP cc_start: 0.9050 (t0) cc_final: 0.8399 (t0) REVERT: F 331 ASN cc_start: 0.9224 (m-40) cc_final: 0.8970 (m-40) REVERT: F 334 LEU cc_start: 0.9666 (mt) cc_final: 0.9388 (pp) REVERT: F 352 ASN cc_start: 0.9219 (m110) cc_final: 0.8971 (p0) REVERT: G 29 ARG cc_start: 0.8302 (mtt180) cc_final: 0.7959 (mtm110) REVERT: G 30 LEU cc_start: 0.8794 (pt) cc_final: 0.8559 (mt) REVERT: G 35 ASP cc_start: 0.8234 (m-30) cc_final: 0.7967 (m-30) REVERT: G 56 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8358 (pp30) REVERT: G 134 HIS cc_start: 0.8671 (t70) cc_final: 0.8054 (t-170) REVERT: G 334 LEU cc_start: 0.9660 (mt) cc_final: 0.9354 (pp) REVERT: G 352 ASN cc_start: 0.9226 (m110) cc_final: 0.8965 (p0) outliers start: 57 outliers final: 12 residues processed: 288 average time/residue: 0.4968 time to fit residues: 163.5677 Evaluate side-chains 211 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 224 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 198 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 213 optimal weight: 0.0770 chunk 128 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 207 HIS D 207 HIS D 279 ASN E 207 HIS E 279 ASN F 207 HIS F 279 ASN G 207 HIS G 279 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.094717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062612 restraints weight = 45059.619| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.51 r_work: 0.2848 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 18375 Z= 0.155 Angle : 0.638 9.858 24927 Z= 0.310 Chirality : 0.038 0.139 2961 Planarity : 0.004 0.076 2975 Dihedral : 4.194 17.175 2359 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.55 % Allowed : 15.07 % Favored : 81.38 % 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: 2.16 (0.19), residues: 2170 helix: 1.86 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : 0.61 (0.27), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 216 TYR 0.016 0.001 TYR G 198 PHE 0.009 0.001 PHE E 333 TRP 0.008 0.001 TRP D 104 HIS 0.013 0.002 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00353 (18361) covalent geometry : angle 0.63612 (24899) SS BOND : bond 0.00301 ( 14) SS BOND : angle 1.42529 ( 28) hydrogen bonds : bond 0.04443 ( 1129) hydrogen bonds : angle 4.31048 ( 3198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 216 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8819 (pt) cc_final: 0.8535 (mt) REVERT: A 56 GLN cc_start: 0.8897 (pp30) cc_final: 0.8513 (pp30) REVERT: A 134 HIS cc_start: 0.8739 (t70) cc_final: 0.8329 (t-170) REVERT: A 227 CYS cc_start: 0.9137 (m) cc_final: 0.8770 (t) REVERT: A 255 ASP cc_start: 0.8957 (t0) cc_final: 0.8301 (t0) REVERT: A 331 ASN cc_start: 0.9213 (m-40) cc_final: 0.8967 (m-40) REVERT: A 334 LEU cc_start: 0.9685 (mt) cc_final: 0.9408 (pp) REVERT: A 352 ASN cc_start: 0.9242 (m110) cc_final: 0.8933 (p0) REVERT: B 30 LEU cc_start: 0.8772 (pt) cc_final: 0.8550 (mt) REVERT: B 56 GLN cc_start: 0.8906 (pp30) cc_final: 0.8527 (pp30) REVERT: B 134 HIS cc_start: 0.8658 (t70) cc_final: 0.8173 (t-170) REVERT: B 255 ASP cc_start: 0.9133 (t0) cc_final: 0.8487 (t0) REVERT: B 331 ASN cc_start: 0.9207 (m-40) cc_final: 0.8982 (m-40) REVERT: B 334 LEU cc_start: 0.9694 (mt) cc_final: 0.9413 (pp) REVERT: B 352 ASN cc_start: 0.9208 (m110) cc_final: 0.8934 (p0) REVERT: C 30 LEU cc_start: 0.8748 (pt) cc_final: 0.8508 (mt) REVERT: C 56 GLN cc_start: 0.8897 (pp30) cc_final: 0.8417 (pp30) REVERT: C 134 HIS cc_start: 0.8768 (t70) cc_final: 0.8320 (t-170) REVERT: C 216 ARG cc_start: 0.8778 (tpp-160) cc_final: 0.8413 (tpp-160) REVERT: C 331 ASN cc_start: 0.9216 (m-40) cc_final: 0.8973 (m-40) REVERT: C 334 LEU cc_start: 0.9656 (mt) cc_final: 0.9384 (pp) REVERT: C 352 ASN cc_start: 0.9215 (m110) cc_final: 0.8962 (p0) REVERT: D 29 ARG cc_start: 0.8218 (mtt180) cc_final: 0.7901 (mtm110) REVERT: D 30 LEU cc_start: 0.8762 (pt) cc_final: 0.8500 (mt) REVERT: D 35 ASP cc_start: 0.8406 (m-30) cc_final: 0.7923 (t70) REVERT: D 56 GLN cc_start: 0.8889 (pp30) cc_final: 0.8425 (pp30) REVERT: D 134 HIS cc_start: 0.8712 (t70) cc_final: 0.8284 (t-170) REVERT: D 227 CYS cc_start: 0.9163 (m) cc_final: 0.8719 (t) REVERT: D 255 ASP cc_start: 0.8974 (t0) cc_final: 0.8255 (t0) REVERT: D 331 ASN cc_start: 0.9228 (m-40) cc_final: 0.8997 (m-40) REVERT: D 334 LEU cc_start: 0.9671 (mt) cc_final: 0.9391 (pp) REVERT: D 352 ASN cc_start: 0.9249 (m110) cc_final: 0.8929 (p0) REVERT: E 29 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7915 (mtm110) REVERT: E 30 LEU cc_start: 0.8807 (pt) cc_final: 0.8533 (mt) REVERT: E 56 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8458 (pp30) REVERT: E 134 HIS cc_start: 0.8699 (t70) cc_final: 0.8178 (t-170) REVERT: E 331 ASN cc_start: 0.9225 (m-40) cc_final: 0.8993 (m-40) REVERT: E 334 LEU cc_start: 0.9674 (mt) cc_final: 0.9381 (pp) REVERT: E 352 ASN cc_start: 0.9253 (m110) cc_final: 0.8955 (p0) REVERT: F 30 LEU cc_start: 0.8824 (pt) cc_final: 0.8554 (mt) REVERT: F 56 GLN cc_start: 0.8840 (pp30) cc_final: 0.8485 (pp30) REVERT: F 57 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: F 134 HIS cc_start: 0.8749 (t70) cc_final: 0.8240 (t-170) REVERT: F 227 CYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8824 (t) REVERT: F 255 ASP cc_start: 0.8996 (t0) cc_final: 0.8303 (t0) REVERT: F 331 ASN cc_start: 0.9203 (m-40) cc_final: 0.8960 (m-40) REVERT: F 334 LEU cc_start: 0.9673 (mt) cc_final: 0.9387 (pp) REVERT: F 352 ASN cc_start: 0.9210 (m110) cc_final: 0.8941 (p0) REVERT: G 29 ARG cc_start: 0.8343 (mtt180) cc_final: 0.8034 (mtm110) REVERT: G 30 LEU cc_start: 0.8793 (pt) cc_final: 0.8540 (mt) REVERT: G 56 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8363 (pp30) REVERT: G 134 HIS cc_start: 0.8605 (t70) cc_final: 0.8035 (t-170) REVERT: G 227 CYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8733 (t) REVERT: G 331 ASN cc_start: 0.9254 (m-40) cc_final: 0.8979 (m-40) REVERT: G 334 LEU cc_start: 0.9672 (mt) cc_final: 0.9401 (pp) REVERT: G 352 ASN cc_start: 0.9206 (m110) cc_final: 0.8917 (p0) outliers start: 72 outliers final: 30 residues processed: 269 average time/residue: 0.4336 time to fit residues: 133.8641 Evaluate side-chains 227 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 227 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 81 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN C 279 ASN D 279 ASN E 279 ASN F 279 ASN G 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.095089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.062861 restraints weight = 44962.712| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.53 r_work: 0.2855 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18375 Z= 0.149 Angle : 0.627 7.746 24927 Z= 0.304 Chirality : 0.038 0.136 2961 Planarity : 0.004 0.059 2975 Dihedral : 4.105 18.442 2359 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.53 % Allowed : 14.83 % Favored : 80.64 % 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: 2.22 (0.20), residues: 2170 helix: 1.92 (0.14), residues: 1491 sheet: -1.03 (0.60), residues: 70 loop : 0.85 (0.30), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 216 TYR 0.010 0.001 TYR G 198 PHE 0.009 0.001 PHE D 333 TRP 0.021 0.001 TRP F 74 HIS 0.010 0.002 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00342 (18361) covalent geometry : angle 0.62568 (24899) SS BOND : bond 0.00282 ( 14) SS BOND : angle 1.35709 ( 28) hydrogen bonds : bond 0.04269 ( 1129) hydrogen bonds : angle 4.21123 ( 3198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 208 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8897 (pp30) cc_final: 0.8521 (pp30) REVERT: A 134 HIS cc_start: 0.8749 (t70) cc_final: 0.8328 (t-170) REVERT: A 227 CYS cc_start: 0.9120 (m) cc_final: 0.8773 (t) REVERT: A 261 ARG cc_start: 0.9014 (mmt-90) cc_final: 0.8721 (mmm-85) REVERT: A 331 ASN cc_start: 0.9205 (m-40) cc_final: 0.8987 (m-40) REVERT: A 334 LEU cc_start: 0.9690 (mt) cc_final: 0.9417 (pp) REVERT: A 352 ASN cc_start: 0.9225 (m110) cc_final: 0.8924 (p0) REVERT: B 56 GLN cc_start: 0.8888 (pp30) cc_final: 0.8481 (pp30) REVERT: B 134 HIS cc_start: 0.8668 (t70) cc_final: 0.8185 (t-170) REVERT: B 331 ASN cc_start: 0.9207 (m-40) cc_final: 0.8990 (m-40) REVERT: B 334 LEU cc_start: 0.9685 (mt) cc_final: 0.9414 (pp) REVERT: C 30 LEU cc_start: 0.8748 (pt) cc_final: 0.8533 (mt) REVERT: C 56 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8404 (pp30) REVERT: C 134 HIS cc_start: 0.8765 (t70) cc_final: 0.8292 (t-170) REVERT: C 281 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8548 (tp) REVERT: C 331 ASN cc_start: 0.9212 (m-40) cc_final: 0.8970 (m-40) REVERT: C 334 LEU cc_start: 0.9655 (mt) cc_final: 0.9397 (pp) REVERT: D 29 ARG cc_start: 0.8246 (mtt180) cc_final: 0.7934 (mtm110) REVERT: D 35 ASP cc_start: 0.8414 (m-30) cc_final: 0.8207 (t70) REVERT: D 56 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8408 (pp30) REVERT: D 134 HIS cc_start: 0.8729 (t70) cc_final: 0.8265 (t-170) REVERT: D 216 ARG cc_start: 0.8891 (tpp-160) cc_final: 0.8583 (tpp-160) REVERT: D 227 CYS cc_start: 0.9134 (m) cc_final: 0.8690 (t) REVERT: D 255 ASP cc_start: 0.8970 (t0) cc_final: 0.8191 (t0) REVERT: D 331 ASN cc_start: 0.9200 (m-40) cc_final: 0.8980 (m-40) REVERT: D 334 LEU cc_start: 0.9673 (mt) cc_final: 0.9395 (pp) REVERT: E 29 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7871 (mtm110) REVERT: E 30 LEU cc_start: 0.8794 (pt) cc_final: 0.8534 (mt) REVERT: E 56 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8422 (pp30) REVERT: E 134 HIS cc_start: 0.8714 (t70) cc_final: 0.8226 (t-170) REVERT: E 255 ASP cc_start: 0.8959 (t0) cc_final: 0.8252 (t0) REVERT: E 331 ASN cc_start: 0.9217 (m-40) cc_final: 0.8985 (m-40) REVERT: E 334 LEU cc_start: 0.9676 (mt) cc_final: 0.9396 (pp) REVERT: F 56 GLN cc_start: 0.8811 (pp30) cc_final: 0.8475 (pp30) REVERT: F 57 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: F 134 HIS cc_start: 0.8719 (t70) cc_final: 0.8205 (t-170) REVERT: F 227 CYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8828 (t) REVERT: F 331 ASN cc_start: 0.9184 (m-40) cc_final: 0.8947 (m-40) REVERT: F 334 LEU cc_start: 0.9665 (mt) cc_final: 0.9382 (pp) REVERT: G 29 ARG cc_start: 0.8374 (mtt180) cc_final: 0.8053 (mtm110) REVERT: G 30 LEU cc_start: 0.8792 (pt) cc_final: 0.8541 (mt) REVERT: G 56 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8329 (pp30) REVERT: G 134 HIS cc_start: 0.8623 (t70) cc_final: 0.8068 (t-170) REVERT: G 227 CYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8735 (t) REVERT: G 281 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8585 (tp) REVERT: G 331 ASN cc_start: 0.9234 (m-40) cc_final: 0.8974 (m-40) REVERT: G 334 LEU cc_start: 0.9677 (mt) cc_final: 0.9408 (pp) outliers start: 92 outliers final: 31 residues processed: 275 average time/residue: 0.4636 time to fit residues: 146.8463 Evaluate side-chains 236 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 227 CYS Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 281 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN C 279 ASN D 279 ASN E 279 ASN F 279 ASN G 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.094690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.062571 restraints weight = 45039.660| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.48 r_work: 0.2847 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18375 Z= 0.170 Angle : 0.643 8.312 24927 Z= 0.317 Chirality : 0.039 0.135 2961 Planarity : 0.004 0.038 2975 Dihedral : 4.108 18.325 2359 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.14 % Allowed : 16.11 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.20), residues: 2170 helix: 1.88 (0.14), residues: 1491 sheet: -1.02 (0.60), residues: 70 loop : 0.87 (0.30), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 216 TYR 0.010 0.001 TYR C 229 PHE 0.009 0.001 PHE D 333 TRP 0.014 0.001 TRP F 74 HIS 0.011 0.002 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00399 (18361) covalent geometry : angle 0.64136 (24899) SS BOND : bond 0.00341 ( 14) SS BOND : angle 1.40529 ( 28) hydrogen bonds : bond 0.04337 ( 1129) hydrogen bonds : angle 4.29433 ( 3198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 204 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8891 (pp30) cc_final: 0.8505 (pp30) REVERT: A 134 HIS cc_start: 0.8757 (t70) cc_final: 0.8356 (t-170) REVERT: A 227 CYS cc_start: 0.9120 (m) cc_final: 0.8767 (t) REVERT: A 261 ARG cc_start: 0.9019 (mmt-90) cc_final: 0.8778 (mmm-85) REVERT: A 331 ASN cc_start: 0.9224 (m-40) cc_final: 0.9010 (m-40) REVERT: A 334 LEU cc_start: 0.9694 (mt) cc_final: 0.9427 (pp) REVERT: B 56 GLN cc_start: 0.8872 (pp30) cc_final: 0.8491 (pp30) REVERT: B 134 HIS cc_start: 0.8697 (t70) cc_final: 0.8200 (t-170) REVERT: B 281 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8479 (tp) REVERT: B 331 ASN cc_start: 0.9200 (m-40) cc_final: 0.8998 (m-40) REVERT: B 334 LEU cc_start: 0.9687 (mt) cc_final: 0.9424 (pp) REVERT: B 352 ASN cc_start: 0.9173 (m110) cc_final: 0.8890 (p0) REVERT: C 35 ASP cc_start: 0.8322 (t70) cc_final: 0.8104 (t70) REVERT: C 56 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8371 (pp30) REVERT: C 134 HIS cc_start: 0.8769 (t70) cc_final: 0.8287 (t-170) REVERT: C 281 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8523 (tp) REVERT: C 331 ASN cc_start: 0.9203 (m-40) cc_final: 0.8952 (m-40) REVERT: C 334 LEU cc_start: 0.9663 (mt) cc_final: 0.9411 (pp) REVERT: C 352 ASN cc_start: 0.9211 (m110) cc_final: 0.8901 (p0) REVERT: D 56 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8387 (pp30) REVERT: D 134 HIS cc_start: 0.8757 (t70) cc_final: 0.8296 (t-170) REVERT: D 227 CYS cc_start: 0.9137 (m) cc_final: 0.8702 (t) REVERT: D 255 ASP cc_start: 0.8981 (t0) cc_final: 0.8216 (t0) REVERT: D 331 ASN cc_start: 0.9182 (m-40) cc_final: 0.8961 (m-40) REVERT: D 334 LEU cc_start: 0.9678 (mt) cc_final: 0.9398 (pp) REVERT: D 352 ASN cc_start: 0.9192 (m110) cc_final: 0.8858 (p0) REVERT: E 29 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7928 (mtm110) REVERT: E 30 LEU cc_start: 0.8815 (pt) cc_final: 0.8574 (mt) REVERT: E 56 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8399 (pp30) REVERT: E 134 HIS cc_start: 0.8716 (t70) cc_final: 0.8209 (t-170) REVERT: E 331 ASN cc_start: 0.9219 (m-40) cc_final: 0.8991 (m-40) REVERT: E 334 LEU cc_start: 0.9678 (mt) cc_final: 0.9398 (pp) REVERT: E 352 ASN cc_start: 0.9154 (m110) cc_final: 0.8798 (p0) REVERT: F 56 GLN cc_start: 0.8813 (pp30) cc_final: 0.8489 (pp30) REVERT: F 57 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: F 134 HIS cc_start: 0.8734 (t70) cc_final: 0.8211 (t-170) REVERT: F 227 CYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8818 (t) REVERT: F 331 ASN cc_start: 0.9176 (m-40) cc_final: 0.8934 (m-40) REVERT: F 334 LEU cc_start: 0.9673 (mt) cc_final: 0.9397 (pp) REVERT: F 352 ASN cc_start: 0.9206 (m110) cc_final: 0.8920 (p0) REVERT: G 29 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8091 (mtm110) REVERT: G 30 LEU cc_start: 0.8821 (pt) cc_final: 0.8578 (mt) REVERT: G 56 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8298 (pp30) REVERT: G 134 HIS cc_start: 0.8626 (t70) cc_final: 0.8126 (t-170) REVERT: G 227 CYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8710 (t) REVERT: G 255 ASP cc_start: 0.9024 (t0) cc_final: 0.8300 (t0) REVERT: G 281 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8481 (tp) REVERT: G 331 ASN cc_start: 0.9233 (m-40) cc_final: 0.8977 (m-40) REVERT: G 334 LEU cc_start: 0.9685 (mt) cc_final: 0.9412 (pp) REVERT: G 352 ASN cc_start: 0.9174 (m110) cc_final: 0.8839 (p0) outliers start: 84 outliers final: 33 residues processed: 266 average time/residue: 0.4594 time to fit residues: 141.2539 Evaluate side-chains 233 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 227 CYS Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 303 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 84 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 279 ASN C 279 ASN D 279 ASN E 279 ASN E 368 ASN F 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.095284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.063119 restraints weight = 45424.413| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.50 r_work: 0.2860 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18375 Z= 0.142 Angle : 0.642 8.246 24927 Z= 0.318 Chirality : 0.038 0.135 2961 Planarity : 0.003 0.071 2975 Dihedral : 4.118 19.382 2359 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.60 % Allowed : 17.14 % Favored : 79.26 % 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: 2.04 (0.20), residues: 2170 helix: 1.75 (0.14), residues: 1498 sheet: -0.94 (0.61), residues: 70 loop : 0.85 (0.31), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 216 TYR 0.011 0.001 TYR A 229 PHE 0.008 0.001 PHE D 333 TRP 0.011 0.001 TRP F 74 HIS 0.008 0.001 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00322 (18361) covalent geometry : angle 0.64072 (24899) SS BOND : bond 0.00251 ( 14) SS BOND : angle 1.30173 ( 28) hydrogen bonds : bond 0.04165 ( 1129) hydrogen bonds : angle 4.27065 ( 3198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 206 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8872 (pp30) cc_final: 0.8495 (pp30) REVERT: A 134 HIS cc_start: 0.8743 (t70) cc_final: 0.8311 (t-170) REVERT: A 227 CYS cc_start: 0.9127 (m) cc_final: 0.8759 (t) REVERT: A 255 ASP cc_start: 0.8928 (t0) cc_final: 0.8193 (t0) REVERT: A 261 ARG cc_start: 0.9033 (mmt-90) cc_final: 0.8796 (mmm-85) REVERT: A 331 ASN cc_start: 0.9204 (m-40) cc_final: 0.8989 (m-40) REVERT: A 334 LEU cc_start: 0.9694 (mt) cc_final: 0.9414 (pp) REVERT: B 56 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8465 (pp30) REVERT: B 134 HIS cc_start: 0.8683 (t70) cc_final: 0.8201 (t-170) REVERT: B 281 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8460 (tp) REVERT: B 331 ASN cc_start: 0.9212 (m-40) cc_final: 0.8992 (m-40) REVERT: B 334 LEU cc_start: 0.9682 (mt) cc_final: 0.9419 (pp) REVERT: B 352 ASN cc_start: 0.9157 (m110) cc_final: 0.8862 (p0) REVERT: C 35 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: C 56 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8412 (pp30) REVERT: C 134 HIS cc_start: 0.8763 (t70) cc_final: 0.8291 (t-170) REVERT: C 216 ARG cc_start: 0.8732 (tpp-160) cc_final: 0.8123 (tpp-160) REVERT: C 331 ASN cc_start: 0.9183 (m-40) cc_final: 0.8936 (m-40) REVERT: C 334 LEU cc_start: 0.9669 (mt) cc_final: 0.9414 (pp) REVERT: C 352 ASN cc_start: 0.9193 (m110) cc_final: 0.8878 (p0) REVERT: D 1 MET cc_start: 0.7388 (tpp) cc_final: 0.7179 (tpt) REVERT: D 56 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8353 (pp30) REVERT: D 134 HIS cc_start: 0.8741 (t70) cc_final: 0.8280 (t-170) REVERT: D 227 CYS cc_start: 0.9132 (m) cc_final: 0.8694 (t) REVERT: D 331 ASN cc_start: 0.9160 (m-40) cc_final: 0.8890 (m-40) REVERT: D 334 LEU cc_start: 0.9674 (mt) cc_final: 0.9388 (pp) REVERT: D 352 ASN cc_start: 0.9203 (m110) cc_final: 0.8867 (p0) REVERT: E 1 MET cc_start: 0.7240 (tpp) cc_final: 0.6867 (tpt) REVERT: E 29 ARG cc_start: 0.8218 (mtt180) cc_final: 0.7920 (mtm110) REVERT: E 30 LEU cc_start: 0.8787 (pt) cc_final: 0.8552 (mt) REVERT: E 35 ASP cc_start: 0.8332 (m-30) cc_final: 0.8090 (t70) REVERT: E 56 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8362 (pp30) REVERT: E 134 HIS cc_start: 0.8712 (t70) cc_final: 0.8201 (t-170) REVERT: E 281 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8505 (tp) REVERT: E 331 ASN cc_start: 0.9202 (m-40) cc_final: 0.8976 (m-40) REVERT: E 334 LEU cc_start: 0.9669 (mt) cc_final: 0.9387 (pp) REVERT: E 352 ASN cc_start: 0.9153 (m110) cc_final: 0.8797 (p0) REVERT: F 56 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8475 (pp30) REVERT: F 57 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: F 134 HIS cc_start: 0.8722 (t70) cc_final: 0.8196 (t-170) REVERT: F 227 CYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8830 (t) REVERT: F 331 ASN cc_start: 0.9155 (m-40) cc_final: 0.8910 (m-40) REVERT: F 334 LEU cc_start: 0.9676 (mt) cc_final: 0.9413 (pp) REVERT: F 352 ASN cc_start: 0.9197 (m110) cc_final: 0.8886 (p0) REVERT: G 29 ARG cc_start: 0.8398 (mtt180) cc_final: 0.8129 (mtm110) REVERT: G 56 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8289 (pp30) REVERT: G 134 HIS cc_start: 0.8619 (t70) cc_final: 0.8072 (t-170) REVERT: G 216 ARG cc_start: 0.8819 (tpp-160) cc_final: 0.8486 (tpp-160) REVERT: G 227 CYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8723 (t) REVERT: G 255 ASP cc_start: 0.9030 (t0) cc_final: 0.8289 (t0) REVERT: G 331 ASN cc_start: 0.9212 (m-40) cc_final: 0.8951 (m-40) REVERT: G 334 LEU cc_start: 0.9680 (mt) cc_final: 0.9412 (pp) REVERT: G 352 ASN cc_start: 0.9161 (m110) cc_final: 0.8827 (p0) outliers start: 73 outliers final: 33 residues processed: 251 average time/residue: 0.5197 time to fit residues: 149.3662 Evaluate side-chains 237 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 227 CYS Chi-restraints excluded: chain G residue 287 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 185 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS C 279 ASN D 5 HIS D 279 ASN E 5 HIS E 279 ASN F 5 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.095185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062465 restraints weight = 44329.572| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.44 r_work: 0.2845 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18375 Z= 0.160 Angle : 0.663 10.587 24927 Z= 0.324 Chirality : 0.039 0.133 2961 Planarity : 0.004 0.076 2975 Dihedral : 4.122 20.598 2359 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.74 % Allowed : 17.88 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.20), residues: 2170 helix: 1.81 (0.14), residues: 1491 sheet: -0.87 (0.63), residues: 70 loop : 0.84 (0.30), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 216 TYR 0.008 0.001 TYR G 212 PHE 0.008 0.001 PHE C 333 TRP 0.011 0.001 TRP F 74 HIS 0.006 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00375 (18361) covalent geometry : angle 0.66192 (24899) SS BOND : bond 0.00313 ( 14) SS BOND : angle 1.34282 ( 28) hydrogen bonds : bond 0.04147 ( 1129) hydrogen bonds : angle 4.27497 ( 3198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 193 time to evaluate : 0.732 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: symmetry clash REVERT: A 56 GLN cc_start: 0.8885 (pp30) cc_final: 0.8517 (pp30) REVERT: A 134 HIS cc_start: 0.8734 (t70) cc_final: 0.8345 (t-170) REVERT: A 227 CYS cc_start: 0.9107 (m) cc_final: 0.8784 (t) REVERT: A 261 ARG cc_start: 0.9050 (mmt-90) cc_final: 0.8820 (mmm-85) REVERT: A 331 ASN cc_start: 0.9200 (m-40) cc_final: 0.8983 (m-40) REVERT: A 334 LEU cc_start: 0.9696 (mt) cc_final: 0.9427 (pp) REVERT: B 1 MET cc_start: 0.7162 (tpp) cc_final: 0.6866 (tpt) REVERT: B 56 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8390 (pp30) REVERT: B 134 HIS cc_start: 0.8665 (t70) cc_final: 0.8167 (t-170) REVERT: B 331 ASN cc_start: 0.9222 (m-40) cc_final: 0.9003 (m-40) REVERT: B 334 LEU cc_start: 0.9698 (mt) cc_final: 0.9446 (pp) REVERT: B 352 ASN cc_start: 0.9161 (m110) cc_final: 0.8871 (p0) REVERT: C 1 MET cc_start: 0.7091 (tpp) cc_final: 0.6605 (tpp) REVERT: C 5 HIS cc_start: 0.8149 (t70) cc_final: 0.7879 (t70) REVERT: C 35 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: C 56 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8385 (pp30) REVERT: C 134 HIS cc_start: 0.8746 (t70) cc_final: 0.8268 (t-170) REVERT: C 216 ARG cc_start: 0.8706 (tpp-160) cc_final: 0.8268 (tpp-160) REVERT: C 227 CYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8934 (t) REVERT: C 281 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8556 (tp) REVERT: C 331 ASN cc_start: 0.9178 (m-40) cc_final: 0.8937 (m-40) REVERT: C 334 LEU cc_start: 0.9669 (mt) cc_final: 0.9432 (pp) REVERT: C 352 ASN cc_start: 0.9198 (m110) cc_final: 0.8904 (p0) REVERT: D 56 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8333 (pp30) REVERT: D 134 HIS cc_start: 0.8747 (t70) cc_final: 0.8282 (t-170) REVERT: D 227 CYS cc_start: 0.9147 (m) cc_final: 0.8712 (t) REVERT: D 331 ASN cc_start: 0.9156 (m-40) cc_final: 0.8937 (m-40) REVERT: D 334 LEU cc_start: 0.9681 (mt) cc_final: 0.9409 (pp) REVERT: D 352 ASN cc_start: 0.9199 (m110) cc_final: 0.8852 (p0) REVERT: E 29 ARG cc_start: 0.8288 (mtt180) cc_final: 0.7995 (mtm110) REVERT: E 30 LEU cc_start: 0.8758 (pt) cc_final: 0.8537 (mt) REVERT: E 35 ASP cc_start: 0.8179 (m-30) cc_final: 0.7730 (t0) REVERT: E 56 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8327 (pp30) REVERT: E 134 HIS cc_start: 0.8739 (t70) cc_final: 0.8225 (t-170) REVERT: E 227 CYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8804 (t) REVERT: E 281 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8495 (tp) REVERT: E 331 ASN cc_start: 0.9201 (m-40) cc_final: 0.8966 (m-40) REVERT: E 334 LEU cc_start: 0.9672 (mt) cc_final: 0.9399 (pp) REVERT: E 352 ASN cc_start: 0.9171 (m110) cc_final: 0.8819 (p0) REVERT: F 56 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8464 (pp30) REVERT: F 57 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: F 134 HIS cc_start: 0.8719 (t70) cc_final: 0.8203 (t-170) REVERT: F 227 CYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8838 (t) REVERT: F 331 ASN cc_start: 0.9172 (m-40) cc_final: 0.8931 (m-40) REVERT: F 334 LEU cc_start: 0.9680 (mt) cc_final: 0.9427 (pp) REVERT: F 352 ASN cc_start: 0.9193 (m110) cc_final: 0.8899 (p0) REVERT: G 30 LEU cc_start: 0.9202 (mt) cc_final: 0.9000 (tp) REVERT: G 56 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8270 (pp30) REVERT: G 134 HIS cc_start: 0.8629 (t70) cc_final: 0.8062 (t-170) REVERT: G 216 ARG cc_start: 0.8798 (tpp-160) cc_final: 0.8478 (tpp-160) REVERT: G 227 CYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8760 (t) REVERT: G 281 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8471 (tp) REVERT: G 331 ASN cc_start: 0.9217 (m-40) cc_final: 0.8968 (m-40) REVERT: G 334 LEU cc_start: 0.9683 (mt) cc_final: 0.9417 (pp) REVERT: G 352 ASN cc_start: 0.9146 (m110) cc_final: 0.8831 (p0) outliers start: 76 outliers final: 38 residues processed: 248 average time/residue: 0.5330 time to fit residues: 150.4574 Evaluate side-chains 238 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 227 CYS Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 227 CYS Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 287 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 212 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 82 optimal weight: 0.0770 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 138 optimal weight: 0.2980 chunk 208 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 279 ASN B 5 HIS B 279 ASN C 279 ASN D 279 ASN E 279 ASN F 279 ASN G 279 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.097061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064759 restraints weight = 43883.588| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.44 r_work: 0.2916 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18375 Z= 0.124 Angle : 0.687 10.277 24927 Z= 0.336 Chirality : 0.038 0.149 2961 Planarity : 0.004 0.092 2975 Dihedral : 4.159 27.529 2359 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.81 % Allowed : 18.77 % Favored : 78.42 % 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: 2.02 (0.20), residues: 2170 helix: 1.73 (0.14), residues: 1498 sheet: -0.61 (0.67), residues: 70 loop : 0.81 (0.30), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 216 TYR 0.010 0.001 TYR D 283 PHE 0.007 0.001 PHE A 220 TRP 0.012 0.001 TRP F 74 HIS 0.005 0.001 HIS B 5 Details of bonding type rmsd covalent geometry : bond 0.00260 (18361) covalent geometry : angle 0.68616 (24899) SS BOND : bond 0.00097 ( 14) SS BOND : angle 1.03604 ( 28) hydrogen bonds : bond 0.03843 ( 1129) hydrogen bonds : angle 4.19877 ( 3198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 0.737 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: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8837 (pp30) cc_final: 0.8461 (pp30) REVERT: A 134 HIS cc_start: 0.8723 (t70) cc_final: 0.8318 (t-170) REVERT: A 216 ARG cc_start: 0.8820 (tpp-160) cc_final: 0.8565 (tpp-160) REVERT: A 227 CYS cc_start: 0.9093 (m) cc_final: 0.8792 (t) REVERT: A 261 ARG cc_start: 0.9046 (mmt-90) cc_final: 0.8815 (mmm-85) REVERT: B 1 MET cc_start: 0.6938 (tpp) cc_final: 0.6638 (tpt) REVERT: B 35 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7964 (t70) REVERT: B 56 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8315 (pp30) REVERT: B 134 HIS cc_start: 0.8657 (t70) cc_final: 0.8165 (t-170) REVERT: B 331 ASN cc_start: 0.9199 (m-40) cc_final: 0.8975 (m-40) REVERT: B 334 LEU cc_start: 0.9670 (mt) cc_final: 0.9387 (pp) REVERT: B 352 ASN cc_start: 0.9147 (m110) cc_final: 0.8834 (p0) REVERT: C 1 MET cc_start: 0.7149 (tpp) cc_final: 0.6877 (tpp) REVERT: C 5 HIS cc_start: 0.8107 (t70) cc_final: 0.7867 (t70) REVERT: C 35 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: C 56 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8303 (pp30) REVERT: C 134 HIS cc_start: 0.8736 (t70) cc_final: 0.8226 (t-170) REVERT: C 216 ARG cc_start: 0.8655 (tpp-160) cc_final: 0.8255 (tpp-160) REVERT: C 331 ASN cc_start: 0.9142 (m-40) cc_final: 0.8888 (m-40) REVERT: C 334 LEU cc_start: 0.9660 (mt) cc_final: 0.9424 (pp) REVERT: C 352 ASN cc_start: 0.9157 (m110) cc_final: 0.8854 (p0) REVERT: D 56 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8243 (pp30) REVERT: D 134 HIS cc_start: 0.8689 (t70) cc_final: 0.8221 (t-170) REVERT: D 227 CYS cc_start: 0.9064 (m) cc_final: 0.8638 (t) REVERT: D 331 ASN cc_start: 0.9148 (m-40) cc_final: 0.8921 (m-40) REVERT: D 334 LEU cc_start: 0.9680 (mt) cc_final: 0.9411 (pp) REVERT: D 352 ASN cc_start: 0.9172 (m110) cc_final: 0.8809 (p0) REVERT: E 1 MET cc_start: 0.6987 (tpt) cc_final: 0.6734 (tpt) REVERT: E 29 ARG cc_start: 0.8296 (mtt180) cc_final: 0.7996 (mtm110) REVERT: E 56 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8268 (pp30) REVERT: E 134 HIS cc_start: 0.8692 (t70) cc_final: 0.8155 (t-170) REVERT: E 331 ASN cc_start: 0.9151 (m-40) cc_final: 0.8922 (m-40) REVERT: E 334 LEU cc_start: 0.9667 (mt) cc_final: 0.9406 (pp) REVERT: E 352 ASN cc_start: 0.9124 (m110) cc_final: 0.8755 (p0) REVERT: F 56 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8359 (pp30) REVERT: F 57 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: F 134 HIS cc_start: 0.8666 (t70) cc_final: 0.8132 (t-170) REVERT: F 227 CYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8814 (t) REVERT: F 331 ASN cc_start: 0.9115 (m-40) cc_final: 0.8880 (m-40) REVERT: F 334 LEU cc_start: 0.9669 (mt) cc_final: 0.9417 (pp) REVERT: F 352 ASN cc_start: 0.9172 (m110) cc_final: 0.8845 (p0) REVERT: G 56 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8220 (pp30) REVERT: G 134 HIS cc_start: 0.8568 (t70) cc_final: 0.7972 (t-170) REVERT: G 216 ARG cc_start: 0.8714 (tpp-160) cc_final: 0.8481 (tpp-160) REVERT: G 227 CYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8702 (t) REVERT: G 331 ASN cc_start: 0.9162 (m-40) cc_final: 0.8891 (m-40) REVERT: G 334 LEU cc_start: 0.9664 (mt) cc_final: 0.9398 (pp) REVERT: G 352 ASN cc_start: 0.9132 (m110) cc_final: 0.8791 (p0) outliers start: 57 outliers final: 29 residues processed: 261 average time/residue: 0.5164 time to fit residues: 154.2879 Evaluate side-chains 230 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 227 CYS Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 287 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 143 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 91 optimal weight: 0.0570 chunk 106 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN C 279 ASN E 5 HIS E 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.096118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.063646 restraints weight = 43814.602| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.42 r_work: 0.2895 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18375 Z= 0.140 Angle : 0.691 11.044 24927 Z= 0.339 Chirality : 0.039 0.238 2961 Planarity : 0.004 0.094 2975 Dihedral : 4.143 21.115 2359 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.77 % Allowed : 20.39 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.20), residues: 2170 helix: 1.71 (0.14), residues: 1498 sheet: -0.57 (0.67), residues: 70 loop : 0.79 (0.30), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 216 TYR 0.009 0.001 TYR C 283 PHE 0.008 0.001 PHE D 333 TRP 0.010 0.001 TRP F 74 HIS 0.004 0.001 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00323 (18361) covalent geometry : angle 0.68990 (24899) SS BOND : bond 0.00236 ( 14) SS BOND : angle 1.20343 ( 28) hydrogen bonds : bond 0.03965 ( 1129) hydrogen bonds : angle 4.27949 ( 3198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.779 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: symmetry clash REVERT: A 56 GLN cc_start: 0.8780 (pp30) cc_final: 0.8430 (pp30) REVERT: A 134 HIS cc_start: 0.8756 (t70) cc_final: 0.8360 (t-170) REVERT: A 216 ARG cc_start: 0.8840 (tpp-160) cc_final: 0.8564 (tpp-160) REVERT: A 227 CYS cc_start: 0.9079 (m) cc_final: 0.8821 (t) REVERT: A 261 ARG cc_start: 0.9053 (mmt-90) cc_final: 0.8820 (mmm-85) REVERT: A 334 LEU cc_start: 0.9709 (mm) cc_final: 0.9470 (pp) REVERT: B 1 MET cc_start: 0.6787 (tpp) cc_final: 0.6568 (tpt) REVERT: B 35 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8044 (t70) REVERT: B 56 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8374 (pp30) REVERT: B 134 HIS cc_start: 0.8670 (t70) cc_final: 0.8196 (t-170) REVERT: B 331 ASN cc_start: 0.9198 (m-40) cc_final: 0.8976 (m-40) REVERT: B 334 LEU cc_start: 0.9677 (mt) cc_final: 0.9394 (pp) REVERT: C 1 MET cc_start: 0.7216 (tpp) cc_final: 0.6866 (tpp) REVERT: C 35 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: C 56 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8344 (pp30) REVERT: C 134 HIS cc_start: 0.8741 (t70) cc_final: 0.8239 (t-170) REVERT: C 216 ARG cc_start: 0.8691 (tpp-160) cc_final: 0.8274 (tpp-160) REVERT: C 331 ASN cc_start: 0.9159 (m-40) cc_final: 0.8908 (m-40) REVERT: C 334 LEU cc_start: 0.9665 (mt) cc_final: 0.9433 (pp) REVERT: C 352 ASN cc_start: 0.9174 (m110) cc_final: 0.8883 (p0) REVERT: D 56 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8250 (pp30) REVERT: D 134 HIS cc_start: 0.8684 (t70) cc_final: 0.8218 (t-170) REVERT: D 227 CYS cc_start: 0.9101 (m) cc_final: 0.8652 (t) REVERT: D 331 ASN cc_start: 0.9191 (m-40) cc_final: 0.8954 (m-40) REVERT: D 334 LEU cc_start: 0.9686 (mt) cc_final: 0.9416 (pp) REVERT: D 352 ASN cc_start: 0.9202 (m110) cc_final: 0.8851 (p0) REVERT: E 1 MET cc_start: 0.7033 (tpt) cc_final: 0.6766 (tpt) REVERT: E 56 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8305 (pp30) REVERT: E 134 HIS cc_start: 0.8700 (t70) cc_final: 0.8183 (OUTLIER) REVERT: E 331 ASN cc_start: 0.9157 (m-40) cc_final: 0.8927 (m-40) REVERT: E 334 LEU cc_start: 0.9686 (mt) cc_final: 0.9423 (pp) REVERT: E 352 ASN cc_start: 0.9154 (m110) cc_final: 0.8788 (p0) REVERT: F 35 ASP cc_start: 0.8119 (t70) cc_final: 0.7614 (t0) REVERT: F 56 GLN cc_start: 0.8673 (pp30) cc_final: 0.8376 (pp30) REVERT: F 57 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: F 134 HIS cc_start: 0.8659 (t70) cc_final: 0.8132 (t-170) REVERT: F 227 CYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8834 (t) REVERT: F 331 ASN cc_start: 0.9119 (m-40) cc_final: 0.8883 (m-40) REVERT: F 334 LEU cc_start: 0.9679 (mt) cc_final: 0.9434 (pp) REVERT: F 352 ASN cc_start: 0.9170 (m110) cc_final: 0.8864 (p0) REVERT: G 35 ASP cc_start: 0.8142 (t70) cc_final: 0.7664 (t0) REVERT: G 56 GLN cc_start: 0.8671 (pp30) cc_final: 0.8201 (pp30) REVERT: G 134 HIS cc_start: 0.8608 (t70) cc_final: 0.8032 (t-170) REVERT: G 216 ARG cc_start: 0.8726 (tpp-160) cc_final: 0.8277 (tpp-160) REVERT: G 227 CYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8699 (t) REVERT: G 331 ASN cc_start: 0.9180 (m-40) cc_final: 0.8933 (m-40) REVERT: G 334 LEU cc_start: 0.9677 (mt) cc_final: 0.9415 (pp) REVERT: G 352 ASN cc_start: 0.9138 (m110) cc_final: 0.8808 (p0) outliers start: 36 outliers final: 25 residues processed: 217 average time/residue: 0.5427 time to fit residues: 134.3161 Evaluate side-chains 225 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 227 CYS Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 287 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 0 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 279 ASN C 279 ASN D 279 ASN E 5 HIS E 279 ASN G 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.096428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.064185 restraints weight = 44085.056| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.41 r_work: 0.2911 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18375 Z= 0.129 Angle : 0.686 10.547 24927 Z= 0.336 Chirality : 0.039 0.176 2961 Planarity : 0.004 0.083 2975 Dihedral : 4.132 19.260 2359 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.97 % Allowed : 20.10 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.20), residues: 2170 helix: 1.69 (0.14), residues: 1498 sheet: -0.44 (0.69), residues: 70 loop : 0.81 (0.30), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 216 TYR 0.008 0.001 TYR E 229 PHE 0.007 0.001 PHE B 333 TRP 0.011 0.001 TRP F 74 HIS 0.003 0.001 HIS A 5 Details of bonding type rmsd covalent geometry : bond 0.00292 (18361) covalent geometry : angle 0.68584 (24899) SS BOND : bond 0.00180 ( 14) SS BOND : angle 1.11071 ( 28) hydrogen bonds : bond 0.03824 ( 1129) hydrogen bonds : angle 4.23647 ( 3198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5870.52 seconds wall clock time: 101 minutes 4.63 seconds (6064.63 seconds total)