Starting phenix.real_space_refine on Thu Feb 5 06:28:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ksp_62553/02_2026/9ksp_62553.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ksp_62553/02_2026/9ksp_62553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ksp_62553/02_2026/9ksp_62553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ksp_62553/02_2026/9ksp_62553.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ksp_62553/02_2026/9ksp_62553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ksp_62553/02_2026/9ksp_62553.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 9793 2.51 5 N 2600 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15319 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2448 Classifications: {'peptide': 320} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 3 Chain: "A" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2563 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 316} Chain breaks: 3 Chain: "B" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2646 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 2 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2554 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 3 Chain: "E" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2554 Classifications: {'peptide': 332} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 315} Chain breaks: 3 Chain: "F" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2554 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N GLY C 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY C 261 " occ=0.00 residue: pdb=" N GLY C 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY C 281 " occ=0.00 residue: pdb=" N GLY A 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 261 " occ=0.00 residue: pdb=" N GLY A 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 281 " occ=0.00 residue: pdb=" N GLY B 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 261 " occ=0.00 residue: pdb=" N GLY B 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 281 " occ=0.00 residue: pdb=" N GLY D 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 261 " occ=0.00 residue: pdb=" N GLY D 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 281 " occ=0.00 residue: pdb=" N GLY E 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY E 261 " occ=0.00 residue: pdb=" N GLY E 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY E 281 " occ=0.00 residue: pdb=" N GLY F 261 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY F 261 " occ=0.00 residue: pdb=" N GLY F 281 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY F 281 " occ=0.00 Time building chain proxies: 2.66, per 1000 atoms: 0.17 Number of scatterers: 15319 At special positions: 0 Unit cell: (156.04, 155.21, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2878 8.00 N 2600 7.00 C 9793 6.00 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: 1.04 Conformation dependent library (CDL) restraints added in 519.4 milliseconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3670 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 29 sheets defined 33.4% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'C' and resid 47 through 60 removed outlier: 4.485A pdb=" N VAL C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 79 Processing helix chain 'C' and resid 128 through 133 removed outlier: 4.304A pdb=" N LYS C 132 " --> pdb=" O THR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 removed outlier: 3.801A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 229 removed outlier: 3.974A pdb=" N ASN C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 255 Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 302 through 313 removed outlier: 4.448A pdb=" N ALA C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 447 removed outlier: 3.635A pdb=" N LYS C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 61 removed outlier: 3.641A pdb=" N VAL A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 83 removed outlier: 3.598A pdb=" N ASN A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.967A pdb=" N GLU A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.340A pdb=" N LYS A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.570A pdb=" N ALA A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.749A pdb=" N VAL A 218 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 removed outlier: 3.740A pdb=" N ALA A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 425 Processing helix chain 'A' and resid 426 through 447 Processing helix chain 'B' and resid 47 through 58 removed outlier: 4.820A pdb=" N VAL B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 83 Processing helix chain 'B' and resid 129 through 134 removed outlier: 4.066A pdb=" N ALA B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 218 through 229 removed outlier: 4.148A pdb=" N ASN B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 removed outlier: 3.796A pdb=" N LEU B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 354 through 359 removed outlier: 4.708A pdb=" N LYS B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.659A pdb=" N ASP B 426 " --> pdb=" O MET B 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 422 through 426' Processing helix chain 'B' and resid 426 through 447 Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 66 through 83 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.884A pdb=" N LYS D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 96 " --> pdb=" O LYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.506A pdb=" N ALA D 133 " --> pdb=" O PRO D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 removed outlier: 3.527A pdb=" N ALA D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 229 removed outlier: 3.725A pdb=" N ASN D 229 " --> pdb=" O GLY D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.552A pdb=" N ALA D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 302 through 309 removed outlier: 3.596A pdb=" N ALA D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 426 removed outlier: 3.990A pdb=" N ASP D 426 " --> pdb=" O MET D 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 422 through 426' Processing helix chain 'D' and resid 426 through 447 Processing helix chain 'E' and resid 46 through 60 removed outlier: 3.962A pdb=" N PHE E 50 " --> pdb=" O MET E 46 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 79 removed outlier: 3.786A pdb=" N LYS E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 97 removed outlier: 3.928A pdb=" N GLU E 96 " --> pdb=" O LYS E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 4.402A pdb=" N LYS E 132 " --> pdb=" O THR E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 161 removed outlier: 3.680A pdb=" N ALA E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 229 removed outlier: 3.798A pdb=" N ASN E 229 " --> pdb=" O GLY E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 255 Processing helix chain 'E' and resid 299 through 303 Processing helix chain 'E' and resid 305 through 312 removed outlier: 3.681A pdb=" N LEU E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 425 removed outlier: 3.546A pdb=" N ASP E 425 " --> pdb=" O MET E 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 422 through 425' Processing helix chain 'E' and resid 426 through 447 Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 66 through 83 removed outlier: 3.576A pdb=" N GLU F 76 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP F 83 " --> pdb=" O LEU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 95 removed outlier: 3.851A pdb=" N LYS F 95 " --> pdb=" O LYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 134 removed outlier: 3.952A pdb=" N LYS F 132 " --> pdb=" O THR F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 162 removed outlier: 3.601A pdb=" N ALA F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 228 Processing helix chain 'F' and resid 246 through 255 Processing helix chain 'F' and resid 256 through 258 No H-bonds generated for 'chain 'F' and resid 256 through 258' Processing helix chain 'F' and resid 300 through 312 removed outlier: 3.704A pdb=" N GLN F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 425 Processing helix chain 'F' and resid 426 through 447 Processing sheet with id=AA1, first strand: chain 'C' and resid 112 through 115 removed outlier: 5.252A pdb=" N LEU C 119 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 139 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 142 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR C 172 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE C 144 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLN C 170 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 197 through 200 removed outlier: 3.675A pdb=" N TYR C 197 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU C 207 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ASP C 238 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL C 209 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE C 235 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU C 293 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU C 237 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 364 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 262 through 266 removed outlier: 6.842A pdb=" N TYR C 277 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER C 265 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU C 275 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 333 removed outlier: 7.190A pdb=" N VAL C 328 " --> pdb=" O THR C 344 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 344 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 111 through 115 removed outlier: 7.735A pdb=" N THR A 111 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 122 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 148 removed outlier: 6.587A pdb=" N THR A 172 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 144 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLN A 170 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 182 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 197 through 200 removed outlier: 6.615A pdb=" N LEU A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP A 238 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 235 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU A 293 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU A 237 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE A 290 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE A 318 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL A 292 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA9, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.723A pdb=" N LYS A 267 " --> pdb=" O ARG A 346 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 346 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 328 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 332 through 333 Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 89 removed outlier: 4.010A pdb=" N LEU B 89 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 339 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 112 through 115 removed outlier: 4.809A pdb=" N LEU B 119 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP B 139 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 112 through 115 removed outlier: 4.809A pdb=" N LEU B 119 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP B 139 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE B 141 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 174 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 196 through 200 removed outlier: 7.149A pdb=" N LEU B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ASP B 238 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 316 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.841A pdb=" N LEU B 275 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER B 265 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR B 277 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 265 " --> pdb=" O TYR B 348 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AB8, first strand: chain 'D' and resid 88 through 89 removed outlier: 3.702A pdb=" N MET D 330 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR D 344 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL D 328 " --> pdb=" O THR D 344 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 112 through 115 removed outlier: 5.506A pdb=" N LEU D 119 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP D 139 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE D 141 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 174 " --> pdb=" O ILE D 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 197 through 200 removed outlier: 6.629A pdb=" N LEU D 207 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASP D 238 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL D 209 " --> pdb=" O ASP D 238 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.990A pdb=" N VAL E 264 " --> pdb=" O TYR E 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 87 through 90 removed outlier: 6.812A pdb=" N GLU E 338 " --> pdb=" O VAL E 334 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE E 342 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET E 330 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL E 328 " --> pdb=" O THR E 344 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 112 through 115 removed outlier: 4.809A pdb=" N LEU E 119 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP E 139 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 112 through 115 removed outlier: 4.809A pdb=" N LEU E 119 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP E 139 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE E 141 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL E 174 " --> pdb=" O ILE E 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 197 through 200 removed outlier: 3.705A pdb=" N ARG E 210 " --> pdb=" O TYR E 197 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU E 207 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ASP E 238 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL E 209 " --> pdb=" O ASP E 238 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 291 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU E 237 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE E 290 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE E 318 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL E 292 " --> pdb=" O ILE E 318 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 112 through 115 Processing sheet with id=AC8, first strand: chain 'F' and resid 147 through 148 removed outlier: 4.924A pdb=" N ILE F 141 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL F 174 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 197 through 199 removed outlier: 6.121A pdb=" N ILE F 235 " --> pdb=" O ALA F 291 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU F 293 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 237 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE F 290 " --> pdb=" O VAL F 316 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE F 318 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL F 292 " --> pdb=" O ILE F 318 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 262 through 265 removed outlier: 7.083A pdb=" N TYR F 277 " --> pdb=" O LEU F 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 327 through 328 removed outlier: 3.630A pdb=" N ALA F 345 " --> pdb=" O VAL F 328 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4923 1.35 - 1.47: 3045 1.47 - 1.59: 7465 1.59 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 15529 Sorted by residual: bond pdb=" CA ALA A 306 " pdb=" C ALA A 306 " ideal model delta sigma weight residual 1.522 1.493 0.029 1.37e-02 5.33e+03 4.48e+00 bond pdb=" CB GLN D 310 " pdb=" CG GLN D 310 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CA VAL F 264 " pdb=" CB VAL F 264 " ideal model delta sigma weight residual 1.551 1.539 0.012 1.08e-02 8.57e+03 1.27e+00 bond pdb=" CA THR A 219 " pdb=" CB THR A 219 " ideal model delta sigma weight residual 1.521 1.537 -0.017 1.48e-02 4.57e+03 1.25e+00 bond pdb=" CB GLU D 272 " pdb=" CG GLU D 272 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 ... (remaining 15524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 20675 2.43 - 4.86: 220 4.86 - 7.29: 17 7.29 - 9.72: 5 9.72 - 12.15: 2 Bond angle restraints: 20919 Sorted by residual: angle pdb=" N VAL E 334 " pdb=" CA VAL E 334 " pdb=" C VAL E 334 " ideal model delta sigma weight residual 113.53 109.05 4.48 9.80e-01 1.04e+00 2.09e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 112.50 117.59 -5.09 1.16e+00 7.43e-01 1.92e+01 angle pdb=" CB MET C 161 " pdb=" CG MET C 161 " pdb=" SD MET C 161 " ideal model delta sigma weight residual 112.70 124.85 -12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" N THR A 219 " pdb=" CA THR A 219 " pdb=" C THR A 219 " ideal model delta sigma weight residual 107.20 114.02 -6.82 1.70e+00 3.46e-01 1.61e+01 angle pdb=" CA GLU D 272 " pdb=" CB GLU D 272 " pdb=" CG GLU D 272 " ideal model delta sigma weight residual 114.10 121.16 -7.06 2.00e+00 2.50e-01 1.25e+01 ... (remaining 20914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8280 18.00 - 36.00: 1038 36.00 - 54.00: 243 54.00 - 71.99: 43 71.99 - 89.99: 24 Dihedral angle restraints: 9628 sinusoidal: 3923 harmonic: 5705 Sorted by residual: dihedral pdb=" CA SER F 151 " pdb=" C SER F 151 " pdb=" N MET F 152 " pdb=" CA MET F 152 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA THR A 219 " pdb=" C THR A 219 " pdb=" N LYS A 220 " pdb=" CA LYS A 220 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ILE F 355 " pdb=" C ILE F 355 " pdb=" N GLN F 356 " pdb=" CA GLN F 356 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 9625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1651 0.037 - 0.075: 528 0.075 - 0.112: 248 0.112 - 0.149: 43 0.149 - 0.186: 4 Chirality restraints: 2474 Sorted by residual: chirality pdb=" CB VAL B 218 " pdb=" CA VAL B 218 " pdb=" CG1 VAL B 218 " pdb=" CG2 VAL B 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CB ILE D 366 " pdb=" CA ILE D 366 " pdb=" CG1 ILE D 366 " pdb=" CG2 ILE D 366 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA ASN A 146 " pdb=" N ASN A 146 " pdb=" C ASN A 146 " pdb=" CB ASN A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 2471 not shown) Planarity restraints: 2629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 242 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B 243 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 214 " -0.014 2.00e-02 2.50e+03 1.16e-02 2.34e+00 pdb=" CG PHE A 214 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 214 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 214 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 214 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 214 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 214 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 128 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO B 129 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.019 5.00e-02 4.00e+02 ... (remaining 2626 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 8490 3.01 - 3.48: 15813 3.48 - 3.96: 23655 3.96 - 4.43: 26467 4.43 - 4.90: 42819 Nonbonded interactions: 117244 Sorted by model distance: nonbonded pdb=" O ASN A 145 " pdb=" OD1 ASN A 146 " model vdw 2.541 3.040 nonbonded pdb=" O SER D 274 " pdb=" OG SER D 274 " model vdw 2.584 3.040 nonbonded pdb=" N VAL A 334 " pdb=" N ASN A 335 " model vdw 2.591 2.560 nonbonded pdb=" N ALA E 357 " pdb=" N LYS E 358 " model vdw 2.608 2.560 nonbonded pdb=" C THR F 286 " pdb=" OG1 THR F 286 " model vdw 2.609 2.616 ... (remaining 117239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 45 through 85 or resid 109 through 447)) selection = (chain 'B' and (resid 45 through 85 or resid 106 or resid 110 through 187 or res \ id 196 through 447)) selection = chain 'C' selection = (chain 'D' and (resid 45 through 85 or resid 109 through 447)) selection = (chain 'E' and (resid 45 through 85 or resid 109 through 447)) selection = (chain 'F' and (resid 45 through 85 or resid 109 through 447)) } 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.440 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5246 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15529 Z= 0.128 Angle : 0.610 12.150 20919 Z= 0.326 Chirality : 0.045 0.186 2474 Planarity : 0.004 0.056 2629 Dihedral : 16.839 89.992 5958 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.64 % Allowed : 25.94 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.63 (0.19), residues: 1947 helix: 0.62 (0.23), residues: 531 sheet: -0.63 (0.30), residues: 321 loop : -0.84 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 314 TYR 0.018 0.001 TYR B 347 PHE 0.026 0.001 PHE A 214 TRP 0.009 0.002 TRP C 439 HIS 0.002 0.000 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00277 (15529) covalent geometry : angle 0.61030 (20919) hydrogen bonds : bond 0.17866 ( 553) hydrogen bonds : angle 7.34340 ( 1560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5368 (mp0) REVERT: C 341 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.6119 (pttp) REVERT: A 434 ASP cc_start: 0.6130 (OUTLIER) cc_final: 0.4688 (t0) REVERT: B 46 MET cc_start: 0.2639 (mmp) cc_final: 0.1773 (tmm) REVERT: B 56 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.6161 (tt0) REVERT: B 114 MET cc_start: 0.8066 (tmm) cc_final: 0.7519 (ttm) REVERT: D 46 MET cc_start: 0.0129 (pmm) cc_final: -0.0612 (mmm) REVERT: D 186 ILE cc_start: 0.4526 (OUTLIER) cc_final: 0.3635 (mt) REVERT: E 114 MET cc_start: 0.7046 (mtt) cc_final: 0.6613 (mtt) REVERT: E 269 LYS cc_start: 0.5210 (ttmt) cc_final: 0.4949 (mmtp) REVERT: E 360 ILE cc_start: 0.7252 (mm) cc_final: 0.6248 (tt) REVERT: E 422 MET cc_start: 0.5416 (mpp) cc_final: 0.5136 (mpp) REVERT: F 235 ILE cc_start: -0.1865 (OUTLIER) cc_final: -0.2396 (mm) outliers start: 62 outliers final: 48 residues processed: 209 average time/residue: 0.0997 time to fit residues: 32.1994 Evaluate side-chains 219 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 439 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 131 TYR Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 427 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.4980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.202028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.170152 restraints weight = 29461.115| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 3.51 r_work: 0.4471 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15529 Z= 0.168 Angle : 0.621 7.131 20919 Z= 0.321 Chirality : 0.046 0.170 2474 Planarity : 0.004 0.044 2629 Dihedral : 7.765 75.043 2197 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 6.63 % Allowed : 23.59 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.95 (0.19), residues: 1947 helix: 0.21 (0.23), residues: 531 sheet: -0.68 (0.27), residues: 374 loop : -1.02 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 314 TYR 0.027 0.002 TYR B 347 PHE 0.022 0.001 PHE A 214 TRP 0.014 0.003 TRP C 439 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00391 (15529) covalent geometry : angle 0.62096 (20919) hydrogen bonds : bond 0.04034 ( 553) hydrogen bonds : angle 5.66899 ( 1560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 162 time to evaluate : 0.637 Fit side-chains REVERT: C 56 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5795 (mp0) REVERT: C 82 LEU cc_start: 0.5378 (OUTLIER) cc_final: 0.4419 (mt) REVERT: C 341 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.4942 (ptmm) REVERT: A 434 ASP cc_start: 0.6358 (OUTLIER) cc_final: 0.4688 (t0) REVERT: B 46 MET cc_start: 0.3219 (mmp) cc_final: 0.2081 (tmm) REVERT: B 56 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6530 (tt0) REVERT: B 114 MET cc_start: 0.8333 (tmm) cc_final: 0.7679 (ttm) REVERT: B 152 MET cc_start: 0.5858 (mpp) cc_final: 0.5453 (mpp) REVERT: D 46 MET cc_start: 0.0177 (pmm) cc_final: -0.0468 (mmm) REVERT: D 136 LYS cc_start: 0.5344 (mmtt) cc_final: 0.5126 (mmtm) REVERT: D 290 ILE cc_start: 0.2924 (OUTLIER) cc_final: 0.2699 (mp) REVERT: D 366 ILE cc_start: 0.5853 (OUTLIER) cc_final: 0.5532 (pp) REVERT: E 47 PHE cc_start: 0.5226 (OUTLIER) cc_final: 0.4889 (t80) REVERT: E 114 MET cc_start: 0.6610 (mtt) cc_final: 0.6172 (mtt) REVERT: E 422 MET cc_start: 0.5721 (OUTLIER) cc_final: 0.5381 (mpp) REVERT: F 115 ARG cc_start: 0.7313 (ptm160) cc_final: 0.6519 (ptp-110) REVERT: F 430 LYS cc_start: 0.4917 (OUTLIER) cc_final: 0.4092 (mttt) outliers start: 113 outliers final: 72 residues processed: 258 average time/residue: 0.1174 time to fit residues: 45.6610 Evaluate side-chains 238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 156 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 439 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 430 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 112 optimal weight: 20.0000 chunk 137 optimal weight: 0.2980 chunk 100 optimal weight: 0.0570 chunk 181 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.206020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.174449 restraints weight = 29256.258| |-----------------------------------------------------------------------------| r_work (start): 0.4736 rms_B_bonded: 3.53 r_work: 0.4537 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5277 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15529 Z= 0.099 Angle : 0.531 10.005 20919 Z= 0.272 Chirality : 0.044 0.194 2474 Planarity : 0.004 0.039 2629 Dihedral : 6.285 58.769 2152 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.16 % Allowed : 25.23 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.19), residues: 1947 helix: 0.87 (0.24), residues: 531 sheet: -0.80 (0.27), residues: 379 loop : -0.85 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.011 0.001 TYR B 347 PHE 0.015 0.001 PHE A 214 TRP 0.007 0.001 TRP C 439 HIS 0.002 0.000 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00220 (15529) covalent geometry : angle 0.53112 (20919) hydrogen bonds : bond 0.03153 ( 553) hydrogen bonds : angle 4.84831 ( 1560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 177 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5684 (mp0) REVERT: A 434 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.4609 (t0) REVERT: B 46 MET cc_start: 0.3345 (mmp) cc_final: 0.2069 (tmm) REVERT: B 56 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6150 (tt0) REVERT: B 114 MET cc_start: 0.8323 (tmm) cc_final: 0.7610 (ttm) REVERT: D 46 MET cc_start: 0.0290 (pmm) cc_final: -0.0484 (mmm) REVERT: D 136 LYS cc_start: 0.5275 (mmtt) cc_final: 0.5005 (mmtm) REVERT: D 186 ILE cc_start: 0.5145 (OUTLIER) cc_final: 0.4365 (mt) REVERT: E 47 PHE cc_start: 0.5012 (OUTLIER) cc_final: 0.4774 (t80) REVERT: E 422 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.5135 (mpp) REVERT: F 289 PRO cc_start: 0.2863 (Cg_exo) cc_final: 0.2538 (Cg_endo) REVERT: F 430 LYS cc_start: 0.4582 (OUTLIER) cc_final: 0.3876 (mttt) outliers start: 88 outliers final: 56 residues processed: 248 average time/residue: 0.1188 time to fit residues: 44.4621 Evaluate side-chains 232 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 439 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 424 ASN Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 430 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 100 optimal weight: 0.0030 chunk 38 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.202907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.172048 restraints weight = 29474.962| |-----------------------------------------------------------------------------| r_work (start): 0.4698 rms_B_bonded: 3.26 r_work (final): 0.4698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5097 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15529 Z= 0.139 Angle : 0.585 10.364 20919 Z= 0.297 Chirality : 0.045 0.189 2474 Planarity : 0.004 0.039 2629 Dihedral : 6.451 58.335 2139 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.51 % Allowed : 24.77 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.82 (0.19), residues: 1947 helix: 0.54 (0.23), residues: 537 sheet: -0.81 (0.27), residues: 377 loop : -0.99 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.023 0.001 TYR B 347 PHE 0.013 0.001 PHE A 214 TRP 0.012 0.002 TRP C 439 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00325 (15529) covalent geometry : angle 0.58503 (20919) hydrogen bonds : bond 0.03318 ( 553) hydrogen bonds : angle 4.96051 ( 1560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 173 time to evaluate : 0.620 Fit side-chains REVERT: C 56 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5793 (mp0) REVERT: C 66 SER cc_start: 0.6594 (OUTLIER) cc_final: 0.6313 (p) REVERT: C 341 LYS cc_start: 0.6402 (OUTLIER) cc_final: 0.4988 (ptmm) REVERT: A 75 ILE cc_start: 0.4867 (OUTLIER) cc_final: 0.4578 (tt) REVERT: A 430 LYS cc_start: 0.4898 (OUTLIER) cc_final: 0.3991 (mttt) REVERT: A 434 ASP cc_start: 0.6088 (OUTLIER) cc_final: 0.4501 (t0) REVERT: B 46 MET cc_start: 0.3417 (mmp) cc_final: 0.2071 (tmm) REVERT: B 56 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5969 (tt0) REVERT: B 114 MET cc_start: 0.7697 (tmm) cc_final: 0.6981 (ttm) REVERT: B 152 MET cc_start: 0.6081 (mpp) cc_final: 0.5698 (mpp) REVERT: D 46 MET cc_start: 0.0417 (pmm) cc_final: -0.0428 (mmm) REVERT: D 186 ILE cc_start: 0.4020 (OUTLIER) cc_final: 0.3223 (mt) REVERT: E 47 PHE cc_start: 0.4686 (OUTLIER) cc_final: 0.4478 (t80) REVERT: E 218 VAL cc_start: 0.4209 (t) cc_final: 0.3982 (t) REVERT: E 422 MET cc_start: 0.5785 (OUTLIER) cc_final: 0.5420 (mpp) REVERT: E 445 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.5642 (ttpp) REVERT: F 115 ARG cc_start: 0.6970 (ptm160) cc_final: 0.6567 (ptp-110) REVERT: F 430 LYS cc_start: 0.4759 (OUTLIER) cc_final: 0.3941 (mttt) outliers start: 111 outliers final: 76 residues processed: 262 average time/residue: 0.1135 time to fit residues: 44.6977 Evaluate side-chains 256 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 168 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 47 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 439 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 430 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 180 optimal weight: 20.0000 chunk 129 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 428 GLN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.205830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.173715 restraints weight = 29139.368| |-----------------------------------------------------------------------------| r_work (start): 0.4721 rms_B_bonded: 3.53 r_work: 0.4547 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5252 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15529 Z= 0.095 Angle : 0.532 9.288 20919 Z= 0.270 Chirality : 0.044 0.201 2474 Planarity : 0.004 0.034 2629 Dihedral : 6.011 55.559 2139 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.11 % Allowed : 26.70 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.62 (0.19), residues: 1947 helix: 0.91 (0.23), residues: 543 sheet: -0.78 (0.27), residues: 379 loop : -0.96 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.010 0.001 TYR B 347 PHE 0.015 0.001 PHE C 214 TRP 0.007 0.001 TRP C 439 HIS 0.002 0.000 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00217 (15529) covalent geometry : angle 0.53194 (20919) hydrogen bonds : bond 0.02806 ( 553) hydrogen bonds : angle 4.53448 ( 1560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 174 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5692 (mp0) REVERT: C 66 SER cc_start: 0.6778 (OUTLIER) cc_final: 0.6511 (p) REVERT: C 114 MET cc_start: 0.7881 (tpp) cc_final: 0.7660 (tpp) REVERT: A 430 LYS cc_start: 0.4809 (OUTLIER) cc_final: 0.3935 (mttt) REVERT: A 434 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.4306 (t0) REVERT: B 46 MET cc_start: 0.3186 (mmp) cc_final: 0.1983 (tmm) REVERT: B 114 MET cc_start: 0.8141 (tmm) cc_final: 0.7681 (tmm) REVERT: B 152 MET cc_start: 0.5727 (OUTLIER) cc_final: 0.5370 (mpp) REVERT: D 46 MET cc_start: 0.0367 (pmm) cc_final: -0.0386 (mmm) REVERT: D 186 ILE cc_start: 0.5085 (OUTLIER) cc_final: 0.4390 (mt) REVERT: E 47 PHE cc_start: 0.4949 (OUTLIER) cc_final: 0.4724 (t80) REVERT: E 145 ASN cc_start: 0.3739 (m110) cc_final: 0.3358 (t0) REVERT: E 422 MET cc_start: 0.5311 (OUTLIER) cc_final: 0.4957 (mpp) REVERT: F 430 LYS cc_start: 0.4653 (OUTLIER) cc_final: 0.3996 (mttt) outliers start: 87 outliers final: 59 residues processed: 241 average time/residue: 0.1046 time to fit residues: 38.7347 Evaluate side-chains 234 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 166 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 47 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 439 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 430 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 126 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 67 optimal weight: 0.0010 chunk 20 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 428 GLN ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.201720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.169886 restraints weight = 29473.151| |-----------------------------------------------------------------------------| r_work (start): 0.4672 rms_B_bonded: 3.27 r_work (final): 0.4672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5176 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15529 Z= 0.163 Angle : 0.617 12.153 20919 Z= 0.312 Chirality : 0.046 0.180 2474 Planarity : 0.004 0.037 2629 Dihedral : 6.364 57.319 2136 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 6.69 % Allowed : 25.47 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.93 (0.19), residues: 1947 helix: 0.44 (0.23), residues: 538 sheet: -0.82 (0.28), residues: 361 loop : -1.08 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.026 0.001 TYR B 347 PHE 0.017 0.001 PHE D 184 TRP 0.014 0.003 TRP C 439 HIS 0.002 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00379 (15529) covalent geometry : angle 0.61709 (20919) hydrogen bonds : bond 0.03432 ( 553) hydrogen bonds : angle 4.94161 ( 1560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 169 time to evaluate : 0.640 Fit side-chains REVERT: C 56 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: C 66 SER cc_start: 0.6644 (OUTLIER) cc_final: 0.6351 (p) REVERT: C 341 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.4946 (ptmm) REVERT: A 75 ILE cc_start: 0.4985 (OUTLIER) cc_final: 0.4685 (tt) REVERT: A 147 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 430 LYS cc_start: 0.4946 (OUTLIER) cc_final: 0.4086 (mttt) REVERT: A 434 ASP cc_start: 0.6204 (OUTLIER) cc_final: 0.4548 (t0) REVERT: B 46 MET cc_start: 0.3437 (mmp) cc_final: 0.2137 (tmm) REVERT: B 114 MET cc_start: 0.7770 (tmm) cc_final: 0.7094 (ttm) REVERT: B 152 MET cc_start: 0.6072 (OUTLIER) cc_final: 0.5712 (mpp) REVERT: D 46 MET cc_start: 0.0527 (pmm) cc_final: -0.0175 (mmm) REVERT: D 186 ILE cc_start: 0.4055 (OUTLIER) cc_final: 0.3327 (mt) REVERT: E 47 PHE cc_start: 0.4766 (OUTLIER) cc_final: 0.4513 (t80) REVERT: E 422 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.5454 (mpp) REVERT: E 445 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.5602 (ttpp) REVERT: F 115 ARG cc_start: 0.7046 (ptm160) cc_final: 0.6553 (ptp-110) REVERT: F 203 GLU cc_start: 0.4644 (OUTLIER) cc_final: 0.2871 (pm20) REVERT: F 430 LYS cc_start: 0.4774 (OUTLIER) cc_final: 0.3985 (mttt) outliers start: 114 outliers final: 77 residues processed: 258 average time/residue: 0.1093 time to fit residues: 42.5016 Evaluate side-chains 254 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 164 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 47 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 439 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 323 PHE Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 430 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 160 optimal weight: 0.5980 chunk 145 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 158 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 71 optimal weight: 0.0170 overall best weight: 0.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.204208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.175267 restraints weight = 29452.161| |-----------------------------------------------------------------------------| r_work (start): 0.4737 rms_B_bonded: 3.08 r_work: 0.4504 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.4504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5349 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15529 Z= 0.103 Angle : 0.555 10.505 20919 Z= 0.280 Chirality : 0.045 0.186 2474 Planarity : 0.004 0.058 2629 Dihedral : 5.944 57.157 2134 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.40 % Allowed : 26.94 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.75 (0.19), residues: 1947 helix: 0.72 (0.23), residues: 543 sheet: -0.85 (0.27), residues: 377 loop : -0.98 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.015 0.001 TYR B 347 PHE 0.012 0.001 PHE A 214 TRP 0.009 0.002 TRP C 439 HIS 0.002 0.000 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00243 (15529) covalent geometry : angle 0.55508 (20919) hydrogen bonds : bond 0.02927 ( 553) hydrogen bonds : angle 4.56421 ( 1560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 171 time to evaluate : 0.659 Fit side-chains REVERT: C 56 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5877 (mp0) REVERT: C 66 SER cc_start: 0.6878 (OUTLIER) cc_final: 0.6601 (p) REVERT: C 341 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.4984 (ptmm) REVERT: A 430 LYS cc_start: 0.4905 (OUTLIER) cc_final: 0.4062 (mttt) REVERT: A 434 ASP cc_start: 0.6279 (OUTLIER) cc_final: 0.4695 (t0) REVERT: B 46 MET cc_start: 0.3235 (mmp) cc_final: 0.2075 (tmm) REVERT: B 152 MET cc_start: 0.5863 (OUTLIER) cc_final: 0.5488 (mpp) REVERT: D 46 MET cc_start: 0.0554 (pmm) cc_final: -0.0110 (mmm) REVERT: D 186 ILE cc_start: 0.4903 (OUTLIER) cc_final: 0.4143 (mt) REVERT: E 47 PHE cc_start: 0.5239 (OUTLIER) cc_final: 0.4929 (t80) REVERT: E 422 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.5222 (mpp) REVERT: F 203 GLU cc_start: 0.4872 (OUTLIER) cc_final: 0.3046 (pm20) REVERT: F 430 LYS cc_start: 0.4623 (OUTLIER) cc_final: 0.3945 (mttt) outliers start: 92 outliers final: 71 residues processed: 243 average time/residue: 0.1084 time to fit residues: 40.0790 Evaluate side-chains 247 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 165 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 47 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 439 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 47 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 424 ASN Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 430 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 32 optimal weight: 8.9990 chunk 156 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 0.0050 chunk 79 optimal weight: 9.9990 chunk 59 optimal weight: 0.0370 chunk 93 optimal weight: 0.4980 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 overall best weight: 0.4474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN D 185 ASN E 229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.206285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.176974 restraints weight = 29968.745| |-----------------------------------------------------------------------------| r_work (start): 0.4760 rms_B_bonded: 3.22 r_work (final): 0.4760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4915 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15529 Z= 0.093 Angle : 0.537 10.700 20919 Z= 0.270 Chirality : 0.044 0.192 2474 Planarity : 0.004 0.050 2629 Dihedral : 5.582 56.876 2134 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.87 % Allowed : 27.64 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1947 helix: 1.00 (0.23), residues: 545 sheet: -0.74 (0.27), residues: 377 loop : -0.94 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 175 TYR 0.011 0.001 TYR B 347 PHE 0.017 0.001 PHE D 184 TRP 0.008 0.001 TRP F 439 HIS 0.004 0.000 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00219 (15529) covalent geometry : angle 0.53683 (20919) hydrogen bonds : bond 0.02670 ( 553) hydrogen bonds : angle 4.28966 ( 1560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 173 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.5638 (mp0) REVERT: C 66 SER cc_start: 0.6523 (OUTLIER) cc_final: 0.6257 (p) REVERT: A 430 LYS cc_start: 0.4539 (OUTLIER) cc_final: 0.3847 (mttt) REVERT: A 434 ASP cc_start: 0.5886 (OUTLIER) cc_final: 0.3976 (t0) REVERT: B 46 MET cc_start: 0.3182 (mmp) cc_final: 0.1939 (tmm) REVERT: B 81 ASN cc_start: 0.6651 (t0) cc_final: 0.6330 (m-40) REVERT: B 114 MET cc_start: 0.7652 (tmm) cc_final: 0.7174 (tmm) REVERT: B 152 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.5596 (mpp) REVERT: D 46 MET cc_start: 0.0053 (pmm) cc_final: -0.0491 (mmm) REVERT: D 186 ILE cc_start: 0.3804 (OUTLIER) cc_final: 0.3161 (mt) REVERT: E 422 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.5106 (mpp) REVERT: F 430 LYS cc_start: 0.4394 (OUTLIER) cc_final: 0.3748 (mttt) outliers start: 83 outliers final: 57 residues processed: 239 average time/residue: 0.1229 time to fit residues: 44.3322 Evaluate side-chains 231 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 166 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 439 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 422 MET Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 424 ASN Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 430 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 89 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.0070 chunk 71 optimal weight: 0.0570 chunk 159 optimal weight: 0.0470 chunk 64 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.206611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.175491 restraints weight = 29373.240| |-----------------------------------------------------------------------------| r_work (start): 0.4744 rms_B_bonded: 3.45 r_work: 0.4563 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5204 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15529 Z= 0.094 Angle : 0.541 11.724 20919 Z= 0.271 Chirality : 0.044 0.189 2474 Planarity : 0.004 0.053 2629 Dihedral : 5.419 56.844 2129 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.52 % Allowed : 27.76 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.50 (0.19), residues: 1947 helix: 1.08 (0.23), residues: 545 sheet: -0.77 (0.27), residues: 379 loop : -0.91 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 115 TYR 0.009 0.001 TYR B 347 PHE 0.022 0.001 PHE D 184 TRP 0.007 0.001 TRP C 439 HIS 0.002 0.000 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00221 (15529) covalent geometry : angle 0.54143 (20919) hydrogen bonds : bond 0.02648 ( 553) hydrogen bonds : angle 4.21497 ( 1560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 171 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5690 (mp0) REVERT: C 66 SER cc_start: 0.6765 (OUTLIER) cc_final: 0.6478 (p) REVERT: A 430 LYS cc_start: 0.4709 (OUTLIER) cc_final: 0.4011 (mttt) REVERT: A 434 ASP cc_start: 0.6071 (OUTLIER) cc_final: 0.4520 (t0) REVERT: B 46 MET cc_start: 0.2877 (mmp) cc_final: 0.1812 (tmm) REVERT: B 81 ASN cc_start: 0.6992 (t0) cc_final: 0.6679 (m-40) REVERT: B 114 MET cc_start: 0.8142 (tmm) cc_final: 0.7640 (tmm) REVERT: B 152 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5448 (mpp) REVERT: D 46 MET cc_start: -0.0000 (pmm) cc_final: -0.0525 (mmm) REVERT: D 183 VAL cc_start: 0.8368 (t) cc_final: 0.8057 (p) REVERT: D 186 ILE cc_start: 0.4588 (OUTLIER) cc_final: 0.3944 (mt) REVERT: D 366 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5333 (pp) REVERT: E 129 PRO cc_start: 0.7492 (Cg_endo) cc_final: 0.7289 (Cg_exo) REVERT: F 115 ARG cc_start: 0.7199 (ptm160) cc_final: 0.6415 (ptm160) REVERT: F 430 LYS cc_start: 0.4376 (OUTLIER) cc_final: 0.3749 (mttt) outliers start: 77 outliers final: 59 residues processed: 231 average time/residue: 0.1119 time to fit residues: 39.2687 Evaluate side-chains 233 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 166 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 439 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 424 ASN Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 430 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 119 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 chunk 188 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 162 optimal weight: 0.0030 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN D 170 GLN D 185 ASN ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.203986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.171941 restraints weight = 29711.001| |-----------------------------------------------------------------------------| r_work (start): 0.4698 rms_B_bonded: 3.77 r_work: 0.4513 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5342 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15529 Z= 0.120 Angle : 0.582 12.039 20919 Z= 0.291 Chirality : 0.045 0.250 2474 Planarity : 0.004 0.055 2629 Dihedral : 5.606 57.125 2128 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.17 % Allowed : 28.35 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.65 (0.19), residues: 1947 helix: 0.84 (0.23), residues: 538 sheet: -0.80 (0.27), residues: 386 loop : -0.94 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 115 TYR 0.018 0.001 TYR B 347 PHE 0.011 0.001 PHE C 47 TRP 0.010 0.002 TRP C 439 HIS 0.002 0.001 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00286 (15529) covalent geometry : angle 0.58207 (20919) hydrogen bonds : bond 0.02874 ( 553) hydrogen bonds : angle 4.41608 ( 1560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 0.641 Fit side-chains REVERT: C 56 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5670 (mp0) REVERT: C 66 SER cc_start: 0.6893 (OUTLIER) cc_final: 0.6604 (p) REVERT: C 147 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.6000 (pt0) REVERT: A 161 MET cc_start: 0.1476 (mtt) cc_final: 0.1250 (mtp) REVERT: A 430 LYS cc_start: 0.4886 (OUTLIER) cc_final: 0.4020 (mttt) REVERT: A 434 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.4691 (t0) REVERT: B 46 MET cc_start: 0.3120 (mmp) cc_final: 0.1975 (tmm) REVERT: B 81 ASN cc_start: 0.7295 (t0) cc_final: 0.7003 (m-40) REVERT: B 152 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5584 (mpp) REVERT: D 46 MET cc_start: 0.0066 (pmm) cc_final: -0.0422 (mmm) REVERT: D 183 VAL cc_start: 0.8455 (t) cc_final: 0.8182 (p) REVERT: D 186 ILE cc_start: 0.4823 (OUTLIER) cc_final: 0.4238 (mt) REVERT: D 366 ILE cc_start: 0.5660 (OUTLIER) cc_final: 0.5344 (pp) REVERT: F 115 ARG cc_start: 0.7350 (ptm160) cc_final: 0.6425 (ptp90) REVERT: F 430 LYS cc_start: 0.4515 (OUTLIER) cc_final: 0.3812 (mttt) outliers start: 71 outliers final: 56 residues processed: 228 average time/residue: 0.1137 time to fit residues: 39.4160 Evaluate side-chains 234 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 169 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 439 TRP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 446 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 424 ASN Chi-restraints excluded: chain F residue 426 ASP Chi-restraints excluded: chain F residue 430 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 69 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.203898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.171980 restraints weight = 28947.834| |-----------------------------------------------------------------------------| r_work (start): 0.4700 rms_B_bonded: 3.35 r_work (final): 0.4700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5078 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 15529 Z= 0.186 Angle : 0.963 59.200 20919 Z= 0.563 Chirality : 0.051 1.098 2474 Planarity : 0.004 0.082 2629 Dihedral : 5.589 57.163 2126 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.11 % Allowed : 28.35 % Favored : 67.55 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.66 (0.19), residues: 1947 helix: 0.82 (0.23), residues: 538 sheet: -0.81 (0.27), residues: 386 loop : -0.94 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 115 TYR 0.019 0.001 TYR B 347 PHE 0.013 0.001 PHE A 214 TRP 0.010 0.002 TRP C 439 HIS 0.002 0.001 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00373 (15529) covalent geometry : angle 0.96269 (20919) hydrogen bonds : bond 0.02899 ( 553) hydrogen bonds : angle 4.41849 ( 1560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3549.88 seconds wall clock time: 61 minutes 54.79 seconds (3714.79 seconds total)