Starting phenix.real_space_refine on Fri Sep 27 20:01:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e78_27937/09_2024/8e78_27937.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e78_27937/09_2024/8e78_27937.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e78_27937/09_2024/8e78_27937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e78_27937/09_2024/8e78_27937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e78_27937/09_2024/8e78_27937.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e78_27937/09_2024/8e78_27937.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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 11200 2.51 5 N 3012 2.21 5 O 3208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17512 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, D Time building chain proxies: 9.16, per 1000 atoms: 0.52 Number of scatterers: 17512 At special positions: 0 Unit cell: (134.16, 132.08, 80.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3208 8.00 N 3012 7.00 C 11200 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: 4.17 Conformation dependent library (CDL) restraints added in 2.1 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: 124 helices and 12 sheets defined 55.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 removed outlier: 4.172A 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 25 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: 3.675A 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: 3.561A pdb=" N LEU A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) 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 125 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 205 through 224 Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.523A pdb=" N ALA A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.574A 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 292 through 307 removed outlier: 3.952A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.876A pdb=" N LYS A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.747A pdb=" N VAL A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.602A pdb=" N ALA A 400 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 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: 3.725A pdb=" N PHE A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 476 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 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 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'B' and resid 1 through 8 removed outlier: 4.172A 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 25 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: 3.675A 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: 3.561A pdb=" N LEU B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) 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 125 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 205 through 224 Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.524A pdb=" N ALA B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.573A 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 292 through 307 removed outlier: 3.952A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 removed outlier: 3.876A pdb=" N LYS B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 350 through 358 removed outlier: 3.747A pdb=" N VAL B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.602A pdb=" N ALA B 400 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 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: 3.725A pdb=" N PHE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 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 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'C' and resid 1 through 8 removed outlier: 4.172A 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 25 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: 3.675A 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: 3.562A pdb=" N LEU C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) 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 125 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 154 through 167 Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 205 through 224 Processing helix chain 'C' and resid 235 through 247 Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.524A pdb=" N ALA C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.573A 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 292 through 307 removed outlier: 3.951A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 317 removed outlier: 3.876A pdb=" N LYS C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 350 through 358 removed outlier: 3.748A pdb=" N VAL C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.602A pdb=" N ALA C 400 " --> pdb=" O THR C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 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: 3.725A pdb=" N PHE C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL C 476 " --> pdb=" O ILE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 483 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 Processing helix chain 'C' and resid 522 through 529 Processing helix chain 'D' and resid 1 through 8 removed outlier: 4.173A 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 25 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: 3.675A 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: 3.561A pdb=" N LEU D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) 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 125 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 154 through 167 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 205 through 224 Processing helix chain 'D' and resid 235 through 247 Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.524A pdb=" N ALA D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.573A 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 292 through 307 removed outlier: 3.951A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 removed outlier: 3.877A pdb=" N LYS D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 350 through 358 removed outlier: 3.748A pdb=" N VAL D 354 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 385 Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.601A pdb=" N ALA D 400 " --> pdb=" O THR D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 411 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: 3.724A pdb=" N PHE D 465 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D 476 " --> pdb=" O ILE D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 483 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 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: 6.428A pdb=" N LEU A 110 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP A 181 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 112 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 134 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL A 178 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 136 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU A 180 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 138 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.401A pdb=" N VAL A 285 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.142A 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: 6.428A pdb=" N LEU B 110 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 181 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 112 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 134 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL B 178 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 136 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 180 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR B 138 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.402A pdb=" N VAL B 285 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 4.141A 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: 6.428A pdb=" N LEU C 110 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP C 181 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 112 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA C 134 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL C 178 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL C 136 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU C 180 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR C 138 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.402A pdb=" N VAL C 285 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 4.142A 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: 6.428A pdb=" N LEU D 110 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP D 181 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 112 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA D 134 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL D 178 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL D 136 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU D 180 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR D 138 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.402A pdb=" N VAL D 285 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 4.142A 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 427 784 hydrogen bonds defined for protein. 2160 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: 5.98 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5760 1.34 - 1.46: 3094 1.46 - 1.57: 8890 1.57 - 1.69: 0 1.69 - 1.81: 148 Bond restraints: 17892 Sorted by residual: bond pdb=" C LEU C 176 " pdb=" O LEU C 176 " ideal model delta sigma weight residual 1.249 1.234 0.015 8.50e-03 1.38e+04 3.11e+00 bond pdb=" C LEU B 176 " pdb=" O LEU B 176 " ideal model delta sigma weight residual 1.249 1.234 0.015 8.50e-03 1.38e+04 3.11e+00 bond pdb=" C LEU A 176 " pdb=" O LEU A 176 " ideal model delta sigma weight residual 1.249 1.234 0.015 8.50e-03 1.38e+04 2.92e+00 bond pdb=" C LEU D 176 " pdb=" O LEU D 176 " ideal model delta sigma weight residual 1.249 1.235 0.014 8.50e-03 1.38e+04 2.76e+00 bond pdb=" CG LEU B 120 " pdb=" CD2 LEU B 120 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 ... (remaining 17887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 23041 1.26 - 2.52: 956 2.52 - 3.78: 179 3.78 - 5.04: 52 5.04 - 6.29: 12 Bond angle restraints: 24240 Sorted by residual: angle pdb=" N GLN A 173 " pdb=" CA GLN A 173 " pdb=" C GLN A 173 " ideal model delta sigma weight residual 114.56 111.55 3.01 1.27e+00 6.20e-01 5.62e+00 angle pdb=" N GLN C 173 " pdb=" CA GLN C 173 " pdb=" C GLN C 173 " ideal model delta sigma weight residual 114.56 111.55 3.01 1.27e+00 6.20e-01 5.61e+00 angle pdb=" N GLN D 173 " pdb=" CA GLN D 173 " pdb=" C GLN D 173 " ideal model delta sigma weight residual 114.56 111.57 2.99 1.27e+00 6.20e-01 5.54e+00 angle pdb=" N GLN B 173 " pdb=" CA GLN B 173 " pdb=" C GLN B 173 " ideal model delta sigma weight residual 114.56 111.62 2.94 1.27e+00 6.20e-01 5.37e+00 angle pdb=" C CYS B 175 " pdb=" N LEU B 176 " pdb=" CA LEU B 176 " ideal model delta sigma weight residual 122.64 120.09 2.55 1.25e+00 6.40e-01 4.15e+00 ... (remaining 24235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 9551 17.51 - 35.02: 1021 35.02 - 52.53: 140 52.53 - 70.04: 32 70.04 - 87.56: 4 Dihedral angle restraints: 10748 sinusoidal: 4324 harmonic: 6424 Sorted by residual: dihedral pdb=" CA PRO D 547 " pdb=" C PRO D 547 " pdb=" N LYS D 548 " pdb=" CA LYS D 548 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA PRO A 547 " pdb=" C PRO A 547 " pdb=" N LYS A 548 " pdb=" CA LYS A 548 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA PRO B 547 " pdb=" C PRO B 547 " pdb=" N LYS B 548 " pdb=" CA LYS B 548 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 10745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1486 0.033 - 0.066: 884 0.066 - 0.099: 239 0.099 - 0.132: 87 0.132 - 0.165: 16 Chirality restraints: 2712 Sorted by residual: chirality pdb=" CA PHE D 445 " pdb=" N PHE D 445 " pdb=" C PHE D 445 " pdb=" CB PHE D 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CA PHE A 445 " pdb=" N PHE A 445 " pdb=" C PHE A 445 " pdb=" CB PHE A 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA PHE B 445 " pdb=" N PHE B 445 " pdb=" C PHE B 445 " pdb=" CB PHE B 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 2709 not shown) Planarity restraints: 3140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 546 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO D 547 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 547 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 547 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 546 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 547 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 547 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 547 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 546 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 547 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 547 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 547 " 0.026 5.00e-02 4.00e+02 ... (remaining 3137 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2868 2.75 - 3.29: 17689 3.29 - 3.83: 30938 3.83 - 4.36: 39442 4.36 - 4.90: 63429 Nonbonded interactions: 154366 Sorted by model distance: nonbonded pdb=" OD1 ASP A 116 " pdb=" OH TYR C 544 " model vdw 2.218 3.040 nonbonded pdb=" O CYS C 407 " pdb=" OG1 THR C 411 " model vdw 2.221 3.040 nonbonded pdb=" O CYS D 407 " pdb=" OG1 THR D 411 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASP B 116 " pdb=" OH TYR D 544 " model vdw 2.222 3.040 nonbonded pdb=" O CYS A 407 " pdb=" OG1 THR A 411 " model vdw 2.222 3.040 ... (remaining 154361 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: 0.00 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.770 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 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 : 0.006 0.049 17892 Z= 0.396 Angle : 0.625 6.295 24240 Z= 0.345 Chirality : 0.045 0.165 2712 Planarity : 0.004 0.047 3140 Dihedral : 14.264 87.556 6636 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: -3.00 (0.16), residues: 2216 helix: -1.90 (0.13), residues: 1024 sheet: -2.70 (0.35), residues: 180 loop : -1.80 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 127 HIS 0.006 0.001 HIS B 333 PHE 0.017 0.002 PHE D 445 TYR 0.016 0.002 TYR B 74 ARG 0.003 0.000 ARG B 105 *********************** 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 181 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 181 average time/residue: 1.3385 time to fit residues: 271.0303 Evaluate side-chains 111 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain D residue 130 ASP 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: 1.9990 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 0.0370 chunk 172 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 199 optimal weight: 0.0470 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 115 HIS A 125 ASN A 226 ASN A 258 GLN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 385 HIS B 52 GLN B 115 HIS B 125 ASN B 226 ASN B 258 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 385 HIS C 52 GLN C 115 HIS C 125 ASN C 226 ASN C 258 GLN ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 385 HIS D 52 GLN D 115 HIS D 125 ASN D 226 ASN D 258 GLN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 385 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17892 Z= 0.209 Angle : 0.622 6.621 24240 Z= 0.317 Chirality : 0.043 0.208 2712 Planarity : 0.004 0.043 3140 Dihedral : 4.697 20.958 2432 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.69 % Allowed : 9.57 % Favored : 89.73 % 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: -1.36 (0.18), residues: 2216 helix: -0.06 (0.16), residues: 1028 sheet: -2.36 (0.38), residues: 180 loop : -1.44 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 319 HIS 0.005 0.001 HIS B 333 PHE 0.012 0.001 PHE D 445 TYR 0.013 0.002 TYR B 517 ARG 0.006 0.001 ARG A 356 *********************** 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 138 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 134 average time/residue: 1.1521 time to fit residues: 175.3229 Evaluate side-chains 114 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 354 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS A 554 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 GLN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17892 Z= 0.201 Angle : 0.592 6.886 24240 Z= 0.297 Chirality : 0.042 0.176 2712 Planarity : 0.004 0.047 3140 Dihedral : 4.422 20.149 2428 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.13 % Allowed : 11.28 % Favored : 86.60 % 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: -0.78 (0.18), residues: 2216 helix: 0.49 (0.17), residues: 1048 sheet: -2.15 (0.39), residues: 180 loop : -1.25 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 319 HIS 0.005 0.001 HIS B 28 PHE 0.015 0.001 PHE B 445 TYR 0.012 0.002 TYR C 74 ARG 0.003 0.000 ARG A 356 *********************** 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 160 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 120 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.4017 (OUTLIER) cc_final: 0.3691 (m-80) REVERT: B 100 TYR cc_start: 0.4010 (OUTLIER) cc_final: 0.3661 (m-80) REVERT: C 100 TYR cc_start: 0.4013 (OUTLIER) cc_final: 0.3695 (m-80) REVERT: D 100 TYR cc_start: 0.4099 (OUTLIER) cc_final: 0.3769 (m-80) outliers start: 40 outliers final: 12 residues processed: 148 average time/residue: 1.1736 time to fit residues: 197.8211 Evaluate side-chains 124 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 134 optimal weight: 0.1980 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS B 554 GLN ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS C 554 GLN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS D 554 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17892 Z= 0.229 Angle : 0.621 7.635 24240 Z= 0.308 Chirality : 0.043 0.178 2712 Planarity : 0.004 0.044 3140 Dihedral : 4.330 16.624 2428 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.01 % Allowed : 14.04 % Favored : 84.95 % 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: -0.60 (0.18), residues: 2216 helix: 0.62 (0.17), residues: 1068 sheet: -1.75 (0.40), residues: 168 loop : -1.26 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 546 HIS 0.004 0.001 HIS A 333 PHE 0.015 0.001 PHE B 445 TYR 0.012 0.002 TYR B 74 ARG 0.004 0.000 ARG D 387 *********************** 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 127 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 120 average time/residue: 1.3097 time to fit residues: 177.2419 Evaluate side-chains 109 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 87 optimal weight: 30.0000 chunk 181 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17892 Z= 0.483 Angle : 0.720 9.166 24240 Z= 0.353 Chirality : 0.045 0.190 2712 Planarity : 0.004 0.050 3140 Dihedral : 4.456 19.356 2428 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.86 % Allowed : 13.67 % 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: -0.32 (0.18), residues: 2216 helix: 0.90 (0.16), residues: 1060 sheet: -1.91 (0.37), residues: 208 loop : -1.02 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 546 HIS 0.003 0.001 HIS C 28 PHE 0.015 0.002 PHE B 445 TYR 0.016 0.002 TYR D 74 ARG 0.008 0.001 ARG B 387 *********************** 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 131 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 96 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 119 average time/residue: 1.2282 time to fit residues: 166.1656 Evaluate side-chains 119 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17892 Z= 0.191 Angle : 0.634 9.975 24240 Z= 0.312 Chirality : 0.042 0.182 2712 Planarity : 0.004 0.051 3140 Dihedral : 4.413 18.092 2428 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.81 % Allowed : 14.73 % Favored : 83.46 % 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: -0.25 (0.18), residues: 2216 helix: 0.95 (0.16), residues: 1064 sheet: -1.44 (0.38), residues: 216 loop : -1.11 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 319 HIS 0.004 0.001 HIS C 333 PHE 0.016 0.001 PHE C 445 TYR 0.013 0.002 TYR A 74 ARG 0.004 0.000 ARG B 387 *********************** 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 140 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 130 average time/residue: 1.1498 time to fit residues: 171.2170 Evaluate side-chains 118 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17892 Z= 0.294 Angle : 0.667 10.719 24240 Z= 0.326 Chirality : 0.043 0.180 2712 Planarity : 0.004 0.054 3140 Dihedral : 4.401 18.804 2428 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.60 % Allowed : 15.90 % Favored : 82.50 % 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: -0.07 (0.18), residues: 2216 helix: 1.04 (0.16), residues: 1060 sheet: -1.19 (0.40), residues: 196 loop : -0.99 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.003 0.001 HIS D 333 PHE 0.014 0.001 PHE B 445 TYR 0.013 0.002 TYR A 74 ARG 0.004 0.000 ARG C 387 *********************** 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 134 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 124 average time/residue: 1.2177 time to fit residues: 171.6437 Evaluate side-chains 127 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 486 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17892 Z= 0.266 Angle : 0.666 11.637 24240 Z= 0.323 Chirality : 0.043 0.184 2712 Planarity : 0.004 0.053 3140 Dihedral : 4.397 18.739 2428 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.70 % Allowed : 16.12 % Favored : 82.18 % 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: -0.07 (0.18), residues: 2216 helix: 1.03 (0.16), residues: 1068 sheet: -1.14 (0.40), residues: 196 loop : -1.01 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 319 HIS 0.003 0.001 HIS D 333 PHE 0.016 0.001 PHE B 445 TYR 0.014 0.002 TYR D 208 ARG 0.003 0.000 ARG C 387 *********************** 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 136 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.4399 (OUTLIER) cc_final: 0.3617 (m-80) REVERT: B 100 TYR cc_start: 0.4375 (OUTLIER) cc_final: 0.3588 (m-80) REVERT: C 100 TYR cc_start: 0.4351 (OUTLIER) cc_final: 0.3608 (m-80) REVERT: D 100 TYR cc_start: 0.4319 (OUTLIER) cc_final: 0.3563 (m-80) outliers start: 32 outliers final: 25 residues processed: 128 average time/residue: 1.1754 time to fit residues: 171.4984 Evaluate side-chains 130 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS A 483 GLN B 282 HIS B 483 GLN C 282 HIS D 282 HIS D 483 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17892 Z= 0.213 Angle : 0.646 12.159 24240 Z= 0.317 Chirality : 0.043 0.181 2712 Planarity : 0.004 0.054 3140 Dihedral : 4.358 18.152 2428 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.86 % Allowed : 16.06 % Favored : 82.07 % 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: -0.00 (0.18), residues: 2216 helix: 1.07 (0.16), residues: 1064 sheet: -1.01 (0.41), residues: 196 loop : -0.97 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 546 HIS 0.003 0.001 HIS C 333 PHE 0.017 0.001 PHE D 341 TYR 0.015 0.001 TYR D 208 ARG 0.003 0.000 ARG B 387 *********************** 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 135 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.4412 (OUTLIER) cc_final: 0.3615 (m-80) REVERT: B 100 TYR cc_start: 0.4526 (OUTLIER) cc_final: 0.3713 (m-80) REVERT: C 100 TYR cc_start: 0.4400 (OUTLIER) cc_final: 0.3619 (m-80) REVERT: D 100 TYR cc_start: 0.4327 (OUTLIER) cc_final: 0.3550 (m-80) outliers start: 35 outliers final: 21 residues processed: 124 average time/residue: 1.1384 time to fit residues: 162.1047 Evaluate side-chains 124 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 219 optimal weight: 0.0040 chunk 201 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 138 optimal weight: 6.9990 overall best weight: 2.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS B 282 HIS B 483 GLN C 282 HIS D 282 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 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 : 0.004 0.046 17892 Z= 0.235 Angle : 0.667 13.256 24240 Z= 0.326 Chirality : 0.043 0.182 2712 Planarity : 0.004 0.051 3140 Dihedral : 4.369 22.431 2428 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.60 % Allowed : 16.86 % Favored : 81.54 % 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: 0.05 (0.18), residues: 2216 helix: 1.07 (0.16), residues: 1068 sheet: -0.95 (0.41), residues: 196 loop : -0.90 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 546 HIS 0.003 0.001 HIS D 333 PHE 0.016 0.001 PHE B 445 TYR 0.016 0.001 TYR D 208 ARG 0.003 0.000 ARG B 387 ********************** 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 131 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.4490 (OUTLIER) cc_final: 0.3815 (m-80) REVERT: B 100 TYR cc_start: 0.4539 (OUTLIER) cc_final: 0.3760 (m-80) REVERT: C 100 TYR cc_start: 0.4483 (OUTLIER) cc_final: 0.3822 (m-80) REVERT: D 100 TYR cc_start: 0.4532 (OUTLIER) cc_final: 0.3730 (m-80) outliers start: 30 outliers final: 19 residues processed: 123 average time/residue: 1.1592 time to fit residues: 163.6829 Evaluate side-chains 120 residues out of total 1880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 0.0980 chunk 174 optimal weight: 9.9990 chunk 73 optimal weight: 0.0770 chunk 179 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 overall best weight: 3.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS B 282 HIS B 483 GLN C 282 HIS D 282 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.040008 restraints weight = 60090.084| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 3.67 r_work: 0.2493 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17892 Z= 0.272 Angle : 0.678 13.254 24240 Z= 0.332 Chirality : 0.043 0.184 2712 Planarity : 0.004 0.051 3140 Dihedral : 4.390 24.292 2428 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.38 % Allowed : 16.91 % Favored : 81.70 % 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: 0.12 (0.18), residues: 2216 helix: 1.11 (0.16), residues: 1068 sheet: -0.94 (0.41), residues: 196 loop : -0.84 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 546 HIS 0.003 0.001 HIS C 333 PHE 0.016 0.001 PHE C 445 TYR 0.016 0.002 TYR C 208 ARG 0.003 0.000 ARG B 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4069.80 seconds wall clock time: 73 minutes 26.41 seconds (4406.41 seconds total)