Starting phenix.real_space_refine on Fri Jul 3 06:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tq7_56126/07_2026/9tq7_56126.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tq7_56126/07_2026/9tq7_56126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tq7_56126/07_2026/9tq7_56126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tq7_56126/07_2026/9tq7_56126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tq7_56126/07_2026/9tq7_56126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tq7_56126/07_2026/9tq7_56126.map" } resolution = 3.58 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 88 5.16 5 C 7628 2.51 5 N 2068 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12156 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2995 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "B" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2995 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "C" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2995 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "D" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2995 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.14, per 1000 atoms: 0.18 Number of scatterers: 12156 At special positions: 0 Unit cell: (117.53, 117.53, 73.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 88 16.00 O 2364 8.00 N 2068 7.00 C 7628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.05 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.05 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.05 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.04 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.05 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.02 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 600 " - " ASN A 88 " " NAG A 601 " - " ASN A 235 " " NAG A 602 " - " ASN A 146 " " NAG B 600 " - " ASN B 88 " " NAG B 601 " - " ASN B 235 " " NAG B 602 " - " ASN B 146 " " NAG C 600 " - " ASN C 88 " " NAG C 601 " - " ASN C 235 " " NAG C 602 " - " ASN C 146 " " NAG D 600 " - " ASN D 88 " " NAG D 601 " - " ASN D 235 " " NAG D 602 " - " ASN D 146 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 526.1 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 28 sheets defined 8.0% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 150 removed outlier: 4.001A pdb=" N GLY A 147 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 149 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 4.011A pdb=" N SER A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.915A pdb=" N THR A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 142 through 150 removed outlier: 4.001A pdb=" N GLY B 147 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 149 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 4.012A pdb=" N SER B 172 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.915A pdb=" N THR B 413 " --> pdb=" O HIS B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 142 through 150 removed outlier: 4.001A pdb=" N GLY C 147 " --> pdb=" O HIS C 144 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE C 149 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 removed outlier: 4.011A pdb=" N SER C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 382 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.914A pdb=" N THR C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 142 through 150 removed outlier: 4.001A pdb=" N GLY D 147 " --> pdb=" O HIS D 144 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE D 149 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 4.011A pdb=" N SER D 172 " --> pdb=" O PRO D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 382 Processing helix chain 'D' and resid 409 through 414 removed outlier: 3.916A pdb=" N THR D 413 " --> pdb=" O HIS D 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102 removed outlier: 5.344A pdb=" N ILE A 99 " --> pdb=" O CYS A 446 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N CYS A 446 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.599A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 157 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 176 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER A 160 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 4.426A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 195 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 184 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP A 214 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR A 208 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 226 removed outlier: 7.485A pdb=" N TYR A 253 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU A 268 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 255 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER A 266 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 257 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 284 removed outlier: 3.727A pdb=" N THR A 289 " --> pdb=" O TYR A 282 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 315 " --> pdb=" O TRP A 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 353 removed outlier: 5.863A pdb=" N LYS A 369 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 396 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 371 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET A 373 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP A 392 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP A 375 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS A 390 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 102 removed outlier: 5.344A pdb=" N ILE B 99 " --> pdb=" O CYS B 446 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N CYS B 446 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.599A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 157 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 176 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER B 160 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE B 174 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 185 removed outlier: 4.427A pdb=" N SER B 180 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 195 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 184 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 214 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR B 208 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE B 212 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 226 removed outlier: 7.484A pdb=" N TYR B 253 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU B 268 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 255 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B 266 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG B 257 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 282 through 284 removed outlier: 3.728A pdb=" N THR B 289 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 315 " --> pdb=" O TRP B 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 352 through 353 removed outlier: 5.862A pdb=" N LYS B 369 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 396 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 371 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET B 373 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP B 392 " --> pdb=" O MET B 373 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TRP B 375 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS B 390 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 97 through 102 removed outlier: 5.344A pdb=" N ILE C 99 " --> pdb=" O CYS C 446 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS C 446 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.600A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR C 157 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 176 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER C 160 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE C 174 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 180 through 185 removed outlier: 4.426A pdb=" N SER C 180 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 195 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS C 184 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C 214 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR C 208 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AC1, first strand: chain 'C' and resid 224 through 226 removed outlier: 7.485A pdb=" N TYR C 253 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU C 268 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 255 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER C 266 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG C 257 " --> pdb=" O ILE C 264 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 282 through 284 removed outlier: 3.727A pdb=" N THR C 289 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 315 " --> pdb=" O TRP C 303 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 352 through 353 removed outlier: 5.863A pdb=" N LYS C 369 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE C 396 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 371 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET C 373 " --> pdb=" O ASP C 392 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP C 392 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP C 375 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS C 390 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 97 through 102 removed outlier: 5.344A pdb=" N ILE D 99 " --> pdb=" O CYS D 446 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N CYS D 446 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.599A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR D 157 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 176 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 180 through 185 removed outlier: 4.426A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 195 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS D 184 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP D 214 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR D 208 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 224 through 226 Processing sheet with id=AC8, first strand: chain 'D' and resid 224 through 226 removed outlier: 7.485A pdb=" N TYR D 253 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU D 268 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE D 255 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER D 266 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG D 257 " --> pdb=" O ILE D 264 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 282 through 284 removed outlier: 3.727A pdb=" N THR D 289 " --> pdb=" O TYR D 282 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY D 315 " --> pdb=" O TRP D 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 352 through 353 removed outlier: 5.863A pdb=" N LYS D 369 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE D 396 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 371 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET D 373 " --> pdb=" O ASP D 392 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP D 392 " --> pdb=" O MET D 373 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP D 375 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS D 390 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 768 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: 1.79 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3920 1.35 - 1.48: 3412 1.48 - 1.61: 5036 1.61 - 1.74: 0 1.74 - 1.87: 108 Bond restraints: 12476 Sorted by residual: bond pdb=" CB CYS C 421 " pdb=" SG CYS C 421 " ideal model delta sigma weight residual 1.808 1.870 -0.062 3.30e-02 9.18e+02 3.49e+00 bond pdb=" CB CYS A 421 " pdb=" SG CYS A 421 " ideal model delta sigma weight residual 1.808 1.870 -0.062 3.30e-02 9.18e+02 3.48e+00 bond pdb=" CB CYS D 421 " pdb=" SG CYS D 421 " ideal model delta sigma weight residual 1.808 1.869 -0.061 3.30e-02 9.18e+02 3.46e+00 bond pdb=" CB CYS B 421 " pdb=" SG CYS B 421 " ideal model delta sigma weight residual 1.808 1.869 -0.061 3.30e-02 9.18e+02 3.45e+00 bond pdb=" N SER B 82 " pdb=" CA SER B 82 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 12471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16571 2.02 - 4.04: 312 4.04 - 6.05: 29 6.05 - 8.07: 8 8.07 - 10.09: 8 Bond angle restraints: 16928 Sorted by residual: angle pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" C CYS B 233 " ideal model delta sigma weight residual 108.76 116.48 -7.72 1.58e+00 4.01e-01 2.39e+01 angle pdb=" N CYS A 233 " pdb=" CA CYS A 233 " pdb=" C CYS A 233 " ideal model delta sigma weight residual 108.76 116.45 -7.69 1.58e+00 4.01e-01 2.37e+01 angle pdb=" N CYS C 233 " pdb=" CA CYS C 233 " pdb=" C CYS C 233 " ideal model delta sigma weight residual 108.76 116.45 -7.69 1.58e+00 4.01e-01 2.37e+01 angle pdb=" N CYS D 233 " pdb=" CA CYS D 233 " pdb=" C CYS D 233 " ideal model delta sigma weight residual 108.76 116.45 -7.69 1.58e+00 4.01e-01 2.37e+01 angle pdb=" CA CYS A 233 " pdb=" CB CYS A 233 " pdb=" SG CYS A 233 " ideal model delta sigma weight residual 114.40 124.49 -10.09 2.30e+00 1.89e-01 1.92e+01 ... (remaining 16923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 6453 16.76 - 33.51: 863 33.51 - 50.27: 184 50.27 - 67.02: 28 67.02 - 83.78: 12 Dihedral angle restraints: 7540 sinusoidal: 3172 harmonic: 4368 Sorted by residual: dihedral pdb=" CB CYS D 233 " pdb=" SG CYS D 233 " pdb=" SG CYS D 238 " pdb=" CB CYS D 238 " ideal model delta sinusoidal sigma weight residual 93.00 27.33 65.67 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS A 233 " pdb=" SG CYS A 233 " pdb=" SG CYS A 238 " pdb=" CB CYS A 238 " ideal model delta sinusoidal sigma weight residual 93.00 27.34 65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS B 233 " pdb=" SG CYS B 233 " pdb=" SG CYS B 238 " pdb=" CB CYS B 238 " ideal model delta sinusoidal sigma weight residual 93.00 27.35 65.65 1 1.00e+01 1.00e-02 5.64e+01 ... (remaining 7537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1281 0.043 - 0.086: 318 0.086 - 0.129: 162 0.129 - 0.172: 27 0.172 - 0.215: 8 Chirality restraints: 1796 Sorted by residual: chirality pdb=" C1 NAG A 600 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 600 " pdb=" O5 NAG A 600 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1 NAG C 600 " pdb=" ND2 ASN C 88 " pdb=" C2 NAG C 600 " pdb=" O5 NAG C 600 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1 NAG B 600 " pdb=" ND2 ASN B 88 " pdb=" C2 NAG B 600 " pdb=" O5 NAG B 600 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1793 not shown) Planarity restraints: 2192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 287 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" CD GLU B 287 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU B 287 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B 287 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 287 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" CD GLU C 287 " -0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU C 287 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU C 287 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 287 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" CD GLU A 287 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU A 287 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 287 " -0.010 2.00e-02 2.50e+03 ... (remaining 2189 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2072 2.76 - 3.30: 12103 3.30 - 3.83: 19346 3.83 - 4.37: 22573 4.37 - 4.90: 41073 Nonbonded interactions: 97167 Sorted by model distance: nonbonded pdb=" O ASP A 284 " pdb=" OD1 ASP A 284 " model vdw 2.227 3.040 nonbonded pdb=" O ASP C 284 " pdb=" OD1 ASP C 284 " model vdw 2.227 3.040 nonbonded pdb=" O ASP B 284 " pdb=" OD1 ASP B 284 " model vdw 2.228 3.040 nonbonded pdb=" O ASP D 284 " pdb=" OD1 ASP D 284 " model vdw 2.228 3.040 nonbonded pdb=" O GLY C 298 " pdb="CA CA C 603 " model vdw 2.254 3.250 ... (remaining 97162 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 1.130 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.160 Find NCS groups from input model: 0.110 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 0.003 0.062 12520 Z= 0.144 Angle : 0.704 10.089 17028 Z= 0.386 Chirality : 0.050 0.215 1796 Planarity : 0.003 0.028 2180 Dihedral : 14.803 83.775 4668 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.35 % Allowed : 32.19 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.14 (0.21), residues: 1540 helix: -2.06 (0.78), residues: 24 sheet: -1.20 (0.23), residues: 580 loop : -1.56 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 173 TYR 0.006 0.001 TYR D 170 PHE 0.008 0.001 PHE C 422 TRP 0.006 0.001 TRP C 219 HIS 0.003 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (12476) covalent geometry : angle 0.68497 / 0.38 (16928) SS BOND : bond 0.00773 / 0.38 ( 32) SS BOND : angle 2.60094 / 1.75 ( 64) hydrogen bonds : bond 0.27637 / 18.61 ( 304) hydrogen bonds : angle 11.86778 / 8.29 ( 768) link_NAG-ASN : bond 0.00300 / 0.21 ( 12) link_NAG-ASN : angle 1.40227 / 0.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 487 time to evaluate : 0.292 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: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8605 (mt) cc_final: 0.8386 (mt) REVERT: A 214 ASP cc_start: 0.7986 (t0) cc_final: 0.7734 (t0) REVERT: A 275 HIS cc_start: 0.7779 (t-90) cc_final: 0.7046 (t-90) REVERT: A 376 ASP cc_start: 0.8225 (t70) cc_final: 0.7862 (t0) REVERT: A 423 TRP cc_start: 0.8480 (p-90) cc_final: 0.8252 (p-90) REVERT: B 275 HIS cc_start: 0.7892 (t-90) cc_final: 0.7366 (t-90) REVERT: B 376 ASP cc_start: 0.8289 (t70) cc_final: 0.8050 (t70) REVERT: B 415 LEU cc_start: 0.8928 (mt) cc_final: 0.8582 (mp) REVERT: B 418 ILE cc_start: 0.8523 (mm) cc_final: 0.8021 (mm) REVERT: B 436 ILE cc_start: 0.9180 (mm) cc_final: 0.8581 (tt) REVERT: C 158 LEU cc_start: 0.8927 (tt) cc_final: 0.8717 (tt) REVERT: C 275 HIS cc_start: 0.8019 (t-90) cc_final: 0.7494 (t-90) REVERT: C 376 ASP cc_start: 0.8281 (t70) cc_final: 0.8046 (t70) REVERT: C 415 LEU cc_start: 0.8883 (mt) cc_final: 0.8558 (mp) REVERT: C 418 ILE cc_start: 0.8546 (mm) cc_final: 0.8027 (mm) REVERT: D 128 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8518 (mt-10) REVERT: D 275 HIS cc_start: 0.7919 (t-90) cc_final: 0.7420 (t-90) REVERT: D 376 ASP cc_start: 0.8197 (t70) cc_final: 0.7925 (t70) REVERT: D 415 LEU cc_start: 0.8918 (mt) cc_final: 0.8563 (mp) REVERT: D 418 ILE cc_start: 0.8584 (mm) cc_final: 0.8086 (mm) REVERT: D 436 ILE cc_start: 0.9240 (mm) cc_final: 0.8765 (tt) outliers start: 18 outliers final: 11 residues processed: 495 average time/residue: 0.0694 time to fit residues: 54.3091 Evaluate side-chains 452 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 441 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 279 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.0470 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN B 144 HIS B 209 ASN B 408 GLN C 144 HIS C 209 ASN C 408 GLN D 209 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122480 restraints weight = 18101.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127889 restraints weight = 9068.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131605 restraints weight = 5683.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134194 restraints weight = 4029.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135915 restraints weight = 3096.050| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12520 Z= 0.165 Angle : 0.693 9.534 17028 Z= 0.358 Chirality : 0.052 0.232 1796 Planarity : 0.004 0.032 2180 Dihedral : 6.485 44.002 1923 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.54 % Allowed : 24.63 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.81 (0.21), residues: 1540 helix: -3.21 (0.57), residues: 24 sheet: -0.77 (0.23), residues: 572 loop : -1.45 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 173 TYR 0.009 0.001 TYR A 170 PHE 0.012 0.001 PHE B 445 TRP 0.006 0.001 TRP C 179 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 (12476) covalent geometry : angle 0.67659 / 0.35 (16928) SS BOND : bond 0.00770 / 0.38 ( 32) SS BOND : angle 2.24297 / 1.48 ( 64) hydrogen bonds : bond 0.03520 / 2.54 ( 304) hydrogen bonds : angle 7.21463 / 4.99 ( 768) link_NAG-ASN : bond 0.00302 / 0.18 ( 12) link_NAG-ASN : angle 1.62329 / 0.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 500 time to evaluate : 0.333 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 214 ASP cc_start: 0.8313 (t0) cc_final: 0.8092 (t0) REVERT: A 228 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7610 (mm-30) REVERT: A 279 CYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6668 (m) REVERT: B 228 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 275 HIS cc_start: 0.8291 (t-90) cc_final: 0.8061 (t-90) REVERT: B 279 CYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6557 (m) REVERT: B 376 ASP cc_start: 0.8022 (t70) cc_final: 0.7817 (t70) REVERT: B 411 GLU cc_start: 0.8125 (mp0) cc_final: 0.7906 (mp0) REVERT: B 415 LEU cc_start: 0.9001 (mt) cc_final: 0.8767 (mp) REVERT: B 436 ILE cc_start: 0.9079 (mm) cc_final: 0.8742 (tt) REVERT: C 268 GLU cc_start: 0.7530 (pm20) cc_final: 0.7188 (pp20) REVERT: C 275 HIS cc_start: 0.8286 (t-90) cc_final: 0.8023 (t-90) REVERT: C 376 ASP cc_start: 0.8018 (t70) cc_final: 0.7599 (t0) REVERT: C 384 ASP cc_start: 0.7771 (t70) cc_final: 0.7281 (t0) REVERT: C 415 LEU cc_start: 0.9003 (mt) cc_final: 0.8790 (mp) REVERT: D 275 HIS cc_start: 0.8285 (t-90) cc_final: 0.8014 (t-90) REVERT: D 376 ASP cc_start: 0.8000 (t70) cc_final: 0.7562 (t0) REVERT: D 411 GLU cc_start: 0.8145 (mp0) cc_final: 0.7911 (mp0) REVERT: D 415 LEU cc_start: 0.9053 (mt) cc_final: 0.8822 (mp) REVERT: D 436 ILE cc_start: 0.9135 (mm) cc_final: 0.8858 (tt) outliers start: 74 outliers final: 47 residues processed: 526 average time/residue: 0.0733 time to fit residues: 60.1891 Evaluate side-chains 514 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 465 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 468 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 140 optimal weight: 0.0050 chunk 0 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.143169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117941 restraints weight = 18132.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123469 restraints weight = 8882.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127436 restraints weight = 5533.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130076 restraints weight = 3932.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131755 restraints weight = 3048.210| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12520 Z= 0.162 Angle : 0.655 9.345 17028 Z= 0.341 Chirality : 0.050 0.231 1796 Planarity : 0.004 0.062 2180 Dihedral : 6.606 50.827 1914 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.61 % Allowed : 25.82 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.92 (0.20), residues: 1540 helix: -4.25 (0.30), residues: 60 sheet: -0.51 (0.23), residues: 552 loop : -1.59 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.012 0.001 TYR B 274 PHE 0.013 0.001 PHE A 445 TRP 0.008 0.001 TRP D 179 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (12476) covalent geometry : angle 0.63853 / 0.33 (16928) SS BOND : bond 0.00764 / 0.38 ( 32) SS BOND : angle 2.27408 / 1.47 ( 64) hydrogen bonds : bond 0.03426 / 2.45 ( 304) hydrogen bonds : angle 6.41737 / 4.45 ( 768) link_NAG-ASN : bond 0.00349 / 0.21 ( 12) link_NAG-ASN : angle 1.50938 / 0.88 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 506 time to evaluate : 0.379 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 214 ASP cc_start: 0.8446 (t0) cc_final: 0.8149 (t0) REVERT: A 228 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7671 (mm-30) REVERT: A 275 HIS cc_start: 0.8408 (t-90) cc_final: 0.8153 (t-90) REVERT: A 277 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6953 (mt-10) REVERT: A 279 CYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6635 (m) REVERT: A 357 VAL cc_start: 0.9241 (t) cc_final: 0.8867 (m) REVERT: A 373 MET cc_start: 0.8070 (mmm) cc_final: 0.7644 (mmm) REVERT: A 376 ASP cc_start: 0.8277 (t70) cc_final: 0.7989 (t70) REVERT: B 113 ASP cc_start: 0.8033 (m-30) cc_final: 0.7793 (m-30) REVERT: B 123 SER cc_start: 0.8584 (m) cc_final: 0.8316 (t) REVERT: B 228 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 268 GLU cc_start: 0.7892 (pm20) cc_final: 0.7642 (pp20) REVERT: B 275 HIS cc_start: 0.8315 (t-90) cc_final: 0.8026 (t-90) REVERT: B 279 CYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6568 (m) REVERT: B 376 ASP cc_start: 0.8155 (t70) cc_final: 0.7669 (t0) REVERT: B 411 GLU cc_start: 0.8283 (mp0) cc_final: 0.8024 (mp0) REVERT: B 415 LEU cc_start: 0.9121 (mt) cc_final: 0.8912 (mp) REVERT: B 436 ILE cc_start: 0.9134 (mm) cc_final: 0.8721 (tt) REVERT: C 123 SER cc_start: 0.8693 (m) cc_final: 0.8474 (t) REVERT: C 207 LYS cc_start: 0.8894 (mtpp) cc_final: 0.8613 (ttmm) REVERT: C 275 HIS cc_start: 0.8288 (t-90) cc_final: 0.7884 (t-90) REVERT: C 284 ASP cc_start: 0.8313 (p0) cc_final: 0.7982 (p0) REVERT: C 287 GLU cc_start: 0.7144 (mp0) cc_final: 0.6923 (mp0) REVERT: C 325 ASN cc_start: 0.7950 (t0) cc_final: 0.7579 (p0) REVERT: C 376 ASP cc_start: 0.8183 (t70) cc_final: 0.7683 (t0) REVERT: C 411 GLU cc_start: 0.8199 (mp0) cc_final: 0.7886 (mp0) REVERT: C 433 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7079 (tm-30) REVERT: D 123 SER cc_start: 0.8722 (m) cc_final: 0.8446 (t) REVERT: D 256 PHE cc_start: 0.8517 (m-80) cc_final: 0.8159 (m-10) REVERT: D 268 GLU cc_start: 0.7825 (pm20) cc_final: 0.7569 (pp20) REVERT: D 275 HIS cc_start: 0.8347 (t-90) cc_final: 0.7990 (t-90) REVERT: D 284 ASP cc_start: 0.8332 (p0) cc_final: 0.7985 (p0) REVERT: D 376 ASP cc_start: 0.8194 (t0) cc_final: 0.7727 (t0) REVERT: D 411 GLU cc_start: 0.8235 (mp0) cc_final: 0.7975 (mp0) REVERT: D 433 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7119 (tm-30) REVERT: D 436 ILE cc_start: 0.9260 (mm) cc_final: 0.8931 (tt) outliers start: 75 outliers final: 47 residues processed: 522 average time/residue: 0.0797 time to fit residues: 64.1867 Evaluate side-chains 479 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 430 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 444 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 409 HIS B 144 HIS B 409 HIS C 144 HIS C 409 HIS D 144 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.146582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122416 restraints weight = 17991.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127666 restraints weight = 8986.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131557 restraints weight = 5639.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134087 restraints weight = 4018.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135987 restraints weight = 3118.873| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12520 Z= 0.139 Angle : 0.653 9.742 17028 Z= 0.338 Chirality : 0.049 0.219 1796 Planarity : 0.004 0.052 2180 Dihedral : 6.747 52.732 1914 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.54 % Allowed : 26.72 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.68 (0.20), residues: 1540 helix: -4.16 (0.35), residues: 60 sheet: -0.25 (0.23), residues: 528 loop : -1.46 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 368 TYR 0.014 0.001 TYR B 274 PHE 0.020 0.002 PHE C 121 TRP 0.009 0.001 TRP D 179 HIS 0.003 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (12476) covalent geometry : angle 0.63491 / 0.33 (16928) SS BOND : bond 0.00689 / 0.35 ( 32) SS BOND : angle 2.39436 / 1.57 ( 64) hydrogen bonds : bond 0.03060 / 2.19 ( 304) hydrogen bonds : angle 5.95188 / 4.14 ( 768) link_NAG-ASN : bond 0.00374 / 0.22 ( 12) link_NAG-ASN : angle 1.41159 / 0.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 466 time to evaluate : 0.500 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 214 ASP cc_start: 0.8403 (t0) cc_final: 0.8123 (t0) REVERT: A 256 PHE cc_start: 0.8489 (m-80) cc_final: 0.8181 (m-10) REVERT: A 279 CYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6573 (m) REVERT: A 357 VAL cc_start: 0.9237 (t) cc_final: 0.8864 (m) REVERT: A 376 ASP cc_start: 0.8129 (t70) cc_final: 0.7864 (t70) REVERT: A 449 ASP cc_start: 0.8199 (m-30) cc_final: 0.7889 (m-30) REVERT: B 113 ASP cc_start: 0.7753 (m-30) cc_final: 0.7487 (m-30) REVERT: B 123 SER cc_start: 0.8600 (m) cc_final: 0.8328 (t) REVERT: B 170 TYR cc_start: 0.8991 (m-10) cc_final: 0.8551 (m-80) REVERT: B 256 PHE cc_start: 0.8454 (m-80) cc_final: 0.8178 (m-10) REVERT: B 264 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8695 (mm) REVERT: B 279 CYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6601 (m) REVERT: B 284 ASP cc_start: 0.8365 (p0) cc_final: 0.8039 (p0) REVERT: B 376 ASP cc_start: 0.7986 (t0) cc_final: 0.7497 (t0) REVERT: B 436 ILE cc_start: 0.9091 (mm) cc_final: 0.8756 (tt) REVERT: C 123 SER cc_start: 0.8725 (m) cc_final: 0.8478 (t) REVERT: C 256 PHE cc_start: 0.8453 (m-80) cc_final: 0.8115 (m-10) REVERT: C 275 HIS cc_start: 0.8267 (t-90) cc_final: 0.7928 (t-90) REVERT: C 287 GLU cc_start: 0.7169 (mp0) cc_final: 0.6934 (mp0) REVERT: C 325 ASN cc_start: 0.7914 (t0) cc_final: 0.7548 (p0) REVERT: C 376 ASP cc_start: 0.8057 (t0) cc_final: 0.7571 (t0) REVERT: C 411 GLU cc_start: 0.8249 (mp0) cc_final: 0.8028 (mp0) REVERT: D 123 SER cc_start: 0.8743 (m) cc_final: 0.8454 (t) REVERT: D 256 PHE cc_start: 0.8440 (m-80) cc_final: 0.7879 (m-10) REVERT: D 264 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.8783 (mm) REVERT: D 275 HIS cc_start: 0.8299 (t-90) cc_final: 0.7994 (t-90) REVERT: D 284 ASP cc_start: 0.8389 (p0) cc_final: 0.8179 (p0) REVERT: D 325 ASN cc_start: 0.7763 (t0) cc_final: 0.7473 (p0) REVERT: D 376 ASP cc_start: 0.8029 (t0) cc_final: 0.7564 (t0) REVERT: D 411 GLU cc_start: 0.8206 (mp0) cc_final: 0.8006 (mp0) REVERT: D 436 ILE cc_start: 0.9247 (mm) cc_final: 0.8987 (tt) REVERT: D 463 LEU cc_start: 0.8698 (pp) cc_final: 0.8382 (mp) outliers start: 74 outliers final: 44 residues processed: 490 average time/residue: 0.0743 time to fit residues: 57.0475 Evaluate side-chains 477 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 429 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 444 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 111 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116580 restraints weight = 18359.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121865 restraints weight = 9260.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125491 restraints weight = 5880.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127960 restraints weight = 4181.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129878 restraints weight = 3261.246| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 12520 Z= 0.233 Angle : 0.739 12.097 17028 Z= 0.379 Chirality : 0.050 0.208 1796 Planarity : 0.004 0.050 2180 Dihedral : 6.964 52.429 1914 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 8.53 % Allowed : 25.15 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.50 (0.21), residues: 1540 helix: -2.92 (0.86), residues: 24 sheet: -0.43 (0.22), residues: 572 loop : -1.32 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 368 TYR 0.015 0.001 TYR B 274 PHE 0.017 0.002 PHE A 445 TRP 0.009 0.001 TRP A 179 HIS 0.005 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (12476) covalent geometry : angle 0.71452 / 0.37 (16928) SS BOND : bond 0.00834 / 0.50 ( 32) SS BOND : angle 3.04162 / 1.99 ( 64) hydrogen bonds : bond 0.03388 / 2.41 ( 304) hydrogen bonds : angle 6.00011 / 4.18 ( 768) link_NAG-ASN : bond 0.00296 / 0.16 ( 12) link_NAG-ASN : angle 1.32199 / 0.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 438 time to evaluate : 0.304 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ASP cc_start: 0.8503 (t70) cc_final: 0.8125 (t0) REVERT: A 228 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 275 HIS cc_start: 0.8534 (t-90) cc_final: 0.8043 (t-90) REVERT: A 279 CYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6817 (m) REVERT: A 357 VAL cc_start: 0.9276 (t) cc_final: 0.8902 (m) REVERT: A 376 ASP cc_start: 0.8435 (t70) cc_final: 0.7999 (t0) REVERT: A 436 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8787 (tt) REVERT: A 449 ASP cc_start: 0.8413 (m-30) cc_final: 0.8070 (m-30) REVERT: B 113 ASP cc_start: 0.7936 (m-30) cc_final: 0.7595 (m-30) REVERT: B 123 SER cc_start: 0.8775 (m) cc_final: 0.8509 (t) REVERT: B 170 TYR cc_start: 0.9058 (m-10) cc_final: 0.8713 (m-80) REVERT: B 275 HIS cc_start: 0.8547 (t-90) cc_final: 0.8321 (t-90) REVERT: B 279 CYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6576 (m) REVERT: B 329 ASN cc_start: 0.8509 (p0) cc_final: 0.8281 (p0) REVERT: B 357 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.8923 (m) REVERT: B 373 MET cc_start: 0.8013 (mmm) cc_final: 0.7629 (mmm) REVERT: B 376 ASP cc_start: 0.8245 (t0) cc_final: 0.7780 (t0) REVERT: B 398 GLU cc_start: 0.7776 (mp0) cc_final: 0.7532 (mp0) REVERT: B 436 ILE cc_start: 0.9250 (mm) cc_final: 0.8841 (tt) REVERT: C 123 SER cc_start: 0.8765 (m) cc_final: 0.8520 (t) REVERT: C 275 HIS cc_start: 0.8390 (t-90) cc_final: 0.7925 (t-90) REVERT: C 284 ASP cc_start: 0.8287 (p0) cc_final: 0.7925 (p0) REVERT: C 287 GLU cc_start: 0.7166 (mp0) cc_final: 0.6901 (mp0) REVERT: C 316 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7735 (m-10) REVERT: C 329 ASN cc_start: 0.8520 (p0) cc_final: 0.8310 (p0) REVERT: C 357 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.8921 (m) REVERT: C 376 ASP cc_start: 0.8275 (t0) cc_final: 0.7801 (t0) REVERT: C 398 GLU cc_start: 0.7792 (mp0) cc_final: 0.7550 (mp0) REVERT: C 433 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7065 (tm-30) REVERT: D 123 SER cc_start: 0.8800 (m) cc_final: 0.8537 (t) REVERT: D 275 HIS cc_start: 0.8450 (t-90) cc_final: 0.8109 (t-90) REVERT: D 277 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7046 (mt-10) REVERT: D 284 ASP cc_start: 0.8331 (p0) cc_final: 0.8092 (p0) REVERT: D 316 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7907 (m-10) REVERT: D 357 VAL cc_start: 0.9284 (t) cc_final: 0.8941 (m) REVERT: D 376 ASP cc_start: 0.8276 (t0) cc_final: 0.7852 (t0) REVERT: D 398 GLU cc_start: 0.7759 (mp0) cc_final: 0.7520 (mp0) REVERT: D 436 ILE cc_start: 0.9335 (mm) cc_final: 0.9014 (tt) REVERT: D 449 ASP cc_start: 0.8431 (m-30) cc_final: 0.8022 (m-30) REVERT: D 463 LEU cc_start: 0.8809 (pp) cc_final: 0.8404 (mp) outliers start: 114 outliers final: 76 residues processed: 491 average time/residue: 0.0740 time to fit residues: 56.4009 Evaluate side-chains 512 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 429 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 444 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 6 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.0010 chunk 101 optimal weight: 0.0970 chunk 141 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS B 409 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.147034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123003 restraints weight = 18112.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128268 restraints weight = 9169.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132143 restraints weight = 5797.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134759 restraints weight = 4125.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136536 restraints weight = 3180.931| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12520 Z= 0.134 Angle : 0.721 12.404 17028 Z= 0.370 Chirality : 0.050 0.202 1796 Planarity : 0.004 0.045 2180 Dihedral : 6.949 53.775 1914 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.91 % Allowed : 27.77 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.49 (0.20), residues: 1540 helix: -4.10 (0.39), residues: 60 sheet: -0.08 (0.23), residues: 528 loop : -1.36 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 368 TYR 0.013 0.001 TYR C 170 PHE 0.019 0.001 PHE A 445 TRP 0.010 0.001 TRP D 179 HIS 0.004 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (12476) covalent geometry : angle 0.70219 / 0.36 (16928) SS BOND : bond 0.00761 / 0.45 ( 32) SS BOND : angle 2.61996 / 1.69 ( 64) hydrogen bonds : bond 0.03014 / 2.13 ( 304) hydrogen bonds : angle 5.72749 / 3.98 ( 768) link_NAG-ASN : bond 0.00376 / 0.22 ( 12) link_NAG-ASN : angle 1.25783 / 0.73 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 441 time to evaluate : 0.310 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7489 (mtm-85) REVERT: A 214 ASP cc_start: 0.8442 (t70) cc_final: 0.8071 (t0) REVERT: A 275 HIS cc_start: 0.8362 (t-90) cc_final: 0.7965 (t-90) REVERT: A 279 CYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6575 (m) REVERT: A 357 VAL cc_start: 0.9248 (t) cc_final: 0.8899 (m) REVERT: A 376 ASP cc_start: 0.8156 (t70) cc_final: 0.7845 (t70) REVERT: A 436 ILE cc_start: 0.9215 (mt) cc_final: 0.8864 (tt) REVERT: A 449 ASP cc_start: 0.8426 (m-30) cc_final: 0.8112 (m-30) REVERT: A 463 LEU cc_start: 0.8824 (pp) cc_final: 0.8356 (mp) REVERT: B 113 ASP cc_start: 0.7941 (m-30) cc_final: 0.7477 (m-30) REVERT: B 136 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8498 (mm-40) REVERT: B 269 MET cc_start: 0.7873 (mtp) cc_final: 0.7589 (ttp) REVERT: B 275 HIS cc_start: 0.8352 (t-90) cc_final: 0.8120 (t-90) REVERT: B 279 CYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6538 (m) REVERT: B 357 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.8858 (m) REVERT: B 376 ASP cc_start: 0.8017 (t0) cc_final: 0.7458 (t0) REVERT: B 436 ILE cc_start: 0.9147 (mm) cc_final: 0.8795 (tt) REVERT: C 275 HIS cc_start: 0.8144 (t-90) cc_final: 0.7794 (t-90) REVERT: C 284 ASP cc_start: 0.8360 (p0) cc_final: 0.7955 (p0) REVERT: C 287 GLU cc_start: 0.7108 (mp0) cc_final: 0.6804 (mp0) REVERT: C 376 ASP cc_start: 0.8048 (t0) cc_final: 0.7507 (t0) REVERT: C 398 GLU cc_start: 0.7640 (mp0) cc_final: 0.7432 (mp0) REVERT: D 268 GLU cc_start: 0.7798 (pm20) cc_final: 0.7527 (pp20) REVERT: D 275 HIS cc_start: 0.8267 (t-90) cc_final: 0.7961 (t-90) REVERT: D 316 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7796 (m-10) REVERT: D 357 VAL cc_start: 0.9273 (t) cc_final: 0.8890 (m) REVERT: D 376 ASP cc_start: 0.8030 (t0) cc_final: 0.7463 (t0) REVERT: D 436 ILE cc_start: 0.9287 (mm) cc_final: 0.9050 (tp) REVERT: D 463 LEU cc_start: 0.8766 (pp) cc_final: 0.8451 (mp) outliers start: 79 outliers final: 58 residues processed: 478 average time/residue: 0.0704 time to fit residues: 52.8547 Evaluate side-chains 476 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 414 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 445 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 109 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS B 409 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119924 restraints weight = 18203.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125093 restraints weight = 9112.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.129010 restraints weight = 5814.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131570 restraints weight = 4128.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133501 restraints weight = 3195.898| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12520 Z= 0.168 Angle : 0.737 12.023 17028 Z= 0.378 Chirality : 0.050 0.203 1796 Planarity : 0.004 0.045 2180 Dihedral : 7.049 56.510 1914 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.21 % Allowed : 29.79 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.49 (0.20), residues: 1540 helix: -4.08 (0.39), residues: 60 sheet: -0.14 (0.23), residues: 552 loop : -1.33 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 368 TYR 0.013 0.001 TYR A 316 PHE 0.020 0.002 PHE C 121 TRP 0.009 0.001 TRP D 179 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (12476) covalent geometry : angle 0.71808 / 0.37 (16928) SS BOND : bond 0.00733 / 0.41 ( 32) SS BOND : angle 2.73652 / 1.82 ( 64) hydrogen bonds : bond 0.03098 / 2.22 ( 304) hydrogen bonds : angle 5.75341 / 4.00 ( 768) link_NAG-ASN : bond 0.00296 / 0.16 ( 12) link_NAG-ASN : angle 1.20664 / 0.70 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 428 time to evaluate : 0.452 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: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.7752 (t0) cc_final: 0.7505 (t0) REVERT: A 214 ASP cc_start: 0.8405 (t70) cc_final: 0.8092 (t0) REVERT: A 275 HIS cc_start: 0.8445 (t-90) cc_final: 0.8239 (t-90) REVERT: A 279 CYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6565 (m) REVERT: A 284 ASP cc_start: 0.8350 (p0) cc_final: 0.8116 (p0) REVERT: A 357 VAL cc_start: 0.9299 (t) cc_final: 0.8953 (m) REVERT: A 376 ASP cc_start: 0.8200 (t70) cc_final: 0.7771 (t0) REVERT: A 436 ILE cc_start: 0.9239 (mt) cc_final: 0.8920 (tt) REVERT: A 449 ASP cc_start: 0.8389 (m-30) cc_final: 0.8182 (m-30) REVERT: A 463 LEU cc_start: 0.8856 (pp) cc_final: 0.8415 (mp) REVERT: B 170 TYR cc_start: 0.9086 (m-10) cc_final: 0.8821 (m-80) REVERT: B 269 MET cc_start: 0.7864 (mtp) cc_final: 0.7594 (ttp) REVERT: B 275 HIS cc_start: 0.8405 (t-90) cc_final: 0.8153 (t-90) REVERT: B 279 CYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6547 (m) REVERT: B 284 ASP cc_start: 0.8361 (p0) cc_final: 0.8055 (p0) REVERT: B 287 GLU cc_start: 0.7223 (mp0) cc_final: 0.6976 (mp0) REVERT: B 357 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.8907 (m) REVERT: B 373 MET cc_start: 0.7918 (mmm) cc_final: 0.7575 (mmm) REVERT: B 376 ASP cc_start: 0.8103 (t0) cc_final: 0.7592 (t0) REVERT: B 436 ILE cc_start: 0.9183 (mm) cc_final: 0.8839 (tt) REVERT: C 275 HIS cc_start: 0.8184 (t-90) cc_final: 0.7927 (t-90) REVERT: C 284 ASP cc_start: 0.8363 (p0) cc_final: 0.7942 (p0) REVERT: C 287 GLU cc_start: 0.7198 (mp0) cc_final: 0.6883 (mp0) REVERT: C 357 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.8897 (m) REVERT: C 373 MET cc_start: 0.7899 (mmm) cc_final: 0.7540 (mmm) REVERT: C 376 ASP cc_start: 0.8120 (t0) cc_final: 0.7594 (t0) REVERT: D 136 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8518 (mm-40) REVERT: D 275 HIS cc_start: 0.8279 (t-90) cc_final: 0.8001 (t-90) REVERT: D 277 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6937 (mt-10) REVERT: D 284 ASP cc_start: 0.8321 (p0) cc_final: 0.8046 (p0) REVERT: D 316 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7714 (m-10) REVERT: D 357 VAL cc_start: 0.9297 (t) cc_final: 0.8964 (m) REVERT: D 373 MET cc_start: 0.7945 (mmm) cc_final: 0.7628 (mmm) REVERT: D 376 ASP cc_start: 0.8047 (t0) cc_final: 0.7570 (t0) REVERT: D 436 ILE cc_start: 0.9300 (mm) cc_final: 0.9064 (tp) REVERT: D 463 LEU cc_start: 0.8778 (pp) cc_final: 0.8469 (mp) outliers start: 83 outliers final: 67 residues processed: 470 average time/residue: 0.0755 time to fit residues: 54.8702 Evaluate side-chains 484 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 412 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 445 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS D 144 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115301 restraints weight = 18535.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120544 restraints weight = 9439.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124209 restraints weight = 6012.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126591 restraints weight = 4336.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128574 restraints weight = 3427.479| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12520 Z= 0.246 Angle : 0.786 12.281 17028 Z= 0.405 Chirality : 0.052 0.236 1796 Planarity : 0.004 0.048 2180 Dihedral : 7.316 57.856 1914 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 6.51 % Allowed : 29.27 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.31 (0.20), residues: 1540 helix: -2.82 (0.94), residues: 24 sheet: -0.24 (0.22), residues: 568 loop : -1.23 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 368 TYR 0.015 0.001 TYR A 316 PHE 0.033 0.002 PHE A 256 TRP 0.010 0.001 TRP A 303 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.25 (12476) covalent geometry : angle 0.76783 / 0.40 (16928) SS BOND : bond 0.00838 / 0.45 ( 32) SS BOND : angle 2.76948 / 1.83 ( 64) hydrogen bonds : bond 0.03391 / 2.43 ( 304) hydrogen bonds : angle 5.92711 / 4.11 ( 768) link_NAG-ASN : bond 0.00278 / 0.16 ( 12) link_NAG-ASN : angle 1.21264 / 0.70 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 435 time to evaluate : 0.325 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 142 ASP cc_start: 0.7988 (t0) cc_final: 0.7736 (t0) REVERT: A 173 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7370 (mtp-110) REVERT: A 214 ASP cc_start: 0.8366 (t70) cc_final: 0.8072 (t0) REVERT: A 228 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 231 CYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5534 (p) REVERT: A 275 HIS cc_start: 0.8399 (t-90) cc_final: 0.7964 (t-90) REVERT: A 284 ASP cc_start: 0.8386 (p0) cc_final: 0.8112 (p0) REVERT: A 357 VAL cc_start: 0.9333 (t) cc_final: 0.9006 (m) REVERT: A 376 ASP cc_start: 0.8199 (t70) cc_final: 0.7579 (t0) REVERT: A 436 ILE cc_start: 0.9279 (mt) cc_final: 0.9038 (tp) REVERT: A 463 LEU cc_start: 0.8849 (pp) cc_final: 0.8429 (mp) REVERT: B 173 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7484 (mtm-85) REVERT: B 228 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7491 (mm-30) REVERT: B 275 HIS cc_start: 0.8436 (t-90) cc_final: 0.8113 (t-90) REVERT: B 284 ASP cc_start: 0.8345 (p0) cc_final: 0.8056 (p0) REVERT: B 357 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.8948 (m) REVERT: B 376 ASP cc_start: 0.8147 (t0) cc_final: 0.7820 (t0) REVERT: B 436 ILE cc_start: 0.9225 (mm) cc_final: 0.8896 (tt) REVERT: B 463 LEU cc_start: 0.8811 (pp) cc_final: 0.8489 (mp) REVERT: C 228 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7498 (mm-30) REVERT: C 230 GLU cc_start: 0.7776 (tt0) cc_final: 0.7543 (tp30) REVERT: C 253 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: C 275 HIS cc_start: 0.8218 (t-90) cc_final: 0.7793 (t-90) REVERT: C 284 ASP cc_start: 0.8343 (p0) cc_final: 0.7973 (p0) REVERT: C 316 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7911 (m-10) REVERT: C 357 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.8938 (m) REVERT: C 376 ASP cc_start: 0.8167 (t0) cc_final: 0.7817 (t0) REVERT: D 84 LYS cc_start: 0.7627 (tttt) cc_final: 0.7250 (tttp) REVERT: D 136 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8579 (mm-40) REVERT: D 173 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7498 (mtm-85) REVERT: D 228 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7615 (mm-30) REVERT: D 275 HIS cc_start: 0.8306 (t-90) cc_final: 0.8030 (t-90) REVERT: D 277 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6999 (mt-10) REVERT: D 284 ASP cc_start: 0.8338 (p0) cc_final: 0.8071 (p0) REVERT: D 316 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7629 (m-10) REVERT: D 329 ASN cc_start: 0.8408 (p0) cc_final: 0.8198 (p0) REVERT: D 357 VAL cc_start: 0.9319 (t) cc_final: 0.9017 (m) REVERT: D 376 ASP cc_start: 0.7984 (t0) cc_final: 0.7590 (t0) REVERT: D 436 ILE cc_start: 0.9275 (mm) cc_final: 0.9051 (tp) REVERT: D 463 LEU cc_start: 0.8792 (pp) cc_final: 0.8474 (mp) outliers start: 87 outliers final: 72 residues processed: 481 average time/residue: 0.0737 time to fit residues: 55.0085 Evaluate side-chains 471 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 393 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 445 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS D 144 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121943 restraints weight = 18034.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127083 restraints weight = 9148.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130971 restraints weight = 5787.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133475 restraints weight = 4121.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135175 restraints weight = 3205.274| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12520 Z= 0.149 Angle : 0.778 11.873 17028 Z= 0.401 Chirality : 0.051 0.198 1796 Planarity : 0.004 0.044 2180 Dihedral : 7.300 59.013 1914 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.09 % Allowed : 31.74 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.48 (0.20), residues: 1540 helix: -4.05 (0.42), residues: 60 sheet: -0.09 (0.23), residues: 540 loop : -1.35 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 368 TYR 0.012 0.001 TYR A 316 PHE 0.029 0.002 PHE A 256 TRP 0.008 0.001 TRP D 179 HIS 0.004 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (12476) covalent geometry : angle 0.76391 / 0.40 (16928) SS BOND : bond 0.00770 / 0.45 ( 32) SS BOND : angle 2.41202 / 1.62 ( 64) hydrogen bonds : bond 0.03047 / 2.19 ( 304) hydrogen bonds : angle 5.73047 / 3.97 ( 768) link_NAG-ASN : bond 0.00325 / 0.20 ( 12) link_NAG-ASN : angle 1.14342 / 0.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 427 time to evaluate : 0.455 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 142 ASP cc_start: 0.7964 (t0) cc_final: 0.7722 (t0) REVERT: A 173 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7352 (mtp-110) REVERT: A 214 ASP cc_start: 0.8407 (t70) cc_final: 0.8022 (t0) REVERT: A 231 CYS cc_start: 0.6156 (OUTLIER) cc_final: 0.5583 (p) REVERT: A 275 HIS cc_start: 0.8354 (t-90) cc_final: 0.7855 (t-90) REVERT: A 357 VAL cc_start: 0.9230 (t) cc_final: 0.8896 (m) REVERT: A 376 ASP cc_start: 0.8242 (t70) cc_final: 0.7759 (t0) REVERT: A 436 ILE cc_start: 0.9343 (mt) cc_final: 0.9057 (tp) REVERT: A 463 LEU cc_start: 0.8937 (pp) cc_final: 0.8577 (mp) REVERT: B 173 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7498 (mtm-85) REVERT: B 275 HIS cc_start: 0.8288 (t-90) cc_final: 0.8021 (t-90) REVERT: B 357 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.8803 (m) REVERT: B 376 ASP cc_start: 0.8071 (t0) cc_final: 0.7518 (t0) REVERT: B 436 ILE cc_start: 0.9267 (mm) cc_final: 0.8889 (tt) REVERT: B 463 LEU cc_start: 0.8907 (pp) cc_final: 0.8609 (mp) REVERT: C 173 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7456 (mtm-85) REVERT: C 230 GLU cc_start: 0.7846 (tt0) cc_final: 0.7593 (tp30) REVERT: C 269 MET cc_start: 0.8004 (mtp) cc_final: 0.7757 (ttp) REVERT: C 275 HIS cc_start: 0.8064 (t-90) cc_final: 0.7536 (t-90) REVERT: C 284 ASP cc_start: 0.8418 (p0) cc_final: 0.8201 (p0) REVERT: C 357 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8765 (m) REVERT: C 376 ASP cc_start: 0.8173 (t0) cc_final: 0.7606 (t0) REVERT: D 136 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8613 (mm-40) REVERT: D 173 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7537 (mtm-85) REVERT: D 228 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7619 (mm-30) REVERT: D 268 GLU cc_start: 0.7929 (pm20) cc_final: 0.7720 (pp20) REVERT: D 275 HIS cc_start: 0.8204 (t-90) cc_final: 0.7778 (t-90) REVERT: D 357 VAL cc_start: 0.9260 (t) cc_final: 0.8912 (m) REVERT: D 376 ASP cc_start: 0.7955 (t0) cc_final: 0.7411 (t0) REVERT: D 463 LEU cc_start: 0.8885 (pp) cc_final: 0.8565 (mp) outliers start: 68 outliers final: 59 residues processed: 462 average time/residue: 0.0699 time to fit residues: 50.6312 Evaluate side-chains 470 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 408 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 445 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS D 144 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118183 restraints weight = 18361.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123421 restraints weight = 9349.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127183 restraints weight = 5975.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129701 restraints weight = 4258.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131378 restraints weight = 3321.931| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12520 Z= 0.195 Angle : 0.799 12.023 17028 Z= 0.411 Chirality : 0.051 0.217 1796 Planarity : 0.004 0.078 2180 Dihedral : 7.327 58.969 1914 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.31 % Allowed : 31.66 % Favored : 63.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.53 (0.20), residues: 1540 helix: -4.03 (0.43), residues: 60 sheet: -0.11 (0.23), residues: 544 loop : -1.41 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 368 TYR 0.012 0.001 TYR A 316 PHE 0.027 0.002 PHE A 256 TRP 0.008 0.001 TRP A 380 HIS 0.003 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (12476) covalent geometry : angle 0.78390 / 0.40 (16928) SS BOND : bond 0.00784 / 0.43 ( 32) SS BOND : angle 2.59888 / 1.74 ( 64) hydrogen bonds : bond 0.03179 / 2.28 ( 304) hydrogen bonds : angle 5.73501 / 3.98 ( 768) link_NAG-ASN : bond 0.00216 / 0.12 ( 12) link_NAG-ASN : angle 1.15334 / 0.68 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 413 time to evaluate : 0.329 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 142 ASP cc_start: 0.7982 (t0) cc_final: 0.7713 (t0) REVERT: A 173 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7440 (mtp-110) REVERT: A 214 ASP cc_start: 0.8353 (t70) cc_final: 0.8027 (t0) REVERT: A 228 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 231 CYS cc_start: 0.6294 (OUTLIER) cc_final: 0.5718 (p) REVERT: A 259 GLU cc_start: 0.7949 (pm20) cc_final: 0.7461 (pm20) REVERT: A 275 HIS cc_start: 0.8385 (t-90) cc_final: 0.7917 (t-90) REVERT: A 284 ASP cc_start: 0.8382 (p0) cc_final: 0.8160 (p0) REVERT: A 376 ASP cc_start: 0.8197 (t70) cc_final: 0.7811 (t0) REVERT: A 436 ILE cc_start: 0.9296 (mt) cc_final: 0.9072 (tp) REVERT: A 463 LEU cc_start: 0.8820 (pp) cc_final: 0.8578 (mp) REVERT: B 136 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8607 (mm-40) REVERT: B 173 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7552 (mtm-85) REVERT: B 275 HIS cc_start: 0.8375 (t-90) cc_final: 0.7965 (t-90) REVERT: B 284 ASP cc_start: 0.8340 (p0) cc_final: 0.8103 (p0) REVERT: B 357 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8885 (m) REVERT: B 376 ASP cc_start: 0.8033 (t0) cc_final: 0.7327 (t0) REVERT: B 436 ILE cc_start: 0.9218 (mm) cc_final: 0.8902 (tt) REVERT: C 136 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8542 (mm-40) REVERT: C 173 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7463 (mtm-85) REVERT: C 228 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7484 (mm-30) REVERT: C 275 HIS cc_start: 0.8071 (t-90) cc_final: 0.7668 (t-90) REVERT: C 357 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.8892 (m) REVERT: C 376 ASP cc_start: 0.8111 (t0) cc_final: 0.7404 (t0) REVERT: C 463 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8422 (mp) REVERT: D 173 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7367 (mtp-110) REVERT: D 228 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7557 (mm-30) REVERT: D 275 HIS cc_start: 0.8203 (t-90) cc_final: 0.7874 (t-90) REVERT: D 277 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6803 (mt-10) REVERT: D 316 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7366 (m-10) REVERT: D 357 VAL cc_start: 0.9286 (t) cc_final: 0.8909 (m) REVERT: D 376 ASP cc_start: 0.7907 (t0) cc_final: 0.7484 (t0) outliers start: 71 outliers final: 62 residues processed: 451 average time/residue: 0.0720 time to fit residues: 50.7031 Evaluate side-chains 473 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 406 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 445 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 144 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 88 optimal weight: 0.0030 chunk 116 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 408 GLN B 144 HIS ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS D 144 HIS ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.142987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118613 restraints weight = 18317.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123813 restraints weight = 9382.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127503 restraints weight = 6036.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129775 restraints weight = 4327.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131939 restraints weight = 3435.016| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12520 Z= 0.181 Angle : 0.797 11.663 17028 Z= 0.409 Chirality : 0.051 0.208 1796 Planarity : 0.004 0.073 2180 Dihedral : 7.329 58.428 1914 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.31 % Allowed : 31.96 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.52 (0.20), residues: 1540 helix: -4.08 (0.40), residues: 60 sheet: -0.17 (0.23), residues: 540 loop : -1.34 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 368 TYR 0.010 0.001 TYR C 170 PHE 0.024 0.002 PHE A 256 TRP 0.011 0.001 TRP A 380 HIS 0.004 0.001 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (12476) covalent geometry : angle 0.78309 / 0.40 (16928) SS BOND : bond 0.00771 / 0.43 ( 32) SS BOND : angle 2.46645 / 1.66 ( 64) hydrogen bonds : bond 0.03157 / 2.27 ( 304) hydrogen bonds : angle 5.70932 / 3.96 ( 768) link_NAG-ASN : bond 0.00220 / 0.13 ( 12) link_NAG-ASN : angle 1.13912 / 0.67 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.01 seconds wall clock time: 32 minutes 3.45 seconds (1923.45 seconds total)