Starting phenix.real_space_refine on Fri Aug 7 23:27:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9srt_55153/08_2026/9srt_55153.cif Found real_map, /net/cci-nas-00/data/ceres_data/9srt_55153/08_2026/9srt_55153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9srt_55153/08_2026/9srt_55153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9srt_55153/08_2026/9srt_55153.map" model { file = "/net/cci-nas-00/data/ceres_data/9srt_55153/08_2026/9srt_55153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9srt_55153/08_2026/9srt_55153.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 S 52 5.16 5 C 7428 2.51 5 N 2064 2.21 5 O 2204 1.98 5 H 11986 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23738 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 5950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 5950 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 13, 'TRANS': 369} Chain breaks: 1 Chain: "C" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 5917 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 13, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 5950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 5950 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 13, 'TRANS': 369} Chain breaks: 1 Chain: "A" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 5917 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 13, 'TRANS': 367} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3706 SG CYS D 257 52.401 77.597 28.327 1.00 57.14 S ATOM 3737 SG CYS D 259 55.201 79.613 26.686 1.00 33.40 S ATOM 3792 SG CYS D 264 55.294 79.139 30.404 1.00 35.58 S ATOM 9620 SG CYS C 257 68.903 93.442 51.094 1.00 63.94 S ATOM 9652 SG CYS C 259 65.288 93.244 52.275 1.00 34.30 S ATOM 9708 SG CYS C 264 66.476 90.922 49.457 1.00 40.84 S ATOM 15573 SG CYS B 257 98.180 71.036 28.354 1.00 58.50 S ATOM 15604 SG CYS B 259 95.354 69.102 26.717 1.00 41.23 S ATOM 15659 SG CYS B 264 95.333 69.589 30.470 1.00 44.95 S ATOM 21487 SG CYS A 257 81.722 55.364 51.117 1.00 65.03 S ATOM 21519 SG CYS A 259 85.297 55.613 52.377 1.00 45.52 S ATOM 21575 SG CYS A 264 84.127 57.906 49.506 1.00 47.71 S Time building chain proxies: 4.04, per 1000 atoms: 0.17 Number of scatterers: 23738 At special positions: 0 Unit cell: (151.574, 149.566, 73.2774, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 52 16.00 O 2204 8.00 N 2064 7.00 C 7428 6.00 H 11986 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 604.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 247 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 259 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 257 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 247 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 259 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 264 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 257 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 247 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 259 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 264 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 257 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 247 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 259 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 264 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 257 " Number of angles added : 12 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 16 sheets defined 52.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.638A pdb=" N LYS D 14 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN D 15 " --> pdb=" O ASP D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 removed outlier: 3.980A pdb=" N ARG D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU D 39 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 57 Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'D' and resid 177 through 187 Processing helix chain 'D' and resid 195 through 207 Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.820A pdb=" N ASN D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 308 through 334 removed outlier: 3.711A pdb=" N ILE D 325 " --> pdb=" O HIS D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 removed outlier: 3.827A pdb=" N LYS D 346 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 363 Proline residue: D 353 - end of helix Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 396 removed outlier: 3.659A pdb=" N VAL D 390 " --> pdb=" O GLY D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 404 removed outlier: 3.699A pdb=" N ILE D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 29 removed outlier: 3.944A pdb=" N THR C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 41 Processing helix chain 'C' and resid 43 through 57 removed outlier: 4.253A pdb=" N LYS C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 139 Processing helix chain 'C' and resid 140 through 143 removed outlier: 3.795A pdb=" N LEU C 143 " --> pdb=" O GLN C 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 177 through 187 removed outlier: 3.857A pdb=" N HIS C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 207 Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 270 through 284 removed outlier: 3.915A pdb=" N GLN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 308 through 334 Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 347 through 363 Proline residue: C 353 - end of helix Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 385 through 396 removed outlier: 4.466A pdb=" N LEU C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 390 " --> pdb=" O GLY C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 405 removed outlier: 3.526A pdb=" N ILE C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.624A pdb=" N LYS B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 15 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 41 removed outlier: 3.537A pdb=" N SER B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 123 through 137 Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 195 through 207 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 270 through 283 removed outlier: 3.779A pdb=" N ASN B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 306 Processing helix chain 'B' and resid 308 through 334 removed outlier: 3.724A pdb=" N ILE B 325 " --> pdb=" O HIS B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.860A pdb=" N LYS B 346 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 363 Proline residue: B 353 - end of helix Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 385 through 396 removed outlier: 4.146A pdb=" N LEU B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.929A pdb=" N ILE B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 29 removed outlier: 3.926A pdb=" N THR A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 41 Processing helix chain 'A' and resid 43 through 57 removed outlier: 4.196A pdb=" N LYS A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 139 Processing helix chain 'A' and resid 140 through 143 removed outlier: 3.733A pdb=" N LEU A 143 " --> pdb=" O GLN A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.733A pdb=" N HIS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 270 through 284 removed outlier: 3.935A pdb=" N GLN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 308 through 334 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 347 through 363 Proline residue: A 353 - end of helix Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.825A pdb=" N VAL A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 removed outlier: 3.800A pdb=" N ILE A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'D' and resid 108 through 115 removed outlier: 6.623A pdb=" N LEU D 101 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU D 111 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU D 99 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER D 113 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE D 97 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N HIS D 86 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER D 148 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR D 191 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE D 149 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLN D 193 " --> pdb=" O ILE D 149 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE D 151 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 156 through 158 removed outlier: 6.652A pdb=" N ILE D 156 " --> pdb=" O HIS D 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 233 through 234 removed outlier: 6.086A pdb=" N ILE D 338 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'C' and resid 108 through 115 removed outlier: 6.282A pdb=" N LEU C 108 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP C 103 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 110 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N HIS C 86 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 149 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 88 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE C 151 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 90 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU C 153 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 92 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 156 through 158 removed outlier: 6.818A pdb=" N ILE C 156 " --> pdb=" O HIS C 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.074A pdb=" N ILE C 338 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 115 removed outlier: 6.667A pdb=" N LEU B 101 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 111 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 99 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 113 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 97 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N HIS B 86 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER B 148 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR B 191 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 149 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLN B 193 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 151 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.760A pdb=" N ILE B 156 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 233 through 234 removed outlier: 6.079A pdb=" N ILE B 338 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AB5, first strand: chain 'A' and resid 108 through 115 removed outlier: 6.102A pdb=" N LEU A 108 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASP A 103 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N HIS A 86 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 149 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU A 88 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE A 151 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 90 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 156 through 158 removed outlier: 6.835A pdb=" N ILE A 156 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 233 through 234 removed outlier: 6.137A pdb=" N ILE A 338 " --> pdb=" O GLU A 374 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.69 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11976 1.03 - 1.23: 50 1.23 - 1.42: 4746 1.42 - 1.62: 7060 1.62 - 1.81: 88 Bond restraints: 23920 Sorted by residual: bond pdb=" CB ARG A 210 " pdb=" CG ARG A 210 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CB ARG C 210 " pdb=" CG ARG C 210 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" C HIS A 321 " pdb=" O HIS A 321 " ideal model delta sigma weight residual 1.236 1.248 -0.012 1.15e-02 7.56e+03 1.03e+00 bond pdb=" C HIS C 321 " pdb=" O HIS C 321 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.82e-01 bond pdb=" CA LEU D 90 " pdb=" CB LEU D 90 " ideal model delta sigma weight residual 1.535 1.517 0.018 1.93e-02 2.68e+03 8.47e-01 ... (remaining 23915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 43016 1.77 - 3.53: 350 3.53 - 5.30: 36 5.30 - 7.06: 1 7.06 - 8.83: 1 Bond angle restraints: 43404 Sorted by residual: angle pdb=" N VAL C 109 " pdb=" CA VAL C 109 " pdb=" C VAL C 109 " ideal model delta sigma weight residual 111.48 107.90 3.58 9.40e-01 1.13e+00 1.45e+01 angle pdb=" N VAL A 109 " pdb=" CA VAL A 109 " pdb=" C VAL A 109 " ideal model delta sigma weight residual 111.48 108.08 3.40 9.40e-01 1.13e+00 1.31e+01 angle pdb=" N ILE A 268 " pdb=" CA ILE A 268 " pdb=" C ILE A 268 " ideal model delta sigma weight residual 113.71 110.99 2.72 9.50e-01 1.11e+00 8.17e+00 angle pdb=" C ARG D 94 " pdb=" CA ARG D 94 " pdb=" CB ARG D 94 " ideal model delta sigma weight residual 110.42 115.71 -5.29 1.99e+00 2.53e-01 7.06e+00 angle pdb=" C ARG B 94 " pdb=" CA ARG B 94 " pdb=" CB ARG B 94 " ideal model delta sigma weight residual 110.42 115.65 -5.23 1.99e+00 2.53e-01 6.92e+00 ... (remaining 43399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10005 17.98 - 35.96: 771 35.96 - 53.95: 232 53.95 - 71.93: 89 71.93 - 89.91: 15 Dihedral angle restraints: 11112 sinusoidal: 6198 harmonic: 4914 Sorted by residual: dihedral pdb=" CG ARG C 324 " pdb=" CD ARG C 324 " pdb=" NE ARG C 324 " pdb=" CZ ARG C 324 " ideal model delta sinusoidal sigma weight residual 90.00 39.08 50.92 2 1.50e+01 4.44e-03 1.29e+01 dihedral pdb=" CA ILE C 47 " pdb=" C ILE C 47 " pdb=" N THR C 48 " pdb=" CA THR C 48 " ideal model delta harmonic sigma weight residual 180.00 -163.10 -16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " pdb=" NE ARG A 256 " pdb=" CZ ARG A 256 " ideal model delta sinusoidal sigma weight residual -90.00 -43.26 -46.74 2 1.50e+01 4.44e-03 1.13e+01 ... (remaining 11109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1163 0.031 - 0.061: 518 0.061 - 0.092: 125 0.092 - 0.122: 110 0.122 - 0.153: 14 Chirality restraints: 1930 Sorted by residual: chirality pdb=" CA ILE D 92 " pdb=" N ILE D 92 " pdb=" C ILE D 92 " pdb=" CB ILE D 92 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ILE B 92 " pdb=" N ILE B 92 " pdb=" C ILE B 92 " pdb=" CB ILE B 92 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE C 149 " pdb=" N ILE C 149 " pdb=" C ILE C 149 " pdb=" CB ILE C 149 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1927 not shown) Planarity restraints: 3546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 256 " -0.209 9.50e-02 1.11e+02 7.02e-02 5.93e+00 pdb=" NE ARG A 256 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 256 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 256 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 256 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 256 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG A 256 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 256 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 256 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 256 " -0.203 9.50e-02 1.11e+02 6.80e-02 5.58e+00 pdb=" NE ARG C 256 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 256 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 256 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 256 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 256 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG C 256 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 256 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 256 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 324 " 0.149 9.50e-02 1.11e+02 4.99e-02 3.03e+00 pdb=" NE ARG C 324 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 324 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 324 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 324 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 324 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG C 324 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 324 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 324 " 0.000 2.00e-02 2.50e+03 ... (remaining 3543 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 998 2.16 - 2.77: 47447 2.77 - 3.38: 67001 3.38 - 3.99: 88291 3.99 - 4.60: 137618 Nonbonded interactions: 341355 Sorted by model distance: nonbonded pdb=" O SER C 285 " pdb=" HE2 HIS C 291 " model vdw 1.554 2.450 nonbonded pdb=" OD1 ASN B 396 " pdb=" H SER B 398 " model vdw 1.587 2.450 nonbonded pdb=" OD1 ASN D 396 " pdb=" H SER D 398 " model vdw 1.611 2.450 nonbonded pdb=" OE1 GLN C 293 " pdb=" H GLN C 293 " model vdw 1.618 2.450 nonbonded pdb=" OD1 ASN C 396 " pdb=" H SER C 398 " model vdw 1.634 2.450 ... (remaining 341350 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 256 or (resid 257 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 258 or (resid 259 and (name N or name CA or name C or name O or name \ CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 260 throu \ gh 263 or (resid 264 and (name N or name CA or name C or name O or name CB or na \ me SG or name H or name HA or name HB2 or name HB3)) or resid 265 through 501)) selection = (chain 'B' and resid 11 through 501) selection = (chain 'C' and (resid 11 through 256 or (resid 257 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 258 or (resid 259 and (name N or name CA or name C or name O or name \ CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 260 throu \ gh 263 or (resid 264 and (name N or name CA or name C or name O or name CB or na \ me SG or name H or name HA or name HB2 or name HB3)) or resid 265 through 501)) selection = (chain 'D' and resid 11 through 501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.170 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.370 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.004 0.042 11950 Z= 0.199 Angle : 0.558 8.830 16188 Z= 0.300 Chirality : 0.042 0.153 1930 Planarity : 0.005 0.092 2078 Dihedral : 15.892 89.912 4408 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.76 % Favored : 95.11 % Rotamer: Outliers : 0.93 % Allowed : 18.87 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.22), residues: 1512 helix: 0.87 (0.20), residues: 666 sheet: 0.49 (0.33), residues: 232 loop : -0.92 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 256 TYR 0.013 0.001 TYR C 87 PHE 0.010 0.001 PHE C 136 TRP 0.012 0.001 TRP A 85 HIS 0.005 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (11934) covalent geometry : angle 0.55620 / 0.30 (16176) hydrogen bonds : bond 0.17293 / 12.22 ( 614) hydrogen bonds : angle 6.83266 / 4.70 ( 1743) metal coordination : bond 0.01600 / 1.26 ( 16) metal coordination : angle 1.71647 / 1.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 TYR cc_start: 0.8801 (m-80) cc_final: 0.8010 (m-80) REVERT: A 62 GLU cc_start: 0.7469 (pm20) cc_final: 0.7138 (pp20) outliers start: 12 outliers final: 8 residues processed: 290 average time/residue: 1.1036 time to fit residues: 347.9086 Evaluate side-chains 283 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 275 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain A residue 240 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN D 161 ASN D 361 GLN C 369 GLN B 86 HIS B 284 GLN B 369 GLN A 223 ASN A 302 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.134147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109568 restraints weight = 49677.618| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.81 r_work: 0.3320 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11950 Z= 0.168 Angle : 0.527 6.634 16188 Z= 0.284 Chirality : 0.042 0.147 1930 Planarity : 0.005 0.060 2078 Dihedral : 5.341 58.021 1644 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 2.48 % Allowed : 16.77 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1512 helix: 0.98 (0.20), residues: 648 sheet: 0.20 (0.33), residues: 234 loop : -0.88 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 256 TYR 0.012 0.001 TYR C 87 PHE 0.008 0.001 PHE C 136 TRP 0.007 0.001 TRP A 85 HIS 0.004 0.001 HIS D 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (11934) covalent geometry : angle 0.52464 / 0.28 (16176) hydrogen bonds : bond 0.05104 / 3.47 ( 614) hydrogen bonds : angle 5.39804 / 3.77 ( 1743) metal coordination : bond 0.01637 / 1.31 ( 16) metal coordination : angle 1.83958 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8182 (mtp) REVERT: A 62 GLU cc_start: 0.7535 (pm20) cc_final: 0.7262 (pp20) outliers start: 32 outliers final: 19 residues processed: 293 average time/residue: 1.1280 time to fit residues: 358.3584 Evaluate side-chains 300 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 280 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 109 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 146 optimal weight: 0.0980 chunk 145 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN D 161 ASN D 361 GLN C 284 GLN C 369 GLN B 27 GLN B 86 HIS B 223 ASN B 369 GLN A 223 ASN A 302 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109688 restraints weight = 50401.106| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.80 r_work: 0.3322 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11950 Z= 0.132 Angle : 0.486 5.496 16188 Z= 0.258 Chirality : 0.041 0.144 1930 Planarity : 0.004 0.073 2078 Dihedral : 4.504 39.596 1634 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.37 % Favored : 95.50 % Rotamer: Outliers : 2.64 % Allowed : 17.00 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1512 helix: 0.98 (0.20), residues: 658 sheet: 0.07 (0.32), residues: 236 loop : -0.90 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 256 TYR 0.012 0.001 TYR C 87 PHE 0.008 0.001 PHE B 98 TRP 0.005 0.001 TRP A 85 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11934) covalent geometry : angle 0.48469 / 0.26 (16176) hydrogen bonds : bond 0.04615 / 3.14 ( 614) hydrogen bonds : angle 5.11571 / 3.59 ( 1743) metal coordination : bond 0.01440 / 1.14 ( 16) metal coordination : angle 1.60544 / 1.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8202 (mtp) REVERT: D 251 ASP cc_start: 0.8029 (t0) cc_final: 0.7752 (t0) REVERT: D 399 LEU cc_start: 0.7860 (tp) cc_final: 0.7635 (tp) REVERT: B 23 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7642 (ttm-80) REVERT: B 58 HIS cc_start: 0.6886 (m170) cc_final: 0.6649 (m170) REVERT: B 244 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8299 (mm-30) REVERT: B 399 LEU cc_start: 0.7937 (tp) cc_final: 0.7714 (tp) REVERT: A 62 GLU cc_start: 0.7504 (pm20) cc_final: 0.7225 (pp20) REVERT: A 158 ASP cc_start: 0.7424 (t0) cc_final: 0.7046 (t0) outliers start: 34 outliers final: 19 residues processed: 284 average time/residue: 1.1053 time to fit residues: 340.7131 Evaluate side-chains 298 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 404 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN D 361 GLN D 369 GLN C 284 GLN C 369 GLN B 27 GLN B 86 HIS B 161 ASN B 223 ASN B 369 GLN A 223 ASN A 302 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108890 restraints weight = 50280.260| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.81 r_work: 0.3308 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11950 Z= 0.172 Angle : 0.498 4.756 16188 Z= 0.266 Chirality : 0.041 0.145 1930 Planarity : 0.005 0.076 2078 Dihedral : 4.391 17.359 1630 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 3.11 % Allowed : 17.08 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1512 helix: 1.00 (0.20), residues: 658 sheet: -0.05 (0.32), residues: 236 loop : -0.99 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 256 TYR 0.013 0.001 TYR C 87 PHE 0.008 0.001 PHE C 135 TRP 0.007 0.001 TRP A 85 HIS 0.004 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (11934) covalent geometry : angle 0.49552 / 0.27 (16176) hydrogen bonds : bond 0.04641 / 3.17 ( 614) hydrogen bonds : angle 5.05897 / 3.55 ( 1743) metal coordination : bond 0.01576 / 1.25 ( 16) metal coordination : angle 1.79679 / 1.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8217 (mtp) REVERT: D 251 ASP cc_start: 0.8049 (t0) cc_final: 0.7735 (t0) REVERT: D 399 LEU cc_start: 0.7893 (tp) cc_final: 0.7676 (tp) REVERT: C 158 ASP cc_start: 0.7217 (t0) cc_final: 0.6913 (t0) REVERT: C 312 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8462 (mtmm) REVERT: B 23 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7705 (ttm-80) REVERT: A 23 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7622 (ttm-80) REVERT: A 62 GLU cc_start: 0.7457 (pm20) cc_final: 0.7249 (pp20) REVERT: A 91 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7834 (ttt-90) REVERT: A 158 ASP cc_start: 0.7459 (t0) cc_final: 0.7074 (t0) outliers start: 40 outliers final: 24 residues processed: 300 average time/residue: 1.1899 time to fit residues: 386.4097 Evaluate side-chains 308 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 107 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN D 161 ASN D 361 GLN D 369 GLN C 284 GLN C 369 GLN B 86 HIS B 161 ASN B 223 ASN B 361 GLN B 369 GLN A 223 ASN A 302 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109483 restraints weight = 50366.471| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.79 r_work: 0.3316 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11950 Z= 0.143 Angle : 0.483 4.808 16188 Z= 0.256 Chirality : 0.041 0.142 1930 Planarity : 0.004 0.082 2078 Dihedral : 4.317 16.855 1630 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.30 % Rotamer: Outliers : 2.87 % Allowed : 17.39 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1512 helix: 1.07 (0.20), residues: 660 sheet: -0.19 (0.32), residues: 236 loop : -1.00 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 256 TYR 0.012 0.001 TYR C 87 PHE 0.010 0.001 PHE B 98 TRP 0.005 0.001 TRP A 85 HIS 0.004 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11934) covalent geometry : angle 0.48128 / 0.26 (16176) hydrogen bonds : bond 0.04381 / 2.98 ( 614) hydrogen bonds : angle 4.96286 / 3.49 ( 1743) metal coordination : bond 0.01481 / 1.18 ( 16) metal coordination : angle 1.55011 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8202 (mtp) REVERT: D 251 ASP cc_start: 0.8042 (t0) cc_final: 0.7721 (t0) REVERT: D 394 MET cc_start: 0.8402 (mmm) cc_final: 0.7991 (mmm) REVERT: D 399 LEU cc_start: 0.7905 (tp) cc_final: 0.7669 (tp) REVERT: B 23 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7661 (ttm-80) REVERT: A 62 GLU cc_start: 0.7434 (pm20) cc_final: 0.7228 (pp20) REVERT: A 91 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7832 (ttt-90) REVERT: A 158 ASP cc_start: 0.7442 (t0) cc_final: 0.7064 (t0) outliers start: 37 outliers final: 22 residues processed: 295 average time/residue: 1.1832 time to fit residues: 377.7648 Evaluate side-chains 300 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 115 optimal weight: 0.0570 chunk 57 optimal weight: 0.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN D 361 GLN D 369 GLN C 284 GLN C 369 GLN B 86 HIS B 161 ASN B 223 ASN B 369 GLN A 223 ASN A 302 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108649 restraints weight = 50479.056| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.83 r_work: 0.3304 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11950 Z= 0.169 Angle : 0.495 4.947 16188 Z= 0.263 Chirality : 0.041 0.143 1930 Planarity : 0.005 0.088 2078 Dihedral : 4.368 17.069 1630 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 2.80 % Allowed : 17.70 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.21), residues: 1512 helix: 1.06 (0.20), residues: 660 sheet: -0.27 (0.32), residues: 236 loop : -1.03 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 256 TYR 0.013 0.001 TYR C 87 PHE 0.008 0.001 PHE C 135 TRP 0.005 0.001 TRP A 85 HIS 0.004 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (11934) covalent geometry : angle 0.49329 / 0.26 (16176) hydrogen bonds : bond 0.04491 / 3.06 ( 614) hydrogen bonds : angle 4.96743 / 3.49 ( 1743) metal coordination : bond 0.01520 / 1.20 ( 16) metal coordination : angle 1.66596 / 1.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8226 (mtp) REVERT: D 251 ASP cc_start: 0.8055 (t0) cc_final: 0.7736 (t0) REVERT: D 399 LEU cc_start: 0.7959 (tp) cc_final: 0.7714 (tp) REVERT: B 244 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8291 (mm-30) REVERT: B 391 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8116 (mmtm) REVERT: A 81 GLU cc_start: 0.7784 (tp30) cc_final: 0.7553 (tp30) REVERT: A 91 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7862 (ttt-90) REVERT: A 158 ASP cc_start: 0.7502 (t0) cc_final: 0.7110 (t0) outliers start: 36 outliers final: 26 residues processed: 289 average time/residue: 1.1824 time to fit residues: 370.9239 Evaluate side-chains 304 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 276 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 101 optimal weight: 0.7980 chunk 116 optimal weight: 0.0170 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN D 161 ASN D 302 GLN D 361 GLN C 284 GLN C 369 GLN B 86 HIS B 161 ASN B 223 ASN B 361 GLN B 369 GLN A 223 ASN A 302 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109285 restraints weight = 50649.776| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.80 r_work: 0.3314 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11950 Z= 0.150 Angle : 0.489 4.908 16188 Z= 0.261 Chirality : 0.041 0.143 1930 Planarity : 0.005 0.093 2078 Dihedral : 4.322 16.941 1630 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.30 % Rotamer: Outliers : 2.48 % Allowed : 18.09 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1512 helix: 1.14 (0.20), residues: 660 sheet: -0.28 (0.32), residues: 236 loop : -1.02 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 256 TYR 0.013 0.001 TYR C 87 PHE 0.010 0.001 PHE D 98 TRP 0.004 0.001 TRP A 85 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (11934) covalent geometry : angle 0.48762 / 0.26 (16176) hydrogen bonds : bond 0.04360 / 2.97 ( 614) hydrogen bonds : angle 4.90607 / 3.44 ( 1743) metal coordination : bond 0.01451 / 1.14 ( 16) metal coordination : angle 1.54887 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8213 (mtp) REVERT: D 251 ASP cc_start: 0.8047 (t0) cc_final: 0.7726 (t0) REVERT: D 394 MET cc_start: 0.8390 (mmm) cc_final: 0.8183 (mmm) REVERT: D 399 LEU cc_start: 0.7952 (tp) cc_final: 0.7749 (tp) REVERT: B 244 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8313 (mm-30) REVERT: B 391 LYS cc_start: 0.8391 (mmtm) cc_final: 0.8115 (mmtm) REVERT: A 81 GLU cc_start: 0.7783 (tp30) cc_final: 0.7526 (tp30) REVERT: A 91 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7849 (ttt-90) outliers start: 32 outliers final: 26 residues processed: 285 average time/residue: 1.1481 time to fit residues: 354.8625 Evaluate side-chains 300 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 145 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN D 361 GLN C 284 GLN C 369 GLN B 86 HIS B 161 ASN B 223 ASN B 369 GLN A 223 ASN A 302 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108879 restraints weight = 50677.535| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.79 r_work: 0.3312 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11950 Z= 0.167 Angle : 0.498 5.382 16188 Z= 0.266 Chirality : 0.041 0.144 1930 Planarity : 0.005 0.098 2078 Dihedral : 4.357 16.999 1630 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % Rotamer: Outliers : 2.56 % Allowed : 18.79 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1512 helix: 1.12 (0.20), residues: 660 sheet: -0.30 (0.32), residues: 236 loop : -1.04 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 256 TYR 0.013 0.001 TYR C 87 PHE 0.008 0.001 PHE C 135 TRP 0.013 0.001 TRP C 85 HIS 0.004 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (11934) covalent geometry : angle 0.49643 / 0.27 (16176) hydrogen bonds : bond 0.04457 / 3.04 ( 614) hydrogen bonds : angle 4.92714 / 3.45 ( 1743) metal coordination : bond 0.01470 / 1.15 ( 16) metal coordination : angle 1.61668 / 1.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8221 (mtp) REVERT: D 251 ASP cc_start: 0.8038 (t0) cc_final: 0.7705 (t0) REVERT: D 298 ASP cc_start: 0.7636 (t0) cc_final: 0.7408 (t0) REVERT: D 394 MET cc_start: 0.8406 (mmm) cc_final: 0.7988 (mmm) REVERT: D 399 LEU cc_start: 0.7955 (tp) cc_final: 0.7724 (tp) REVERT: B 244 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8313 (mm-30) REVERT: B 391 LYS cc_start: 0.8378 (mmtm) cc_final: 0.8105 (mmtm) REVERT: A 81 GLU cc_start: 0.7793 (tp30) cc_final: 0.7532 (tp30) REVERT: A 107 LYS cc_start: 0.8212 (tttp) cc_final: 0.8001 (tttp) outliers start: 33 outliers final: 29 residues processed: 287 average time/residue: 1.1616 time to fit residues: 361.3593 Evaluate side-chains 305 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN D 302 GLN D 361 GLN C 284 GLN C 369 GLN B 86 HIS B 114 GLN B 161 ASN B 223 ASN B 361 GLN B 369 GLN A 223 ASN A 302 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109132 restraints weight = 50908.219| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.81 r_work: 0.3315 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11950 Z= 0.150 Angle : 0.498 4.934 16188 Z= 0.264 Chirality : 0.041 0.143 1930 Planarity : 0.005 0.100 2078 Dihedral : 4.309 17.023 1630 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 2.41 % Allowed : 19.33 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1512 helix: 1.19 (0.20), residues: 660 sheet: -0.31 (0.32), residues: 236 loop : -1.01 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 256 TYR 0.013 0.001 TYR C 87 PHE 0.010 0.001 PHE D 98 TRP 0.006 0.001 TRP C 85 HIS 0.004 0.001 HIS B 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (11934) covalent geometry : angle 0.49677 / 0.26 (16176) hydrogen bonds : bond 0.04332 / 2.95 ( 614) hydrogen bonds : angle 4.88201 / 3.42 ( 1743) metal coordination : bond 0.01420 / 1.11 ( 16) metal coordination : angle 1.51339 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8207 (mtp) REVERT: D 251 ASP cc_start: 0.8040 (t0) cc_final: 0.7720 (t0) REVERT: D 394 MET cc_start: 0.8418 (mmm) cc_final: 0.8007 (mmm) REVERT: D 399 LEU cc_start: 0.7938 (tp) cc_final: 0.7681 (tp) REVERT: C 81 GLU cc_start: 0.7554 (tp30) cc_final: 0.7228 (tp30) REVERT: B 244 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8311 (mm-30) REVERT: B 255 LYS cc_start: 0.8743 (mtmm) cc_final: 0.8426 (mtmt) REVERT: B 391 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8166 (mmtp) REVERT: A 81 GLU cc_start: 0.7812 (tp30) cc_final: 0.7551 (tp30) REVERT: A 107 LYS cc_start: 0.8179 (tttp) cc_final: 0.7955 (tttp) outliers start: 31 outliers final: 26 residues processed: 288 average time/residue: 1.1365 time to fit residues: 354.8711 Evaluate side-chains 304 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 chunk 126 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 70 optimal weight: 0.0870 chunk 96 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN C 284 GLN C 369 GLN B 86 HIS B 114 GLN B 161 ASN B 223 ASN B 361 GLN B 369 GLN A 223 ASN A 302 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109344 restraints weight = 50901.140| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.81 r_work: 0.3319 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11950 Z= 0.135 Angle : 0.493 4.882 16188 Z= 0.261 Chirality : 0.041 0.142 1930 Planarity : 0.005 0.102 2078 Dihedral : 4.252 17.057 1630 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.10 % Allowed : 19.88 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1512 helix: 1.24 (0.20), residues: 660 sheet: -0.30 (0.32), residues: 236 loop : -0.97 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 256 TYR 0.012 0.001 TYR C 87 PHE 0.006 0.001 PHE C 136 TRP 0.006 0.001 TRP C 85 HIS 0.004 0.001 HIS B 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11934) covalent geometry : angle 0.49157 / 0.26 (16176) hydrogen bonds : bond 0.04219 / 2.87 ( 614) hydrogen bonds : angle 4.84567 / 3.39 ( 1743) metal coordination : bond 0.01358 / 1.06 ( 16) metal coordination : angle 1.45316 / 1.31 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: D 251 ASP cc_start: 0.8031 (t0) cc_final: 0.7712 (t0) REVERT: D 394 MET cc_start: 0.8406 (mmm) cc_final: 0.7987 (mmm) REVERT: C 81 GLU cc_start: 0.7532 (tp30) cc_final: 0.7198 (tp30) REVERT: B 244 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8306 (mm-30) REVERT: B 391 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8163 (mmtp) REVERT: A 81 GLU cc_start: 0.7799 (tp30) cc_final: 0.7546 (tp30) REVERT: A 107 LYS cc_start: 0.8166 (tttp) cc_final: 0.7937 (tttp) outliers start: 27 outliers final: 25 residues processed: 290 average time/residue: 1.1340 time to fit residues: 356.1837 Evaluate side-chains 302 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN C 284 GLN C 369 GLN B 86 HIS B 114 GLN B 161 ASN B 223 ASN B 361 GLN B 369 GLN A 223 ASN A 302 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109185 restraints weight = 50112.358| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.79 r_work: 0.3313 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11950 Z= 0.164 Angle : 0.513 6.534 16188 Z= 0.272 Chirality : 0.041 0.144 1930 Planarity : 0.005 0.099 2078 Dihedral : 4.319 16.967 1630 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.25 % Allowed : 19.72 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1512 helix: 1.21 (0.20), residues: 660 sheet: -0.31 (0.32), residues: 236 loop : -0.98 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 256 TYR 0.013 0.001 TYR C 87 PHE 0.010 0.001 PHE D 98 TRP 0.007 0.001 TRP C 85 HIS 0.004 0.001 HIS B 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (11934) covalent geometry : angle 0.51153 / 0.27 (16176) hydrogen bonds : bond 0.04396 / 3.00 ( 614) hydrogen bonds : angle 4.89125 / 3.42 ( 1743) metal coordination : bond 0.01466 / 1.16 ( 16) metal coordination : angle 1.58550 / 1.44 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8684.41 seconds wall clock time: 146 minutes 56.49 seconds (8816.49 seconds total)