Starting phenix.real_space_refine on Sun Aug 24 06:26:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e8o_27945/08_2025/8e8o_27945.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e8o_27945/08_2025/8e8o_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 { model { file = "/net/cci-nas-00/data/ceres_data/8e8o_27945/08_2025/8e8o_27945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e8o_27945/08_2025/8e8o_27945.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e8o_27945/08_2025/8e8o_27945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e8o_27945/08_2025/8e8o_27945.map" } 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-2.0-5787/lib/python3.9/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: 3.71, per 1000 atoms: 0.21 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: 1.31 Conformation dependent library (CDL) restraints added in 591.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.70 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: 3.15 Time building geometry restraints manager: 1.74 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: 9708 17.26 - 34.51: 1020 34.51 - 51.77: 236 51.77 - 69.03: 44 69.03 - 86.29: 8 Dihedral angle restraints: 11016 sinusoidal: 4592 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 11013 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: 0.04 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: 0.610 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 14.956 86.285 6904 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 aren 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 covalent geometry : bond 0.00744 (18100) covalent geometry : angle 0.74507 (24560) hydrogen bonds : bond 0.17832 ( 788) hydrogen bonds : angle 7.28684 ( 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 : 0.449 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: 0.6011 time to fit residues: 74.6013 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 : 0.470 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 28 HIS 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 28 HIS 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 D 395 ASN D 474 GLN D 479 GLN D 554 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.052290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.039074 restraints weight = 63259.994| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 3.37 r_work: 0.2496 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18100 Z= 0.201 Angle : 0.628 9.230 24560 Z= 0.314 Chirality : 0.043 0.158 2744 Planarity : 0.004 0.034 3152 Dihedral : 9.997 58.255 2696 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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 aren not related in a simple way. whole: -1.54 (0.17), residues: 2216 helix: -0.26 (0.15), residues: 1084 sheet: -1.78 (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 0.001 PHE A 445 TRP 0.002 0.001 TRP C 546 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00443 (18100) covalent geometry : angle 0.62767 (24560) hydrogen bonds : bond 0.04402 ( 788) hydrogen bonds : angle 4.89572 ( 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 98 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.650 Fit side-chains REVERT: A 15 MET cc_start: 0.9234 (mtm) cc_final: 0.8913 (mtm) REVERT: A 196 ILE cc_start: 0.9281 (pt) cc_final: 0.8846 (pp) REVERT: B 15 MET cc_start: 0.9221 (mtm) cc_final: 0.8901 (mtm) REVERT: B 196 ILE cc_start: 0.9274 (pt) cc_final: 0.8837 (pp) REVERT: C 15 MET cc_start: 0.9212 (mtm) cc_final: 0.8888 (mtm) REVERT: C 196 ILE cc_start: 0.9281 (pt) cc_final: 0.8842 (pp) REVERT: D 15 MET cc_start: 0.9209 (mtm) cc_final: 0.8890 (mtm) REVERT: D 196 ILE cc_start: 0.9279 (pt) cc_final: 0.8841 (pp) outliers start: 16 outliers final: 4 residues processed: 94 average time/residue: 0.4488 time to fit residues: 48.7579 Evaluate side-chains 82 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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: 9.9990 chunk 125 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 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: 10.0000 chunk 8 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.052819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.039619 restraints weight = 63379.014| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.45 r_work: 0.2515 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18100 Z= 0.148 Angle : 0.576 8.368 24560 Z= 0.284 Chirality : 0.042 0.153 2744 Planarity : 0.003 0.033 3152 Dihedral : 9.371 59.065 2696 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.06 % Allowed : 10.21 % Favored : 88.72 % 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 aren not related in a simple way. whole: -0.98 (0.17), residues: 2216 helix: 0.23 (0.16), residues: 1096 sheet: -1.65 (0.39), residues: 192 loop : -1.43 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.014 0.002 TYR C 517 PHE 0.016 0.001 PHE B 445 TRP 0.002 0.001 TRP B 319 HIS 0.002 0.001 HIS B 200 Details of bonding type rmsd covalent geometry : bond 0.00333 (18100) covalent geometry : angle 0.57633 (24560) hydrogen bonds : bond 0.03669 ( 788) hydrogen bonds : angle 4.59107 ( 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 : 0.419 Fit side-chains REVERT: A 15 MET cc_start: 0.9187 (mtm) cc_final: 0.8868 (mtm) REVERT: A 196 ILE cc_start: 0.9274 (pt) cc_final: 0.8834 (pp) REVERT: B 15 MET cc_start: 0.9174 (mtm) cc_final: 0.8854 (mtm) REVERT: B 196 ILE cc_start: 0.9269 (pt) cc_final: 0.8827 (pp) REVERT: C 15 MET cc_start: 0.9171 (mtm) cc_final: 0.8847 (mtm) REVERT: C 196 ILE cc_start: 0.9269 (pt) cc_final: 0.8828 (pp) REVERT: D 15 MET cc_start: 0.9166 (mtm) cc_final: 0.8846 (mtm) REVERT: D 196 ILE cc_start: 0.9269 (pt) cc_final: 0.8828 (pp) outliers start: 20 outliers final: 4 residues processed: 88 average time/residue: 0.4658 time to fit residues: 47.2428 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 : 0.448 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.039051 restraints weight = 62842.051| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.41 r_work: 0.2520 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2080 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= 0.152 Angle : 0.561 9.152 24560 Z= 0.276 Chirality : 0.042 0.155 2744 Planarity : 0.003 0.033 3152 Dihedral : 9.079 59.619 2696 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % 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 aren not related in a simple way. whole: -0.55 (0.18), residues: 2216 helix: 0.60 (0.16), residues: 1096 sheet: -1.64 (0.39), residues: 192 loop : -1.19 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 1 TYR 0.013 0.001 TYR C 517 PHE 0.016 0.001 PHE D 445 TRP 0.001 0.000 TRP D 546 HIS 0.002 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00341 (18100) covalent geometry : angle 0.56129 (24560) hydrogen bonds : bond 0.03348 ( 788) hydrogen bonds : angle 4.41515 ( 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 : 0.542 Fit side-chains REVERT: A 15 MET cc_start: 0.9183 (mtm) cc_final: 0.8879 (mtm) REVERT: A 196 ILE cc_start: 0.9275 (pt) cc_final: 0.8821 (pp) REVERT: A 252 MET cc_start: 0.9283 (ppp) cc_final: 0.9066 (tmm) REVERT: B 15 MET cc_start: 0.9172 (mtm) cc_final: 0.8868 (mtm) REVERT: B 196 ILE cc_start: 0.9262 (pt) cc_final: 0.8812 (pp) REVERT: B 252 MET cc_start: 0.9285 (ppp) cc_final: 0.9071 (tmm) REVERT: C 15 MET cc_start: 0.9176 (mtm) cc_final: 0.8872 (mtm) REVERT: C 196 ILE cc_start: 0.9266 (pt) cc_final: 0.8813 (pp) REVERT: C 252 MET cc_start: 0.9278 (ppp) cc_final: 0.9059 (tmm) REVERT: D 15 MET cc_start: 0.9164 (mtm) cc_final: 0.8859 (mtm) REVERT: D 196 ILE cc_start: 0.9266 (pt) cc_final: 0.8814 (pp) REVERT: D 252 MET cc_start: 0.9281 (ppp) cc_final: 0.9066 (tmm) outliers start: 20 outliers final: 4 residues processed: 92 average time/residue: 0.4945 time to fit residues: 52.4614 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 : 0.627 ------------------------------------------------------------------------------- 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: 2.9990 chunk 206 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.050928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.037919 restraints weight = 63439.956| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 3.39 r_work: 0.2484 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18100 Z= 0.207 Angle : 0.592 10.098 24560 Z= 0.288 Chirality : 0.042 0.154 2744 Planarity : 0.003 0.031 3152 Dihedral : 8.924 59.903 2696 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.28 % Allowed : 12.98 % Favored : 85.74 % 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 aren not related in a simple way. whole: -0.36 (0.18), residues: 2216 helix: 0.78 (0.16), residues: 1096 sheet: -1.58 (0.39), residues: 192 loop : -1.11 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 202 TYR 0.013 0.002 TYR C 517 PHE 0.015 0.001 PHE B 445 TRP 0.002 0.001 TRP A 546 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00457 (18100) covalent geometry : angle 0.59239 (24560) hydrogen bonds : bond 0.03392 ( 788) hydrogen bonds : angle 4.43874 ( 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 96 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.727 Fit side-chains REVERT: A 15 MET cc_start: 0.9211 (mtm) cc_final: 0.8854 (mtm) REVERT: B 15 MET cc_start: 0.9203 (mtm) cc_final: 0.8843 (mtm) REVERT: C 15 MET cc_start: 0.9201 (mtm) cc_final: 0.8838 (mtm) REVERT: D 15 MET cc_start: 0.9195 (mtm) cc_final: 0.8834 (mtm) outliers start: 24 outliers final: 12 residues processed: 92 average time/residue: 0.5477 time to fit residues: 58.3143 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 : 0.745 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 1 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.050516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.037299 restraints weight = 63313.651| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 3.48 r_work: 0.2472 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18100 Z= 0.269 Angle : 0.645 10.479 24560 Z= 0.312 Chirality : 0.044 0.154 2744 Planarity : 0.004 0.030 3152 Dihedral : 8.854 59.900 2696 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.33 % Allowed : 13.35 % 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 aren not related in a simple way. whole: -0.27 (0.18), residues: 2216 helix: 0.87 (0.16), residues: 1096 sheet: -1.58 (0.39), residues: 192 loop : -1.08 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 51 TYR 0.014 0.002 TYR D 517 PHE 0.014 0.001 PHE B 445 TRP 0.003 0.001 TRP B 319 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00597 (18100) covalent geometry : angle 0.64532 (24560) hydrogen bonds : bond 0.03558 ( 788) hydrogen bonds : angle 4.56483 ( 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 101 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.726 Fit side-chains REVERT: A 15 MET cc_start: 0.9260 (mtm) cc_final: 0.8883 (mtm) REVERT: B 15 MET cc_start: 0.9264 (mtm) cc_final: 0.8887 (mtm) REVERT: C 15 MET cc_start: 0.9268 (mtm) cc_final: 0.8894 (mtm) REVERT: D 15 MET cc_start: 0.9263 (mtm) cc_final: 0.8886 (mtm) outliers start: 25 outliers final: 8 residues processed: 96 average time/residue: 0.6419 time to fit residues: 69.8423 Evaluate side-chains 80 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 95 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.038780 restraints weight = 62824.444| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.53 r_work: 0.2516 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2522 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= 0.137 Angle : 0.614 11.030 24560 Z= 0.294 Chirality : 0.042 0.154 2744 Planarity : 0.003 0.031 3152 Dihedral : 8.985 59.055 2696 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.64 % Allowed : 14.47 % Favored : 84.89 % 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 aren not related in a simple way. whole: -0.21 (0.18), residues: 2216 helix: 0.90 (0.16), residues: 1100 sheet: -1.49 (0.39), residues: 192 loop : -1.05 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.013 0.001 TYR A 208 PHE 0.016 0.001 PHE A 445 TRP 0.002 0.001 TRP B 546 HIS 0.003 0.001 HIS B 200 Details of bonding type rmsd covalent geometry : bond 0.00314 (18100) covalent geometry : angle 0.61444 (24560) hydrogen bonds : bond 0.03232 ( 788) hydrogen bonds : angle 4.39234 ( 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 84 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.918 Fit side-chains REVERT: A 15 MET cc_start: 0.9161 (mtm) cc_final: 0.8816 (mtm) REVERT: A 252 MET cc_start: 0.9311 (ppp) cc_final: 0.9071 (tmm) REVERT: B 15 MET cc_start: 0.9161 (mtm) cc_final: 0.8813 (mtm) REVERT: B 252 MET cc_start: 0.9308 (ppp) cc_final: 0.9072 (tmm) REVERT: C 15 MET cc_start: 0.9158 (mtm) cc_final: 0.8810 (mtm) REVERT: C 252 MET cc_start: 0.9315 (ppp) cc_final: 0.9074 (tmm) REVERT: D 15 MET cc_start: 0.9155 (mtm) cc_final: 0.8806 (mtm) REVERT: D 252 MET cc_start: 0.9313 (ppp) cc_final: 0.9076 (tmm) outliers start: 12 outliers final: 12 residues processed: 80 average time/residue: 0.6116 time to fit residues: 56.0791 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 : 0.766 ------------------------------------------------------------------------------- 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: 3.9990 chunk 96 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.0030 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.052052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.038795 restraints weight = 62592.905| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 3.52 r_work: 0.2511 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18100 Z= 0.147 Angle : 0.604 11.805 24560 Z= 0.289 Chirality : 0.042 0.147 2744 Planarity : 0.003 0.032 3152 Dihedral : 8.936 59.328 2696 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.64 % Allowed : 14.89 % Favored : 84.47 % 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 aren not related in a simple way. whole: -0.12 (0.18), residues: 2216 helix: 0.97 (0.16), residues: 1076 sheet: -1.44 (0.39), residues: 192 loop : -0.96 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 108 TYR 0.012 0.001 TYR A 208 PHE 0.015 0.001 PHE C 445 TRP 0.001 0.000 TRP A 319 HIS 0.003 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00336 (18100) covalent geometry : angle 0.60414 (24560) hydrogen bonds : bond 0.03194 ( 788) hydrogen bonds : angle 4.39833 ( 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 84 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.695 Fit side-chains REVERT: A 15 MET cc_start: 0.9185 (mtm) cc_final: 0.8846 (mtm) REVERT: B 15 MET cc_start: 0.9174 (mtm) cc_final: 0.8833 (mtm) REVERT: C 15 MET cc_start: 0.9185 (mtm) cc_final: 0.8844 (mtm) REVERT: D 15 MET cc_start: 0.9175 (mtm) cc_final: 0.8834 (mtm) outliers start: 12 outliers final: 12 residues processed: 80 average time/residue: 0.6144 time to fit residues: 55.9020 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 : 0.712 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 19 optimal weight: 0.6980 chunk 176 optimal weight: 7.9990 chunk 214 optimal weight: 8.9990 chunk 74 optimal weight: 0.0030 chunk 215 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 198 optimal weight: 0.0040 chunk 102 optimal weight: 2.9990 overall best weight: 0.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.053518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.040339 restraints weight = 62440.408| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.56 r_work: 0.2571 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18100 Z= 0.103 Angle : 0.599 12.069 24560 Z= 0.284 Chirality : 0.042 0.151 2744 Planarity : 0.003 0.034 3152 Dihedral : 8.854 59.208 2696 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.85 % Allowed : 14.68 % Favored : 84.47 % 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 aren not related in a simple way. whole: -0.10 (0.17), residues: 2216 helix: 0.97 (0.16), residues: 1076 sheet: -1.32 (0.37), residues: 216 loop : -0.92 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 458 TYR 0.014 0.001 TYR A 208 PHE 0.017 0.001 PHE C 445 TRP 0.001 0.000 TRP D 127 HIS 0.003 0.001 HIS B 200 Details of bonding type rmsd covalent geometry : bond 0.00237 (18100) covalent geometry : angle 0.59937 (24560) hydrogen bonds : bond 0.02973 ( 788) hydrogen bonds : angle 4.31541 ( 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 100 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.770 Fit side-chains REVERT: A 15 MET cc_start: 0.9175 (mtm) cc_final: 0.8747 (mtm) REVERT: B 15 MET cc_start: 0.9171 (mtm) cc_final: 0.8741 (mtm) REVERT: C 15 MET cc_start: 0.9170 (mtm) cc_final: 0.8741 (mtm) REVERT: D 15 MET cc_start: 0.9168 (mtm) cc_final: 0.8739 (mtm) outliers start: 16 outliers final: 8 residues processed: 96 average time/residue: 0.5232 time to fit residues: 58.3455 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 : 0.767 ------------------------------------------------------------------------------- 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: 0.9980 chunk 123 optimal weight: 0.0470 chunk 72 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS D 28 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.052611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.039438 restraints weight = 62283.218| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.52 r_work: 0.2538 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2878 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= 0.141 Angle : 0.641 13.985 24560 Z= 0.301 Chirality : 0.043 0.280 2744 Planarity : 0.003 0.033 3152 Dihedral : 8.597 59.009 2696 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.21 % Allowed : 15.32 % Favored : 84.47 % 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 aren not related in a simple way. whole: -0.00 (0.18), residues: 2216 helix: 1.03 (0.16), residues: 1076 sheet: -1.19 (0.37), residues: 216 loop : -0.87 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.012 0.001 TYR A 208 PHE 0.015 0.001 PHE C 445 TRP 0.001 0.000 TRP B 319 HIS 0.003 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00323 (18100) covalent geometry : angle 0.64082 (24560) hydrogen bonds : bond 0.03058 ( 788) hydrogen bonds : angle 4.33898 ( 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 81 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.705 Fit side-chains REVERT: A 15 MET cc_start: 0.9189 (mtm) cc_final: 0.8749 (mtm) REVERT: A 395 ASN cc_start: 0.8871 (p0) cc_final: 0.8643 (m-40) REVERT: B 15 MET cc_start: 0.9190 (mtm) cc_final: 0.8752 (mtm) REVERT: B 395 ASN cc_start: 0.8912 (p0) cc_final: 0.8683 (m110) REVERT: C 15 MET cc_start: 0.9204 (mtm) cc_final: 0.8769 (mtm) REVERT: C 395 ASN cc_start: 0.8864 (p0) cc_final: 0.8638 (m-40) REVERT: D 15 MET cc_start: 0.9193 (mtm) cc_final: 0.8756 (mtm) REVERT: D 395 ASN cc_start: 0.8871 (p0) cc_final: 0.8643 (m-40) outliers start: 4 outliers final: 4 residues processed: 81 average time/residue: 0.6220 time to fit residues: 57.4755 Evaluate side-chains 81 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 162 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 180 optimal weight: 5.9990 chunk 8 optimal weight: 0.0040 chunk 197 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 184 optimal weight: 0.0060 chunk 189 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 overall best weight: 1.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.040017 restraints weight = 62386.793| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.55 r_work: 0.2564 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18100 Z= 0.115 Angle : 0.630 12.547 24560 Z= 0.296 Chirality : 0.043 0.266 2744 Planarity : 0.003 0.034 3152 Dihedral : 8.438 58.593 2696 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.43 % Allowed : 15.11 % Favored : 84.47 % 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 aren not related in a simple way. whole: 0.03 (0.17), residues: 2216 helix: 1.02 (0.16), residues: 1076 sheet: -1.09 (0.37), residues: 216 loop : -0.83 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.013 0.001 TYR C 208 PHE 0.016 0.001 PHE C 445 TRP 0.001 0.000 TRP B 319 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00266 (18100) covalent geometry : angle 0.63004 (24560) hydrogen bonds : bond 0.03003 ( 788) hydrogen bonds : angle 4.31496 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3811.13 seconds wall clock time: 66 minutes 50.54 seconds (4010.54 seconds total)