Starting phenix.real_space_refine on Sun Sep 13 22:28:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ltm_63373/09_2026/9ltm_63373.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ltm_63373/09_2026/9ltm_63373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ltm_63373/09_2026/9ltm_63373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ltm_63373/09_2026/9ltm_63373.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ltm_63373/09_2026/9ltm_63373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ltm_63373/09_2026/9ltm_63373.map" } resolution = 2.3 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= -0.003 sd= 0.206 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 138 5.16 5 C 16470 2.51 5 N 4356 2.21 5 O 4962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25956 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "B" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "C" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "D" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "E" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "F" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "I" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "K" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Time building chain proxies: 5.47, per 1000 atoms: 0.21 Number of scatterers: 25956 At special positions: 0 Unit cell: (144.45, 141.24, 109.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 30 15.00 O 4962 8.00 N 4356 7.00 C 16470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5916 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 12 sheets defined 63.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 40 through 49 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 96 through 105 removed outlier: 4.586A pdb=" N ARG A 100 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 105 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 160 through 167 removed outlier: 4.233A pdb=" N TRP A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.767A pdb=" N LYS A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 231 removed outlier: 3.723A pdb=" N SER A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.668A pdb=" N SER A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.505A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) 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: 3.871A 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: 3.544A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 461 removed outlier: 3.840A pdb=" N LEU A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 removed outlier: 3.660A 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 519 Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 96 through 105 removed outlier: 4.304A pdb=" N ARG B 100 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.532A pdb=" N LYS B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 160 through 167 removed outlier: 4.209A pdb=" N TRP B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.687A pdb=" N LYS B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 231 removed outlier: 3.558A pdb=" N SER B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 266 removed outlier: 3.826A pdb=" N TYR B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.584A pdb=" N SER B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.780A pdb=" N LYS B 309 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.547A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) 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: 3.909A 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 445 removed outlier: 3.543A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 461 removed outlier: 3.933A pdb=" N LEU B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 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 519 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 96 through 105 removed outlier: 4.383A pdb=" N ARG C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 140 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 160 through 167 removed outlier: 4.409A pdb=" N TRP C 164 " --> pdb=" O HIS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.638A pdb=" N LYS C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 231 removed outlier: 3.534A pdb=" N SER C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 3.544A 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 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.647A pdb=" N SER C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.828A pdb=" N LYS C 309 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 329 Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.703A pdb=" N VAL C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) 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: 3.963A 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 401 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 Processing helix chain 'C' and resid 447 through 461 removed outlier: 3.896A pdb=" N LEU C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 470 removed outlier: 3.592A pdb=" N ILE C 467 " --> pdb=" O TYR C 463 " (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 519 Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 40 through 49 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 140 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 160 through 167 removed outlier: 4.393A pdb=" N TRP D 164 " --> pdb=" O HIS D 160 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 Processing helix chain 'D' and resid 186 through 198 Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.612A pdb=" N SER D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.717A pdb=" N SER D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.562A pdb=" N LYS D 309 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 329 Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.524A pdb=" N VAL D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 365 removed outlier: 4.417A pdb=" N THR D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN D 353 " --> pdb=" O TYR D 349 " (cutoff:3.500A) 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: 3.953A 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 Processing helix chain 'D' and resid 447 through 461 removed outlier: 3.914A pdb=" N LEU D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 470 removed outlier: 3.667A 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 519 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 96 through 105 removed outlier: 4.350A pdb=" N ARG E 100 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N PHE E 101 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN E 105 " --> pdb=" O ILE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 140 Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 160 through 167 removed outlier: 4.169A pdb=" N TRP E 164 " --> pdb=" O HIS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 176 Processing helix chain 'E' and resid 186 through 199 removed outlier: 3.735A pdb=" N LYS E 199 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 231 removed outlier: 3.610A pdb=" N SER E 214 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA E 223 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 3.500A 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 286 through 295 removed outlier: 3.726A pdb=" N SER E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 309 removed outlier: 3.612A pdb=" N LYS E 309 " --> pdb=" O ASP E 306 " (cutoff:3.500A) 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: 3.990A 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 Processing helix chain 'E' and resid 447 through 460 Processing helix chain 'E' and resid 463 through 469 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 519 Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 40 through 49 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 removed outlier: 3.676A pdb=" N ASN F 105 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 140 Processing helix chain 'F' and resid 152 through 157 Processing helix chain 'F' and resid 160 through 167 removed outlier: 4.211A pdb=" N TRP F 164 " --> pdb=" O HIS F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 178 removed outlier: 4.283A pdb=" N THR F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 Processing helix chain 'F' and resid 186 through 199 removed outlier: 3.721A pdb=" N LYS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 231 removed outlier: 3.511A pdb=" N SER F 214 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 265 Processing helix chain 'F' and resid 286 through 295 removed outlier: 3.564A pdb=" N SER F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 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 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: 3.874A 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 445 Processing helix chain 'F' and resid 447 through 461 removed outlier: 3.837A pdb=" N LEU F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 470 removed outlier: 3.588A 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 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.569A pdb=" N LEU A 234 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AA5, first strand: chain 'C' and resid 63 through 68 Processing sheet with id=AA6, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.606A pdb=" N LEU C 234 " --> pdb=" O TYR C 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 68 Processing sheet with id=AA8, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.564A pdb=" N LEU D 234 " --> pdb=" O TYR D 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 63 through 68 Processing sheet with id=AB1, first strand: chain 'E' and resid 234 through 238 removed outlier: 4.513A pdb=" N LEU E 234 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 63 through 68 Processing sheet with id=AB3, first strand: chain 'F' and resid 234 through 238 removed outlier: 4.646A pdb=" N LEU F 234 " --> pdb=" O TYR F 245 " (cutoff:3.500A) 1334 hydrogen bonds defined for protein. 3786 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: 4.81 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8330 1.34 - 1.46: 6606 1.46 - 1.58: 11464 1.58 - 1.70: 54 1.70 - 1.82: 192 Bond restraints: 26646 Sorted by residual: bond pdb=" C3' DA L 30 " pdb=" C2' DA L 30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA H 10 " pdb=" C2' DA H 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA G 4 " pdb=" O3' DA G 4 " ideal model delta sigma weight residual 1.435 1.403 0.032 1.30e-02 5.92e+03 5.95e+00 bond pdb=" C3' DA K 24 " pdb=" O3' DA K 24 " ideal model delta sigma weight residual 1.435 1.406 0.029 1.30e-02 5.92e+03 4.87e+00 bond pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " ideal model delta sigma weight residual 1.435 1.408 0.027 1.30e-02 5.92e+03 4.33e+00 ... (remaining 26641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 35719 1.83 - 3.66: 417 3.66 - 5.49: 42 5.49 - 7.33: 11 7.33 - 9.16: 3 Bond angle restraints: 36192 Sorted by residual: angle pdb=" C ARG E 55 " pdb=" N SER E 56 " pdb=" CA SER E 56 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 angle pdb=" O4' DA G 5 " pdb=" C4' DA G 5 " pdb=" C3' DA G 5 " ideal model delta sigma weight residual 106.00 103.62 2.38 6.00e-01 2.78e+00 1.58e+01 angle pdb=" O4' DA K 25 " pdb=" C4' DA K 25 " pdb=" C3' DA K 25 " ideal model delta sigma weight residual 106.00 103.72 2.28 6.00e-01 2.78e+00 1.45e+01 angle pdb=" C4' DA L 30 " pdb=" O4' DA L 30 " pdb=" C1' DA L 30 " ideal model delta sigma weight residual 110.10 106.63 3.47 1.00e+00 1.00e+00 1.20e+01 angle pdb=" N GLY E 25 " pdb=" CA GLY E 25 " pdb=" C GLY E 25 " ideal model delta sigma weight residual 115.32 110.78 4.54 1.31e+00 5.83e-01 1.20e+01 ... (remaining 36187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.81: 15072 28.81 - 57.61: 753 57.61 - 86.42: 98 86.42 - 115.22: 4 115.22 - 144.03: 3 Dihedral angle restraints: 15930 sinusoidal: 6732 harmonic: 9198 Sorted by residual: dihedral pdb=" C4' DA G 3 " pdb=" C3' DA G 3 " pdb=" O3' DA G 3 " pdb=" P DA G 4 " ideal model delta sinusoidal sigma weight residual 220.00 75.97 144.03 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DA J 18 " pdb=" C3' DA J 18 " pdb=" O3' DA J 18 " pdb=" P DA J 19 " ideal model delta sinusoidal sigma weight residual 220.00 77.28 142.72 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DA K 23 " pdb=" C3' DA K 23 " pdb=" O3' DA K 23 " pdb=" P DA K 24 " ideal model delta sinusoidal sigma weight residual 220.00 80.10 139.90 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 15927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2194 0.029 - 0.057: 1112 0.057 - 0.086: 418 0.086 - 0.115: 136 0.115 - 0.143: 40 Chirality restraints: 3900 Sorted by residual: chirality pdb=" CA GLU B 126 " pdb=" N GLU B 126 " pdb=" C GLU B 126 " pdb=" CB GLU B 126 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE B 30 " pdb=" N ILE B 30 " pdb=" C ILE B 30 " pdb=" CB ILE B 30 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" C3' DA K 24 " pdb=" C4' DA K 24 " pdb=" O3' DA K 24 " pdb=" C2' DA K 24 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 3897 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 126 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C GLU B 126 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU B 126 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP B 127 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 209 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO E 210 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 306 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" CG ASP F 306 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP F 306 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP F 306 " 0.011 2.00e-02 2.50e+03 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 223 2.62 - 3.19: 23138 3.19 - 3.76: 42964 3.76 - 4.33: 61159 4.33 - 4.90: 96760 Nonbonded interactions: 224244 Sorted by model distance: nonbonded pdb=" OE2 GLU A 202 " pdb=" OG1 THR C 203 " model vdw 2.052 3.040 nonbonded pdb=" OG SER C 340 " pdb=" OH TYR C 371 " model vdw 2.190 3.040 nonbonded pdb=" NH2 ARG E 301 " pdb=" N7 DA K 21 " model vdw 2.204 3.200 nonbonded pdb=" OG1 THR B 283 " pdb=" O ASN B 285 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASP E 320 " pdb=" OH TYR E 357 " model vdw 2.219 3.040 ... (remaining 224239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 23.130 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26646 Z= 0.171 Angle : 0.530 9.158 36192 Z= 0.322 Chirality : 0.041 0.143 3900 Planarity : 0.004 0.049 4536 Dihedral : 16.231 144.030 10014 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.85 % Favored : 97.92 % Rotamer: Outliers : 0.95 % Allowed : 11.12 % Favored : 87.92 % 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: 1.41 (0.15), residues: 3078 helix: 1.72 (0.12), residues: 1734 sheet: -0.45 (0.35), residues: 204 loop : 0.10 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 54 TYR 0.020 0.001 TYR A 380 PHE 0.013 0.001 PHE F 140 TRP 0.014 0.002 TRP E 363 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (26646) covalent geometry : angle 0.53002 / 0.32 (36192) hydrogen bonds : bond 0.13943 / 9.81 ( 1334) hydrogen bonds : angle 5.13296 / 3.73 ( 3786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 312 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: B 113 ASP cc_start: 0.8089 (t0) cc_final: 0.7871 (t70) REVERT: D 160 HIS cc_start: 0.8814 (m-70) cc_final: 0.8602 (m170) REVERT: E 261 MET cc_start: 0.8322 (mmm) cc_final: 0.8096 (mtp) outliers start: 27 outliers final: 21 residues processed: 334 average time/residue: 0.7172 time to fit residues: 274.5905 Evaluate side-chains 319 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 298 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 347 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 378 HIS C 107 ASN C 171 ASN C 324 GLN D 23 GLN E 324 GLN F 160 HIS F 378 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128260 restraints weight = 26373.738| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.34 r_work: 0.3372 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 26646 Z= 0.176 Angle : 0.544 9.070 36192 Z= 0.302 Chirality : 0.042 0.184 3900 Planarity : 0.005 0.054 4536 Dihedral : 12.283 144.165 3842 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.05 % Favored : 97.73 % Rotamer: Outliers : 2.01 % Allowed : 9.85 % Favored : 88.14 % 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: 1.46 (0.15), residues: 3078 helix: 1.72 (0.12), residues: 1740 sheet: -0.58 (0.34), residues: 204 loop : 0.20 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 54 TYR 0.021 0.002 TYR B 475 PHE 0.016 0.002 PHE F 140 TRP 0.010 0.002 TRP F 471 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (26646) covalent geometry : angle 0.54425 / 0.30 (36192) hydrogen bonds : bond 0.05503 / 3.70 ( 1334) hydrogen bonds : angle 4.50403 / 3.28 ( 3786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 309 time to evaluate : 1.045 Fit side-chains REVERT: A 304 ASP cc_start: 0.7284 (t0) cc_final: 0.6996 (t70) REVERT: B 75 ARG cc_start: 0.8159 (ttp-170) cc_final: 0.7936 (ttp-170) REVERT: B 129 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7197 (tp30) REVERT: B 286 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: C 135 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: C 400 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: D 160 HIS cc_start: 0.8819 (m-70) cc_final: 0.8592 (m170) REVERT: D 315 VAL cc_start: 0.9274 (t) cc_final: 0.9003 (p) REVERT: D 449 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: E 462 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7369 (t0) REVERT: F 97 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: F 247 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8613 (mttp) REVERT: F 450 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8160 (mmtm) outliers start: 57 outliers final: 20 residues processed: 338 average time/residue: 0.7847 time to fit residues: 302.4401 Evaluate side-chains 329 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 455 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 215 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 304 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS B 160 HIS C 171 ASN D 23 GLN E 324 GLN F 17 HIS F 378 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128829 restraints weight = 26492.033| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.34 r_work: 0.3380 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 26646 Z= 0.147 Angle : 0.507 8.822 36192 Z= 0.281 Chirality : 0.041 0.175 3900 Planarity : 0.004 0.048 4536 Dihedral : 12.049 144.570 3817 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.92 % Favored : 97.86 % Rotamer: Outliers : 2.30 % Allowed : 9.89 % Favored : 87.82 % 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: 1.49 (0.15), residues: 3078 helix: 1.78 (0.12), residues: 1746 sheet: -0.63 (0.34), residues: 204 loop : 0.16 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 54 TYR 0.019 0.002 TYR F 475 PHE 0.013 0.001 PHE F 140 TRP 0.011 0.002 TRP F 471 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (26646) covalent geometry : angle 0.50652 / 0.28 (36192) hydrogen bonds : bond 0.05007 / 3.35 ( 1334) hydrogen bonds : angle 4.35504 / 3.17 ( 3786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 313 time to evaluate : 1.147 Fit side-chains REVERT: A 304 ASP cc_start: 0.7226 (t0) cc_final: 0.6825 (t70) REVERT: B 11 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8682 (t80) REVERT: B 106 GLU cc_start: 0.7822 (pm20) cc_final: 0.7617 (pm20) REVERT: B 113 ASP cc_start: 0.8312 (t0) cc_final: 0.8060 (t70) REVERT: B 129 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7166 (tp30) REVERT: B 286 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: B 386 GLU cc_start: 0.7636 (pm20) cc_final: 0.7370 (tt0) REVERT: B 388 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8488 (ttmm) REVERT: C 135 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: C 400 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: D 145 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8971 (ttpm) REVERT: D 160 HIS cc_start: 0.8828 (m-70) cc_final: 0.8550 (m170) REVERT: D 315 VAL cc_start: 0.9265 (t) cc_final: 0.8960 (p) REVERT: D 358 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8800 (mp) REVERT: D 449 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: E 117 ASP cc_start: 0.8342 (p0) cc_final: 0.8140 (p0) REVERT: E 388 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8729 (tmtm) REVERT: E 462 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7366 (t0) REVERT: F 54 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7477 (tmm160) REVERT: F 97 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: F 247 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8582 (mttp) REVERT: F 450 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8155 (mmtm) outliers start: 65 outliers final: 27 residues processed: 356 average time/residue: 0.7627 time to fit residues: 310.6366 Evaluate side-chains 344 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 302 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 388 LYS Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 455 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 221 optimal weight: 0.0000 chunk 77 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 260 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN A 378 HIS B 171 ASN C 171 ASN D 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127070 restraints weight = 26192.737| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.33 r_work: 0.3357 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 26646 Z= 0.191 Angle : 0.554 9.473 36192 Z= 0.306 Chirality : 0.043 0.178 3900 Planarity : 0.005 0.054 4536 Dihedral : 12.146 146.006 3817 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.95 % Favored : 97.82 % Rotamer: Outliers : 2.51 % Allowed : 10.03 % Favored : 87.46 % 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: 1.37 (0.15), residues: 3078 helix: 1.69 (0.12), residues: 1746 sheet: -0.59 (0.34), residues: 204 loop : 0.06 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 100 TYR 0.023 0.002 TYR F 475 PHE 0.018 0.002 PHE F 140 TRP 0.013 0.002 TRP F 471 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (26646) covalent geometry : angle 0.55407 / 0.31 (36192) hydrogen bonds : bond 0.05478 / 3.64 ( 1334) hydrogen bonds : angle 4.41022 / 3.21 ( 3786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 311 time to evaluate : 1.073 Fit side-chains REVERT: A 304 ASP cc_start: 0.7178 (t0) cc_final: 0.6971 (t0) REVERT: B 10 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8357 (tp) REVERT: B 11 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8621 (t80) REVERT: B 129 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7246 (tp30) REVERT: B 286 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: B 386 GLU cc_start: 0.7647 (pm20) cc_final: 0.7363 (tt0) REVERT: B 498 TYR cc_start: 0.8587 (m-80) cc_final: 0.8272 (m-80) REVERT: C 37 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7969 (mtt180) REVERT: C 135 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: C 400 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: D 145 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8935 (ttpm) REVERT: D 160 HIS cc_start: 0.8846 (m-70) cc_final: 0.8581 (m170) REVERT: D 315 VAL cc_start: 0.9269 (t) cc_final: 0.8979 (p) REVERT: D 358 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8588 (tp) REVERT: D 449 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: E 117 ASP cc_start: 0.8356 (p0) cc_final: 0.8119 (p0) REVERT: E 457 ASP cc_start: 0.8371 (m-30) cc_final: 0.8121 (m-30) REVERT: E 462 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7365 (t0) REVERT: F 54 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7492 (tmm160) REVERT: F 97 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: F 247 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8598 (mttp) REVERT: F 450 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8179 (mmtm) outliers start: 71 outliers final: 34 residues processed: 355 average time/residue: 0.7640 time to fit residues: 310.1054 Evaluate side-chains 348 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 455 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 293 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 0.2980 chunk 116 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN A 378 HIS B 171 ASN C 171 ASN C 257 HIS D 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127127 restraints weight = 26200.090| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.33 r_work: 0.3358 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 26646 Z= 0.185 Angle : 0.545 9.241 36192 Z= 0.302 Chirality : 0.043 0.181 3900 Planarity : 0.005 0.050 4536 Dihedral : 12.128 146.248 3817 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.69 % Favored : 98.08 % Rotamer: Outliers : 2.61 % Allowed : 10.20 % Favored : 87.18 % 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: 1.36 (0.15), residues: 3078 helix: 1.70 (0.12), residues: 1740 sheet: -0.60 (0.34), residues: 204 loop : 0.04 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 227 TYR 0.022 0.002 TYR F 475 PHE 0.018 0.002 PHE F 140 TRP 0.013 0.002 TRP F 471 HIS 0.007 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (26646) covalent geometry : angle 0.54516 / 0.30 (36192) hydrogen bonds : bond 0.05347 / 3.56 ( 1334) hydrogen bonds : angle 4.39484 / 3.20 ( 3786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 309 time to evaluate : 1.276 Fit side-chains REVERT: B 10 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8379 (tp) REVERT: B 11 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8616 (t80) REVERT: B 113 ASP cc_start: 0.8374 (t0) cc_final: 0.8170 (t70) REVERT: B 129 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: B 386 GLU cc_start: 0.7608 (pm20) cc_final: 0.7369 (tt0) REVERT: C 54 ARG cc_start: 0.7264 (ttp80) cc_final: 0.7038 (ttp80) REVERT: C 135 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: C 227 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7993 (mmm160) REVERT: C 301 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7458 (mtt90) REVERT: C 400 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: D 145 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8927 (ttpm) REVERT: D 315 VAL cc_start: 0.9265 (t) cc_final: 0.8976 (p) REVERT: D 358 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8598 (tp) REVERT: D 449 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: D 495 MET cc_start: 0.8812 (mtp) cc_final: 0.8458 (mtp) REVERT: E 117 ASP cc_start: 0.8352 (p0) cc_final: 0.8121 (p0) REVERT: E 457 ASP cc_start: 0.8359 (m-30) cc_final: 0.8109 (m-30) REVERT: E 462 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7458 (t0) REVERT: F 7 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8452 (mtpm) REVERT: F 54 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7502 (tmm160) REVERT: F 97 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: F 450 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8197 (mmtm) outliers start: 74 outliers final: 36 residues processed: 356 average time/residue: 0.7680 time to fit residues: 312.5684 Evaluate side-chains 356 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 305 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 455 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 78 optimal weight: 7.9990 chunk 207 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 258 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 270 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN B 171 ASN C 171 ASN D 23 GLN D 160 HIS E 186 HIS E 324 GLN F 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128733 restraints weight = 26255.554| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.33 r_work: 0.3378 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26646 Z= 0.134 Angle : 0.500 8.305 36192 Z= 0.277 Chirality : 0.040 0.177 3900 Planarity : 0.004 0.047 4536 Dihedral : 12.027 145.188 3817 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.95 % Favored : 97.82 % Rotamer: Outliers : 2.33 % Allowed : 10.56 % Favored : 87.11 % 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: 1.49 (0.15), residues: 3078 helix: 1.83 (0.12), residues: 1740 sheet: -0.63 (0.34), residues: 204 loop : 0.07 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 227 TYR 0.018 0.001 TYR F 475 PHE 0.013 0.001 PHE F 140 TRP 0.012 0.002 TRP F 471 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (26646) covalent geometry : angle 0.50001 / 0.28 (36192) hydrogen bonds : bond 0.04735 / 3.15 ( 1334) hydrogen bonds : angle 4.28970 / 3.12 ( 3786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 315 time to evaluate : 1.068 Fit side-chains REVERT: B 10 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8437 (tp) REVERT: B 11 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8699 (t80) REVERT: B 106 GLU cc_start: 0.7762 (pm20) cc_final: 0.7539 (pm20) REVERT: B 113 ASP cc_start: 0.8314 (t0) cc_final: 0.8055 (t70) REVERT: B 129 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: B 286 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: B 386 GLU cc_start: 0.7565 (pm20) cc_final: 0.7196 (tt0) REVERT: B 393 GLU cc_start: 0.8604 (tp30) cc_final: 0.8394 (tp30) REVERT: C 37 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7940 (mtt180) REVERT: C 75 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8034 (ttp80) REVERT: C 135 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: C 227 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7959 (mmm160) REVERT: C 301 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7486 (mtt90) REVERT: C 400 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: D 145 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8957 (ttpm) REVERT: D 241 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8003 (t70) REVERT: D 315 VAL cc_start: 0.9246 (t) cc_final: 0.8951 (p) REVERT: D 358 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8590 (tp) REVERT: D 449 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: D 495 MET cc_start: 0.8802 (mtp) cc_final: 0.8443 (mtp) REVERT: E 117 ASP cc_start: 0.8334 (p0) cc_final: 0.8113 (p0) REVERT: E 457 ASP cc_start: 0.8340 (m-30) cc_final: 0.8085 (m-30) REVERT: E 462 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7439 (t0) REVERT: F 7 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8423 (mtpm) REVERT: F 54 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7502 (tmm160) REVERT: F 97 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: F 450 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8173 (mmtm) outliers start: 66 outliers final: 31 residues processed: 352 average time/residue: 0.7685 time to fit residues: 309.2072 Evaluate side-chains 355 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 306 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 455 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 179 optimal weight: 0.0870 chunk 21 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 284 optimal weight: 0.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN A 378 HIS B 171 ASN B 401 ASN C 171 ASN D 23 GLN D 160 HIS E 324 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127656 restraints weight = 26150.293| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.33 r_work: 0.3371 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 26646 Z= 0.170 Angle : 0.532 8.892 36192 Z= 0.293 Chirality : 0.042 0.178 3900 Planarity : 0.004 0.047 4536 Dihedral : 12.049 145.709 3817 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.82 % Favored : 97.95 % Rotamer: Outliers : 2.37 % Allowed : 10.42 % Favored : 87.22 % 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: 1.42 (0.15), residues: 3078 helix: 1.78 (0.12), residues: 1740 sheet: -0.63 (0.34), residues: 204 loop : 0.04 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 54 TYR 0.021 0.002 TYR F 475 PHE 0.017 0.002 PHE F 140 TRP 0.012 0.002 TRP F 471 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (26646) covalent geometry : angle 0.53165 / 0.29 (36192) hydrogen bonds : bond 0.05113 / 3.40 ( 1334) hydrogen bonds : angle 4.32027 / 3.14 ( 3786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 309 time to evaluate : 1.080 Fit side-chains REVERT: A 460 LYS cc_start: 0.8182 (mtmp) cc_final: 0.7851 (mppt) REVERT: B 10 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8444 (tp) REVERT: B 11 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8623 (t80) REVERT: B 106 GLU cc_start: 0.7777 (pm20) cc_final: 0.7553 (pm20) REVERT: B 113 ASP cc_start: 0.8383 (t0) cc_final: 0.8148 (t70) REVERT: B 129 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: B 286 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: B 386 GLU cc_start: 0.7601 (pm20) cc_final: 0.7263 (tt0) REVERT: B 393 GLU cc_start: 0.8600 (tp30) cc_final: 0.8389 (tp30) REVERT: C 75 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8061 (ttp80) REVERT: C 135 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: C 227 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7984 (mmm160) REVERT: C 301 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7498 (mtt90) REVERT: C 400 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: D 145 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8938 (ttpm) REVERT: D 315 VAL cc_start: 0.9259 (t) cc_final: 0.8966 (p) REVERT: D 358 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8594 (tp) REVERT: D 495 MET cc_start: 0.8817 (mtp) cc_final: 0.8464 (mtp) REVERT: E 117 ASP cc_start: 0.8369 (p0) cc_final: 0.8089 (p0) REVERT: E 416 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7866 (ttmt) REVERT: E 457 ASP cc_start: 0.8355 (m-30) cc_final: 0.8103 (m-30) REVERT: E 462 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7440 (t0) REVERT: F 7 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8453 (mtpm) REVERT: F 54 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7510 (tmm160) REVERT: F 97 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: F 450 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8181 (mmtm) outliers start: 67 outliers final: 31 residues processed: 350 average time/residue: 0.7755 time to fit residues: 310.5628 Evaluate side-chains 348 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 455 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 63 optimal weight: 0.6980 chunk 191 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 53 optimal weight: 0.0670 chunk 17 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 overall best weight: 3.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN A 378 HIS B 171 ASN C 171 ASN D 23 GLN D 160 HIS D 401 ASN E 324 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127405 restraints weight = 26334.247| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.33 r_work: 0.3362 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 26646 Z= 0.182 Angle : 0.547 9.042 36192 Z= 0.302 Chirality : 0.042 0.182 3900 Planarity : 0.005 0.048 4536 Dihedral : 12.092 145.934 3817 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.85 % Favored : 97.92 % Rotamer: Outliers : 2.30 % Allowed : 10.49 % Favored : 87.22 % 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: 1.34 (0.15), residues: 3078 helix: 1.72 (0.12), residues: 1746 sheet: -0.64 (0.34), residues: 204 loop : -0.02 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 54 TYR 0.022 0.002 TYR F 475 PHE 0.018 0.002 PHE F 140 TRP 0.013 0.002 TRP F 471 HIS 0.007 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (26646) covalent geometry : angle 0.54677 / 0.30 (36192) hydrogen bonds : bond 0.05251 / 3.49 ( 1334) hydrogen bonds : angle 4.35024 / 3.17 ( 3786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 311 time to evaluate : 1.093 Fit side-chains REVERT: B 10 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8384 (tp) REVERT: B 11 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8628 (t80) REVERT: B 106 GLU cc_start: 0.7873 (pm20) cc_final: 0.7629 (pm20) REVERT: B 113 ASP cc_start: 0.8428 (t0) cc_final: 0.8193 (t70) REVERT: B 129 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: B 286 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: B 386 GLU cc_start: 0.7631 (pm20) cc_final: 0.7285 (tt0) REVERT: B 393 GLU cc_start: 0.8612 (tp30) cc_final: 0.8398 (tp30) REVERT: C 75 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8052 (ttp80) REVERT: C 135 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: C 227 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7948 (mmm160) REVERT: C 301 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7488 (mtt90) REVERT: C 400 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: D 145 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8942 (ttpm) REVERT: D 241 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8169 (t70) REVERT: D 315 VAL cc_start: 0.9246 (t) cc_final: 0.8958 (p) REVERT: D 358 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8603 (tp) REVERT: D 367 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8868 (ptm) REVERT: D 495 MET cc_start: 0.8786 (mtp) cc_final: 0.8429 (mtp) REVERT: E 117 ASP cc_start: 0.8384 (p0) cc_final: 0.8105 (p0) REVERT: E 416 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7878 (ttmt) REVERT: E 457 ASP cc_start: 0.8338 (m-30) cc_final: 0.8089 (m-30) REVERT: E 462 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7419 (t0) REVERT: F 7 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8473 (mtpm) REVERT: F 54 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7512 (tmm160) REVERT: F 97 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: F 450 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8184 (mmtm) outliers start: 65 outliers final: 35 residues processed: 352 average time/residue: 0.7785 time to fit residues: 312.9636 Evaluate side-chains 357 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 304 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 455 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 50 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN A 353 GLN A 378 HIS B 171 ASN C 171 ASN D 23 GLN D 160 HIS E 324 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.128057 restraints weight = 26301.128| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.33 r_work: 0.3377 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 26646 Z= 0.155 Angle : 0.524 8.675 36192 Z= 0.289 Chirality : 0.041 0.180 3900 Planarity : 0.004 0.047 4536 Dihedral : 12.012 145.687 3817 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.88 % Favored : 97.89 % Rotamer: Outliers : 2.30 % Allowed : 10.63 % Favored : 87.08 % 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: 1.40 (0.15), residues: 3078 helix: 1.75 (0.12), residues: 1752 sheet: -0.63 (0.34), residues: 204 loop : 0.03 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 134 TYR 0.020 0.002 TYR F 475 PHE 0.015 0.002 PHE F 140 TRP 0.013 0.002 TRP F 471 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (26646) covalent geometry : angle 0.52358 / 0.29 (36192) hydrogen bonds : bond 0.04922 / 3.27 ( 1334) hydrogen bonds : angle 4.29773 / 3.13 ( 3786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 310 time to evaluate : 1.214 Fit side-chains REVERT: A 460 LYS cc_start: 0.8182 (mtmp) cc_final: 0.7861 (mppt) REVERT: B 10 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8446 (tp) REVERT: B 11 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8701 (t80) REVERT: B 113 ASP cc_start: 0.8386 (t0) cc_final: 0.8149 (t70) REVERT: B 129 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: B 286 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: B 386 GLU cc_start: 0.7660 (pm20) cc_final: 0.7324 (tt0) REVERT: B 393 GLU cc_start: 0.8607 (tp30) cc_final: 0.8392 (tp30) REVERT: C 37 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7949 (mtt180) REVERT: C 75 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8051 (ttp80) REVERT: C 135 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: C 227 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7960 (mmm160) REVERT: C 301 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7438 (mtt90) REVERT: C 400 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: D 145 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8936 (ttpm) REVERT: D 241 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8192 (t70) REVERT: D 315 VAL cc_start: 0.9243 (t) cc_final: 0.8947 (p) REVERT: D 358 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8595 (tp) REVERT: D 367 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8879 (ptm) REVERT: D 495 MET cc_start: 0.8808 (mtp) cc_final: 0.8450 (mtp) REVERT: E 416 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7871 (ttmt) REVERT: E 457 ASP cc_start: 0.8321 (m-30) cc_final: 0.8064 (m-30) REVERT: E 462 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7427 (t0) REVERT: F 7 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8458 (mtpm) REVERT: F 54 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7495 (tmm160) REVERT: F 97 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: F 450 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8176 (mmtm) outliers start: 65 outliers final: 36 residues processed: 348 average time/residue: 0.7749 time to fit residues: 308.3457 Evaluate side-chains 361 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 306 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 144 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 206 optimal weight: 0.0980 chunk 180 optimal weight: 0.4980 chunk 104 optimal weight: 0.2980 chunk 238 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN B 95 ASN B 171 ASN C 171 ASN D 23 GLN D 160 HIS E 324 GLN F 95 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132078 restraints weight = 26462.579| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.32 r_work: 0.3425 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26646 Z= 0.104 Angle : 0.470 9.125 36192 Z= 0.259 Chirality : 0.039 0.189 3900 Planarity : 0.004 0.045 4536 Dihedral : 11.813 143.269 3817 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.08 % Favored : 97.69 % Rotamer: Outliers : 1.52 % Allowed : 11.51 % Favored : 86.97 % 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: 1.73 (0.15), residues: 3078 helix: 2.08 (0.12), residues: 1716 sheet: -0.62 (0.34), residues: 204 loop : 0.16 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 134 TYR 0.016 0.001 TYR B 349 PHE 0.009 0.001 PHE F 454 TRP 0.013 0.002 TRP F 471 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (26646) covalent geometry : angle 0.47029 / 0.26 (36192) hydrogen bonds : bond 0.03919 / 2.61 ( 1334) hydrogen bonds : angle 4.14808 / 3.02 ( 3786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 324 time to evaluate : 1.212 Fit side-chains REVERT: A 380 TYR cc_start: 0.7450 (m-80) cc_final: 0.6879 (m-80) REVERT: A 460 LYS cc_start: 0.8137 (mtmp) cc_final: 0.7839 (mppt) REVERT: B 10 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8485 (tp) REVERT: B 106 GLU cc_start: 0.7858 (pm20) cc_final: 0.7568 (pm20) REVERT: B 113 ASP cc_start: 0.8308 (t0) cc_final: 0.8057 (t70) REVERT: B 129 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7227 (tp30) REVERT: B 386 GLU cc_start: 0.7467 (pm20) cc_final: 0.7080 (tt0) REVERT: C 75 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.7979 (ttp80) REVERT: C 135 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: C 227 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7891 (mmm160) REVERT: C 400 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: C 462 ASP cc_start: 0.7892 (t70) cc_final: 0.7454 (t70) REVERT: D 241 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8116 (t70) REVERT: D 315 VAL cc_start: 0.9208 (t) cc_final: 0.8916 (p) REVERT: D 358 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8575 (tp) REVERT: E 307 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8436 (mt) REVERT: E 457 ASP cc_start: 0.8325 (m-30) cc_final: 0.8088 (m-30) REVERT: F 7 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8389 (mtpm) REVERT: F 54 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7504 (tmm160) REVERT: F 450 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8185 (mmtm) REVERT: F 488 ASN cc_start: 0.8491 (p0) cc_final: 0.8239 (p0) outliers start: 43 outliers final: 20 residues processed: 348 average time/residue: 0.7630 time to fit residues: 304.3375 Evaluate side-chains 342 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 311 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 103 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 0.0980 chunk 111 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 216 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN A 378 HIS B 171 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 ASN C 324 GLN D 23 GLN D 160 HIS E 324 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132091 restraints weight = 26464.326| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.33 r_work: 0.3426 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26646 Z= 0.107 Angle : 0.476 9.275 36192 Z= 0.261 Chirality : 0.039 0.187 3900 Planarity : 0.004 0.045 4536 Dihedral : 11.734 142.631 3817 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.92 % Favored : 97.86 % Rotamer: Outliers : 1.09 % Allowed : 11.94 % Favored : 86.97 % 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: 1.80 (0.15), residues: 3078 helix: 2.13 (0.12), residues: 1716 sheet: -0.54 (0.35), residues: 204 loop : 0.19 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 134 TYR 0.016 0.001 TYR B 349 PHE 0.009 0.001 PHE C 140 TRP 0.012 0.001 TRP B 471 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (26646) covalent geometry : angle 0.47614 / 0.26 (36192) hydrogen bonds : bond 0.03976 / 2.65 ( 1334) hydrogen bonds : angle 4.08737 / 2.98 ( 3786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10651.81 seconds wall clock time: 182 minutes 24.97 seconds (10944.97 seconds total)