Starting phenix.real_space_refine on Sat Aug 8 06:53:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21rs_67950/08_2026/21rs_67950.cif Found real_map, /net/cci-nas-00/data/ceres_data/21rs_67950/08_2026/21rs_67950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21rs_67950/08_2026/21rs_67950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21rs_67950/08_2026/21rs_67950.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21rs_67950/08_2026/21rs_67950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21rs_67950/08_2026/21rs_67950.map" } resolution = 2.76 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= 0.002 sd= 0.021 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 18 5.49 5 Mg 12 5.21 5 S 144 5.16 5 C 16338 2.51 5 N 4290 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25740 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4237 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 499} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 2, 'GMP%rna2p': 1, 'T8T': 1} Classifications: {'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 4.17, per 1000 atoms: 0.16 Number of scatterers: 25740 At special positions: 0 Unit cell: (144.2, 138.432, 104.648, 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 144 16.00 P 18 15.00 Mg 12 11.99 O 4938 8.00 N 4290 7.00 C 16338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 876.1 milliseconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 12 sheets defined 64.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 127 through 139 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 168 through 179 removed outlier: 4.485A pdb=" N ASN A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 4.134A pdb=" N LYS A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 231 removed outlier: 4.012A pdb=" N SER A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.545A pdb=" N THR A 275 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.763A pdb=" N SER A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 350 through 365 Processing helix chain 'A' and resid 366 through 370 Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 371 through 376 removed outlier: 4.340A pdb=" N LEU A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 385 through 402 Processing helix chain 'A' and resid 403 through 417 Processing helix chain 'A' and resid 422 through 433 Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.527A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 461 removed outlier: 3.517A pdb=" N LEU A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 removed outlier: 3.631A pdb=" N TYR A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 510 through 520 Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 168 Processing helix chain 'B' and resid 168 through 179 removed outlier: 4.485A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 4.134A pdb=" N LYS B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 231 removed outlier: 4.011A pdb=" N SER B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 265 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.545A pdb=" N THR B 275 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.764A pdb=" N SER B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 365 Processing helix chain 'B' and resid 366 through 370 Proline residue: B 370 - end of helix Processing helix chain 'B' and resid 371 through 376 removed outlier: 4.340A pdb=" N LEU B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 385 through 402 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 434 through 444 removed outlier: 3.527A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 461 removed outlier: 3.516A pdb=" N LEU B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 470 removed outlier: 3.631A pdb=" N TYR B 470 " --> pdb=" O ASP B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 510 through 520 Processing helix chain 'C' and resid 6 through 17 Processing helix chain 'C' and resid 40 through 50 Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 168 Processing helix chain 'C' and resid 168 through 179 removed outlier: 4.485A pdb=" N ASN C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 199 removed outlier: 4.134A pdb=" N LYS C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 231 removed outlier: 4.011A pdb=" N SER C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 265 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.545A pdb=" N THR C 275 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.764A pdb=" N SER C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 311 through 329 Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 350 through 365 Processing helix chain 'C' and resid 366 through 370 Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 371 through 376 removed outlier: 4.340A pdb=" N LEU C 375 " --> pdb=" O TYR C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 385 through 402 Processing helix chain 'C' and resid 403 through 417 Processing helix chain 'C' and resid 422 through 433 Processing helix chain 'C' and resid 434 through 444 removed outlier: 3.527A pdb=" N SER C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 461 removed outlier: 3.517A pdb=" N LEU C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 470 removed outlier: 3.631A pdb=" N TYR C 470 " --> pdb=" O ASP C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'C' and resid 510 through 520 Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 127 through 139 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 168 through 179 removed outlier: 4.485A pdb=" N ASN D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 199 removed outlier: 4.133A pdb=" N LYS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.011A pdb=" N SER D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.545A pdb=" N THR D 275 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.764A pdb=" N SER D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 311 through 329 Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 347 through 349 No H-bonds generated for 'chain 'D' and resid 347 through 349' Processing helix chain 'D' and resid 350 through 365 Processing helix chain 'D' and resid 366 through 370 Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 371 through 376 removed outlier: 4.340A pdb=" N LEU D 375 " --> pdb=" O TYR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 379 No H-bonds generated for 'chain 'D' and resid 377 through 379' Processing helix chain 'D' and resid 385 through 402 Processing helix chain 'D' and resid 403 through 417 Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 434 through 444 removed outlier: 3.527A pdb=" N SER D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 461 removed outlier: 3.516A pdb=" N LEU D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 470 removed outlier: 3.632A pdb=" N TYR D 470 " --> pdb=" O ASP D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'D' and resid 510 through 520 Processing helix chain 'E' and resid 6 through 17 Processing helix chain 'E' and resid 40 through 50 Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 101 through 105 Processing helix chain 'E' and resid 127 through 139 Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 161 through 168 Processing helix chain 'E' and resid 168 through 179 removed outlier: 4.485A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 199 removed outlier: 4.134A pdb=" N LYS E 199 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 231 removed outlier: 4.012A pdb=" N SER E 214 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA E 223 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 265 Processing helix chain 'E' and resid 271 through 275 removed outlier: 3.545A pdb=" N THR E 275 " --> pdb=" O LEU E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.764A pdb=" N SER E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 309 Processing helix chain 'E' and resid 311 through 329 Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 350 through 365 Processing helix chain 'E' and resid 366 through 370 Proline residue: E 370 - end of helix Processing helix chain 'E' and resid 371 through 376 removed outlier: 4.339A pdb=" N LEU E 375 " --> pdb=" O TYR E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 379 No H-bonds generated for 'chain 'E' and resid 377 through 379' Processing helix chain 'E' and resid 385 through 402 Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 434 through 444 removed outlier: 3.527A pdb=" N SER E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 461 removed outlier: 3.517A pdb=" N LEU E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 470 removed outlier: 3.632A pdb=" N TYR E 470 " --> pdb=" O ASP E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 480 Processing helix chain 'E' and resid 490 through 498 Processing helix chain 'E' and resid 510 through 520 Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 81 through 95 Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 127 through 139 Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 161 through 168 Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.485A pdb=" N ASN F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 199 removed outlier: 4.133A pdb=" N LYS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 231 removed outlier: 4.011A pdb=" N SER F 214 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 265 Processing helix chain 'F' and resid 271 through 275 removed outlier: 3.545A pdb=" N THR F 275 " --> pdb=" O LEU F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.764A pdb=" N SER F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 311 through 329 Processing helix chain 'F' and resid 333 through 343 Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'F' and resid 350 through 365 Processing helix chain 'F' and resid 366 through 370 Proline residue: F 370 - end of helix Processing helix chain 'F' and resid 371 through 376 removed outlier: 4.340A pdb=" N LEU F 375 " --> pdb=" O TYR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 379 No H-bonds generated for 'chain 'F' and resid 377 through 379' Processing helix chain 'F' and resid 385 through 402 Processing helix chain 'F' and resid 403 through 417 Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 434 through 444 removed outlier: 3.528A pdb=" N SER F 444 " --> pdb=" O LEU F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 461 removed outlier: 3.517A pdb=" N LEU F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 470 removed outlier: 3.631A pdb=" N TYR F 470 " --> pdb=" O ASP F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 480 Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'F' and resid 510 through 520 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 237 Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 237 Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 68 Processing sheet with id=AA6, first strand: chain 'C' and resid 235 through 237 Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 68 Processing sheet with id=AA8, first strand: chain 'D' and resid 235 through 237 Processing sheet with id=AA9, first strand: chain 'E' and resid 62 through 68 Processing sheet with id=AB1, first strand: chain 'E' and resid 235 through 237 Processing sheet with id=AB2, first strand: chain 'F' and resid 62 through 68 Processing sheet with id=AB3, first strand: chain 'F' and resid 235 through 237 1321 hydrogen bonds defined for protein. 3801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 11051 1.39 - 1.56: 15085 1.56 - 1.74: 24 1.74 - 1.91: 192 1.91 - 2.08: 6 Bond restraints: 26358 Sorted by residual: bond pdb=" O3B T8T E 601 " pdb=" PG T8T E 601 " ideal model delta sigma weight residual 1.778 1.604 0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" O3B T8T C 601 " pdb=" PG T8T C 601 " ideal model delta sigma weight residual 1.778 1.604 0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" O3B T8T A 601 " pdb=" PG T8T A 601 " ideal model delta sigma weight residual 1.778 1.605 0.173 2.00e-02 2.50e+03 7.50e+01 bond pdb=" O3B T8T B 601 " pdb=" PG T8T B 601 " ideal model delta sigma weight residual 1.778 1.605 0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" O3B T8T F 601 " pdb=" PG T8T F 601 " ideal model delta sigma weight residual 1.778 1.605 0.173 2.00e-02 2.50e+03 7.48e+01 ... (remaining 26353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 35342 1.77 - 3.54: 278 3.54 - 5.32: 84 5.32 - 7.09: 32 7.09 - 8.86: 12 Bond angle restraints: 35748 Sorted by residual: angle pdb=" PB T8T E 601 " pdb=" O3B T8T E 601 " pdb=" PG T8T E 601 " ideal model delta sigma weight residual 123.53 132.39 -8.86 3.00e+00 1.11e-01 8.72e+00 angle pdb=" PB T8T C 601 " pdb=" O3B T8T C 601 " pdb=" PG T8T C 601 " ideal model delta sigma weight residual 123.53 132.39 -8.86 3.00e+00 1.11e-01 8.72e+00 angle pdb=" PB T8T B 601 " pdb=" O3B T8T B 601 " pdb=" PG T8T B 601 " ideal model delta sigma weight residual 123.53 132.36 -8.83 3.00e+00 1.11e-01 8.66e+00 angle pdb=" PB T8T A 601 " pdb=" O3B T8T A 601 " pdb=" PG T8T A 601 " ideal model delta sigma weight residual 123.53 132.35 -8.82 3.00e+00 1.11e-01 8.65e+00 angle pdb=" PB T8T D 601 " pdb=" O3B T8T D 601 " pdb=" PG T8T D 601 " ideal model delta sigma weight residual 123.53 132.35 -8.82 3.00e+00 1.11e-01 8.65e+00 ... (remaining 35743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.23: 14772 28.23 - 56.45: 1044 56.45 - 84.68: 102 84.68 - 112.90: 6 112.90 - 141.13: 18 Dihedral angle restraints: 15942 sinusoidal: 6708 harmonic: 9234 Sorted by residual: dihedral pdb=" O2A T8T E 601 " pdb=" O3A T8T E 601 " pdb=" PA T8T E 601 " pdb=" PB T8T E 601 " ideal model delta sinusoidal sigma weight residual -63.32 77.81 -141.13 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O2A T8T C 601 " pdb=" O3A T8T C 601 " pdb=" PA T8T C 601 " pdb=" PB T8T C 601 " ideal model delta sinusoidal sigma weight residual -63.32 77.80 -141.12 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O2A T8T A 601 " pdb=" O3A T8T A 601 " pdb=" PA T8T A 601 " pdb=" PB T8T A 601 " ideal model delta sinusoidal sigma weight residual -63.32 77.77 -141.09 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 15939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2382 0.026 - 0.053: 845 0.053 - 0.079: 418 0.079 - 0.105: 113 0.105 - 0.132: 82 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE F 79 " pdb=" N ILE F 79 " pdb=" C ILE F 79 " pdb=" CB ILE F 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE E 79 " pdb=" N ILE E 79 " pdb=" C ILE E 79 " pdb=" CB ILE E 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 3837 not shown) Planarity restraints: 4548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 40 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.49e+00 pdb=" N PRO D 41 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 41 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 41 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 40 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 41 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 40 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO B 41 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " 0.017 5.00e-02 4.00e+02 ... (remaining 4545 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 72 2.42 - 3.04: 15860 3.04 - 3.66: 39364 3.66 - 4.28: 60552 4.28 - 4.90: 101511 Nonbonded interactions: 217359 Sorted by model distance: nonbonded pdb=" O3A T8T F 601 " pdb="MG MG F 602 " model vdw 1.801 2.170 nonbonded pdb=" O3A T8T A 601 " pdb="MG MG A 602 " model vdw 1.802 2.170 nonbonded pdb=" O3A T8T E 601 " pdb="MG MG E 602 " model vdw 1.802 2.170 nonbonded pdb=" O3A T8T C 601 " pdb="MG MG C 602 " model vdw 1.802 2.170 nonbonded pdb=" O3A T8T B 601 " pdb="MG MG B 602 " model vdw 1.802 2.170 ... (remaining 217354 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.530 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 26358 Z= 0.214 Angle : 0.497 8.858 35748 Z= 0.231 Chirality : 0.037 0.132 3840 Planarity : 0.003 0.031 4548 Dihedral : 18.939 141.125 10002 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.84 % Allowed : 24.79 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.15), residues: 3090 helix: 1.51 (0.12), residues: 1776 sheet: 0.30 (0.42), residues: 210 loop : -0.03 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 54 TYR 0.016 0.001 TYR F 11 PHE 0.005 0.001 PHE D 318 TRP 0.005 0.001 TRP B 471 HIS 0.003 0.000 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (26358) covalent geometry : angle 0.49666 / 0.23 (35748) hydrogen bonds : bond 0.17816 / 11.76 ( 1321) hydrogen bonds : angle 5.94372 / 4.16 ( 3801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.160 Fit side-chains REVERT: A 70 TYR cc_start: 0.8726 (p90) cc_final: 0.8454 (p90) REVERT: A 328 GLN cc_start: 0.8779 (pt0) cc_final: 0.8541 (tm-30) REVERT: A 355 TYR cc_start: 0.8952 (t80) cc_final: 0.8741 (t80) REVERT: A 380 TYR cc_start: 0.7168 (t80) cc_final: 0.6815 (t80) REVERT: A 420 ASP cc_start: 0.9073 (m-30) cc_final: 0.8502 (m-30) REVERT: B 23 GLN cc_start: 0.9254 (mt0) cc_final: 0.8907 (mt0) REVERT: B 70 TYR cc_start: 0.8760 (p90) cc_final: 0.8517 (p90) REVERT: B 306 ASP cc_start: 0.9225 (t0) cc_final: 0.8946 (m-30) REVERT: B 380 TYR cc_start: 0.7077 (t80) cc_final: 0.6611 (t80) REVERT: B 400 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8337 (mm-30) REVERT: C 380 TYR cc_start: 0.7363 (t80) cc_final: 0.6997 (t80) REVERT: C 400 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8380 (mm-30) REVERT: D 70 TYR cc_start: 0.8733 (p90) cc_final: 0.8480 (p90) REVERT: D 328 GLN cc_start: 0.8761 (pt0) cc_final: 0.8518 (tm-30) REVERT: D 380 TYR cc_start: 0.7278 (t80) cc_final: 0.6722 (t80) REVERT: E 380 TYR cc_start: 0.7380 (t80) cc_final: 0.6819 (t80) REVERT: E 400 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8345 (mm-30) REVERT: F 23 GLN cc_start: 0.9230 (mt0) cc_final: 0.8872 (mt0) REVERT: F 70 TYR cc_start: 0.8773 (p90) cc_final: 0.8550 (p90) REVERT: F 380 TYR cc_start: 0.7181 (t80) cc_final: 0.6674 (t80) REVERT: F 400 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8303 (mm-30) outliers start: 24 outliers final: 10 residues processed: 219 average time/residue: 0.6212 time to fit residues: 157.7484 Evaluate side-chains 202 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 308 ASN A 517 HIS B 201 ASN B 308 ASN B 517 HIS C 201 ASN C 308 ASN C 517 HIS D 201 ASN D 308 ASN D 517 HIS E 201 ASN E 308 ASN E 517 HIS F 201 ASN F 308 ASN F 517 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.061709 restraints weight = 47700.170| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.92 r_work: 0.2632 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26358 Z= 0.111 Angle : 0.427 5.009 35748 Z= 0.229 Chirality : 0.038 0.126 3840 Planarity : 0.003 0.032 4548 Dihedral : 11.728 119.544 3794 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.39 % Allowed : 23.98 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.15), residues: 3090 helix: 2.03 (0.12), residues: 1770 sheet: 0.33 (0.42), residues: 210 loop : 0.20 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 54 TYR 0.010 0.001 TYR B 475 PHE 0.006 0.001 PHE D 318 TRP 0.004 0.001 TRP C 187 HIS 0.003 0.000 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (26358) covalent geometry : angle 0.42743 / 0.23 (35748) hydrogen bonds : bond 0.04326 / 2.85 ( 1321) hydrogen bonds : angle 4.52653 / 3.16 ( 3801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 1.001 Fit side-chains REVERT: A 70 TYR cc_start: 0.8674 (p90) cc_final: 0.8345 (p90) REVERT: A 328 GLN cc_start: 0.8787 (pt0) cc_final: 0.8536 (tm-30) REVERT: A 380 TYR cc_start: 0.7190 (t80) cc_final: 0.6835 (t80) REVERT: A 420 ASP cc_start: 0.9083 (m-30) cc_final: 0.8532 (m-30) REVERT: B 70 TYR cc_start: 0.8759 (p90) cc_final: 0.8442 (p90) REVERT: B 328 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8538 (tm-30) REVERT: B 380 TYR cc_start: 0.7112 (t80) cc_final: 0.6636 (t80) REVERT: B 400 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8380 (mm-30) REVERT: C 70 TYR cc_start: 0.8682 (p90) cc_final: 0.8419 (p90) REVERT: C 283 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8583 (p) REVERT: C 328 GLN cc_start: 0.8780 (pt0) cc_final: 0.8496 (tm-30) REVERT: C 380 TYR cc_start: 0.7376 (t80) cc_final: 0.7014 (t80) REVERT: C 400 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8432 (mm-30) REVERT: C 517 HIS cc_start: 0.7774 (m-70) cc_final: 0.7558 (m170) REVERT: D 70 TYR cc_start: 0.8694 (p90) cc_final: 0.8381 (p90) REVERT: D 328 GLN cc_start: 0.8765 (pt0) cc_final: 0.8496 (tm-30) REVERT: D 380 TYR cc_start: 0.7315 (t80) cc_final: 0.6981 (t80) REVERT: E 283 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8593 (p) REVERT: E 328 GLN cc_start: 0.8753 (pt0) cc_final: 0.8493 (tm-30) REVERT: E 380 TYR cc_start: 0.7401 (t80) cc_final: 0.7063 (t80) REVERT: E 400 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8390 (mm-30) REVERT: F 23 GLN cc_start: 0.9272 (mt0) cc_final: 0.8867 (mt0) REVERT: F 70 TYR cc_start: 0.8784 (p90) cc_final: 0.8483 (p90) REVERT: F 328 GLN cc_start: 0.8730 (pt0) cc_final: 0.8523 (tm-30) REVERT: F 380 TYR cc_start: 0.7184 (t80) cc_final: 0.6682 (t80) REVERT: F 400 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8294 (mm-30) outliers start: 68 outliers final: 13 residues processed: 280 average time/residue: 0.5539 time to fit residues: 181.3070 Evaluate side-chains 226 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 287 ASN Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 256 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 182 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 217 optimal weight: 0.0020 chunk 174 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 HIS ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS D 517 HIS E 517 HIS F 517 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.079087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.062273 restraints weight = 47604.803| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.94 r_work: 0.2631 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26358 Z= 0.090 Angle : 0.406 4.754 35748 Z= 0.215 Chirality : 0.038 0.132 3840 Planarity : 0.003 0.031 4548 Dihedral : 10.184 108.044 3782 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.64 % Allowed : 23.80 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.16), residues: 3090 helix: 2.10 (0.12), residues: 1776 sheet: 0.35 (0.42), residues: 210 loop : 0.21 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 54 TYR 0.010 0.001 TYR D 65 PHE 0.007 0.001 PHE D 318 TRP 0.005 0.001 TRP C 187 HIS 0.003 0.000 HIS E 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (26358) covalent geometry : angle 0.40638 / 0.21 (35748) hydrogen bonds : bond 0.03569 / 2.35 ( 1321) hydrogen bonds : angle 4.16346 / 2.91 ( 3801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 229 time to evaluate : 0.825 Fit side-chains REVERT: A 70 TYR cc_start: 0.8644 (p90) cc_final: 0.8422 (p90) REVERT: A 328 GLN cc_start: 0.8730 (pt0) cc_final: 0.8508 (tm-30) REVERT: A 380 TYR cc_start: 0.7164 (t80) cc_final: 0.6814 (t80) REVERT: B 70 TYR cc_start: 0.8710 (p90) cc_final: 0.8509 (p90) REVERT: B 380 TYR cc_start: 0.7081 (t80) cc_final: 0.6589 (t80) REVERT: C 283 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8576 (p) REVERT: C 328 GLN cc_start: 0.8725 (pt0) cc_final: 0.8501 (tm-30) REVERT: C 380 TYR cc_start: 0.7347 (t80) cc_final: 0.6986 (t80) REVERT: C 400 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8396 (mm-30) REVERT: D 70 TYR cc_start: 0.8647 (p90) cc_final: 0.8419 (p90) REVERT: D 328 GLN cc_start: 0.8719 (pt0) cc_final: 0.8502 (tm-30) REVERT: D 380 TYR cc_start: 0.7312 (t80) cc_final: 0.6965 (t80) REVERT: E 283 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8588 (p) REVERT: E 380 TYR cc_start: 0.7390 (t80) cc_final: 0.7031 (t80) REVERT: E 400 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8381 (mm-30) REVERT: F 11 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8520 (t80) REVERT: F 380 TYR cc_start: 0.7166 (t80) cc_final: 0.6665 (t80) REVERT: F 400 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8301 (mm-30) outliers start: 75 outliers final: 18 residues processed: 294 average time/residue: 0.5976 time to fit residues: 204.6902 Evaluate side-chains 230 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 283 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 295 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 117 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 159 optimal weight: 0.4980 chunk 150 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 HIS B 517 HIS C 517 HIS D 23 GLN D 517 HIS E 517 HIS F 517 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.079244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.062595 restraints weight = 47387.016| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.92 r_work: 0.2630 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26358 Z= 0.087 Angle : 0.409 4.896 35748 Z= 0.216 Chirality : 0.038 0.132 3840 Planarity : 0.003 0.032 4548 Dihedral : 9.201 99.136 3774 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.20 % Allowed : 23.56 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.16), residues: 3090 helix: 2.17 (0.12), residues: 1776 sheet: 0.33 (0.41), residues: 210 loop : 0.23 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 54 TYR 0.010 0.001 TYR D 65 PHE 0.009 0.001 PHE D 432 TRP 0.005 0.001 TRP E 187 HIS 0.003 0.000 HIS E 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (26358) covalent geometry : angle 0.40941 / 0.22 (35748) hydrogen bonds : bond 0.03291 / 2.15 ( 1321) hydrogen bonds : angle 4.03590 / 2.82 ( 3801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 217 time to evaluate : 0.932 Fit side-chains REVERT: A 70 TYR cc_start: 0.8676 (p90) cc_final: 0.8468 (p90) REVERT: A 380 TYR cc_start: 0.7131 (t80) cc_final: 0.6770 (t80) REVERT: A 490 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8455 (mmtp) REVERT: B 135 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: B 380 TYR cc_start: 0.7060 (t80) cc_final: 0.6592 (t80) REVERT: C 283 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8589 (p) REVERT: C 380 TYR cc_start: 0.7324 (t80) cc_final: 0.6998 (t80) REVERT: D 70 TYR cc_start: 0.8690 (p90) cc_final: 0.8467 (p90) REVERT: D 313 SER cc_start: 0.8631 (m) cc_final: 0.8406 (p) REVERT: D 380 TYR cc_start: 0.7321 (t80) cc_final: 0.7013 (t80) REVERT: D 490 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8473 (mmtp) REVERT: E 283 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8612 (p) REVERT: E 380 TYR cc_start: 0.7374 (t80) cc_final: 0.7022 (t80) REVERT: F 58 GLN cc_start: 0.8669 (mt0) cc_final: 0.8228 (mt0) REVERT: F 135 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: F 380 TYR cc_start: 0.7138 (t80) cc_final: 0.6644 (t80) outliers start: 91 outliers final: 31 residues processed: 298 average time/residue: 0.5777 time to fit residues: 199.5512 Evaluate side-chains 240 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 490 LYS Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 228 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 HIS B 517 HIS C 517 HIS D 517 HIS E 517 HIS F 517 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.073715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.056514 restraints weight = 47876.733| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 2.92 r_work: 0.2444 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26358 Z= 0.203 Angle : 0.471 5.462 35748 Z= 0.249 Chirality : 0.041 0.136 3840 Planarity : 0.004 0.033 4548 Dihedral : 9.085 95.851 3774 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.32 % Allowed : 23.70 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.16), residues: 3090 helix: 2.16 (0.12), residues: 1770 sheet: 0.30 (0.41), residues: 210 loop : 0.17 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 54 TYR 0.014 0.001 TYR F 238 PHE 0.011 0.001 PHE D 154 TRP 0.006 0.001 TRP C 471 HIS 0.005 0.001 HIS E 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (26358) covalent geometry : angle 0.47109 / 0.25 (35748) hydrogen bonds : bond 0.03963 / 2.60 ( 1321) hydrogen bonds : angle 4.07584 / 2.85 ( 3801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 186 time to evaluate : 0.669 Fit side-chains REVERT: A 70 TYR cc_start: 0.8776 (p90) cc_final: 0.8575 (p90) REVERT: A 380 TYR cc_start: 0.7279 (t80) cc_final: 0.6931 (t80) REVERT: A 490 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8536 (mmtp) REVERT: B 11 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.8614 (t80) REVERT: B 135 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: B 380 TYR cc_start: 0.7181 (t80) cc_final: 0.6669 (t80) REVERT: C 23 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8607 (mt0) REVERT: C 283 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8725 (p) REVERT: C 380 TYR cc_start: 0.7422 (t80) cc_final: 0.7080 (t80) REVERT: D 70 TYR cc_start: 0.8808 (p90) cc_final: 0.8606 (p90) REVERT: D 380 TYR cc_start: 0.7392 (t80) cc_final: 0.7087 (t80) REVERT: D 490 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8561 (mmtp) REVERT: E 23 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8574 (mt0) REVERT: E 283 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8729 (p) REVERT: E 328 GLN cc_start: 0.8746 (pt0) cc_final: 0.8525 (tm-30) REVERT: E 380 TYR cc_start: 0.7424 (t80) cc_final: 0.7092 (t80) REVERT: F 11 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8624 (t80) REVERT: F 135 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: F 380 TYR cc_start: 0.7273 (t80) cc_final: 0.6777 (t80) REVERT: F 513 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.6793 (mp0) outliers start: 66 outliers final: 34 residues processed: 252 average time/residue: 0.6311 time to fit residues: 183.5935 Evaluate side-chains 225 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 490 LYS Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 513 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 229 optimal weight: 0.9990 chunk 270 optimal weight: 0.6980 chunk 303 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 HIS B 517 HIS C 517 HIS D 517 HIS E 517 HIS F 517 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.074352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.057145 restraints weight = 47626.579| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 2.92 r_work: 0.2457 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26358 Z= 0.144 Angle : 0.438 5.593 35748 Z= 0.233 Chirality : 0.039 0.138 3840 Planarity : 0.003 0.033 4548 Dihedral : 8.655 88.491 3774 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.39 % Allowed : 23.59 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.16), residues: 3090 helix: 2.20 (0.12), residues: 1770 sheet: 0.37 (0.39), residues: 240 loop : 0.25 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 54 TYR 0.012 0.001 TYR A 475 PHE 0.009 0.001 PHE A 432 TRP 0.005 0.001 TRP B 288 HIS 0.003 0.000 HIS E 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (26358) covalent geometry : angle 0.43769 / 0.23 (35748) hydrogen bonds : bond 0.03643 / 2.39 ( 1321) hydrogen bonds : angle 4.02792 / 2.82 ( 3801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 187 time to evaluate : 0.996 Fit side-chains REVERT: A 375 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9055 (mt) REVERT: A 380 TYR cc_start: 0.7294 (t80) cc_final: 0.6943 (t80) REVERT: A 490 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8517 (mmtp) REVERT: A 507 ASN cc_start: 0.9124 (p0) cc_final: 0.8864 (m-40) REVERT: B 11 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8643 (t80) REVERT: B 135 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8523 (tt0) REVERT: B 380 TYR cc_start: 0.7208 (t80) cc_final: 0.6710 (t80) REVERT: C 23 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8587 (mt0) REVERT: C 380 TYR cc_start: 0.7406 (t80) cc_final: 0.7065 (t80) REVERT: D 70 TYR cc_start: 0.8849 (p90) cc_final: 0.8633 (p90) REVERT: D 375 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9057 (mt) REVERT: D 380 TYR cc_start: 0.7415 (t80) cc_final: 0.7098 (t80) REVERT: D 490 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8548 (mmtp) REVERT: D 507 ASN cc_start: 0.9119 (p0) cc_final: 0.8821 (m-40) REVERT: E 23 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8593 (mt0) REVERT: E 283 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8725 (p) REVERT: E 328 GLN cc_start: 0.8716 (pt0) cc_final: 0.8486 (tm-30) REVERT: E 380 TYR cc_start: 0.7428 (t80) cc_final: 0.7096 (t80) REVERT: E 513 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: F 11 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8657 (t80) REVERT: F 58 GLN cc_start: 0.8770 (mt0) cc_final: 0.8370 (mt0) REVERT: F 135 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: F 380 TYR cc_start: 0.7265 (t80) cc_final: 0.6759 (t80) REVERT: F 513 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.6802 (mp0) outliers start: 68 outliers final: 37 residues processed: 248 average time/residue: 0.6569 time to fit residues: 188.1621 Evaluate side-chains 235 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 490 LYS Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 513 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 164 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN A 517 HIS B 517 HIS C 308 ASN C 517 HIS D 305 GLN D 517 HIS E 308 ASN F 517 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.073178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.056117 restraints weight = 47902.728| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 2.89 r_work: 0.2439 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26358 Z= 0.172 Angle : 0.462 6.560 35748 Z= 0.245 Chirality : 0.040 0.140 3840 Planarity : 0.004 0.034 4548 Dihedral : 8.429 82.184 3774 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.67 % Allowed : 23.00 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.16), residues: 3090 helix: 2.23 (0.12), residues: 1758 sheet: 0.22 (0.41), residues: 210 loop : 0.11 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 54 TYR 0.021 0.001 TYR A 70 PHE 0.009 0.001 PHE D 432 TRP 0.005 0.001 TRP B 288 HIS 0.004 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (26358) covalent geometry : angle 0.46162 / 0.25 (35748) hydrogen bonds : bond 0.03848 / 2.52 ( 1321) hydrogen bonds : angle 4.03871 / 2.82 ( 3801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 188 time to evaluate : 0.971 Fit side-chains REVERT: A 375 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9054 (mt) REVERT: A 380 TYR cc_start: 0.7310 (t80) cc_final: 0.6992 (t80) REVERT: A 490 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8530 (mmtp) REVERT: A 507 ASN cc_start: 0.9102 (p0) cc_final: 0.8852 (m-40) REVERT: B 11 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8612 (t80) REVERT: B 58 GLN cc_start: 0.8761 (mt0) cc_final: 0.8369 (mp10) REVERT: B 135 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: B 380 TYR cc_start: 0.7278 (t80) cc_final: 0.6763 (t80) REVERT: B 513 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: C 23 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8538 (mt0) REVERT: C 380 TYR cc_start: 0.7451 (t80) cc_final: 0.7139 (t80) REVERT: C 507 ASN cc_start: 0.9173 (p0) cc_final: 0.8893 (m-40) REVERT: C 513 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: D 70 TYR cc_start: 0.8905 (p90) cc_final: 0.8637 (p90) REVERT: D 375 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9055 (mt) REVERT: D 380 TYR cc_start: 0.7449 (t80) cc_final: 0.7148 (t80) REVERT: D 507 ASN cc_start: 0.9108 (p0) cc_final: 0.8837 (m-40) REVERT: E 23 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8544 (mt0) REVERT: E 283 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8781 (p) REVERT: E 328 GLN cc_start: 0.8730 (pt0) cc_final: 0.8518 (tm130) REVERT: E 380 TYR cc_start: 0.7454 (t80) cc_final: 0.7140 (t80) REVERT: E 507 ASN cc_start: 0.9164 (p0) cc_final: 0.8881 (m-40) REVERT: E 513 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: F 11 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8626 (t80) REVERT: F 58 GLN cc_start: 0.8781 (mt0) cc_final: 0.8387 (mt0) REVERT: F 135 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: F 380 TYR cc_start: 0.7302 (t80) cc_final: 0.6811 (t80) REVERT: F 513 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.6758 (mp0) outliers start: 76 outliers final: 38 residues processed: 259 average time/residue: 0.6291 time to fit residues: 187.9111 Evaluate side-chains 236 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 513 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 257 optimal weight: 0.0770 chunk 39 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 284 optimal weight: 0.1980 chunk 159 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 143 optimal weight: 0.0870 chunk 52 optimal weight: 0.6980 chunk 287 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN A 517 HIS B 517 HIS C 23 GLN C 308 ASN C 517 HIS D 305 GLN D 517 HIS E 23 GLN E 308 ASN F 517 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.076438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.059507 restraints weight = 47241.691| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.87 r_work: 0.2511 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26358 Z= 0.086 Angle : 0.419 5.400 35748 Z= 0.224 Chirality : 0.038 0.137 3840 Planarity : 0.003 0.033 4548 Dihedral : 7.899 80.747 3774 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.90 % Allowed : 24.16 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.16), residues: 3090 helix: 2.15 (0.12), residues: 1788 sheet: 0.30 (0.40), residues: 210 loop : 0.26 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 54 TYR 0.023 0.001 TYR A 70 PHE 0.011 0.001 PHE A 432 TRP 0.008 0.001 TRP A 187 HIS 0.003 0.000 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.09 (26358) covalent geometry : angle 0.41905 / 0.22 (35748) hydrogen bonds : bond 0.03119 / 2.03 ( 1321) hydrogen bonds : angle 3.90969 / 2.74 ( 3801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 1.031 Fit side-chains REVERT: A 375 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9032 (mt) REVERT: A 380 TYR cc_start: 0.7252 (t80) cc_final: 0.6933 (t80) REVERT: A 507 ASN cc_start: 0.9087 (p0) cc_final: 0.8815 (m-40) REVERT: B 58 GLN cc_start: 0.8687 (mt0) cc_final: 0.8299 (mp10) REVERT: B 135 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: B 380 TYR cc_start: 0.7204 (t80) cc_final: 0.6757 (t80) REVERT: C 328 GLN cc_start: 0.8985 (tt0) cc_final: 0.8600 (tm-30) REVERT: C 380 TYR cc_start: 0.7399 (t80) cc_final: 0.7084 (t80) REVERT: C 507 ASN cc_start: 0.9154 (p0) cc_final: 0.8872 (m-40) REVERT: C 513 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: D 375 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9022 (mt) REVERT: D 380 TYR cc_start: 0.7375 (t80) cc_final: 0.7057 (t80) REVERT: D 507 ASN cc_start: 0.9093 (p0) cc_final: 0.8772 (m-40) REVERT: E 283 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8666 (p) REVERT: E 380 TYR cc_start: 0.7389 (t80) cc_final: 0.7072 (t80) REVERT: E 513 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: F 58 GLN cc_start: 0.8658 (mt0) cc_final: 0.8277 (mt0) REVERT: F 135 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: F 380 TYR cc_start: 0.7253 (t80) cc_final: 0.6802 (t80) REVERT: F 513 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.6772 (mp0) outliers start: 54 outliers final: 18 residues processed: 259 average time/residue: 0.6091 time to fit residues: 182.4769 Evaluate side-chains 220 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 513 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 55 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 268 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 200 optimal weight: 0.1980 chunk 190 optimal weight: 0.8980 chunk 291 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 HIS B 517 HIS C 517 HIS D 305 GLN D 517 HIS F 517 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.075156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.057914 restraints weight = 47793.776| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 2.94 r_work: 0.2467 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26358 Z= 0.128 Angle : 0.440 6.699 35748 Z= 0.234 Chirality : 0.039 0.136 3840 Planarity : 0.003 0.033 4548 Dihedral : 7.898 79.091 3774 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.51 % Allowed : 24.96 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.16), residues: 3090 helix: 2.23 (0.12), residues: 1770 sheet: 0.27 (0.40), residues: 210 loop : 0.19 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 54 TYR 0.022 0.001 TYR A 70 PHE 0.017 0.001 PHE D 432 TRP 0.006 0.001 TRP F 187 HIS 0.004 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (26358) covalent geometry : angle 0.44041 / 0.23 (35748) hydrogen bonds : bond 0.03454 / 2.26 ( 1321) hydrogen bonds : angle 3.92367 / 2.75 ( 3801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.634 Fit side-chains REVERT: A 375 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9035 (mt) REVERT: A 380 TYR cc_start: 0.7313 (t80) cc_final: 0.7003 (t80) REVERT: A 507 ASN cc_start: 0.9069 (p0) cc_final: 0.8791 (m-40) REVERT: B 58 GLN cc_start: 0.8728 (mt0) cc_final: 0.8347 (mp10) REVERT: B 135 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: B 380 TYR cc_start: 0.7290 (t80) cc_final: 0.6845 (t80) REVERT: C 328 GLN cc_start: 0.8978 (tt0) cc_final: 0.8623 (tm-30) REVERT: C 380 TYR cc_start: 0.7440 (t80) cc_final: 0.7143 (t80) REVERT: C 507 ASN cc_start: 0.9163 (p0) cc_final: 0.8878 (m-40) REVERT: D 375 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9028 (mt) REVERT: D 380 TYR cc_start: 0.7426 (t80) cc_final: 0.7123 (t80) REVERT: D 507 ASN cc_start: 0.9098 (p0) cc_final: 0.8753 (m-40) REVERT: E 283 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8704 (p) REVERT: E 380 TYR cc_start: 0.7436 (t80) cc_final: 0.7128 (t80) REVERT: E 507 ASN cc_start: 0.9150 (p0) cc_final: 0.8861 (m-40) REVERT: E 513 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: F 58 GLN cc_start: 0.8683 (mt0) cc_final: 0.8315 (mt0) REVERT: F 135 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8512 (tt0) REVERT: F 380 TYR cc_start: 0.7312 (t80) cc_final: 0.6864 (t80) REVERT: F 513 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.6766 (mp0) outliers start: 43 outliers final: 23 residues processed: 229 average time/residue: 0.6117 time to fit residues: 161.5591 Evaluate side-chains 215 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 491 CYS Chi-restraints excluded: chain F residue 513 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 128 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN A 517 HIS B 517 HIS D 517 HIS F 517 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.075719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.058585 restraints weight = 47389.402| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.89 r_work: 0.2493 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26358 Z= 0.101 Angle : 0.432 7.265 35748 Z= 0.229 Chirality : 0.038 0.135 3840 Planarity : 0.003 0.036 4548 Dihedral : 7.777 81.049 3774 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.55 % Allowed : 24.75 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.16), residues: 3090 helix: 2.23 (0.12), residues: 1770 sheet: 0.26 (0.40), residues: 210 loop : 0.18 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 54 TYR 0.023 0.001 TYR A 70 PHE 0.015 0.001 PHE A 432 TRP 0.007 0.001 TRP F 187 HIS 0.003 0.000 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (26358) covalent geometry : angle 0.43171 / 0.23 (35748) hydrogen bonds : bond 0.03284 / 2.14 ( 1321) hydrogen bonds : angle 3.88705 / 2.73 ( 3801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.669 Fit side-chains REVERT: A 380 TYR cc_start: 0.7321 (t80) cc_final: 0.7033 (t80) REVERT: A 507 ASN cc_start: 0.9058 (p0) cc_final: 0.8786 (m-40) REVERT: B 58 GLN cc_start: 0.8693 (mt0) cc_final: 0.8314 (mp10) REVERT: B 135 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: B 380 TYR cc_start: 0.7251 (t80) cc_final: 0.6802 (t80) REVERT: C 380 TYR cc_start: 0.7431 (t80) cc_final: 0.7134 (t80) REVERT: C 507 ASN cc_start: 0.9153 (p0) cc_final: 0.8874 (m-40) REVERT: D 380 TYR cc_start: 0.7349 (t80) cc_final: 0.7042 (t80) REVERT: D 507 ASN cc_start: 0.9117 (p0) cc_final: 0.8781 (m-40) REVERT: E 283 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8686 (p) REVERT: E 380 TYR cc_start: 0.7417 (t80) cc_final: 0.7116 (t80) REVERT: E 513 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: F 58 GLN cc_start: 0.8645 (mt0) cc_final: 0.8271 (mt0) REVERT: F 135 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: F 380 TYR cc_start: 0.7315 (t80) cc_final: 0.6859 (t80) REVERT: F 513 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.6770 (mp0) outliers start: 44 outliers final: 26 residues processed: 230 average time/residue: 0.5895 time to fit residues: 156.4282 Evaluate side-chains 217 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 513 GLU Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 491 CYS Chi-restraints excluded: chain F residue 513 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 160 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 278 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 517 HIS ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS D 305 GLN D 517 HIS ** F 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 517 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.075690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.058649 restraints weight = 47354.646| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.88 r_work: 0.2495 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26358 Z= 0.103 Angle : 0.437 6.918 35748 Z= 0.232 Chirality : 0.038 0.135 3840 Planarity : 0.003 0.037 4548 Dihedral : 7.702 81.695 3774 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.34 % Allowed : 25.07 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.16), residues: 3090 helix: 2.21 (0.12), residues: 1776 sheet: 0.27 (0.40), residues: 210 loop : 0.20 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 54 TYR 0.024 0.001 TYR D 70 PHE 0.020 0.001 PHE D 432 TRP 0.007 0.001 TRP E 187 HIS 0.003 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (26358) covalent geometry : angle 0.43712 / 0.23 (35748) hydrogen bonds : bond 0.03274 / 2.14 ( 1321) hydrogen bonds : angle 3.86946 / 2.72 ( 3801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5361.22 seconds wall clock time: 92 minutes 52.71 seconds (5572.71 seconds total)