Starting phenix.real_space_refine on Sat Jul 4 02:09:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e8o_27945/07_2026/8e8o_27945.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e8o_27945/07_2026/8e8o_27945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e8o_27945/07_2026/8e8o_27945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e8o_27945/07_2026/8e8o_27945.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e8o_27945/07_2026/8e8o_27945.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e8o_27945/07_2026/8e8o_27945.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e8o_27945/07_2026/8e8o_27945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e8o_27945/07_2026/8e8o_27945.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 12 5.49 5 S 92 5.16 5 C 11284 2.51 5 N 3040 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17704 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4378 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 529} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.14, per 1000 atoms: 0.23 Number of scatterers: 17704 At special positions: 0 Unit cell: (132.08, 80.08, 134.16, 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 92 16.00 P 12 15.00 O 3276 8.00 N 3040 7.00 C 11284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 991.8 milliseconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4112 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 12 sheets defined 57.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.793A pdb=" N ASP A 4 " --> pdb=" O ARG A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.818A pdb=" N ASP A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 91 through 99 removed outlier: 3.772A pdb=" N LEU A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.876A pdb=" N TRP A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 205 through 224 Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.682A pdb=" N ALA A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 290 through 307 removed outlier: 3.523A pdb=" N GLY A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.954A pdb=" N MET A 340 " --> pdb=" O HIS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 removed outlier: 4.146A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.882A pdb=" N PHE A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 476 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.537A pdb=" N GLN A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 511 removed outlier: 3.555A pdb=" N LYS A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'B' and resid 1 through 6 removed outlier: 3.793A pdb=" N ASP B 4 " --> pdb=" O ARG B 1 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.818A pdb=" N ASP B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 89 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 91 through 99 removed outlier: 3.772A pdb=" N LEU B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.876A pdb=" N TRP B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 205 through 224 Processing helix chain 'B' and resid 235 through 246 Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.682A pdb=" N ALA B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 290 through 307 removed outlier: 3.523A pdb=" N GLY B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 316 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.954A pdb=" N MET B 340 " --> pdb=" O HIS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 removed outlier: 4.146A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'B' and resid 444 through 456 Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.882A pdb=" N PHE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 removed outlier: 3.537A pdb=" N GLN B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 492 through 511 removed outlier: 3.555A pdb=" N LYS B 503 " --> pdb=" O ARG B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.793A pdb=" N ASP C 4 " --> pdb=" O ARG C 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.818A pdb=" N ASP C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.772A pdb=" N LEU C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.876A pdb=" N TRP C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 205 through 224 Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.682A pdb=" N ALA C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 290 through 307 removed outlier: 3.523A pdb=" N GLY C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.954A pdb=" N MET C 340 " --> pdb=" O HIS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 358 removed outlier: 4.146A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 440 through 443 Processing helix chain 'C' and resid 444 through 456 Processing helix chain 'C' and resid 461 through 476 removed outlier: 3.882A pdb=" N PHE C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 476 " --> pdb=" O ILE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 483 removed outlier: 3.537A pdb=" N GLN C 483 " --> pdb=" O GLN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 492 through 511 removed outlier: 3.555A pdb=" N LYS C 503 " --> pdb=" O ARG C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 529 Processing helix chain 'D' and resid 1 through 6 removed outlier: 3.793A pdb=" N ASP D 4 " --> pdb=" O ARG D 1 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 17 Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.818A pdb=" N ASP D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 91 through 99 removed outlier: 3.772A pdb=" N LEU D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.876A pdb=" N TRP D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 154 through 167 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 205 through 224 Processing helix chain 'D' and resid 235 through 246 Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.682A pdb=" N ALA D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 290 through 307 removed outlier: 3.523A pdb=" N GLY D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.954A pdb=" N MET D 340 " --> pdb=" O HIS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 358 removed outlier: 4.146A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 385 Processing helix chain 'D' and resid 403 through 411 Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.882A pdb=" N PHE D 465 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 476 " --> pdb=" O ILE D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 483 removed outlier: 3.537A pdb=" N GLN D 483 " --> pdb=" O GLN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 492 through 511 removed outlier: 3.555A pdb=" N LYS D 503 " --> pdb=" O ARG D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 529 Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA A 134 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 178 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 136 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU A 180 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR A 138 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 135 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU A 232 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 137 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.259A pdb=" N VAL A 285 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 437 " --> pdb=" O PHE A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA B 134 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 178 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 136 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU B 180 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR B 138 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 135 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU B 232 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 137 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.259A pdb=" N VAL B 285 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY B 437 " --> pdb=" O PHE B 417 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 426 through 427 Processing sheet with id=AA7, first strand: chain 'C' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA C 134 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL C 178 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 136 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU C 180 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR C 138 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL C 135 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU C 232 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 137 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.259A pdb=" N VAL C 285 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY C 437 " --> pdb=" O PHE C 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 426 through 427 Processing sheet with id=AB1, first strand: chain 'D' and resid 110 through 113 removed outlier: 6.797A pdb=" N ALA D 134 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL D 178 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL D 136 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU D 180 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR D 138 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL D 135 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU D 232 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D 137 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.259A pdb=" N VAL D 285 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY D 437 " --> pdb=" O PHE D 417 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 426 through 427 788 hydrogen bonds defined for protein. 2232 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: 3.02 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4972 1.33 - 1.45: 2836 1.45 - 1.57: 10124 1.57 - 1.68: 20 1.68 - 1.80: 148 Bond restraints: 18100 Sorted by residual: bond pdb=" O2B NAP D 601 " pdb=" P2B NAP D 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" O2B NAP B 601 " pdb=" P2B NAP B 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" O2B NAP C 601 " pdb=" P2B NAP C 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" O2B NAP A 601 " pdb=" P2B NAP A 601 " ideal model delta sigma weight residual 1.736 1.608 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C4A NAP D 601 " pdb=" C5A NAP D 601 " ideal model delta sigma weight residual 1.385 1.465 -0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 18095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 23812 1.81 - 3.61: 604 3.61 - 5.42: 104 5.42 - 7.22: 24 7.22 - 9.03: 16 Bond angle restraints: 24560 Sorted by residual: angle pdb=" N LYS C 324 " pdb=" CA LYS C 324 " pdb=" C LYS C 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N LYS B 324 " pdb=" CA LYS B 324 " pdb=" C LYS B 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N LYS D 324 " pdb=" CA LYS D 324 " pdb=" C LYS D 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N LYS A 324 " pdb=" CA LYS A 324 " pdb=" C LYS A 324 " ideal model delta sigma weight residual 114.75 109.88 4.87 1.26e+00 6.30e-01 1.50e+01 angle pdb=" C2A NAP B 601 " pdb=" N3A NAP B 601 " pdb=" C4A NAP B 601 " ideal model delta sigma weight residual 111.82 120.85 -9.03 3.00e+00 1.11e-01 9.05e+00 ... (remaining 24555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 9660 17.26 - 34.51: 984 34.51 - 51.77: 148 51.77 - 69.03: 32 69.03 - 86.29: 8 Dihedral angle restraints: 10832 sinusoidal: 4408 harmonic: 6424 Sorted by residual: dihedral pdb=" CA GLY C 330 " pdb=" C GLY C 330 " pdb=" N ARG C 331 " pdb=" CA ARG C 331 " ideal model delta harmonic sigma weight residual 180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLY B 330 " pdb=" C GLY B 330 " pdb=" N ARG B 331 " pdb=" CA ARG B 331 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLY D 330 " pdb=" C GLY D 330 " pdb=" N ARG D 331 " pdb=" CA ARG D 331 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 10829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1656 0.039 - 0.079: 832 0.079 - 0.118: 212 0.118 - 0.158: 36 0.158 - 0.197: 8 Chirality restraints: 2744 Sorted by residual: chirality pdb=" C1B NAP A 601 " pdb=" C2B NAP A 601 " pdb=" N9A NAP A 601 " pdb=" O4B NAP A 601 " both_signs ideal model delta sigma weight residual False 2.31 2.51 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C1B NAP C 601 " pdb=" C2B NAP C 601 " pdb=" N9A NAP C 601 " pdb=" O4B NAP C 601 " both_signs ideal model delta sigma weight residual False 2.31 2.51 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C1B NAP B 601 " pdb=" C2B NAP B 601 " pdb=" N9A NAP B 601 " pdb=" O4B NAP B 601 " both_signs ideal model delta sigma weight residual False 2.31 2.51 -0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 2741 not shown) Planarity restraints: 3152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 345 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO D 346 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 346 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 346 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 345 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 346 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 346 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 346 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 345 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO C 346 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 346 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 346 " -0.018 5.00e-02 4.00e+02 ... (remaining 3149 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 480 2.70 - 3.25: 18532 3.25 - 3.80: 30784 3.80 - 4.35: 41384 4.35 - 4.90: 66248 Nonbonded interactions: 157428 Sorted by model distance: nonbonded pdb=" OG SER B 350 " pdb=" OE1 GLU B 353 " model vdw 2.148 3.040 nonbonded pdb=" OG SER A 350 " pdb=" OE1 GLU A 353 " model vdw 2.148 3.040 nonbonded pdb=" OG SER C 350 " pdb=" OE1 GLU C 353 " model vdw 2.148 3.040 nonbonded pdb=" OG SER D 350 " pdb=" OE1 GLU D 353 " model vdw 2.148 3.040 nonbonded pdb=" OG SER A 394 " pdb=" OE2 GLU A 401 " model vdw 2.186 3.040 ... (remaining 157423 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.630 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.007 0.128 18100 Z= 0.331 Angle : 0.745 9.026 24560 Z= 0.382 Chirality : 0.047 0.197 2744 Planarity : 0.004 0.032 3152 Dihedral : 13.977 86.285 6720 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.16), residues: 2216 helix: -1.69 (0.14), residues: 1044 sheet: -2.52 (0.34), residues: 216 loop : -1.73 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 387 TYR 0.015 0.002 TYR D 74 PHE 0.017 0.002 PHE D 445 TRP 0.005 0.001 TRP A 319 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.33 (18100) covalent geometry : angle 0.74507 / 0.38 (24560) hydrogen bonds : bond 0.17832 / 11.76 ( 788) hydrogen bonds : angle 7.28684 / 5.23 ( 2232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.7241 time to fit residues: 90.1330 Evaluate side-chains 76 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 52 GLN A 66 GLN A 226 ASN A 282 HIS A 335 ASN A 385 HIS A 395 ASN A 474 GLN A 479 GLN A 554 GLN B 8 ASN B 52 GLN B 66 GLN B 226 ASN B 282 HIS B 335 ASN ** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 474 GLN B 479 GLN B 554 GLN C 8 ASN C 52 GLN C 66 GLN C 226 ASN C 282 HIS C 335 ASN C 385 HIS C 395 ASN C 474 GLN C 479 GLN C 554 GLN D 8 ASN D 52 GLN D 66 GLN D 226 ASN D 282 HIS D 335 ASN ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN D 474 GLN D 479 GLN D 554 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.052233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.039074 restraints weight = 63319.059| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 3.40 r_work: 0.2497 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18100 Z= 0.195 Angle : 0.626 9.555 24560 Z= 0.313 Chirality : 0.043 0.154 2744 Planarity : 0.004 0.034 3152 Dihedral : 6.466 49.286 2512 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.85 % Allowed : 9.36 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.50 (0.17), residues: 2216 helix: -0.22 (0.15), residues: 1084 sheet: -1.77 (0.39), residues: 192 loop : -1.68 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.019 0.002 TYR B 517 PHE 0.015 0.002 PHE A 445 TRP 0.002 0.001 TRP C 546 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (18100) covalent geometry : angle 0.62586 / 0.31 (24560) hydrogen bonds : bond 0.04218 / 2.79 ( 788) hydrogen bonds : angle 4.83324 / 3.45 ( 2232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.782 Fit side-chains REVERT: A 15 MET cc_start: 0.9238 (mtm) cc_final: 0.8914 (mtm) REVERT: A 196 ILE cc_start: 0.9260 (pt) cc_final: 0.8827 (pp) REVERT: B 15 MET cc_start: 0.9234 (mtm) cc_final: 0.8909 (mtm) REVERT: B 196 ILE cc_start: 0.9249 (pt) cc_final: 0.8815 (pp) REVERT: C 15 MET cc_start: 0.9222 (mtm) cc_final: 0.8894 (mtm) REVERT: C 196 ILE cc_start: 0.9260 (pt) cc_final: 0.8827 (pp) REVERT: D 15 MET cc_start: 0.9219 (mtm) cc_final: 0.8893 (mtm) REVERT: D 196 ILE cc_start: 0.9255 (pt) cc_final: 0.8820 (pp) outliers start: 16 outliers final: 4 residues processed: 92 average time/residue: 0.5206 time to fit residues: 55.5611 Evaluate side-chains 80 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 193 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 385 HIS D 385 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.052958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.039664 restraints weight = 63621.499| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.47 r_work: 0.2523 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18100 Z= 0.135 Angle : 0.568 8.672 24560 Z= 0.279 Chirality : 0.042 0.153 2744 Planarity : 0.003 0.033 3152 Dihedral : 6.023 45.185 2512 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.06 % Allowed : 10.85 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2216 helix: 0.27 (0.16), residues: 1092 sheet: -1.60 (0.39), residues: 192 loop : -1.44 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.014 0.001 TYR C 517 PHE 0.016 0.001 PHE A 445 TRP 0.003 0.001 TRP B 319 HIS 0.002 0.001 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (18100) covalent geometry : angle 0.56809 / 0.28 (24560) hydrogen bonds : bond 0.03601 / 2.40 ( 788) hydrogen bonds : angle 4.56580 / 3.25 ( 2232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.830 Fit side-chains REVERT: A 15 MET cc_start: 0.9186 (mtm) cc_final: 0.8891 (mtm) REVERT: A 196 ILE cc_start: 0.9256 (pt) cc_final: 0.8837 (pp) REVERT: B 15 MET cc_start: 0.9168 (mtm) cc_final: 0.8872 (mtm) REVERT: B 196 ILE cc_start: 0.9245 (pt) cc_final: 0.8826 (pp) REVERT: C 15 MET cc_start: 0.9169 (mtm) cc_final: 0.8872 (mtm) REVERT: C 196 ILE cc_start: 0.9249 (pt) cc_final: 0.8829 (pp) REVERT: D 15 MET cc_start: 0.9169 (mtm) cc_final: 0.8875 (mtm) REVERT: D 196 ILE cc_start: 0.9248 (pt) cc_final: 0.8828 (pp) outliers start: 20 outliers final: 4 residues processed: 88 average time/residue: 0.5436 time to fit residues: 55.1765 Evaluate side-chains 80 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 127 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.052737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.039662 restraints weight = 63071.008| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.45 r_work: 0.2526 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18100 Z= 0.140 Angle : 0.560 9.160 24560 Z= 0.274 Chirality : 0.042 0.155 2744 Planarity : 0.003 0.033 3152 Dihedral : 5.692 48.091 2512 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.06 % Allowed : 12.13 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.18), residues: 2216 helix: 0.59 (0.16), residues: 1088 sheet: -1.52 (0.39), residues: 192 loop : -1.18 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 108 TYR 0.013 0.001 TYR C 517 PHE 0.016 0.001 PHE A 445 TRP 0.002 0.000 TRP B 319 HIS 0.002 0.001 HIS C 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (18100) covalent geometry : angle 0.56015 / 0.27 (24560) hydrogen bonds : bond 0.03348 / 2.22 ( 788) hydrogen bonds : angle 4.40356 / 3.12 ( 2232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.745 Fit side-chains REVERT: A 15 MET cc_start: 0.9142 (mtm) cc_final: 0.8832 (mtm) REVERT: A 196 ILE cc_start: 0.9277 (pt) cc_final: 0.8836 (pp) REVERT: B 15 MET cc_start: 0.9144 (mtm) cc_final: 0.8837 (mtm) REVERT: B 196 ILE cc_start: 0.9263 (pt) cc_final: 0.8824 (pp) REVERT: C 15 MET cc_start: 0.9137 (mtm) cc_final: 0.8827 (mtm) REVERT: C 196 ILE cc_start: 0.9266 (pt) cc_final: 0.8828 (pp) REVERT: D 15 MET cc_start: 0.9128 (mtm) cc_final: 0.8818 (mtm) REVERT: D 196 ILE cc_start: 0.9269 (pt) cc_final: 0.8830 (pp) outliers start: 20 outliers final: 4 residues processed: 92 average time/residue: 0.5311 time to fit residues: 56.5211 Evaluate side-chains 80 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 16 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.051187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.038166 restraints weight = 63853.837| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 3.39 r_work: 0.2489 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18100 Z= 0.209 Angle : 0.592 10.114 24560 Z= 0.288 Chirality : 0.042 0.153 2744 Planarity : 0.003 0.031 3152 Dihedral : 5.417 52.224 2512 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.06 % Allowed : 12.77 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2216 helix: 0.78 (0.16), residues: 1096 sheet: -1.47 (0.39), residues: 192 loop : -1.12 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.014 0.001 TYR C 517 PHE 0.015 0.001 PHE D 445 TRP 0.002 0.001 TRP D 319 HIS 0.002 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (18100) covalent geometry : angle 0.59185 / 0.29 (24560) hydrogen bonds : bond 0.03383 / 2.25 ( 788) hydrogen bonds : angle 4.44518 / 3.15 ( 2232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.733 Fit side-chains REVERT: A 15 MET cc_start: 0.9202 (mtm) cc_final: 0.8836 (mtm) REVERT: B 15 MET cc_start: 0.9201 (mtm) cc_final: 0.8835 (mtm) REVERT: C 15 MET cc_start: 0.9201 (mtm) cc_final: 0.8832 (mtm) REVERT: D 15 MET cc_start: 0.9193 (mtm) cc_final: 0.8826 (mtm) outliers start: 20 outliers final: 4 residues processed: 88 average time/residue: 0.5509 time to fit residues: 55.9190 Evaluate side-chains 76 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 1 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 165 optimal weight: 0.0670 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.051972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.038936 restraints weight = 62842.090| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.47 r_work: 0.2522 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18100 Z= 0.133 Angle : 0.554 9.501 24560 Z= 0.269 Chirality : 0.042 0.155 2744 Planarity : 0.003 0.032 3152 Dihedral : 5.222 53.787 2512 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.85 % Allowed : 13.83 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 2216 helix: 0.87 (0.16), residues: 1096 sheet: -1.35 (0.40), residues: 192 loop : -1.08 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.013 0.001 TYR D 208 PHE 0.017 0.001 PHE A 445 TRP 0.001 0.000 TRP A 319 HIS 0.002 0.001 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (18100) covalent geometry : angle 0.55391 / 0.27 (24560) hydrogen bonds : bond 0.03186 / 2.12 ( 788) hydrogen bonds : angle 4.35062 / 3.08 ( 2232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.752 Fit side-chains REVERT: A 15 MET cc_start: 0.9123 (mtm) cc_final: 0.8754 (mtm) REVERT: B 15 MET cc_start: 0.9126 (mtm) cc_final: 0.8758 (mtm) REVERT: C 15 MET cc_start: 0.9118 (mtm) cc_final: 0.8745 (mtm) REVERT: D 15 MET cc_start: 0.9121 (mtm) cc_final: 0.8751 (mtm) outliers start: 16 outliers final: 8 residues processed: 88 average time/residue: 0.6102 time to fit residues: 61.2840 Evaluate side-chains 84 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 416 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 95 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.051881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.038863 restraints weight = 63495.279| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.45 r_work: 0.2514 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18100 Z= 0.159 Angle : 0.611 12.130 24560 Z= 0.290 Chirality : 0.042 0.158 2744 Planarity : 0.003 0.033 3152 Dihedral : 5.152 55.296 2512 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.85 % Allowed : 14.89 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2216 helix: 0.91 (0.16), residues: 1096 sheet: -1.36 (0.39), residues: 192 loop : -1.01 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 202 TYR 0.013 0.001 TYR D 208 PHE 0.015 0.001 PHE B 445 TRP 0.002 0.000 TRP B 319 HIS 0.002 0.001 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (18100) covalent geometry : angle 0.61078 / 0.29 (24560) hydrogen bonds : bond 0.03183 / 2.12 ( 788) hydrogen bonds : angle 4.35369 / 3.08 ( 2232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.727 Fit side-chains REVERT: A 15 MET cc_start: 0.9174 (mtm) cc_final: 0.8817 (mtm) REVERT: B 15 MET cc_start: 0.9166 (mtm) cc_final: 0.8811 (mtm) REVERT: C 15 MET cc_start: 0.9176 (mtm) cc_final: 0.8819 (mtm) REVERT: D 15 MET cc_start: 0.9176 (mtm) cc_final: 0.8822 (mtm) outliers start: 16 outliers final: 12 residues processed: 84 average time/residue: 0.5759 time to fit residues: 55.7259 Evaluate side-chains 84 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 416 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 193 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 chunk 119 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.053106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.039964 restraints weight = 62671.818| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.53 r_work: 0.2562 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18100 Z= 0.102 Angle : 0.591 13.197 24560 Z= 0.279 Chirality : 0.041 0.152 2744 Planarity : 0.003 0.034 3152 Dihedral : 5.097 55.704 2512 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.06 % Allowed : 14.79 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2216 helix: 0.95 (0.16), residues: 1076 sheet: -1.30 (0.38), residues: 216 loop : -0.88 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 108 TYR 0.014 0.001 TYR B 208 PHE 0.018 0.001 PHE D 445 TRP 0.001 0.000 TRP A 127 HIS 0.003 0.000 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (18100) covalent geometry : angle 0.59114 / 0.28 (24560) hydrogen bonds : bond 0.02972 / 1.98 ( 788) hydrogen bonds : angle 4.27783 / 3.01 ( 2232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.877 Fit side-chains REVERT: A 15 MET cc_start: 0.9142 (mtm) cc_final: 0.8682 (mtm) REVERT: B 15 MET cc_start: 0.9132 (mtm) cc_final: 0.8670 (mtm) REVERT: C 15 MET cc_start: 0.9129 (mtm) cc_final: 0.8667 (mtm) REVERT: D 15 MET cc_start: 0.9126 (mtm) cc_final: 0.8662 (mtm) outliers start: 20 outliers final: 4 residues processed: 96 average time/residue: 0.5077 time to fit residues: 56.7805 Evaluate side-chains 76 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 416 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 19 optimal weight: 7.9990 chunk 176 optimal weight: 0.0770 chunk 214 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 198 optimal weight: 0.0570 chunk 102 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.054031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.040682 restraints weight = 62430.513| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.61 r_work: 0.2572 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18100 Z= 0.104 Angle : 0.627 13.590 24560 Z= 0.292 Chirality : 0.043 0.281 2744 Planarity : 0.003 0.034 3152 Dihedral : 4.898 56.796 2512 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.43 % Allowed : 15.53 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.18), residues: 2216 helix: 0.98 (0.16), residues: 1068 sheet: -1.15 (0.38), residues: 216 loop : -0.79 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 108 TYR 0.014 0.001 TYR B 208 PHE 0.016 0.001 PHE D 445 TRP 0.001 0.000 TRP A 319 HIS 0.003 0.001 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (18100) covalent geometry : angle 0.62658 / 0.29 (24560) hydrogen bonds : bond 0.02918 / 1.94 ( 788) hydrogen bonds : angle 4.27379 / 3.01 ( 2232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.800 Fit side-chains REVERT: A 15 MET cc_start: 0.9171 (mtm) cc_final: 0.8771 (mtm) REVERT: A 395 ASN cc_start: 0.8970 (p0) cc_final: 0.8690 (m-40) REVERT: B 15 MET cc_start: 0.9175 (mtm) cc_final: 0.8773 (mtm) REVERT: B 395 ASN cc_start: 0.8975 (p0) cc_final: 0.8696 (m-40) REVERT: C 15 MET cc_start: 0.9181 (mtm) cc_final: 0.8782 (mtm) REVERT: C 395 ASN cc_start: 0.8967 (p0) cc_final: 0.8686 (m-40) REVERT: D 15 MET cc_start: 0.9166 (mtm) cc_final: 0.8764 (mtm) REVERT: D 395 ASN cc_start: 0.8972 (p0) cc_final: 0.8690 (m-40) outliers start: 8 outliers final: 8 residues processed: 88 average time/residue: 0.5486 time to fit residues: 55.7866 Evaluate side-chains 84 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 133 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS B 28 HIS C 28 HIS D 28 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.051947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.038911 restraints weight = 63242.348| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.52 r_work: 0.2512 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18100 Z= 0.195 Angle : 0.666 13.965 24560 Z= 0.311 Chirality : 0.044 0.270 2744 Planarity : 0.003 0.032 3152 Dihedral : 4.880 58.931 2512 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.32 % Allowed : 15.85 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2216 helix: 1.11 (0.16), residues: 1072 sheet: -1.25 (0.37), residues: 228 loop : -0.68 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.012 0.002 TYR B 208 PHE 0.013 0.001 PHE D 445 TRP 0.001 0.000 TRP B 546 HIS 0.003 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (18100) covalent geometry : angle 0.66621 / 0.31 (24560) hydrogen bonds : bond 0.03172 / 2.10 ( 788) hydrogen bonds : angle 4.38601 / 3.09 ( 2232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.786 Fit side-chains REVERT: A 15 MET cc_start: 0.9201 (mtm) cc_final: 0.8901 (mtm) REVERT: A 395 ASN cc_start: 0.8986 (p0) cc_final: 0.8659 (m110) REVERT: B 15 MET cc_start: 0.9199 (mtm) cc_final: 0.8899 (mtm) REVERT: B 395 ASN cc_start: 0.8987 (p0) cc_final: 0.8662 (m110) REVERT: C 15 MET cc_start: 0.9207 (mtm) cc_final: 0.8906 (mtm) REVERT: C 395 ASN cc_start: 0.8988 (p0) cc_final: 0.8660 (m110) REVERT: D 15 MET cc_start: 0.9205 (mtm) cc_final: 0.8905 (mtm) REVERT: D 395 ASN cc_start: 0.8984 (p0) cc_final: 0.8656 (m110) outliers start: 6 outliers final: 2 residues processed: 80 average time/residue: 0.5971 time to fit residues: 54.5952 Evaluate side-chains 74 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain D residue 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 162 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.039675 restraints weight = 62935.405| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.53 r_work: 0.2538 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18100 Z= 0.129 Angle : 0.633 12.490 24560 Z= 0.295 Chirality : 0.043 0.247 2744 Planarity : 0.003 0.033 3152 Dihedral : 4.855 59.242 2512 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.64 % Allowed : 15.53 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 2216 helix: 1.08 (0.16), residues: 1072 sheet: -1.19 (0.37), residues: 228 loop : -0.70 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 108 TYR 0.013 0.001 TYR D 208 PHE 0.016 0.001 PHE D 445 TRP 0.001 0.000 TRP A 127 HIS 0.003 0.001 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (18100) covalent geometry : angle 0.63337 / 0.29 (24560) hydrogen bonds : bond 0.03041 / 2.02 ( 788) hydrogen bonds : angle 4.33841 / 3.05 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3987.72 seconds wall clock time: 69 minutes 40.96 seconds (4180.96 seconds total)