Starting phenix.real_space_refine on Sun Jun 15 18:35:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e8o_27945/06_2025/8e8o_27945.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e8o_27945/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e8o_27945/06_2025/8e8o_27945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e8o_27945/06_2025/8e8o_27945.map" model { file = "/net/cci-nas-00/data/ceres_data/8e8o_27945/06_2025/8e8o_27945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e8o_27945/06_2025/8e8o_27945.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 9.71, per 1000 atoms: 0.55 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: 4.68 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.08 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: 5.80 Time building geometry restraints manager: 5.46 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 40.780 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP A 319 HIS 0.005 0.001 HIS A 200 PHE 0.017 0.002 PHE D 445 TYR 0.015 0.002 TYR D 74 ARG 0.005 0.001 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.17832 ( 788) hydrogen bonds : angle 7.28684 ( 2232) covalent geometry : bond 0.00744 (18100) covalent geometry : angle 0.74507 (24560) *********************** 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 : 2.080 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: 1.5291 time to fit residues: 190.6403 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 : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 D 395 ASN D 474 GLN D 479 GLN D 554 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.040541 restraints weight = 62212.795| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.46 r_work: 0.2542 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18100 Z= 0.128 Angle : 0.597 9.477 24560 Z= 0.300 Chirality : 0.042 0.156 2744 Planarity : 0.004 0.035 3152 Dihedral : 9.877 58.742 2696 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2216 helix: -0.35 (0.15), residues: 1084 sheet: -1.72 (0.39), residues: 192 loop : -1.59 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 319 HIS 0.004 0.001 HIS A 200 PHE 0.015 0.002 PHE D 445 TYR 0.018 0.002 TYR A 517 ARG 0.003 0.000 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 788) hydrogen bonds : angle 4.76588 ( 2232) covalent geometry : bond 0.00280 (18100) covalent geometry : angle 0.59749 (24560) *********************** 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 100 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 2.022 Fit side-chains REVERT: A 196 ILE cc_start: 0.9250 (pt) cc_final: 0.8840 (pp) REVERT: B 196 ILE cc_start: 0.9244 (pt) cc_final: 0.8832 (pp) REVERT: C 196 ILE cc_start: 0.9248 (pt) cc_final: 0.8839 (pp) REVERT: D 196 ILE cc_start: 0.9247 (pt) cc_final: 0.8840 (pp) outliers start: 16 outliers final: 4 residues processed: 96 average time/residue: 1.1014 time to fit residues: 123.4342 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 : 2.054 ------------------------------------------------------------------------------- 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 147 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 214 optimal weight: 8.9990 chunk 8 optimal weight: 0.2980 chunk 140 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- 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 = 0.3058 r_free = 0.3058 target = 0.050947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.037738 restraints weight = 64514.840| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.38 r_work: 0.2469 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18100 Z= 0.276 Angle : 0.645 8.193 24560 Z= 0.318 Chirality : 0.044 0.152 2744 Planarity : 0.004 0.033 3152 Dihedral : 9.320 59.990 2696 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.28 % Allowed : 10.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2216 helix: 0.35 (0.16), residues: 1088 sheet: -1.73 (0.39), residues: 192 loop : -1.49 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 127 HIS 0.004 0.001 HIS B 115 PHE 0.014 0.002 PHE D 445 TYR 0.016 0.002 TYR D 517 ARG 0.003 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 788) hydrogen bonds : angle 4.70744 ( 2232) covalent geometry : bond 0.00607 (18100) covalent geometry : angle 0.64459 (24560) *********************** 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: 24 poor density : 72 time to evaluate : 3.326 Fit side-chains REVERT: A 15 MET cc_start: 0.9323 (mtm) cc_final: 0.8955 (mtm) REVERT: B 15 MET cc_start: 0.9319 (mtm) cc_final: 0.8946 (mtm) REVERT: C 15 MET cc_start: 0.9314 (mtm) cc_final: 0.8940 (mtm) REVERT: D 15 MET cc_start: 0.9321 (mtm) cc_final: 0.8947 (mtm) outliers start: 24 outliers final: 4 residues processed: 88 average time/residue: 1.2385 time to fit residues: 126.4134 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 : 1.948 ------------------------------------------------------------------------------- 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 188 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 204 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.3078 r_free = 0.3078 target = 0.051663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.038485 restraints weight = 62552.729| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.48 r_work: 0.2497 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2069 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= 0.165 Angle : 0.570 9.052 24560 Z= 0.281 Chirality : 0.042 0.160 2744 Planarity : 0.003 0.033 3152 Dihedral : 9.091 59.532 2696 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.49 % Allowed : 11.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2216 helix: 0.65 (0.16), residues: 1096 sheet: -1.73 (0.39), residues: 192 loop : -1.23 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 319 HIS 0.002 0.001 HIS C 200 PHE 0.017 0.001 PHE D 445 TYR 0.013 0.001 TYR D 517 ARG 0.002 0.000 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 788) hydrogen bonds : angle 4.48026 ( 2232) covalent geometry : bond 0.00371 (18100) covalent geometry : angle 0.56980 (24560) *********************** 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 100 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 2.231 Fit side-chains REVERT: A 15 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8925 (mtm) REVERT: A 351 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9301 (tt) REVERT: B 15 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8920 (mtm) REVERT: B 351 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9300 (tt) REVERT: C 15 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8928 (mtm) REVERT: C 351 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9300 (tt) REVERT: D 15 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8915 (mtm) REVERT: D 351 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9298 (tt) outliers start: 28 outliers final: 4 residues processed: 92 average time/residue: 1.1689 time to fit residues: 125.2556 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 : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 351 LEU 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 98 optimal weight: 20.0000 chunk 219 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 205 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 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 = 0.3063 r_free = 0.3063 target = 0.050898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.037901 restraints weight = 63496.094| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 3.39 r_work: 0.2482 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18100 Z= 0.210 Angle : 0.597 10.118 24560 Z= 0.290 Chirality : 0.043 0.152 2744 Planarity : 0.003 0.032 3152 Dihedral : 8.983 59.818 2696 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.28 % Allowed : 13.19 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2216 helix: 0.76 (0.16), residues: 1096 sheet: -1.66 (0.39), residues: 192 loop : -1.14 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 546 HIS 0.002 0.001 HIS C 336 PHE 0.014 0.001 PHE B 445 TYR 0.014 0.002 TYR A 517 ARG 0.002 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 788) hydrogen bonds : angle 4.48564 ( 2232) covalent geometry : bond 0.00467 (18100) covalent geometry : angle 0.59688 (24560) *********************** 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 : 2.149 Fit side-chains REVERT: A 15 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.9025 (mtm) REVERT: B 15 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.9033 (mtm) REVERT: C 15 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.9025 (mtm) REVERT: D 15 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.9021 (mtm) outliers start: 24 outliers final: 8 residues processed: 88 average time/residue: 1.1500 time to fit residues: 117.0484 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 : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 15 MET 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 29 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 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 = 0.3068 r_free = 0.3068 target = 0.051157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.037927 restraints weight = 63126.714| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.50 r_work: 0.2480 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2379 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= 0.205 Angle : 0.593 9.065 24560 Z= 0.287 Chirality : 0.043 0.154 2744 Planarity : 0.003 0.032 3152 Dihedral : 8.888 59.917 2696 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.28 % Allowed : 13.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2216 helix: 0.86 (0.16), residues: 1096 sheet: -1.59 (0.39), residues: 192 loop : -1.09 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 319 HIS 0.002 0.001 HIS D 200 PHE 0.015 0.001 PHE A 445 TYR 0.013 0.001 TYR A 517 ARG 0.002 0.000 ARG D 202 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 788) hydrogen bonds : angle 4.45525 ( 2232) covalent geometry : bond 0.00458 (18100) covalent geometry : angle 0.59299 (24560) *********************** 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 100 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 2.094 Fit side-chains REVERT: A 15 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.9011 (mtm) REVERT: B 15 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.9018 (mtm) REVERT: C 15 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.9028 (mtm) REVERT: D 15 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.9019 (mtm) outliers start: 24 outliers final: 4 residues processed: 92 average time/residue: 1.3857 time to fit residues: 144.1099 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 : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 15 MET 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 131 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 198 optimal weight: 0.3980 chunk 75 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.050836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.037685 restraints weight = 63337.016| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 3.48 r_work: 0.2473 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18100 Z= 0.229 Angle : 0.641 10.344 24560 Z= 0.310 Chirality : 0.043 0.152 2744 Planarity : 0.003 0.032 3152 Dihedral : 8.972 59.936 2696 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.28 % Allowed : 14.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2216 helix: 0.90 (0.16), residues: 1096 sheet: -1.63 (0.39), residues: 192 loop : -1.05 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 319 HIS 0.002 0.001 HIS D 200 PHE 0.014 0.001 PHE C 445 TYR 0.013 0.002 TYR B 517 ARG 0.002 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 788) hydrogen bonds : angle 4.50550 ( 2232) covalent geometry : bond 0.00512 (18100) covalent geometry : angle 0.64130 (24560) *********************** 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 96 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 2.106 Fit side-chains REVERT: A 15 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9047 (mtm) REVERT: B 15 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9041 (mtm) REVERT: C 15 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.9044 (mtm) REVERT: D 15 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.9045 (mtm) outliers start: 24 outliers final: 8 residues processed: 84 average time/residue: 1.3290 time to fit residues: 128.1723 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 : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 64 optimal weight: 0.3980 chunk 171 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3109 r_free = 0.3109 target = 0.052725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.039752 restraints weight = 62244.172| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.48 r_work: 0.2537 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2658 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= 0.107 Angle : 0.600 11.740 24560 Z= 0.286 Chirality : 0.042 0.153 2744 Planarity : 0.003 0.032 3152 Dihedral : 9.012 59.295 2696 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2216 helix: 0.93 (0.16), residues: 1076 sheet: -1.58 (0.39), residues: 192 loop : -0.97 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 127 HIS 0.003 0.001 HIS D 200 PHE 0.017 0.001 PHE D 445 TYR 0.013 0.001 TYR A 208 ARG 0.002 0.000 ARG D 356 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 788) hydrogen bonds : angle 4.37342 ( 2232) covalent geometry : bond 0.00247 (18100) covalent geometry : angle 0.60044 (24560) *********************** 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 92 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 2.251 Fit side-chains REVERT: A 15 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8732 (mtm) REVERT: B 15 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8730 (mtm) REVERT: C 15 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8729 (mtm) REVERT: D 15 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8726 (mtm) outliers start: 16 outliers final: 8 residues processed: 84 average time/residue: 1.7824 time to fit residues: 171.5411 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 : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 15 MET 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 172 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.3077 r_free = 0.3077 target = 0.051476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.038350 restraints weight = 63490.164| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.50 r_work: 0.2492 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18100 Z= 0.199 Angle : 0.660 13.562 24560 Z= 0.309 Chirality : 0.043 0.149 2744 Planarity : 0.003 0.032 3152 Dihedral : 8.931 59.722 2696 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.64 % Allowed : 15.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2216 helix: 1.02 (0.16), residues: 1076 sheet: -1.50 (0.39), residues: 192 loop : -0.93 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 319 HIS 0.002 0.001 HIS D 200 PHE 0.014 0.001 PHE C 445 TYR 0.012 0.001 TYR D 208 ARG 0.002 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 788) hydrogen bonds : angle 4.46083 ( 2232) covalent geometry : bond 0.00447 (18100) covalent geometry : angle 0.65993 (24560) *********************** 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 88 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 2.433 Fit side-chains REVERT: A 15 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8883 (mtm) REVERT: B 15 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8880 (mtm) REVERT: C 15 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8894 (mtm) REVERT: D 15 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8876 (mtm) outliers start: 12 outliers final: 4 residues processed: 84 average time/residue: 1.3667 time to fit residues: 130.9864 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 : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 358 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 145 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.052949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.039882 restraints weight = 62352.837| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.57 r_work: 0.2559 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18100 Z= 0.110 Angle : 0.638 13.674 24560 Z= 0.300 Chirality : 0.043 0.278 2744 Planarity : 0.003 0.037 3152 Dihedral : 8.750 58.561 2696 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.85 % Allowed : 14.47 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2216 helix: 0.98 (0.16), residues: 1076 sheet: -1.34 (0.39), residues: 192 loop : -0.94 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 127 HIS 0.003 0.001 HIS D 200 PHE 0.018 0.001 PHE B 445 TYR 0.014 0.001 TYR A 208 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 788) hydrogen bonds : angle 4.36961 ( 2232) covalent geometry : bond 0.00254 (18100) covalent geometry : angle 0.63794 (24560) ********************** 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 100 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 2.004 Fit side-chains REVERT: A 15 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8780 (mtm) REVERT: B 15 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8764 (mtm) REVERT: C 15 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8769 (mtm) REVERT: D 15 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8763 (mtm) outliers start: 16 outliers final: 4 residues processed: 92 average time/residue: 1.1897 time to fit residues: 126.4747 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 : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 15 MET Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 15 MET 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 193 optimal weight: 6.9990 chunk 63 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 178 optimal weight: 0.0970 chunk 140 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 176 optimal weight: 0.3980 chunk 47 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.052989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.039805 restraints weight = 62546.238| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.55 r_work: 0.2552 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2927 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= 0.117 Angle : 0.632 12.545 24560 Z= 0.295 Chirality : 0.042 0.146 2744 Planarity : 0.003 0.033 3152 Dihedral : 8.752 58.840 2696 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.85 % Allowed : 15.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2216 helix: 1.01 (0.16), residues: 1076 sheet: -1.15 (0.39), residues: 192 loop : -0.85 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 319 HIS 0.003 0.001 HIS D 200 PHE 0.015 0.001 PHE A 445 TYR 0.013 0.001 TYR B 208 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 788) hydrogen bonds : angle 4.37690 ( 2232) covalent geometry : bond 0.00271 (18100) covalent geometry : angle 0.63238 (24560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9025.85 seconds wall clock time: 163 minutes 6.64 seconds (9786.64 seconds total)