Starting phenix.real_space_refine on Mon Apr 6 18:22:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uri_64458/04_2026/9uri_64458_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uri_64458/04_2026/9uri_64458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uri_64458/04_2026/9uri_64458_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uri_64458/04_2026/9uri_64458_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uri_64458/04_2026/9uri_64458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uri_64458/04_2026/9uri_64458.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 52 5.16 5 C 13204 2.51 5 N 3648 2.21 5 O 3664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5142 Classifications: {'peptide': 622} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 595} Chain breaks: 5 Restraints were copied for chains: B, C, D Time building chain proxies: 5.02, per 1000 atoms: 0.24 Number of scatterers: 20568 At special positions: 0 Unit cell: (141.913, 109.221, 128.539, 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 52 16.00 O 3664 8.00 N 3648 7.00 C 13204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 863.5 milliseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4784 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 20 sheets defined 45.5% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 Processing helix chain 'A' and resid 31 through 63 removed outlier: 3.685A pdb=" N PHE A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 41 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 105 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.530A pdb=" N PHE A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.588A pdb=" N ILE A 210 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.679A pdb=" N ASP A 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 301 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 302 " --> pdb=" O ASP A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.721A pdb=" N LEU A 311 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 312 " --> pdb=" O ALA A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 312' Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.952A pdb=" N LYS A 326 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.618A pdb=" N ALA A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 removed outlier: 3.526A pdb=" N LEU A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.704A pdb=" N ALA A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 493 removed outlier: 4.139A pdb=" N GLU A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 527 removed outlier: 3.574A pdb=" N LEU A 513 " --> pdb=" O ASN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 556 Processing helix chain 'A' and resid 600 through 603 removed outlier: 3.697A pdb=" N ASP A 603 " --> pdb=" O ASN A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 630 through 646 removed outlier: 3.721A pdb=" N GLN A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 685 Processing helix chain 'B' and resid 9 through 23 Processing helix chain 'B' and resid 31 through 63 removed outlier: 3.685A pdb=" N PHE B 38 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY B 40 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 41 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 105 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 150 removed outlier: 3.530A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.588A pdb=" N ILE B 210 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 280 Processing helix chain 'B' and resid 296 through 303 removed outlier: 3.679A pdb=" N ASP B 299 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 301 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 302 " --> pdb=" O ASP B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.721A pdb=" N LEU B 311 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 312 " --> pdb=" O ALA B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 312' Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.952A pdb=" N LYS B 326 " --> pdb=" O TRP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 removed outlier: 3.618A pdb=" N ALA B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.526A pdb=" N LEU B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 393 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.704A pdb=" N ALA B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 493 removed outlier: 4.139A pdb=" N GLU B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 527 removed outlier: 3.574A pdb=" N LEU B 513 " --> pdb=" O ASN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 556 Processing helix chain 'B' and resid 600 through 603 removed outlier: 3.697A pdb=" N ASP B 603 " --> pdb=" O ASN B 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 600 through 603' Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.721A pdb=" N GLN B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 685 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 31 through 63 removed outlier: 3.685A pdb=" N PHE C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY C 40 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 41 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 105 Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.530A pdb=" N PHE C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.588A pdb=" N ILE C 210 " --> pdb=" O CYS C 206 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 296 through 303 removed outlier: 3.679A pdb=" N ASP C 299 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 301 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 302 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 removed outlier: 3.721A pdb=" N LEU C 311 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 312 " --> pdb=" O ALA C 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 312' Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.952A pdb=" N LYS C 326 " --> pdb=" O TRP C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 339 removed outlier: 3.618A pdb=" N ALA C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 removed outlier: 3.526A pdb=" N LEU C 354 " --> pdb=" O PHE C 350 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 393 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.704A pdb=" N ALA C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 493 removed outlier: 4.139A pdb=" N GLU C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 527 removed outlier: 3.574A pdb=" N LEU C 513 " --> pdb=" O ASN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 556 Processing helix chain 'C' and resid 600 through 603 removed outlier: 3.697A pdb=" N ASP C 603 " --> pdb=" O ASN C 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 600 through 603' Processing helix chain 'C' and resid 614 through 620 Processing helix chain 'C' and resid 630 through 646 removed outlier: 3.721A pdb=" N GLN C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 685 Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 31 through 63 removed outlier: 3.685A pdb=" N PHE D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 39 " --> pdb=" O ARG D 35 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY D 40 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE D 41 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 105 Processing helix chain 'D' and resid 117 through 130 Processing helix chain 'D' and resid 145 through 150 removed outlier: 3.530A pdb=" N PHE D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 206 Processing helix chain 'D' and resid 206 through 212 removed outlier: 3.588A pdb=" N ILE D 210 " --> pdb=" O CYS D 206 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 296 through 303 removed outlier: 3.679A pdb=" N ASP D 299 " --> pdb=" O ASN D 296 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE D 301 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN D 302 " --> pdb=" O ASP D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 312 removed outlier: 3.721A pdb=" N LEU D 311 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 312 " --> pdb=" O ALA D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 312' Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.952A pdb=" N LYS D 326 " --> pdb=" O TRP D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 339 removed outlier: 3.618A pdb=" N ALA D 335 " --> pdb=" O ASN D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 removed outlier: 3.526A pdb=" N LEU D 354 " --> pdb=" O PHE D 350 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 393 Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.704A pdb=" N ALA D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 493 removed outlier: 4.139A pdb=" N GLU D 483 " --> pdb=" O ARG D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 527 removed outlier: 3.574A pdb=" N LEU D 513 " --> pdb=" O ASN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 556 Processing helix chain 'D' and resid 600 through 603 removed outlier: 3.697A pdb=" N ASP D 603 " --> pdb=" O ASN D 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 600 through 603' Processing helix chain 'D' and resid 614 through 620 Processing helix chain 'D' and resid 630 through 646 removed outlier: 3.721A pdb=" N GLN D 635 " --> pdb=" O PRO D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.329A pdb=" N PHE A 108 " --> pdb=" O MET A 196 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU A 198 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 4.596A pdb=" N TYR A 154 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET A 227 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE A 262 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.961A pdb=" N LYS A 437 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A 438 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE A 371 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 440 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 369 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 442 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 367 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR A 397 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 369 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL A 399 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 371 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU A 401 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ILE A 373 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 396 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 426 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 398 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER A 428 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 400 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 505 removed outlier: 6.482A pdb=" N ILE A 533 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.329A pdb=" N PHE B 108 " --> pdb=" O MET B 196 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU B 198 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 139 removed outlier: 4.596A pdb=" N TYR B 154 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET B 227 " --> pdb=" O TYR B 154 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE B 262 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.961A pdb=" N LYS B 437 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 438 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE B 371 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 440 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE B 369 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER B 442 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU B 367 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR B 397 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 369 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL B 399 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 371 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU B 401 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ILE B 373 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 396 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE B 426 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 398 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER B 428 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 400 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AB1, first strand: chain 'B' and resid 504 through 505 removed outlier: 6.482A pdb=" N ILE B 533 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.329A pdb=" N PHE C 108 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU C 198 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 138 through 139 removed outlier: 4.596A pdb=" N TYR C 154 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET C 227 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE C 262 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.961A pdb=" N LYS C 437 " --> pdb=" O GLY C 456 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C 438 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE C 371 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 440 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE C 369 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER C 442 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU C 367 " --> pdb=" O LYS C 395 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR C 397 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 369 " --> pdb=" O THR C 397 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL C 399 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 371 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU C 401 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ILE C 373 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 396 " --> pdb=" O HIS C 424 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE C 426 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 398 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER C 428 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C 400 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AB6, first strand: chain 'C' and resid 504 through 505 removed outlier: 6.482A pdb=" N ILE C 533 " --> pdb=" O ASN C 560 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 107 through 109 removed outlier: 6.329A pdb=" N PHE D 108 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU D 198 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 138 through 139 removed outlier: 4.596A pdb=" N TYR D 154 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET D 227 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE D 262 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 341 through 345 removed outlier: 3.961A pdb=" N LYS D 437 " --> pdb=" O GLY D 456 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU D 438 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE D 371 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU D 440 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE D 369 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER D 442 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU D 367 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR D 397 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE D 369 " --> pdb=" O THR D 397 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL D 399 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 371 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU D 401 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ILE D 373 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL D 396 " --> pdb=" O HIS D 424 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE D 426 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 398 " --> pdb=" O ILE D 426 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER D 428 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL D 400 " --> pdb=" O SER D 428 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 341 through 345 Processing sheet with id=AC2, first strand: chain 'D' and resid 504 through 505 removed outlier: 6.482A pdb=" N ILE D 533 " --> pdb=" O ASN D 560 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 1.72 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: 6796 1.34 - 1.46: 2760 1.46 - 1.57: 11320 1.57 - 1.69: 0 1.69 - 1.80: 96 Bond restraints: 20972 Sorted by residual: bond pdb=" N PRO B 530 " pdb=" CD PRO B 530 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" N PRO C 530 " pdb=" CD PRO C 530 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" N PRO D 530 " pdb=" CD PRO D 530 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" N PRO A 530 " pdb=" CD PRO A 530 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" N PHE A 297 " pdb=" CA PHE A 297 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.33e-02 5.65e+03 7.53e+00 ... (remaining 20967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 27592 1.40 - 2.79: 584 2.79 - 4.19: 100 4.19 - 5.58: 32 5.58 - 6.98: 16 Bond angle restraints: 28324 Sorted by residual: angle pdb=" N LYS D 670 " pdb=" CA LYS D 670 " pdb=" CB LYS D 670 " ideal model delta sigma weight residual 109.94 116.10 -6.16 1.60e+00 3.91e-01 1.48e+01 angle pdb=" N LYS C 670 " pdb=" CA LYS C 670 " pdb=" CB LYS C 670 " ideal model delta sigma weight residual 109.94 116.10 -6.16 1.60e+00 3.91e-01 1.48e+01 angle pdb=" N LYS B 670 " pdb=" CA LYS B 670 " pdb=" CB LYS B 670 " ideal model delta sigma weight residual 109.94 116.10 -6.16 1.60e+00 3.91e-01 1.48e+01 angle pdb=" N LYS A 670 " pdb=" CA LYS A 670 " pdb=" CB LYS A 670 " ideal model delta sigma weight residual 109.94 116.10 -6.16 1.60e+00 3.91e-01 1.48e+01 angle pdb=" CA ASN D 296 " pdb=" C ASN D 296 " pdb=" O ASN D 296 " ideal model delta sigma weight residual 122.14 117.37 4.77 1.24e+00 6.50e-01 1.48e+01 ... (remaining 28319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 10720 17.73 - 35.47: 1552 35.47 - 53.20: 480 53.20 - 70.94: 52 70.94 - 88.67: 20 Dihedral angle restraints: 12824 sinusoidal: 5444 harmonic: 7380 Sorted by residual: dihedral pdb=" CA LEU A 438 " pdb=" C LEU A 438 " pdb=" N PHE A 439 " pdb=" CA PHE A 439 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU C 438 " pdb=" C LEU C 438 " pdb=" N PHE C 439 " pdb=" CA PHE C 439 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU B 438 " pdb=" C LEU B 438 " pdb=" N PHE B 439 " pdb=" CA PHE B 439 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 12821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1848 0.031 - 0.062: 888 0.062 - 0.092: 228 0.092 - 0.123: 152 0.123 - 0.154: 24 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA PHE A 297 " pdb=" N PHE A 297 " pdb=" C PHE A 297 " pdb=" CB PHE A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA PHE B 297 " pdb=" N PHE B 297 " pdb=" C PHE B 297 " pdb=" CB PHE B 297 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA PHE D 297 " pdb=" N PHE D 297 " pdb=" C PHE D 297 " pdb=" CB PHE D 297 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 3137 not shown) Planarity restraints: 3644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 293 " 0.379 9.50e-02 1.11e+02 1.70e-01 1.76e+01 pdb=" NE ARG B 293 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 293 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 293 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 293 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 293 " -0.379 9.50e-02 1.11e+02 1.70e-01 1.76e+01 pdb=" NE ARG A 293 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 293 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 293 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 293 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 293 " 0.379 9.50e-02 1.11e+02 1.70e-01 1.76e+01 pdb=" NE ARG C 293 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C 293 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 293 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 293 " 0.013 2.00e-02 2.50e+03 ... (remaining 3641 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1376 2.74 - 3.28: 19068 3.28 - 3.82: 32586 3.82 - 4.36: 40064 4.36 - 4.90: 71580 Nonbonded interactions: 164674 Sorted by model distance: nonbonded pdb=" O ALA B 415 " pdb=" OG1 THR B 419 " model vdw 2.199 3.040 nonbonded pdb=" O ALA A 415 " pdb=" OG1 THR A 419 " model vdw 2.199 3.040 nonbonded pdb=" O ALA D 415 " pdb=" OG1 THR D 419 " model vdw 2.199 3.040 nonbonded pdb=" O ALA C 415 " pdb=" OG1 THR C 419 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP C 542 " pdb=" OG1 THR C 615 " model vdw 2.338 3.040 ... (remaining 164669 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: 0.03 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.350 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.004 0.046 20972 Z= 0.173 Angle : 0.539 6.978 28324 Z= 0.311 Chirality : 0.043 0.154 3140 Planarity : 0.007 0.170 3644 Dihedral : 17.642 88.671 8040 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 24.73 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2440 helix: 1.63 (0.17), residues: 1012 sheet: 0.04 (0.23), residues: 496 loop : -0.17 (0.23), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 277 TYR 0.007 0.001 TYR D 42 PHE 0.024 0.001 PHE C 439 TRP 0.006 0.001 TRP D 14 HIS 0.003 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00357 (20972) covalent geometry : angle 0.53889 (28324) hydrogen bonds : bond 0.13848 ( 948) hydrogen bonds : angle 5.59215 ( 2760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.796 Fit side-chains REVERT: A 59 ARG cc_start: 0.7270 (mtm-85) cc_final: 0.7010 (mtm180) REVERT: A 229 ARG cc_start: 0.7499 (ttm110) cc_final: 0.6706 (mmp80) REVERT: A 277 ARG cc_start: 0.7926 (mtm110) cc_final: 0.6793 (mmm160) REVERT: A 375 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7922 (mtm180) REVERT: A 669 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.7551 (mtm-85) REVERT: B 59 ARG cc_start: 0.7277 (mtm-85) cc_final: 0.7015 (mtm180) REVERT: B 229 ARG cc_start: 0.7502 (ttm110) cc_final: 0.6708 (mmp80) REVERT: B 277 ARG cc_start: 0.7931 (mtm110) cc_final: 0.6793 (mmm160) REVERT: B 375 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7916 (mtm180) REVERT: B 669 ARG cc_start: 0.7766 (mtp-110) cc_final: 0.7551 (mtm-85) REVERT: C 59 ARG cc_start: 0.7270 (mtm-85) cc_final: 0.7010 (mtm180) REVERT: C 229 ARG cc_start: 0.7498 (ttm110) cc_final: 0.6709 (mmp80) REVERT: C 277 ARG cc_start: 0.7928 (mtm110) cc_final: 0.6795 (mmm160) REVERT: C 375 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7916 (mtm180) REVERT: C 669 ARG cc_start: 0.7763 (mtp-110) cc_final: 0.7551 (mtm-85) REVERT: D 59 ARG cc_start: 0.7271 (mtm-85) cc_final: 0.7010 (mtm180) REVERT: D 229 ARG cc_start: 0.7498 (ttm110) cc_final: 0.6706 (mmp80) REVERT: D 277 ARG cc_start: 0.7925 (mtm110) cc_final: 0.6792 (mmm160) REVERT: D 375 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7915 (mtm180) REVERT: D 669 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.7550 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1832 time to fit residues: 73.4510 Evaluate side-chains 262 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 459 ASN A 686 GLN B 114 GLN B 459 ASN B 686 GLN C 114 GLN C 459 ASN C 686 GLN D 114 GLN D 459 ASN D 686 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115672 restraints weight = 24627.624| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.44 r_work: 0.3206 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20972 Z= 0.126 Angle : 0.446 6.496 28324 Z= 0.233 Chirality : 0.041 0.144 3140 Planarity : 0.003 0.025 3644 Dihedral : 3.866 20.369 2820 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.38 % Allowed : 21.53 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.18), residues: 2440 helix: 1.92 (0.16), residues: 1024 sheet: 0.31 (0.24), residues: 488 loop : -0.08 (0.23), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.007 0.001 TYR C 680 PHE 0.024 0.001 PHE D 439 TRP 0.005 0.001 TRP A 14 HIS 0.003 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00299 (20972) covalent geometry : angle 0.44626 (28324) hydrogen bonds : bond 0.03937 ( 948) hydrogen bonds : angle 4.24345 ( 2760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 296 time to evaluate : 0.545 Fit side-chains REVERT: A 59 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7143 (mtm180) REVERT: A 229 ARG cc_start: 0.7621 (ttm110) cc_final: 0.6846 (mmp80) REVERT: A 277 ARG cc_start: 0.8173 (mtm110) cc_final: 0.6874 (mmm160) REVERT: A 435 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.6994 (tp40) REVERT: A 669 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7781 (mtm-85) REVERT: B 59 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7149 (mtm180) REVERT: B 229 ARG cc_start: 0.7621 (ttm110) cc_final: 0.6839 (mmp80) REVERT: B 277 ARG cc_start: 0.8170 (mtm110) cc_final: 0.6880 (mmm160) REVERT: B 435 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.6986 (tp40) REVERT: B 669 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7783 (mtm-85) REVERT: C 59 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7153 (mtm180) REVERT: C 229 ARG cc_start: 0.7631 (ttm110) cc_final: 0.6852 (mmp80) REVERT: C 277 ARG cc_start: 0.8176 (mtm110) cc_final: 0.6880 (mmm160) REVERT: C 435 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6996 (tp40) REVERT: C 669 ARG cc_start: 0.8017 (mtp-110) cc_final: 0.7786 (mtm-85) REVERT: D 59 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.7154 (mtm180) REVERT: D 229 ARG cc_start: 0.7621 (ttm110) cc_final: 0.6852 (mmp80) REVERT: D 277 ARG cc_start: 0.8169 (mtm110) cc_final: 0.6874 (mmm160) REVERT: D 435 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6998 (tp40) REVERT: D 669 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7779 (mtm-85) outliers start: 76 outliers final: 44 residues processed: 352 average time/residue: 0.1689 time to fit residues: 87.0382 Evaluate side-chains 328 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 498 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 46 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 686 GLN B 459 ASN B 686 GLN C 459 ASN C 686 GLN D 459 ASN D 686 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113636 restraints weight = 24791.771| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.43 r_work: 0.3179 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20972 Z= 0.167 Angle : 0.468 7.676 28324 Z= 0.242 Chirality : 0.042 0.143 3140 Planarity : 0.004 0.034 3644 Dihedral : 3.981 20.729 2820 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.74 % Allowed : 21.71 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.18), residues: 2440 helix: 1.91 (0.16), residues: 1024 sheet: 0.37 (0.24), residues: 488 loop : -0.01 (0.23), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 564 TYR 0.009 0.001 TYR A 42 PHE 0.025 0.001 PHE C 439 TRP 0.005 0.001 TRP A 14 HIS 0.004 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00409 (20972) covalent geometry : angle 0.46782 (28324) hydrogen bonds : bond 0.04159 ( 948) hydrogen bonds : angle 4.20969 ( 2760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 292 time to evaluate : 0.795 Fit side-chains REVERT: A 59 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7141 (mtm180) REVERT: A 229 ARG cc_start: 0.7681 (ttm110) cc_final: 0.6981 (mmp80) REVERT: A 277 ARG cc_start: 0.8192 (mtm110) cc_final: 0.6898 (mmm160) REVERT: A 375 ARG cc_start: 0.8296 (mtm180) cc_final: 0.8014 (mtm180) REVERT: A 435 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7060 (tp40) REVERT: A 562 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8755 (tt) REVERT: A 669 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7771 (mtm-85) REVERT: B 59 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7155 (mtm180) REVERT: B 229 ARG cc_start: 0.7682 (ttm110) cc_final: 0.6987 (mmp80) REVERT: B 277 ARG cc_start: 0.8186 (mtm110) cc_final: 0.6900 (mmm160) REVERT: B 375 ARG cc_start: 0.8299 (mtm180) cc_final: 0.8020 (mtm180) REVERT: B 435 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7049 (tp40) REVERT: B 562 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8755 (tt) REVERT: B 669 ARG cc_start: 0.8074 (mtp-110) cc_final: 0.7766 (mtm-85) REVERT: C 59 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.7162 (mtm180) REVERT: C 229 ARG cc_start: 0.7683 (ttm110) cc_final: 0.6982 (mmp80) REVERT: C 277 ARG cc_start: 0.8192 (mtm110) cc_final: 0.6903 (mmm160) REVERT: C 375 ARG cc_start: 0.8293 (mtm180) cc_final: 0.8013 (mtm180) REVERT: C 435 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7066 (tp40) REVERT: C 562 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8761 (tt) REVERT: C 669 ARG cc_start: 0.8079 (mtp-110) cc_final: 0.7774 (mtm-85) REVERT: D 59 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7154 (mtm180) REVERT: D 229 ARG cc_start: 0.7687 (ttm110) cc_final: 0.6988 (mmp80) REVERT: D 277 ARG cc_start: 0.8185 (mtm110) cc_final: 0.6894 (mmm160) REVERT: D 375 ARG cc_start: 0.8295 (mtm180) cc_final: 0.8014 (mtm180) REVERT: D 435 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7062 (tp40) REVERT: D 562 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8755 (tt) REVERT: D 669 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7762 (mtm-85) outliers start: 84 outliers final: 52 residues processed: 344 average time/residue: 0.1788 time to fit residues: 88.8104 Evaluate side-chains 332 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 562 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 203 optimal weight: 0.0370 chunk 208 optimal weight: 0.4980 chunk 175 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 overall best weight: 1.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 686 GLN B 459 ASN B 686 GLN C 459 ASN C 686 GLN D 459 ASN D 686 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113688 restraints weight = 24640.237| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.38 r_work: 0.3200 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20972 Z= 0.124 Angle : 0.422 5.784 28324 Z= 0.222 Chirality : 0.041 0.143 3140 Planarity : 0.003 0.024 3644 Dihedral : 3.859 20.297 2820 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.27 % Allowed : 21.71 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.18), residues: 2440 helix: 2.04 (0.16), residues: 1024 sheet: 0.51 (0.23), residues: 488 loop : 0.03 (0.23), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 104 TYR 0.010 0.001 TYR A 596 PHE 0.024 0.001 PHE D 439 TRP 0.005 0.001 TRP B 14 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00298 (20972) covalent geometry : angle 0.42179 (28324) hydrogen bonds : bond 0.03607 ( 948) hydrogen bonds : angle 3.94929 ( 2760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 296 time to evaluate : 0.881 Fit side-chains REVERT: A 59 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7116 (mtm180) REVERT: A 229 ARG cc_start: 0.7704 (ttm110) cc_final: 0.6982 (mmp80) REVERT: A 277 ARG cc_start: 0.8148 (mtm110) cc_final: 0.6890 (mmm160) REVERT: A 435 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6966 (tp40) REVERT: A 562 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8711 (tt) REVERT: A 669 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7779 (mtm-85) REVERT: B 59 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.7129 (mtm180) REVERT: B 229 ARG cc_start: 0.7704 (ttm110) cc_final: 0.6984 (mmp80) REVERT: B 277 ARG cc_start: 0.8146 (mtm110) cc_final: 0.6899 (mmm160) REVERT: B 435 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6961 (tp40) REVERT: B 562 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8705 (tt) REVERT: B 669 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7767 (mtm-85) REVERT: C 59 ARG cc_start: 0.7367 (mtm-85) cc_final: 0.7133 (mtm180) REVERT: C 229 ARG cc_start: 0.7704 (ttm110) cc_final: 0.6983 (mmp80) REVERT: C 277 ARG cc_start: 0.8153 (mtm110) cc_final: 0.6898 (mmm160) REVERT: C 435 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.6971 (tp40) REVERT: C 562 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8716 (tt) REVERT: C 669 ARG cc_start: 0.8076 (mtp-110) cc_final: 0.7779 (mtm-85) REVERT: D 59 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.7126 (mtm180) REVERT: D 229 ARG cc_start: 0.7708 (ttm110) cc_final: 0.6990 (mmp80) REVERT: D 277 ARG cc_start: 0.8144 (mtm110) cc_final: 0.6891 (mmm160) REVERT: D 435 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.6967 (tp40) REVERT: D 562 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8705 (tt) REVERT: D 669 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7770 (mtm-85) outliers start: 96 outliers final: 56 residues processed: 360 average time/residue: 0.1671 time to fit residues: 88.4623 Evaluate side-chains 348 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 284 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 562 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 208 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 173 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 686 GLN B 310 ASN B 686 GLN C 310 ASN C 686 GLN D 310 ASN D 686 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115609 restraints weight = 24482.100| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.38 r_work: 0.3228 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 20972 Z= 0.095 Angle : 0.397 5.107 28324 Z= 0.211 Chirality : 0.040 0.144 3140 Planarity : 0.003 0.023 3644 Dihedral : 3.715 19.585 2820 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.91 % Allowed : 21.17 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.18), residues: 2440 helix: 2.25 (0.16), residues: 1012 sheet: 0.63 (0.23), residues: 488 loop : 0.06 (0.23), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.008 0.001 TYR B 596 PHE 0.023 0.001 PHE A 439 TRP 0.006 0.001 TRP B 14 HIS 0.003 0.000 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00218 (20972) covalent geometry : angle 0.39702 (28324) hydrogen bonds : bond 0.03175 ( 948) hydrogen bonds : angle 3.75602 ( 2760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 292 time to evaluate : 0.785 Fit side-chains REVERT: A 59 ARG cc_start: 0.7308 (mtm-85) cc_final: 0.7080 (mtm180) REVERT: A 229 ARG cc_start: 0.7684 (ttm110) cc_final: 0.6930 (mmp80) REVERT: A 277 ARG cc_start: 0.8163 (mtm110) cc_final: 0.6898 (mmm160) REVERT: A 435 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6806 (tp40) REVERT: A 562 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8720 (tt) REVERT: A 669 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.7761 (mtm-85) REVERT: A 685 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6256 (mm-30) REVERT: B 59 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.7098 (mtm180) REVERT: B 229 ARG cc_start: 0.7681 (ttm110) cc_final: 0.6935 (mmp80) REVERT: B 277 ARG cc_start: 0.8159 (mtm110) cc_final: 0.6900 (mmm160) REVERT: B 435 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6803 (tp40) REVERT: B 562 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8715 (tt) REVERT: B 669 ARG cc_start: 0.8062 (mtp-110) cc_final: 0.7754 (mtm-85) REVERT: B 685 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6268 (mm-30) REVERT: C 59 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.7093 (mtm180) REVERT: C 229 ARG cc_start: 0.7688 (ttm110) cc_final: 0.6932 (mmp80) REVERT: C 277 ARG cc_start: 0.8162 (mtm110) cc_final: 0.6898 (mmm160) REVERT: C 435 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6821 (tp40) REVERT: C 562 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8727 (tt) REVERT: C 669 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.7759 (mtm-85) REVERT: C 685 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6260 (mm-30) REVERT: D 59 ARG cc_start: 0.7314 (mtm-85) cc_final: 0.7087 (mtm180) REVERT: D 229 ARG cc_start: 0.7679 (ttm110) cc_final: 0.6937 (mmp80) REVERT: D 277 ARG cc_start: 0.8159 (mtm110) cc_final: 0.6895 (mmm160) REVERT: D 435 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6816 (tp40) REVERT: D 562 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8716 (tt) REVERT: D 669 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7750 (mtm-85) REVERT: D 685 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6261 (mm-30) outliers start: 88 outliers final: 56 residues processed: 348 average time/residue: 0.1632 time to fit residues: 85.2211 Evaluate side-chains 332 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 268 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 562 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 102 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 120 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 210 optimal weight: 0.0870 chunk 23 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 overall best weight: 0.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN B 686 GLN C 686 GLN D 686 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.094204 restraints weight = 25294.062| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.05 r_work: 0.2854 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 20972 Z= 0.102 Angle : 0.396 4.494 28324 Z= 0.209 Chirality : 0.040 0.143 3140 Planarity : 0.003 0.023 3644 Dihedral : 3.676 18.688 2820 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.74 % Allowed : 21.71 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.18), residues: 2440 helix: 2.29 (0.16), residues: 1012 sheet: 0.66 (0.23), residues: 488 loop : 0.14 (0.23), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.008 0.001 TYR C 596 PHE 0.023 0.001 PHE C 439 TRP 0.005 0.001 TRP B 14 HIS 0.002 0.000 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00240 (20972) covalent geometry : angle 0.39611 (28324) hydrogen bonds : bond 0.03206 ( 948) hydrogen bonds : angle 3.71618 ( 2760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 295 time to evaluate : 0.635 Fit side-chains REVERT: A 59 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.7137 (mtm180) REVERT: A 229 ARG cc_start: 0.7779 (ttm110) cc_final: 0.6963 (mmp80) REVERT: A 277 ARG cc_start: 0.8211 (mtm110) cc_final: 0.6957 (mmm160) REVERT: A 435 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6838 (tp40) REVERT: A 562 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8792 (tt) REVERT: B 59 ARG cc_start: 0.7378 (mtm-85) cc_final: 0.7161 (mtm180) REVERT: B 229 ARG cc_start: 0.7759 (ttm110) cc_final: 0.6964 (mmp80) REVERT: B 277 ARG cc_start: 0.8200 (mtm110) cc_final: 0.6952 (mmm160) REVERT: B 435 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6853 (tp40) REVERT: B 562 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8779 (tt) REVERT: C 59 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7140 (mtm180) REVERT: C 229 ARG cc_start: 0.7767 (ttm110) cc_final: 0.6959 (mmp80) REVERT: C 277 ARG cc_start: 0.8201 (mtm110) cc_final: 0.6956 (mmm160) REVERT: C 435 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6853 (tp40) REVERT: C 562 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8796 (tt) REVERT: D 59 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.7141 (mtm180) REVERT: D 229 ARG cc_start: 0.7779 (ttm110) cc_final: 0.6965 (mmp80) REVERT: D 277 ARG cc_start: 0.8199 (mtm110) cc_final: 0.6942 (mmm160) REVERT: D 435 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6860 (tp40) REVERT: D 562 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8783 (tt) outliers start: 84 outliers final: 60 residues processed: 343 average time/residue: 0.1534 time to fit residues: 78.2929 Evaluate side-chains 351 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 283 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 562 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 207 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 112 optimal weight: 0.0770 chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 686 GLN B 459 ASN B 686 GLN C 459 ASN C 686 GLN D 459 ASN D 686 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.117641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.094228 restraints weight = 25450.681| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.05 r_work: 0.2859 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 20972 Z= 0.107 Angle : 0.401 4.850 28324 Z= 0.212 Chirality : 0.041 0.143 3140 Planarity : 0.003 0.023 3644 Dihedral : 3.671 18.986 2820 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.38 % Allowed : 23.13 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.18), residues: 2440 helix: 2.35 (0.16), residues: 1008 sheet: 0.70 (0.23), residues: 488 loop : 0.15 (0.23), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.007 0.001 TYR B 596 PHE 0.023 0.001 PHE B 439 TRP 0.005 0.001 TRP C 14 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00253 (20972) covalent geometry : angle 0.40100 (28324) hydrogen bonds : bond 0.03226 ( 948) hydrogen bonds : angle 3.71273 ( 2760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 296 time to evaluate : 0.770 Fit side-chains REVERT: A 59 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.7151 (mtm180) REVERT: A 229 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7058 (mmp80) REVERT: A 277 ARG cc_start: 0.8216 (mtm110) cc_final: 0.6969 (mmm160) REVERT: A 435 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6816 (tp40) REVERT: A 562 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8795 (tt) REVERT: A 685 GLU cc_start: 0.6630 (mm-30) cc_final: 0.6402 (mm-30) REVERT: B 59 ARG cc_start: 0.7402 (mtm-85) cc_final: 0.7182 (mtm180) REVERT: B 229 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7063 (mmp80) REVERT: B 277 ARG cc_start: 0.8211 (mtm110) cc_final: 0.6971 (mmm160) REVERT: B 435 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6824 (tp40) REVERT: B 562 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8783 (tt) REVERT: B 685 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6429 (mm-30) REVERT: C 59 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.7155 (mtm180) REVERT: C 229 ARG cc_start: 0.7801 (ttm110) cc_final: 0.7050 (mmp80) REVERT: C 277 ARG cc_start: 0.8213 (mtm110) cc_final: 0.6971 (mmm160) REVERT: C 435 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6824 (tp40) REVERT: C 562 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8801 (tt) REVERT: C 685 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6428 (mm-30) REVERT: D 59 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.7165 (mtm180) REVERT: D 229 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7061 (mmp80) REVERT: D 277 ARG cc_start: 0.8217 (mtm110) cc_final: 0.6963 (mmm160) REVERT: D 435 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6831 (tp40) REVERT: D 562 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8790 (tt) REVERT: D 685 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6441 (mm-30) outliers start: 76 outliers final: 60 residues processed: 340 average time/residue: 0.1672 time to fit residues: 84.3649 Evaluate side-chains 348 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 280 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 562 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 0.0570 chunk 54 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 246 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN B 686 GLN C 686 GLN D 686 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.097248 restraints weight = 25284.672| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.06 r_work: 0.2894 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 20972 Z= 0.076 Angle : 0.373 4.025 28324 Z= 0.198 Chirality : 0.040 0.138 3140 Planarity : 0.003 0.024 3644 Dihedral : 3.475 17.628 2820 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.02 % Allowed : 23.49 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.18), residues: 2440 helix: 2.45 (0.16), residues: 1008 sheet: 0.75 (0.23), residues: 488 loop : 0.20 (0.23), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.007 0.001 TYR D 596 PHE 0.021 0.001 PHE B 439 TRP 0.006 0.001 TRP A 14 HIS 0.001 0.000 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00168 (20972) covalent geometry : angle 0.37294 (28324) hydrogen bonds : bond 0.02691 ( 948) hydrogen bonds : angle 3.52373 ( 2760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 316 time to evaluate : 0.581 Fit side-chains REVERT: A 229 ARG cc_start: 0.7806 (ttm110) cc_final: 0.6971 (mmp80) REVERT: A 277 ARG cc_start: 0.8187 (mtm110) cc_final: 0.6927 (mmm160) REVERT: A 435 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7076 (tp40) REVERT: A 444 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8472 (ttpt) REVERT: B 229 ARG cc_start: 0.7812 (ttm110) cc_final: 0.6978 (mmp80) REVERT: B 277 ARG cc_start: 0.8179 (mtm110) cc_final: 0.6928 (mmm160) REVERT: B 435 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7069 (tp40) REVERT: B 444 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8468 (ttpt) REVERT: C 229 ARG cc_start: 0.7799 (ttm110) cc_final: 0.6966 (mmp80) REVERT: C 277 ARG cc_start: 0.8173 (mtm110) cc_final: 0.6917 (mmm160) REVERT: C 435 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7057 (tp40) REVERT: C 444 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8475 (ttpt) REVERT: D 229 ARG cc_start: 0.7817 (ttm110) cc_final: 0.6984 (mmp80) REVERT: D 277 ARG cc_start: 0.8180 (mtm110) cc_final: 0.6919 (mmm160) REVERT: D 435 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7067 (tp40) REVERT: D 444 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8459 (ttpt) outliers start: 68 outliers final: 52 residues processed: 352 average time/residue: 0.1654 time to fit residues: 86.2336 Evaluate side-chains 352 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 498 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 96 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 39 optimal weight: 0.0010 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 205 optimal weight: 0.3980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN B 686 GLN C 686 GLN D 686 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.096334 restraints weight = 25227.810| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.06 r_work: 0.2904 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 20972 Z= 0.083 Angle : 0.389 5.874 28324 Z= 0.203 Chirality : 0.040 0.139 3140 Planarity : 0.003 0.023 3644 Dihedral : 3.467 17.913 2820 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.20 % Allowed : 22.78 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.18), residues: 2440 helix: 2.53 (0.16), residues: 1008 sheet: 0.83 (0.23), residues: 488 loop : 0.25 (0.23), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.006 0.001 TYR B 596 PHE 0.021 0.001 PHE B 439 TRP 0.005 0.001 TRP A 14 HIS 0.001 0.000 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00187 (20972) covalent geometry : angle 0.38864 (28324) hydrogen bonds : bond 0.02802 ( 948) hydrogen bonds : angle 3.51546 ( 2760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 308 time to evaluate : 0.800 Fit side-chains REVERT: A 229 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7021 (mmp80) REVERT: A 277 ARG cc_start: 0.8251 (mtm110) cc_final: 0.7025 (mmm160) REVERT: A 435 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7116 (tp40) REVERT: A 444 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8495 (ttpt) REVERT: B 229 ARG cc_start: 0.7790 (ttm110) cc_final: 0.7023 (mmp80) REVERT: B 277 ARG cc_start: 0.8235 (mtm110) cc_final: 0.7019 (mmm160) REVERT: B 435 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7115 (tp40) REVERT: B 444 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8489 (ttpt) REVERT: C 229 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7012 (mmp80) REVERT: C 277 ARG cc_start: 0.8226 (mtm110) cc_final: 0.7010 (mmm160) REVERT: C 435 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7099 (tp40) REVERT: C 444 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8495 (ttpt) REVERT: D 229 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7021 (mmp80) REVERT: D 277 ARG cc_start: 0.8244 (mtm110) cc_final: 0.7018 (mmm160) REVERT: D 435 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7122 (tp40) REVERT: D 444 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8476 (ttpt) outliers start: 72 outliers final: 64 residues processed: 348 average time/residue: 0.1647 time to fit residues: 84.7980 Evaluate side-chains 368 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 300 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 194 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 177 optimal weight: 0.1980 chunk 178 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN B 686 GLN C 686 GLN D 686 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.095625 restraints weight = 25392.343| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.05 r_work: 0.2883 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 20972 Z= 0.091 Angle : 0.398 5.852 28324 Z= 0.208 Chirality : 0.040 0.140 3140 Planarity : 0.003 0.023 3644 Dihedral : 3.508 18.143 2820 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.85 % Allowed : 23.49 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.18), residues: 2440 helix: 2.53 (0.16), residues: 1008 sheet: 0.85 (0.23), residues: 488 loop : 0.25 (0.23), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.007 0.001 TYR B 596 PHE 0.022 0.001 PHE B 439 TRP 0.005 0.001 TRP A 14 HIS 0.002 0.000 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00211 (20972) covalent geometry : angle 0.39795 (28324) hydrogen bonds : bond 0.02929 ( 948) hydrogen bonds : angle 3.55420 ( 2760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 308 time to evaluate : 0.673 Fit side-chains REVERT: A 63 ILE cc_start: 0.6037 (mt) cc_final: 0.5755 (mt) REVERT: A 229 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7038 (mmp80) REVERT: A 277 ARG cc_start: 0.8198 (mtm110) cc_final: 0.6992 (mmm160) REVERT: A 435 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7111 (tp40) REVERT: A 444 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8485 (ttpt) REVERT: B 63 ILE cc_start: 0.6108 (mt) cc_final: 0.5825 (mt) REVERT: B 229 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7039 (mmp80) REVERT: B 277 ARG cc_start: 0.8193 (mtm110) cc_final: 0.6992 (mmm160) REVERT: B 435 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7107 (tp40) REVERT: B 444 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8479 (ttpt) REVERT: C 63 ILE cc_start: 0.6063 (mt) cc_final: 0.5782 (mt) REVERT: C 229 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7031 (mmp80) REVERT: C 277 ARG cc_start: 0.8183 (mtm110) cc_final: 0.6984 (mmm160) REVERT: C 435 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7083 (tp40) REVERT: C 444 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8491 (ttpt) REVERT: D 63 ILE cc_start: 0.6088 (mt) cc_final: 0.5801 (mt) REVERT: D 229 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7040 (mmp80) REVERT: D 277 ARG cc_start: 0.8192 (mtm110) cc_final: 0.6983 (mmm160) REVERT: D 435 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7116 (tp40) REVERT: D 444 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8471 (ttpt) outliers start: 64 outliers final: 60 residues processed: 344 average time/residue: 0.1654 time to fit residues: 84.4970 Evaluate side-chains 368 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 304 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 328 GLN Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.0405 > 50: distance: 69 - 73: 16.267 distance: 73 - 74: 25.739 distance: 74 - 75: 40.304 distance: 74 - 77: 34.948 distance: 75 - 76: 25.559 distance: 75 - 84: 21.990 distance: 77 - 78: 9.080 distance: 78 - 79: 11.644 distance: 78 - 80: 8.484 distance: 79 - 81: 8.683 distance: 80 - 82: 4.231 distance: 81 - 83: 3.528 distance: 82 - 83: 4.238 distance: 84 - 85: 43.375 distance: 84 - 159: 24.434 distance: 85 - 86: 26.217 distance: 85 - 88: 24.436 distance: 86 - 87: 5.034 distance: 86 - 91: 22.004 distance: 87 - 156: 19.936 distance: 88 - 89: 12.106 distance: 88 - 90: 17.628 distance: 91 - 92: 34.108 distance: 92 - 93: 33.561 distance: 92 - 95: 22.979 distance: 93 - 94: 29.888 distance: 93 - 99: 7.838 distance: 95 - 96: 16.850 distance: 96 - 97: 31.104 distance: 96 - 98: 23.226 distance: 99 - 100: 7.728 distance: 100 - 101: 19.351 distance: 100 - 103: 12.619 distance: 101 - 102: 27.168 distance: 101 - 107: 24.629 distance: 103 - 104: 21.839 distance: 104 - 105: 16.726 distance: 104 - 106: 25.351 distance: 107 - 108: 30.358 distance: 107 - 113: 37.578 distance: 108 - 109: 41.083 distance: 108 - 111: 37.137 distance: 109 - 110: 23.494 distance: 109 - 114: 28.589 distance: 111 - 112: 31.081 distance: 112 - 113: 36.001 distance: 114 - 115: 17.198 distance: 114 - 120: 11.073 distance: 115 - 116: 20.953 distance: 115 - 118: 28.661 distance: 116 - 117: 17.490 distance: 118 - 119: 11.752 distance: 119 - 120: 17.418 distance: 121 - 122: 20.576 distance: 122 - 123: 22.267 distance: 122 - 125: 23.424 distance: 123 - 124: 22.030 distance: 123 - 132: 18.352 distance: 125 - 126: 7.187 distance: 126 - 127: 8.624 distance: 127 - 128: 5.872 distance: 128 - 129: 4.015 distance: 129 - 131: 3.120 distance: 132 - 133: 15.344 distance: 133 - 134: 8.550 distance: 133 - 136: 7.535 distance: 134 - 135: 16.514 distance: 134 - 141: 24.448 distance: 136 - 137: 13.936 distance: 137 - 138: 11.988 distance: 138 - 139: 15.806 distance: 139 - 140: 8.457 distance: 141 - 142: 24.556 distance: 141 - 147: 12.878 distance: 142 - 143: 21.131 distance: 142 - 145: 26.891 distance: 143 - 144: 19.320 distance: 143 - 148: 19.356 distance: 145 - 146: 18.365 distance: 146 - 147: 12.640 distance: 148 - 149: 15.922 distance: 149 - 150: 9.516 distance: 149 - 152: 11.748 distance: 150 - 151: 9.781 distance: 152 - 153: 4.974 distance: 153 - 154: 3.334 distance: 154 - 155: 5.832