Starting phenix.real_space_refine on Thu Oct 29 01:02:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/38kl_78879/10_2026/38kl_78879.cif Found real_map, /net/cci-nas-00/data/ceres_data/38kl_78879/10_2026/38kl_78879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/38kl_78879/10_2026/38kl_78879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/38kl_78879/10_2026/38kl_78879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/38kl_78879/10_2026/38kl_78879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/38kl_78879/10_2026/38kl_78879.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 163 5.16 5 C 18754 2.51 5 N 5046 2.21 5 O 5765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29743 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2913 Chain: "B" Number of atoms: 2913 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2929 Chain: "C" Number of atoms: 2919 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2922 Chain: "D" Number of atoms: 2925 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2915 Chain: "E" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2933 Chain: "X" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4604 Classifications: {'peptide': 610} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 584} Chain: "Y" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4604 Classifications: {'peptide': 610} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 584} Chain: "a" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain: "b" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain: "c" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain: "d" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1088 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 1 Chain: "e" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1135 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 4, 'TRANS': 140} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.91, per 1000 atoms: 0.30 Number of scatterers: 29743 At special positions: 0 Unit cell: (135.05, 134.32, 202.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 163 16.00 P 10 15.00 Mg 5 11.99 O 5765 8.00 N 5046 7.00 C 18754 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: 2.69 Conformation dependent library (CDL) restraints added in 1.7 seconds 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7118 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 59 sheets defined 33.6% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.596A pdb=" N GLN A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.603A pdb=" N ILE A 77 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 224 through 233 removed outlier: 4.463A pdb=" N ALA A 233 " --> pdb=" O MET A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.596A pdb=" N CYS A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 263 through 264 No H-bonds generated for 'chain 'A' and resid 263 through 264' Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 291 through 297 removed outlier: 3.528A pdb=" N ALA A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.907A pdb=" N GLN A 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.529A pdb=" N GLN B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.728A pdb=" N ILE B 77 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.684A pdb=" N HIS B 103 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 308 removed outlier: 4.308A pdb=" N TYR B 308 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 351 through 357 removed outlier: 4.250A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.798A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.831A pdb=" N GLN C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.906A pdb=" N ILE C 77 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'C' and resid 174 through 177 removed outlier: 3.566A pdb=" N ILE C 177 " --> pdb=" O PRO C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 177' Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.703A pdb=" N THR C 196 " --> pdb=" O MET C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 291 through 297 removed outlier: 3.708A pdb=" N ALA C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.587A pdb=" N THR C 306 " --> pdb=" O GLY C 303 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR C 308 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 352 through 355 Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 371 through 376 Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.777A pdb=" N ILE D 77 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 94 Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.645A pdb=" N HIS D 103 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'D' and resid 174 through 177 removed outlier: 3.594A pdb=" N ILE D 177 " --> pdb=" O PRO D 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 177' Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 204 through 219 Processing helix chain 'D' and resid 224 through 231 Processing helix chain 'D' and resid 254 through 262 Proline residue: D 260 - end of helix Processing helix chain 'D' and resid 263 through 264 No H-bonds generated for 'chain 'D' and resid 263 through 264' Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 288 through 297 removed outlier: 4.292A pdb=" N LYS D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.098A pdb=" N TYR D 308 " --> pdb=" O THR D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 352 through 357 removed outlier: 4.025A pdb=" N GLN D 356 " --> pdb=" O THR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 371 through 376 Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.516A pdb=" N GLN E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 4.091A pdb=" N ILE E 77 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 94 removed outlier: 3.615A pdb=" N MET E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.585A pdb=" N HIS E 103 " --> pdb=" O PRO E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'E' and resid 139 through 147 removed outlier: 3.563A pdb=" N SER E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 177 removed outlier: 3.611A pdb=" N ILE E 177 " --> pdb=" O PRO E 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 174 through 177' Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.577A pdb=" N THR E 196 " --> pdb=" O MET E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 219 Processing helix chain 'E' and resid 224 through 231 Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.518A pdb=" N CYS E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 264 Processing helix chain 'E' and resid 265 through 270 Processing helix chain 'E' and resid 275 through 286 Processing helix chain 'E' and resid 291 through 298 Processing helix chain 'E' and resid 304 through 308 removed outlier: 4.189A pdb=" N TYR E 308 " --> pdb=" O THR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 323 removed outlier: 3.664A pdb=" N ARG E 314 " --> pdb=" O GLY E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 349 Processing helix chain 'E' and resid 351 through 358 removed outlier: 4.637A pdb=" N GLN E 356 " --> pdb=" O THR E 353 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP E 358 " --> pdb=" O GLN E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 368 Processing helix chain 'E' and resid 370 through 376 removed outlier: 3.860A pdb=" N ARG E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'X' and resid 282 through 285 Processing helix chain 'X' and resid 401 through 405 removed outlier: 3.871A pdb=" N LYS X 404 " --> pdb=" O ASP X 401 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA X 405 " --> pdb=" O SER X 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 401 through 405' Processing helix chain 'Y' and resid 282 through 285 Processing helix chain 'Y' and resid 401 through 405 removed outlier: 3.506A pdb=" N LYS Y 404 " --> pdb=" O ASP Y 401 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.869A pdb=" N LYS a 12 " --> pdb=" O ASP a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 61 removed outlier: 3.531A pdb=" N PHE a 53 " --> pdb=" O PRO a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 122 removed outlier: 4.912A pdb=" N ARG a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA a 116 " --> pdb=" O SER a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 137 Processing helix chain 'a' and resid 138 through 148 Processing helix chain 'b' and resid 8 through 21 removed outlier: 3.689A pdb=" N LYS b 12 " --> pdb=" O ASP b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 61 removed outlier: 3.561A pdb=" N PHE b 53 " --> pdb=" O PRO b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 122 removed outlier: 4.902A pdb=" N ARG b 115 " --> pdb=" O ALA b 111 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA b 116 " --> pdb=" O SER b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 137 Processing helix chain 'b' and resid 138 through 148 Processing helix chain 'c' and resid 8 through 20 removed outlier: 3.896A pdb=" N LYS c 12 " --> pdb=" O ASP c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 61 removed outlier: 3.718A pdb=" N PHE c 53 " --> pdb=" O PRO c 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 122 removed outlier: 4.910A pdb=" N ARG c 115 " --> pdb=" O ALA c 111 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA c 116 " --> pdb=" O SER c 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 133 through 137 Processing helix chain 'c' and resid 138 through 149 removed outlier: 3.547A pdb=" N ASN c 149 " --> pdb=" O ASP c 145 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 20 removed outlier: 3.812A pdb=" N LEU d 18 " --> pdb=" O ALA d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 61 Processing helix chain 'd' and resid 103 through 120 removed outlier: 4.672A pdb=" N ARG d 115 " --> pdb=" O ALA d 111 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA d 116 " --> pdb=" O SER d 112 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER d 120 " --> pdb=" O ALA d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 137 Processing helix chain 'd' and resid 138 through 148 Processing helix chain 'e' and resid 8 through 21 removed outlier: 4.138A pdb=" N LYS e 12 " --> pdb=" O ASP e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 61 removed outlier: 3.504A pdb=" N PHE e 53 " --> pdb=" O PRO e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 122 removed outlier: 4.567A pdb=" N ARG e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA e 116 " --> pdb=" O SER e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 137 Processing helix chain 'e' and resid 138 through 150 removed outlier: 3.764A pdb=" N ASN e 149 " --> pdb=" O ASP e 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.831A pdb=" N LEU A 10 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 108 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N CYS A 12 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 6.321A pdb=" N ASN A 299 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 243 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.509A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA8, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.252A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.530A pdb=" N THR C 108 " --> pdb=" O CYS C 12 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN C 14 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'C' and resid 171 through 172 removed outlier: 6.419A pdb=" N ASN C 299 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 240 through 243 Processing sheet with id=AB7, first strand: chain 'D' and resid 31 through 34 removed outlier: 6.569A pdb=" N LEU D 10 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR D 108 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N CYS D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AB9, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AC1, first strand: chain 'D' and resid 171 through 172 removed outlier: 6.379A pdb=" N ASN D 299 " --> pdb=" O ILE D 332 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 240 through 243 Processing sheet with id=AC3, first strand: chain 'E' and resid 31 through 34 removed outlier: 6.543A pdb=" N LEU E 10 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR E 108 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N CYS E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC5, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AC6, first strand: chain 'E' and resid 171 through 172 removed outlier: 6.176A pdb=" N ILE E 153 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER E 302 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU E 155 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN E 299 " --> pdb=" O ILE E 332 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 240 through 243 Processing sheet with id=AC8, first strand: chain 'X' and resid 5 through 10 removed outlier: 5.542A pdb=" N GLN X 6 " --> pdb=" O ASN X 608 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN X 608 " --> pdb=" O GLN X 6 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA X 8 " --> pdb=" O PHE X 606 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'X' and resid 62 through 67 removed outlier: 6.855A pdb=" N GLY X 77 " --> pdb=" O THR X 63 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA X 65 " --> pdb=" O ALA X 75 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA X 75 " --> pdb=" O ALA X 65 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR X 67 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TYR X 73 " --> pdb=" O THR X 67 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN X 82 " --> pdb=" O ASP X 78 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP X 87 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU X 95 " --> pdb=" O ASP X 87 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 106 through 111 removed outlier: 8.217A pdb=" N GLY X 129 " --> pdb=" O ASN X 142 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN X 142 " --> pdb=" O GLY X 129 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL X 131 " --> pdb=" O ASN X 140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 150 through 155 removed outlier: 3.509A pdb=" N SER X 152 " --> pdb=" O GLY X 166 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 193 through 198 removed outlier: 3.539A pdb=" N SER X 195 " --> pdb=" O THR X 208 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE X 214 " --> pdb=" O PHE X 228 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASN X 218 " --> pdb=" O LYS X 224 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS X 224 " --> pdb=" O ASN X 218 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 242 through 247 removed outlier: 3.665A pdb=" N THR X 262 " --> pdb=" O SER X 258 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASN X 267 " --> pdb=" O VAL X 273 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL X 273 " --> pdb=" O ASN X 267 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 287 through 292 removed outlier: 3.690A pdb=" N GLY X 289 " --> pdb=" O ILE X 300 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU X 297 " --> pdb=" O VAL X 309 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE X 306 " --> pdb=" O VAL X 319 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL X 319 " --> pdb=" O ILE X 306 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE X 308 " --> pdb=" O ASP X 317 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER X 315 " --> pdb=" O ASN X 310 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 327 through 332 Processing sheet with id=AD8, first strand: chain 'X' and resid 370 through 375 removed outlier: 3.739A pdb=" N GLY X 372 " --> pdb=" O VAL X 384 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS X 389 " --> pdb=" O SER X 385 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 414 through 419 removed outlier: 3.931A pdb=" N HIS X 433 " --> pdb=" O CYS X 430 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 451 through 456 removed outlier: 6.786A pdb=" N GLY X 466 " --> pdb=" O SER X 452 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL X 454 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA X 464 " --> pdb=" O VAL X 454 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU X 456 " --> pdb=" O PHE X 462 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE X 462 " --> pdb=" O LEU X 456 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS X 471 " --> pdb=" O GLY X 467 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL X 472 " --> pdb=" O THR X 487 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR X 487 " --> pdb=" O VAL X 472 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL X 474 " --> pdb=" O VAL X 485 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 494 through 499 removed outlier: 3.796A pdb=" N SER X 496 " --> pdb=" O THR X 509 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU X 525 " --> pdb=" O SER X 519 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 539 through 544 Processing sheet with id=AE4, first strand: chain 'Y' and resid 5 through 10 removed outlier: 5.590A pdb=" N GLN Y 6 " --> pdb=" O ASN Y 608 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN Y 608 " --> pdb=" O GLN Y 6 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA Y 8 " --> pdb=" O PHE Y 606 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR Y 594 " --> pdb=" O LEU Y 590 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 25 through 26 Processing sheet with id=AE6, first strand: chain 'Y' and resid 62 through 67 removed outlier: 3.774A pdb=" N VAL Y 64 " --> pdb=" O GLY Y 77 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN Y 82 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP Y 87 " --> pdb=" O LEU Y 95 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU Y 95 " --> pdb=" O ASP Y 87 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 106 through 111 removed outlier: 7.776A pdb=" N GLY Y 129 " --> pdb=" O ASN Y 142 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN Y 142 " --> pdb=" O GLY Y 129 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL Y 131 " --> pdb=" O ASN Y 140 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 154 through 155 removed outlier: 6.061A pdb=" N GLU Y 176 " --> pdb=" O PHE Y 182 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE Y 182 " --> pdb=" O GLU Y 176 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 193 through 198 removed outlier: 7.103A pdb=" N THR Y 208 " --> pdb=" O HIS Y 194 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL Y 196 " --> pdb=" O ALA Y 206 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA Y 206 " --> pdb=" O VAL Y 196 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR Y 198 " --> pdb=" O LEU Y 204 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU Y 204 " --> pdb=" O TYR Y 198 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE Y 214 " --> pdb=" O VAL Y 227 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL Y 227 " --> pdb=" O ILE Y 214 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU Y 216 " --> pdb=" O THR Y 225 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 242 through 247 removed outlier: 3.525A pdb=" N GLY Y 244 " --> pdb=" O ALA Y 257 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR Y 262 " --> pdb=" O SER Y 258 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE Y 263 " --> pdb=" O THR Y 276 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR Y 276 " --> pdb=" O ILE Y 263 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE Y 265 " --> pdb=" O GLU Y 274 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 287 through 292 removed outlier: 3.724A pdb=" N GLY Y 289 " --> pdb=" O ILE Y 300 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU Y 297 " --> pdb=" O VAL Y 309 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN Y 318 " --> pdb=" O PHE Y 308 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN Y 310 " --> pdb=" O ILE Y 316 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE Y 316 " --> pdb=" O ASN Y 310 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 327 through 332 Processing sheet with id=AF4, first strand: chain 'Y' and resid 370 through 375 removed outlier: 3.706A pdb=" N GLY Y 372 " --> pdb=" O VAL Y 384 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS Y 389 " --> pdb=" O SER Y 385 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 414 through 419 removed outlier: 6.647A pdb=" N ALA Y 429 " --> pdb=" O LEU Y 415 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU Y 417 " --> pdb=" O VAL Y 427 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL Y 427 " --> pdb=" O LEU Y 417 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL Y 419 " --> pdb=" O ILE Y 425 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE Y 425 " --> pdb=" O VAL Y 419 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS Y 433 " --> pdb=" O CYS Y 430 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 451 through 456 removed outlier: 6.871A pdb=" N GLY Y 466 " --> pdb=" O SER Y 452 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL Y 454 " --> pdb=" O ALA Y 464 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA Y 464 " --> pdb=" O VAL Y 454 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU Y 456 " --> pdb=" O PHE Y 462 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE Y 462 " --> pdb=" O LEU Y 456 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS Y 471 " --> pdb=" O GLY Y 467 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS Y 476 " --> pdb=" O GLU Y 484 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU Y 484 " --> pdb=" O LYS Y 476 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 494 through 499 removed outlier: 3.746A pdb=" N SER Y 496 " --> pdb=" O THR Y 509 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU Y 525 " --> pdb=" O SER Y 519 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 539 through 544 Processing sheet with id=AF9, first strand: chain 'a' and resid 6 through 7 removed outlier: 6.940A pdb=" N LYS a 6 " --> pdb=" O ILE a 38 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N VAL a 40 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL a 40 " --> pdb=" O LYS a 30 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS a 30 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE a 127 " --> pdb=" O VAL a 92 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.044A pdb=" N LYS b 6 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N VAL b 40 " --> pdb=" O LYS b 6 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL b 40 " --> pdb=" O LYS b 30 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS b 30 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N PHE b 127 " --> pdb=" O ASN b 90 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL b 92 " --> pdb=" O PHE b 127 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL b 129 " --> pdb=" O VAL b 92 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE b 94 " --> pdb=" O VAL b 129 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA b 131 " --> pdb=" O PHE b 94 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLN b 96 " --> pdb=" O ALA b 131 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'c' and resid 6 through 7 removed outlier: 6.858A pdb=" N LYS c 6 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N VAL c 40 " --> pdb=" O LYS c 6 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE c 38 " --> pdb=" O ASP c 32 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP c 32 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL c 40 " --> pdb=" O LYS c 30 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS c 30 " --> pdb=" O VAL c 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE c 127 " --> pdb=" O VAL c 92 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'd' and resid 6 through 7 removed outlier: 6.881A pdb=" N LYS d 6 " --> pdb=" O ILE d 38 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N VAL d 40 " --> pdb=" O LYS d 6 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'd' and resid 68 through 74 removed outlier: 8.969A pdb=" N VAL d 129 " --> pdb=" O VAL d 92 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE d 94 " --> pdb=" O VAL d 129 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA d 131 " --> pdb=" O PHE d 94 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLN d 96 " --> pdb=" O ALA d 131 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.253A pdb=" N LYS e 6 " --> pdb=" O ILE e 38 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N VAL e 40 " --> pdb=" O LYS e 6 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL e 40 " --> pdb=" O LYS e 30 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS e 30 " --> pdb=" O VAL e 40 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE e 127 " --> pdb=" O VAL e 92 " (cutoff:3.500A) 1296 hydrogen bonds defined for protein. 3391 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: 6.45 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9708 1.34 - 1.46: 6485 1.46 - 1.58: 13905 1.58 - 1.70: 15 1.70 - 1.82: 276 Bond restraints: 30389 Sorted by residual: bond pdb=" C PRO Y 178 " pdb=" N PRO Y 179 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.35e+00 bond pdb=" C PRO X 178 " pdb=" N PRO X 179 " ideal model delta sigma weight residual 1.334 1.365 -0.032 2.34e-02 1.83e+03 1.82e+00 bond pdb=" C4 ADP B 400 " pdb=" C5 ADP B 400 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.28e+00 bond pdb=" C4 ADP E 400 " pdb=" C5 ADP E 400 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C4 ADP C 400 " pdb=" C5 ADP C 400 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.16e+00 ... (remaining 30384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 40763 2.05 - 4.11: 424 4.11 - 6.16: 65 6.16 - 8.21: 4 8.21 - 10.26: 3 Bond angle restraints: 41259 Sorted by residual: angle pdb=" N ILE D 66 " pdb=" CA ILE D 66 " pdb=" C ILE D 66 " ideal model delta sigma weight residual 111.91 108.55 3.36 8.90e-01 1.26e+00 1.43e+01 angle pdb=" CG1 ILE E 73 " pdb=" CB ILE E 73 " pdb=" CG2 ILE E 73 " ideal model delta sigma weight residual 110.70 100.44 10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CG1 ILE C 73 " pdb=" CB ILE C 73 " pdb=" CG2 ILE C 73 " ideal model delta sigma weight residual 110.70 101.97 8.73 3.00e+00 1.11e-01 8.47e+00 angle pdb=" N GLU A 119 " pdb=" CA GLU A 119 " pdb=" CB GLU A 119 " ideal model delta sigma weight residual 110.12 114.31 -4.19 1.47e+00 4.63e-01 8.12e+00 angle pdb=" CG1 ILE d 27 " pdb=" CB ILE d 27 " pdb=" CG2 ILE d 27 " ideal model delta sigma weight residual 110.70 102.29 8.41 3.00e+00 1.11e-01 7.86e+00 ... (remaining 41254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 17071 17.63 - 35.25: 972 35.25 - 52.88: 162 52.88 - 70.51: 50 70.51 - 88.14: 26 Dihedral angle restraints: 18281 sinusoidal: 7184 harmonic: 11097 Sorted by residual: dihedral pdb=" CA PHE X 362 " pdb=" C PHE X 362 " pdb=" N PRO X 363 " pdb=" CA PRO X 363 " ideal model delta harmonic sigma weight residual -180.00 -119.72 -60.28 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA PRO Y 178 " pdb=" C PRO Y 178 " pdb=" N PRO Y 179 " pdb=" CA PRO Y 179 " ideal model delta harmonic sigma weight residual -180.00 -133.67 -46.33 0 5.00e+00 4.00e-02 8.59e+01 dihedral pdb=" CA PRO X 178 " pdb=" C PRO X 178 " pdb=" N PRO X 179 " pdb=" CA PRO X 179 " ideal model delta harmonic sigma weight residual 180.00 -138.99 -41.01 0 5.00e+00 4.00e-02 6.73e+01 ... (remaining 18278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3411 0.047 - 0.095: 891 0.095 - 0.142: 329 0.142 - 0.189: 7 0.189 - 0.237: 4 Chirality restraints: 4642 Sorted by residual: chirality pdb=" CB ILE d 27 " pdb=" CA ILE d 27 " pdb=" CG1 ILE d 27 " pdb=" CG2 ILE d 27 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB ILE E 73 " pdb=" CA ILE E 73 " pdb=" CG1 ILE E 73 " pdb=" CG2 ILE E 73 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE D 73 " pdb=" CA ILE D 73 " pdb=" CG1 ILE D 73 " pdb=" CG2 ILE D 73 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 4639 not shown) Planarity restraints: 5298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE X 362 " 0.062 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO X 363 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO X 363 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO X 363 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO Y 178 " 0.058 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO Y 179 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO Y 179 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO Y 179 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO Y 178 " 0.010 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C PRO Y 178 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO Y 178 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO Y 179 " 0.011 2.00e-02 2.50e+03 ... (remaining 5295 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 13 2.58 - 3.16: 24576 3.16 - 3.74: 45517 3.74 - 4.32: 69144 4.32 - 4.90: 112955 Nonbonded interactions: 252205 Sorted by model distance: nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.004 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.008 2.170 nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.019 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.050 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.065 2.170 ... (remaining 252200 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 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 92 or resid 94 through 170 or resid 172 through 174 or resid 176 throu \ gh 401)) selection = (chain 'B' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 92 or resid 94 through 170 or resid 172 through 174 or resid 176 throu \ gh 401)) selection = (chain 'C' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 92 or resid 94 through 170 or resid 172 through 174 or resid 176 throu \ gh 401)) selection = (chain 'D' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 92 or resid 94 through 170 or resid 172 through 174 or resid 176 throu \ gh 401)) selection = (chain 'E' and (resid 8 through 53 or resid 55 through 58 or resid 60 or resid 6 \ 2 through 92 or resid 94 through 170 or resid 172 through 174 or resid 176 throu \ gh 401)) } ncs_group { reference = chain 'X' selection = chain 'Y' } ncs_group { reference = (chain 'a' and (resid 1 through 76 or resid 89 through 150)) selection = (chain 'b' and (resid 1 through 76 or resid 89 through 150)) selection = (chain 'c' and (resid 1 through 76 or resid 89 through 150)) selection = chain 'd' selection = (chain 'e' and (resid 1 through 76 or resid 89 through 150)) } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.210 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: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 30.680 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30389 Z= 0.117 Angle : 0.557 10.263 41259 Z= 0.287 Chirality : 0.047 0.237 4642 Planarity : 0.004 0.095 5298 Dihedral : 12.182 88.137 11163 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 0.06 % Allowed : 0.34 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3800 helix: 0.41 (0.16), residues: 1027 sheet: 0.20 (0.16), residues: 1060 loop : 0.42 (0.16), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 115 TYR 0.015 0.001 TYR Y 198 PHE 0.025 0.001 PHE X 362 TRP 0.019 0.002 TRP C 358 HIS 0.006 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (30389) covalent geometry : angle 0.55736 / 0.29 (41259) hydrogen bonds : bond 0.12331 / 8.37 ( 1286) hydrogen bonds : angle 6.39519 / 4.45 ( 3391) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8476 (mpt180) cc_final: 0.7238 (mmt180) REVERT: A 84 MET cc_start: 0.9195 (tpt) cc_final: 0.8929 (tpt) REVERT: C 49 MET cc_start: 0.6455 (mpp) cc_final: 0.6093 (ttt) REVERT: E 46 MET cc_start: 0.6710 (mmm) cc_final: 0.6269 (mpt) REVERT: a 147 MET cc_start: 0.8955 (mtt) cc_final: 0.8728 (mtm) REVERT: b 145 ASP cc_start: 0.9065 (m-30) cc_final: 0.8754 (m-30) REVERT: c 32 ASP cc_start: 0.8132 (t0) cc_final: 0.7682 (t0) REVERT: d 36 THR cc_start: 0.9111 (m) cc_final: 0.8895 (p) REVERT: d 52 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8259 (tm-30) REVERT: d 55 GLU cc_start: 0.7801 (pp20) cc_final: 0.7551 (pp20) REVERT: d 126 LEU cc_start: 0.8049 (mp) cc_final: 0.7478 (pt) REVERT: e 16 ASP cc_start: 0.8941 (m-30) cc_final: 0.8608 (p0) outliers start: 0 outliers final: 1 residues processed: 263 average time/residue: 0.7554 time to fit residues: 230.2406 Evaluate side-chains 189 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 31 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN X 433 HIS Y 603 ASN a 96 GLN a 128 GLN b 47 ASN d 22 HIS d 96 GLN d 128 GLN e 13 ASN e 19 HIS e 47 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.061807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.042124 restraints weight = 243584.247| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 4.50 r_work: 0.2580 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 30389 Z= 0.319 Angle : 0.643 8.391 41259 Z= 0.332 Chirality : 0.051 0.197 4642 Planarity : 0.005 0.087 5298 Dihedral : 6.107 81.287 4197 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 0.61 % Allowed : 4.83 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.41 (0.14), residues: 3800 helix: 0.57 (0.16), residues: 1033 sheet: 0.25 (0.16), residues: 1071 loop : 0.30 (0.16), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 115 TYR 0.026 0.002 TYR D 145 PHE 0.024 0.002 PHE b 29 TRP 0.015 0.002 TRP X 563 HIS 0.007 0.001 HIS d 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.32 (30389) covalent geometry : angle 0.64345 / 0.33 (41259) hydrogen bonds : bond 0.04770 / 3.21 ( 1286) hydrogen bonds : angle 5.23394 / 3.69 ( 3391) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8705 (mpt180) cc_final: 0.7336 (mmt180) REVERT: C 46 MET cc_start: 0.6493 (mpp) cc_final: 0.6251 (mpp) REVERT: C 49 MET cc_start: 0.6768 (mpp) cc_final: 0.5716 (ttt) REVERT: E 327 MET cc_start: 0.8963 (tpp) cc_final: 0.8751 (tpp) REVERT: a 147 MET cc_start: 0.8910 (mtt) cc_final: 0.8693 (mtm) REVERT: b 145 ASP cc_start: 0.9022 (m-30) cc_final: 0.8726 (m-30) REVERT: c 6 LYS cc_start: 0.8374 (mptt) cc_final: 0.8025 (mmtm) REVERT: c 8 ASP cc_start: 0.8329 (t70) cc_final: 0.8064 (t70) REVERT: c 32 ASP cc_start: 0.8155 (t0) cc_final: 0.7618 (t0) REVERT: d 126 LEU cc_start: 0.8184 (mp) cc_final: 0.7587 (pt) REVERT: e 138 ASP cc_start: 0.8155 (t0) cc_final: 0.7827 (t0) REVERT: e 149 ASN cc_start: 0.6962 (p0) cc_final: 0.6124 (p0) REVERT: e 150 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7063 (pm20) outliers start: 18 outliers final: 4 residues processed: 199 average time/residue: 0.7033 time to fit residues: 163.9522 Evaluate side-chains 192 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain d residue 89 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [74, 27, 188, 253, 288, 92, 6, 343, 100, 268, 49] chunk 74 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 253 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 343 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 140 ASN Y 6 GLN b 47 ASN d 22 HIS e 13 ASN e 47 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.063518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.043813 restraints weight = 245453.126| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 4.56 r_work: 0.2631 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30389 Z= 0.112 Angle : 0.532 8.124 41259 Z= 0.272 Chirality : 0.046 0.181 4642 Planarity : 0.004 0.079 5298 Dihedral : 5.768 74.898 4195 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 0.61 % Allowed : 5.07 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 (0.14), residues: 3800 helix: 0.86 (0.17), residues: 1033 sheet: 0.31 (0.16), residues: 1053 loop : 0.38 (0.16), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 41 TYR 0.013 0.001 TYR e 15 PHE 0.021 0.001 PHE d 94 TRP 0.012 0.001 TRP Y 563 HIS 0.003 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (30389) covalent geometry : angle 0.53210 / 0.27 (41259) hydrogen bonds : bond 0.03535 / 2.34 ( 1286) hydrogen bonds : angle 4.87414 / 3.44 ( 3391) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8712 (mpt180) cc_final: 0.7359 (mmt180) REVERT: B 357 MET cc_start: 0.9230 (mmm) cc_final: 0.8770 (mtp) REVERT: C 46 MET cc_start: 0.6657 (mpp) cc_final: 0.6432 (mpp) REVERT: C 49 MET cc_start: 0.6734 (mpp) cc_final: 0.5725 (ttt) REVERT: E 327 MET cc_start: 0.8935 (tpp) cc_final: 0.8730 (tpp) REVERT: X 126 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7578 (mp0) REVERT: a 147 MET cc_start: 0.8858 (mtt) cc_final: 0.8658 (mtm) REVERT: b 145 ASP cc_start: 0.9031 (m-30) cc_final: 0.8727 (m-30) REVERT: c 6 LYS cc_start: 0.8332 (mptt) cc_final: 0.7953 (mmtm) REVERT: c 8 ASP cc_start: 0.8342 (t70) cc_final: 0.8022 (t70) REVERT: c 32 ASP cc_start: 0.8172 (t0) cc_final: 0.7698 (t0) REVERT: c 138 ASP cc_start: 0.8603 (t0) cc_final: 0.8344 (t0) REVERT: d 36 THR cc_start: 0.8792 (m) cc_final: 0.8516 (p) REVERT: d 126 LEU cc_start: 0.8167 (mp) cc_final: 0.7574 (pt) REVERT: e 138 ASP cc_start: 0.8100 (t0) cc_final: 0.7779 (t0) REVERT: e 149 ASN cc_start: 0.6909 (p0) cc_final: 0.5945 (p0) REVERT: e 150 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7040 (pm20) outliers start: 17 outliers final: 5 residues processed: 203 average time/residue: 0.6999 time to fit residues: 166.5200 Evaluate side-chains 188 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 183 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain X residue 422 ASP Chi-restraints excluded: chain d residue 121 LEU Chi-restraints excluded: chain e residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [218, 372, 117, 298, 228, 21, 168, 325, 327, 355, 377] chunk 218 optimal weight: 9.9990 chunk 372 optimal weight: 0.0470 chunk 117 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 chunk 325 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 355 optimal weight: 20.0000 chunk 377 optimal weight: 9.9990 overall best weight: 2.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 47 ASN e 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.062637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.042855 restraints weight = 266561.883| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 4.68 r_work: 0.2590 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30389 Z= 0.183 Angle : 0.552 8.455 41259 Z= 0.282 Chirality : 0.048 0.190 4642 Planarity : 0.004 0.079 5298 Dihedral : 5.776 74.965 4195 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 0.55 % Allowed : 6.03 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 (0.14), residues: 3800 helix: 0.90 (0.17), residues: 1033 sheet: 0.27 (0.16), residues: 1073 loop : 0.39 (0.16), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 374 TYR 0.013 0.001 TYR D 145 PHE 0.031 0.001 PHE d 94 TRP 0.013 0.001 TRP C 342 HIS 0.004 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (30389) covalent geometry : angle 0.55207 / 0.28 (41259) hydrogen bonds : bond 0.03789 / 2.52 ( 1286) hydrogen bonds : angle 4.79994 / 3.40 ( 3391) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8725 (mpt180) cc_final: 0.7370 (mmt180) REVERT: B 357 MET cc_start: 0.9281 (mmm) cc_final: 0.8798 (mtp) REVERT: C 46 MET cc_start: 0.6751 (mpp) cc_final: 0.6510 (mpp) REVERT: C 49 MET cc_start: 0.6736 (mpp) cc_final: 0.5756 (ttt) REVERT: X 126 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7637 (mp0) REVERT: a 147 MET cc_start: 0.8883 (mtt) cc_final: 0.8665 (mtm) REVERT: b 145 ASP cc_start: 0.9048 (m-30) cc_final: 0.8756 (m-30) REVERT: c 6 LYS cc_start: 0.8386 (mptt) cc_final: 0.7997 (mmtm) REVERT: c 8 ASP cc_start: 0.8397 (t70) cc_final: 0.8071 (t70) REVERT: c 32 ASP cc_start: 0.8189 (t0) cc_final: 0.7715 (t0) REVERT: c 138 ASP cc_start: 0.8717 (t0) cc_final: 0.8397 (t70) REVERT: d 126 LEU cc_start: 0.8185 (mp) cc_final: 0.7599 (pt) REVERT: e 138 ASP cc_start: 0.8141 (t0) cc_final: 0.7825 (t0) outliers start: 15 outliers final: 6 residues processed: 194 average time/residue: 0.6832 time to fit residues: 155.9243 Evaluate side-chains 186 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 180 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain d residue 121 LEU Chi-restraints excluded: chain e residue 61 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [10, 366, 271, 132, 69, 210, 17, 376, 23, 288, 81] chunk 10 optimal weight: 2.9990 chunk 366 optimal weight: 20.0000 chunk 271 optimal weight: 0.0470 chunk 132 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 210 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 376 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 288 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 47 ASN ** d 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.063972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.044295 restraints weight = 245749.702| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 4.58 r_work: 0.2644 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30389 Z= 0.102 Angle : 0.513 8.386 41259 Z= 0.259 Chirality : 0.046 0.203 4642 Planarity : 0.004 0.075 5298 Dihedral : 5.517 70.558 4195 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 0.52 % Allowed : 6.76 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.72 (0.14), residues: 3800 helix: 1.04 (0.17), residues: 1033 sheet: 0.28 (0.16), residues: 1079 loop : 0.44 (0.16), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 374 TYR 0.011 0.001 TYR b 15 PHE 0.025 0.001 PHE d 94 TRP 0.012 0.001 TRP Y 563 HIS 0.003 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (30389) covalent geometry : angle 0.51262 / 0.26 (41259) hydrogen bonds : bond 0.03064 / 2.02 ( 1286) hydrogen bonds : angle 4.59885 / 3.26 ( 3391) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8694 (mpt180) cc_final: 0.7139 (tpt170) REVERT: B 357 MET cc_start: 0.9210 (mmm) cc_final: 0.8716 (mtp) REVERT: C 46 MET cc_start: 0.6715 (mpp) cc_final: 0.6463 (mpp) REVERT: C 49 MET cc_start: 0.6732 (mpp) cc_final: 0.5725 (ttt) REVERT: X 234 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8548 (mptt) REVERT: a 147 MET cc_start: 0.8840 (mtt) cc_final: 0.8634 (mtm) REVERT: b 145 ASP cc_start: 0.9027 (m-30) cc_final: 0.8733 (m-30) REVERT: c 6 LYS cc_start: 0.8367 (mptt) cc_final: 0.7993 (mmtm) REVERT: c 8 ASP cc_start: 0.8362 (t70) cc_final: 0.7998 (t70) REVERT: c 32 ASP cc_start: 0.8133 (t0) cc_final: 0.7675 (t0) REVERT: c 138 ASP cc_start: 0.8740 (t0) cc_final: 0.8348 (t70) REVERT: d 36 THR cc_start: 0.8972 (m) cc_final: 0.8586 (p) REVERT: d 126 LEU cc_start: 0.8172 (mp) cc_final: 0.7552 (pt) REVERT: e 138 ASP cc_start: 0.8124 (t0) cc_final: 0.7831 (t0) outliers start: 14 outliers final: 6 residues processed: 204 average time/residue: 0.6701 time to fit residues: 161.2323 Evaluate side-chains 190 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 184 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain a residue 138 ASP Chi-restraints excluded: chain d residue 121 LEU Chi-restraints excluded: chain e residue 61 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [27, 132, 267, 213, 68, 25, 50, 340, 1, 332, 288] chunk 27 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 267 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 340 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN b 47 ASN ** d 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.042819 restraints weight = 249712.823| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 4.57 r_work: 0.2594 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30389 Z= 0.203 Angle : 0.559 9.179 41259 Z= 0.284 Chirality : 0.048 0.190 4642 Planarity : 0.004 0.078 5298 Dihedral : 5.699 71.220 4195 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 0.52 % Allowed : 7.44 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.70 (0.14), residues: 3800 helix: 0.99 (0.17), residues: 1036 sheet: 0.29 (0.16), residues: 1087 loop : 0.44 (0.16), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 374 TYR 0.015 0.001 TYR D 145 PHE 0.042 0.001 PHE d 94 TRP 0.013 0.001 TRP C 342 HIS 0.004 0.001 HIS Y 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (30389) covalent geometry : angle 0.55944 / 0.28 (41259) hydrogen bonds : bond 0.03793 / 2.53 ( 1286) hydrogen bonds : angle 4.69513 / 3.33 ( 3391) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8697 (mpt180) cc_final: 0.7363 (mmt180) REVERT: B 357 MET cc_start: 0.9265 (mmm) cc_final: 0.8756 (mtp) REVERT: C 46 MET cc_start: 0.6795 (mpp) cc_final: 0.6538 (mpp) REVERT: C 49 MET cc_start: 0.6760 (mpp) cc_final: 0.5768 (ttp) REVERT: X 234 LYS cc_start: 0.9032 (mmmt) cc_final: 0.8584 (mptt) REVERT: b 145 ASP cc_start: 0.9026 (m-30) cc_final: 0.8742 (m-30) REVERT: c 6 LYS cc_start: 0.8403 (mptt) cc_final: 0.8056 (mptt) REVERT: c 8 ASP cc_start: 0.8435 (t70) cc_final: 0.8130 (t0) REVERT: c 32 ASP cc_start: 0.8121 (t0) cc_final: 0.7652 (t0) REVERT: c 36 THR cc_start: 0.9060 (p) cc_final: 0.8418 (t) REVERT: c 138 ASP cc_start: 0.8774 (t0) cc_final: 0.8372 (t70) REVERT: d 126 LEU cc_start: 0.8217 (mp) cc_final: 0.7622 (pt) REVERT: e 138 ASP cc_start: 0.8251 (t0) cc_final: 0.7970 (t0) outliers start: 14 outliers final: 5 residues processed: 195 average time/residue: 0.7148 time to fit residues: 163.3050 Evaluate side-chains 186 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 181 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 121 LEU Chi-restraints excluded: chain e residue 61 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [78, 91, 186, 197, 134, 174, 298, 143, 212, 81, 179] chunk 78 optimal weight: 0.0060 chunk 91 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 212 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 overall best weight: 3.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 ASN ** d 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.062440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.042835 restraints weight = 240721.468| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 4.50 r_work: 0.2602 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30389 Z= 0.191 Angle : 0.557 9.412 41259 Z= 0.282 Chirality : 0.048 0.185 4642 Planarity : 0.004 0.078 5298 Dihedral : 5.768 75.082 4195 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 0.55 % Allowed : 7.72 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.71 (0.14), residues: 3800 helix: 1.02 (0.17), residues: 1036 sheet: 0.30 (0.16), residues: 1073 loop : 0.42 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 374 TYR 0.013 0.001 TYR b 15 PHE 0.020 0.001 PHE d 94 TRP 0.012 0.001 TRP C 342 HIS 0.003 0.001 HIS Y 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (30389) covalent geometry : angle 0.55655 / 0.28 (41259) hydrogen bonds : bond 0.03700 / 2.47 ( 1286) hydrogen bonds : angle 4.68772 / 3.32 ( 3391) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 1.201 Fit side-chains REVERT: A 64 ARG cc_start: 0.8713 (mpt180) cc_final: 0.7363 (mmt180) REVERT: B 357 MET cc_start: 0.9269 (mmm) cc_final: 0.8755 (mtp) REVERT: C 46 MET cc_start: 0.6848 (mpp) cc_final: 0.6592 (mpp) REVERT: C 49 MET cc_start: 0.6771 (mpp) cc_final: 0.5780 (ttt) REVERT: X 234 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8590 (mptt) REVERT: b 145 ASP cc_start: 0.9014 (m-30) cc_final: 0.8724 (m-30) REVERT: c 6 LYS cc_start: 0.8424 (mptt) cc_final: 0.8136 (mptt) REVERT: c 8 ASP cc_start: 0.8461 (t70) cc_final: 0.8109 (t70) REVERT: c 32 ASP cc_start: 0.8095 (t0) cc_final: 0.7628 (t0) REVERT: c 138 ASP cc_start: 0.8803 (t0) cc_final: 0.8419 (t70) REVERT: d 126 LEU cc_start: 0.8219 (mp) cc_final: 0.7625 (pt) REVERT: e 138 ASP cc_start: 0.8273 (t0) cc_final: 0.7981 (t0) outliers start: 15 outliers final: 6 residues processed: 198 average time/residue: 0.7104 time to fit residues: 164.5893 Evaluate side-chains 188 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain e residue 61 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [11, 269, 80, 193, 120, 280, 137, 37, 126, 360, 158] chunk 11 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 280 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 360 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 ASN ** d 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.062929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.043267 restraints weight = 253732.574| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 4.60 r_work: 0.2615 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30389 Z= 0.143 Angle : 0.538 10.819 41259 Z= 0.271 Chirality : 0.047 0.239 4642 Planarity : 0.004 0.077 5298 Dihedral : 5.669 72.061 4195 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 0.46 % Allowed : 8.02 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.76 (0.14), residues: 3800 helix: 1.11 (0.17), residues: 1036 sheet: 0.32 (0.16), residues: 1073 loop : 0.43 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 374 TYR 0.013 0.001 TYR b 15 PHE 0.033 0.001 PHE d 94 TRP 0.012 0.001 TRP C 342 HIS 0.008 0.001 HIS d 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (30389) covalent geometry : angle 0.53752 / 0.27 (41259) hydrogen bonds : bond 0.03413 / 2.26 ( 1286) hydrogen bonds : angle 4.59859 / 3.26 ( 3391) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 1.131 Fit side-chains REVERT: A 64 ARG cc_start: 0.8695 (mpt180) cc_final: 0.7363 (mmt180) REVERT: B 357 MET cc_start: 0.9252 (mmm) cc_final: 0.8737 (mtp) REVERT: C 46 MET cc_start: 0.6861 (mpp) cc_final: 0.6598 (mpp) REVERT: C 49 MET cc_start: 0.6756 (mpp) cc_final: 0.5843 (ttt) REVERT: X 234 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8586 (mptt) REVERT: b 145 ASP cc_start: 0.9011 (m-30) cc_final: 0.8724 (m-30) REVERT: c 6 LYS cc_start: 0.8437 (mptt) cc_final: 0.8143 (mptt) REVERT: c 8 ASP cc_start: 0.8452 (t70) cc_final: 0.8091 (t70) REVERT: c 32 ASP cc_start: 0.8105 (t0) cc_final: 0.7656 (t0) REVERT: c 138 ASP cc_start: 0.8809 (t0) cc_final: 0.8421 (t70) REVERT: d 126 LEU cc_start: 0.8189 (mp) cc_final: 0.7583 (pt) REVERT: d 147 MET cc_start: 0.8429 (ptm) cc_final: 0.8204 (mmt) REVERT: e 138 ASP cc_start: 0.8286 (t0) cc_final: 0.7992 (t0) outliers start: 12 outliers final: 6 residues processed: 195 average time/residue: 0.6914 time to fit residues: 157.8417 Evaluate side-chains 187 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain a residue 138 ASP Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain e residue 61 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [216, 25, 100, 213, 296, 31, 50, 66, 355, 250, 238] chunk 216 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 355 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.042690 restraints weight = 290199.742| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 5.02 r_work: 0.2577 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30389 Z= 0.190 Angle : 0.562 11.856 41259 Z= 0.283 Chirality : 0.048 0.297 4642 Planarity : 0.004 0.077 5298 Dihedral : 5.746 74.129 4195 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 0.40 % Allowed : 8.15 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.72 (0.14), residues: 3800 helix: 1.06 (0.17), residues: 1036 sheet: 0.32 (0.16), residues: 1073 loop : 0.41 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 374 TYR 0.014 0.001 TYR b 15 PHE 0.018 0.001 PHE b 29 TRP 0.013 0.001 TRP C 342 HIS 0.003 0.001 HIS Y 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (30389) covalent geometry : angle 0.56198 / 0.28 (41259) hydrogen bonds : bond 0.03699 / 2.46 ( 1286) hydrogen bonds : angle 4.66344 / 3.31 ( 3391) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 1.249 Fit side-chains REVERT: A 64 ARG cc_start: 0.8739 (mpt180) cc_final: 0.7378 (mmt180) REVERT: C 46 MET cc_start: 0.6925 (mpp) cc_final: 0.6665 (mpp) REVERT: C 49 MET cc_start: 0.6835 (mpp) cc_final: 0.5863 (ttt) REVERT: E 49 MET cc_start: 0.7579 (pmm) cc_final: 0.7217 (ttt) REVERT: X 234 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8589 (mptt) REVERT: b 145 ASP cc_start: 0.9010 (m-30) cc_final: 0.8730 (m-30) REVERT: c 6 LYS cc_start: 0.8468 (mptt) cc_final: 0.8171 (mptt) REVERT: c 8 ASP cc_start: 0.8457 (t70) cc_final: 0.8154 (t0) REVERT: c 32 ASP cc_start: 0.8116 (t0) cc_final: 0.7661 (t0) REVERT: c 138 ASP cc_start: 0.8822 (t0) cc_final: 0.8427 (t70) REVERT: d 126 LEU cc_start: 0.8241 (mp) cc_final: 0.7661 (pt) outliers start: 10 outliers final: 4 residues processed: 193 average time/residue: 0.7024 time to fit residues: 159.1010 Evaluate side-chains 183 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain e residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [10, 179, 5, 187, 319, 142, 77, 366, 8, 302, 134] chunk 10 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 187 optimal weight: 9.9990 chunk 319 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 366 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 302 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.063406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.043794 restraints weight = 243230.770| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 4.54 r_work: 0.2633 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30389 Z= 0.112 Angle : 0.529 12.250 41259 Z= 0.266 Chirality : 0.046 0.207 4642 Planarity : 0.004 0.075 5298 Dihedral : 5.557 71.755 4195 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Rotamer: Outliers : 0.28 % Allowed : 8.39 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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 (0.14), residues: 3800 helix: 1.20 (0.17), residues: 1036 sheet: 0.36 (0.16), residues: 1071 loop : 0.44 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 374 TYR 0.012 0.001 TYR b 15 PHE 0.014 0.001 PHE a 29 TRP 0.012 0.001 TRP Y 563 HIS 0.002 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (30389) covalent geometry : angle 0.52896 / 0.27 (41259) hydrogen bonds : bond 0.03177 / 2.10 ( 1286) hydrogen bonds : angle 4.52666 / 3.21 ( 3391) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 1.061 Fit side-chains REVERT: A 64 ARG cc_start: 0.8685 (mpt180) cc_final: 0.7369 (mmt180) REVERT: B 357 MET cc_start: 0.9138 (mmm) cc_final: 0.8510 (mtm) REVERT: C 46 MET cc_start: 0.6879 (mpp) cc_final: 0.6614 (mpp) REVERT: C 49 MET cc_start: 0.6770 (mpp) cc_final: 0.5832 (ttt) REVERT: E 49 MET cc_start: 0.7486 (pmm) cc_final: 0.7189 (ttt) REVERT: X 234 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8590 (mptt) REVERT: b 145 ASP cc_start: 0.9006 (m-30) cc_final: 0.8723 (m-30) REVERT: c 6 LYS cc_start: 0.8457 (mptt) cc_final: 0.8158 (mptt) REVERT: c 8 ASP cc_start: 0.8431 (t70) cc_final: 0.8053 (t70) REVERT: c 32 ASP cc_start: 0.8099 (t0) cc_final: 0.7659 (t0) REVERT: c 138 ASP cc_start: 0.8795 (t0) cc_final: 0.8391 (t70) REVERT: d 123 LEU cc_start: 0.6516 (pp) cc_final: 0.6070 (pp) REVERT: d 126 LEU cc_start: 0.8202 (mp) cc_final: 0.7629 (pt) REVERT: e 138 ASP cc_start: 0.8176 (t0) cc_final: 0.7861 (t0) REVERT: e 150 GLN cc_start: 0.7798 (tm-30) cc_final: 0.6608 (mp10) outliers start: 6 outliers final: 6 residues processed: 192 average time/residue: 0.7035 time to fit residues: 158.7085 Evaluate side-chains 191 residues out of total 3215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 185 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain a residue 138 ASP Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain d residue 121 LEU Chi-restraints excluded: chain e residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: [24, 291, 178, 129, 217, 282, 74, 6, 352, 342, 122] chunk 24 optimal weight: 3.9990 chunk 291 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 chunk 282 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 352 optimal weight: 0.7980 chunk 342 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.063546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.043882 restraints weight = 266567.040| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 4.88 r_work: 0.2614 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30389 Z= 0.117 Angle : 0.533 13.043 41259 Z= 0.265 Chirality : 0.046 0.202 4642 Planarity : 0.004 0.075 5298 Dihedral : 5.455 72.532 4195 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 0.37 % Allowed : 8.39 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: 0.86 (0.14), residues: 3800 helix: 1.24 (0.17), residues: 1033 sheet: 0.40 (0.16), residues: 1071 loop : 0.45 (0.16), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 374 TYR 0.011 0.001 TYR b 15 PHE 0.014 0.001 PHE a 29 TRP 0.011 0.001 TRP C 342 HIS 0.003 0.001 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (30389) covalent geometry : angle 0.53262 / 0.27 (41259) hydrogen bonds : bond 0.03128 / 2.07 ( 1286) hydrogen bonds : angle 4.48458 / 3.18 ( 3391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10352.34 seconds wall clock time: 176 minutes 56.08 seconds (10616.08 seconds total)