Starting phenix.real_space_refine on Wed Aug 5 21:03:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ean_47837/08_2026/9ean_47837.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ean_47837/08_2026/9ean_47837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ean_47837/08_2026/9ean_47837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ean_47837/08_2026/9ean_47837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ean_47837/08_2026/9ean_47837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ean_47837/08_2026/9ean_47837.map" } resolution = 2.4 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= 0.011 sd= 0.154 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 48 5.16 5 C 7603 2.51 5 N 1942 2.21 5 O 2205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11798 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3953 Classifications: {'peptide': 515} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 468} Chain: "B" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3963 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 470} Chain: "C" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3882 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 459} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.40, per 1000 atoms: 0.20 Number of scatterers: 11798 At special positions: 0 Unit cell: (119.9, 116.6, 122.1, 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 48 16.00 O 2205 8.00 N 1942 7.00 C 7603 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: 0.59 Conformation dependent library (CDL) restraints added in 415.1 milliseconds 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2842 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 19 sheets defined 9.7% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.500A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.926A pdb=" N ASN A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.846A pdb=" N THR A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.520A pdb=" N LEU B 88 " --> pdb=" O GLY B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 52 through 58 removed outlier: 3.936A pdb=" N ASN C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.933A pdb=" N THR C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.788A pdb=" N VAL C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.796A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASN A 105 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 212 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 103 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN A 214 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY A 101 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.796A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASN A 105 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 212 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 103 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN A 214 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY A 101 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83 removed outlier: 7.273A pdb=" N ILE A 78 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 185 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS A 121 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ALA A 119 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451 Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451 removed outlier: 5.409A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 487 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA A 472 " --> pdb=" O TRP A 520 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP A 520 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 474 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 358 removed outlier: 6.964A pdb=" N SER A 332 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A 401 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLU A 338 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLN A 340 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ALA A 393 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N GLU A 342 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N VAL A 391 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 389 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA A 290 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 69 removed outlier: 6.809A pdb=" N LEU B 205 " --> pdb=" O CYS B 62 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N LEU B 64 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N GLY B 203 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N GLU B 66 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 11.626A pdb=" N VAL B 201 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.823A pdb=" N CYS B 183 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP B 81 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU B 181 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS B 121 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA B 119 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB1, first strand: chain 'B' and resid 447 through 451 removed outlier: 4.548A pdb=" N GLU B 447 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU B 252 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 289 through 298 removed outlier: 4.119A pdb=" N ALA B 290 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE B 375 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE B 358 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLN B 334 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY B 400 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU B 336 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE B 398 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLU B 338 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG B 396 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLN B 340 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N VAL B 394 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N GLU B 342 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 13.296A pdb=" N ARG B 392 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 427 through 429 removed outlier: 5.337A pdb=" N SER B 500 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLU B 488 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B 477 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 488 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 475 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS B 490 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 473 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 519 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG B 476 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL B 517 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG B 478 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N PHE B 515 " --> pdb=" O ARG B 478 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.743A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY C 101 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.743A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY C 101 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 78 through 83 removed outlier: 6.497A pdb=" N CYS C 183 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP C 81 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU C 181 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS C 121 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 448 through 451 removed outlier: 4.640A pdb=" N LEU C 252 " --> pdb=" O PHE C 509 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 289 through 296 removed outlier: 4.362A pdb=" N ALA C 290 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE C 375 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE C 358 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 337 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER C 332 " --> pdb=" O PHE C 401 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE C 401 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 397 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU C 338 " --> pdb=" O PRO C 395 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N GLN C 340 " --> pdb=" O ALA C 393 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ALA C 393 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N GLU C 342 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N VAL C 391 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 289 " --> pdb=" O ALA C 393 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 427 through 429 removed outlier: 7.018A pdb=" N TYR C 477 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 427 through 429 removed outlier: 3.856A pdb=" N ALA C 472 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 519 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG C 476 " --> pdb=" O VAL C 517 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL C 517 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ARG C 478 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE C 515 " --> pdb=" O ARG C 478 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 843 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: 1.86 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3365 1.33 - 1.45: 2116 1.45 - 1.58: 6571 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 12124 Sorted by residual: bond pdb=" C ASP B 231 " pdb=" N LEU B 232 " ideal model delta sigma weight residual 1.327 1.275 0.052 1.71e-02 3.42e+03 9.14e+00 bond pdb=" CB ASN B 192 " pdb=" CG ASN B 192 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.98e+00 bond pdb=" CB ASN A 115 " pdb=" CG ASN A 115 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.91e+00 bond pdb=" CB THR C 191 " pdb=" CG2 THR C 191 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" CB PRO B 23 " pdb=" CG PRO B 23 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.51e+00 ... (remaining 12119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 16391 2.93 - 5.86: 213 5.86 - 8.78: 18 8.78 - 11.71: 1 11.71 - 14.64: 1 Bond angle restraints: 16624 Sorted by residual: angle pdb=" N GLY A 104 " pdb=" CA GLY A 104 " pdb=" C GLY A 104 " ideal model delta sigma weight residual 111.63 118.63 -7.00 1.15e+00 7.56e-01 3.71e+01 angle pdb=" N GLY B 104 " pdb=" CA GLY B 104 " pdb=" C GLY B 104 " ideal model delta sigma weight residual 111.63 117.98 -6.35 1.15e+00 7.56e-01 3.05e+01 angle pdb=" CA VAL C 216 " pdb=" C VAL C 216 " pdb=" N TYR C 217 " ideal model delta sigma weight residual 117.37 120.72 -3.35 7.40e-01 1.83e+00 2.05e+01 angle pdb=" C GLY C 347 " pdb=" N GLU C 348 " pdb=" CA GLU C 348 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C PHE C 215 " pdb=" N VAL C 216 " pdb=" CA VAL C 216 " ideal model delta sigma weight residual 122.97 118.76 4.21 9.80e-01 1.04e+00 1.84e+01 ... (remaining 16619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6212 17.95 - 35.91: 698 35.91 - 53.86: 208 53.86 - 71.82: 53 71.82 - 89.77: 21 Dihedral angle restraints: 7192 sinusoidal: 2761 harmonic: 4431 Sorted by residual: dihedral pdb=" CA GLY B 195 " pdb=" C GLY B 195 " pdb=" N ASP B 196 " pdb=" CA ASP B 196 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLY A 421 " pdb=" C GLY A 421 " pdb=" N PRO A 422 " pdb=" CA PRO A 422 " ideal model delta harmonic sigma weight residual 0.00 -27.43 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA SER B 17 " pdb=" C SER B 17 " pdb=" N GLY B 18 " pdb=" CA GLY B 18 " ideal model delta harmonic sigma weight residual -180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 7189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1272 0.048 - 0.095: 454 0.095 - 0.143: 152 0.143 - 0.191: 9 0.191 - 0.238: 4 Chirality restraints: 1891 Sorted by residual: chirality pdb=" CA PRO B 23 " pdb=" N PRO B 23 " pdb=" C PRO B 23 " pdb=" CB PRO B 23 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP B 196 " pdb=" N ASP B 196 " pdb=" C ASP B 196 " pdb=" CB ASP B 196 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL A 103 " pdb=" CA VAL A 103 " pdb=" CG1 VAL A 103 " pdb=" CG2 VAL A 103 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1888 not shown) Planarity restraints: 2178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 22 " -0.096 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO B 23 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO B 23 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 23 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 471 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" CD GLU B 471 " 0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU B 471 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU B 471 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 62 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO B 63 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " 0.034 5.00e-02 4.00e+02 ... (remaining 2175 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 112 2.65 - 3.21: 9660 3.21 - 3.78: 16935 3.78 - 4.34: 23891 4.34 - 4.90: 39530 Nonbonded interactions: 90128 Sorted by model distance: nonbonded pdb=" ND2 ASN B 49 " pdb=" O VAL B 216 " model vdw 2.091 3.120 nonbonded pdb=" NH1 ARG C 244 " pdb=" OD2 ASP C 330 " model vdw 2.248 3.120 nonbonded pdb=" ND1 HIS B 270 " pdb=" OD1 ASP B 272 " model vdw 2.256 3.120 nonbonded pdb=" O ILE C 358 " pdb=" NE2 GLN C 367 " model vdw 2.262 3.120 nonbonded pdb=" O SER A 198 " pdb=" OG SER A 198 " model vdw 2.264 3.040 ... (remaining 90123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 529 or (resid 530 and (name N or name CA or nam \ e C or name O or name CB or name CG2)))) selection = (chain 'B' and (resid 27 through 529 or (resid 530 and (name N or name CA or nam \ e C or name O or name CB or name CG2)))) selection = chain 'C' } 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: 12.810 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.430 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0240 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 12124 Z= 0.251 Angle : 0.843 14.641 16624 Z= 0.466 Chirality : 0.053 0.238 1891 Planarity : 0.007 0.144 2178 Dihedral : 17.817 89.770 4350 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.49 % Favored : 94.31 % Rotamer: Outliers : 2.75 % Allowed : 26.91 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -0.84 (0.20), residues: 1529 helix: -0.54 (0.63), residues: 50 sheet: -0.10 (0.23), residues: 449 loop : -0.77 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 152 TYR 0.032 0.003 TYR C 217 PHE 0.022 0.003 PHE A 289 TRP 0.015 0.002 TRP B 102 HIS 0.007 0.003 HIS B 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 (12124) covalent geometry : angle 0.84297 / 0.47 (16624) hydrogen bonds : bond 0.17408 / 11.15 ( 305) hydrogen bonds : angle 7.57402 / 5.29 ( 843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 366 ASP cc_start: 0.1673 (p0) cc_final: 0.1230 (m-30) REVERT: C 95 LEU cc_start: 0.1607 (OUTLIER) cc_final: 0.1358 (mt) outliers start: 35 outliers final: 15 residues processed: 125 average time/residue: 0.4042 time to fit residues: 55.9964 Evaluate side-chains 64 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 374 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.3272 > 50:) chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN B 270 HIS B 409 ASN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.244144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.203425 restraints weight = 12286.437| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 1.27 r_work: 0.3876 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0709 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12124 Z= 0.142 Angle : 0.676 9.779 16624 Z= 0.339 Chirality : 0.046 0.210 1891 Planarity : 0.006 0.139 2178 Dihedral : 5.961 67.045 1681 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.79 % Favored : 95.95 % Rotamer: Outliers : 3.38 % Allowed : 25.18 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.71 (0.20), residues: 1529 helix: -1.51 (0.57), residues: 59 sheet: 0.14 (0.23), residues: 459 loop : -0.70 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 523 TYR 0.016 0.002 TYR B 496 PHE 0.024 0.002 PHE B 144 TRP 0.012 0.002 TRP A 460 HIS 0.007 0.002 HIS B 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (12124) covalent geometry : angle 0.67648 / 0.34 (16624) hydrogen bonds : bond 0.03555 / 2.34 ( 305) hydrogen bonds : angle 5.82624 / 4.02 ( 843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 64 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.2022 (OUTLIER) cc_final: 0.1713 (tp) REVERT: B 23 PRO cc_start: 0.1294 (Cg_exo) cc_final: 0.1077 (Cg_endo) REVERT: B 315 SER cc_start: 0.2363 (t) cc_final: 0.1995 (p) outliers start: 43 outliers final: 17 residues processed: 99 average time/residue: 0.3427 time to fit residues: 38.6854 Evaluate side-chains 66 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 9.9990 chunk 112 optimal weight: 0.0370 chunk 52 optimal weight: 0.2980 chunk 127 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 42 optimal weight: 30.0000 overall best weight: 3.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 146 HIS ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN A 265 GLN A 312 GLN A 464 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 146 HIS B 173 GLN B 340 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN B 484 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 175 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN C 270 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.294563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.270159 restraints weight = 15531.226| |-----------------------------------------------------------------------------| r_work (start): 0.4791 rms_B_bonded: 1.56 r_work: 0.4468 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5450 moved from start: 0.9366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.181 12124 Z= 0.417 Angle : 1.192 22.239 16624 Z= 0.633 Chirality : 0.062 0.375 1891 Planarity : 0.010 0.124 2178 Dihedral : 7.706 53.688 1662 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.33 % Favored : 92.48 % Rotamer: Outliers : 5.51 % Allowed : 23.84 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.29 % 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: -1.51 (0.20), residues: 1529 helix: -2.19 (0.55), residues: 50 sheet: -0.05 (0.24), residues: 430 loop : -1.44 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 165 TYR 0.040 0.004 TYR A 91 PHE 0.062 0.004 PHE B 401 TRP 0.036 0.005 TRP C 264 HIS 0.031 0.006 HIS C 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.42 (12124) covalent geometry : angle 1.19164 / 0.63 (16624) hydrogen bonds : bond 0.06294 / 4.11 ( 305) hydrogen bonds : angle 7.77891 / 5.26 ( 843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 90 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.1509 (OUTLIER) cc_final: 0.1248 (mt0) REVERT: A 312 GLN cc_start: 0.3097 (OUTLIER) cc_final: 0.1746 (pm20) REVERT: A 350 LEU cc_start: 0.2239 (OUTLIER) cc_final: 0.1913 (tp) REVERT: B 23 PRO cc_start: 0.5190 (Cg_exo) cc_final: 0.4951 (Cg_endo) REVERT: B 229 MET cc_start: 0.3209 (OUTLIER) cc_final: 0.2965 (pmm) REVERT: B 436 MET cc_start: 0.2643 (OUTLIER) cc_final: 0.2198 (pp-130) REVERT: C 263 GLN cc_start: 0.2471 (OUTLIER) cc_final: 0.1830 (pt0) REVERT: C 342 GLU cc_start: 0.3401 (OUTLIER) cc_final: 0.1119 (mm-30) outliers start: 70 outliers final: 18 residues processed: 149 average time/residue: 0.4349 time to fit residues: 71.5550 Evaluate side-chains 82 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 387 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN A 146 HIS A 242 HIS A 340 GLN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 146 HIS ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN C 73 ASN C 173 GLN C 214 ASN C 265 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.278282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.243690 restraints weight = 13316.216| |-----------------------------------------------------------------------------| r_work (start): 0.4557 rms_B_bonded: 1.47 r_work: 0.4350 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4313 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 1.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 12124 Z= 0.215 Angle : 0.860 12.245 16624 Z= 0.445 Chirality : 0.050 0.201 1891 Planarity : 0.008 0.126 2178 Dihedral : 6.254 51.766 1659 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.97 % Favored : 94.83 % Rotamer: Outliers : 4.72 % Allowed : 23.68 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % 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: -1.20 (0.20), residues: 1529 helix: -1.58 (0.56), residues: 51 sheet: 0.12 (0.25), residues: 411 loop : -1.20 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 166 TYR 0.056 0.002 TYR A 91 PHE 0.034 0.003 PHE B 117 TRP 0.026 0.002 TRP C 264 HIS 0.013 0.002 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (12124) covalent geometry : angle 0.86010 / 0.44 (16624) hydrogen bonds : bond 0.04912 / 3.37 ( 305) hydrogen bonds : angle 6.27853 / 4.36 ( 843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 74 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8227 (mtm110) REVERT: A 434 THR cc_start: 0.2117 (OUTLIER) cc_final: 0.1763 (p) REVERT: B 225 THR cc_start: 0.3326 (OUTLIER) cc_final: 0.3108 (p) REVERT: B 436 MET cc_start: 0.3301 (mtm) cc_final: 0.0603 (ttp) REVERT: C 47 GLN cc_start: 0.5317 (mt0) cc_final: 0.4488 (pm20) REVERT: C 106 MET cc_start: 0.8737 (mtt) cc_final: 0.8497 (mtt) REVERT: C 187 THR cc_start: 0.8343 (m) cc_final: 0.7986 (p) REVERT: C 196 ASP cc_start: 0.5982 (p0) cc_final: 0.5747 (p0) REVERT: C 342 GLU cc_start: 0.2723 (OUTLIER) cc_final: 0.0875 (mm-30) outliers start: 60 outliers final: 16 residues processed: 124 average time/residue: 0.5547 time to fit residues: 74.5624 Evaluate side-chains 74 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 450 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 104 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 121 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 28 optimal weight: 40.0000 chunk 107 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 86 optimal weight: 30.0000 chunk 44 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 214 ASN A 312 GLN B 73 ASN B 455 GLN C 146 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.272826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.242996 restraints weight = 12989.917| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 1.38 r_work: 0.4287 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4242 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 1.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12124 Z= 0.127 Angle : 0.681 22.490 16624 Z= 0.336 Chirality : 0.047 0.228 1891 Planarity : 0.007 0.188 2178 Dihedral : 5.314 33.985 1659 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.09 % Rotamer: Outliers : 2.99 % Allowed : 24.86 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % 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: -0.94 (0.20), residues: 1529 helix: -1.50 (0.55), residues: 65 sheet: 0.20 (0.25), residues: 412 loop : -0.94 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 228 TYR 0.013 0.001 TYR B 99 PHE 0.018 0.002 PHE A 56 TRP 0.017 0.001 TRP C 264 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (12124) covalent geometry : angle 0.68061 / 0.34 (16624) hydrogen bonds : bond 0.03458 / 2.27 ( 305) hydrogen bonds : angle 5.75816 / 4.02 ( 843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 64 time to evaluate : 0.308 Fit side-chains REVERT: A 357 MET cc_start: 0.2079 (tmt) cc_final: 0.0843 (pmm) REVERT: B 141 ILE cc_start: 0.5966 (OUTLIER) cc_final: 0.5448 (mt) REVERT: B 436 MET cc_start: 0.3052 (mtm) cc_final: 0.1148 (ttp) REVERT: C 47 GLN cc_start: 0.5522 (mt0) cc_final: 0.4627 (pm20) REVERT: C 342 GLU cc_start: 0.2862 (OUTLIER) cc_final: 0.0988 (mp0) REVERT: C 357 MET cc_start: 0.3054 (tpt) cc_final: 0.2775 (mmm) REVERT: C 493 ASN cc_start: 0.7899 (t0) cc_final: 0.7695 (t0) outliers start: 38 outliers final: 14 residues processed: 97 average time/residue: 0.5294 time to fit residues: 55.8176 Evaluate side-chains 71 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 86 optimal weight: 0.0970 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN B 265 GLN B 270 HIS B 526 GLN C 242 HIS C 340 GLN C 493 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.257930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.194529 restraints weight = 12088.663| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 6.48 r_work: 0.3410 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 1.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 12124 Z= 0.227 Angle : 0.879 25.539 16624 Z= 0.446 Chirality : 0.052 0.231 1891 Planarity : 0.008 0.195 2178 Dihedral : 6.195 40.199 1659 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.95 % Favored : 93.85 % Rotamer: Outliers : 2.99 % Allowed : 23.92 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.07 % 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: -1.13 (0.20), residues: 1529 helix: -1.93 (0.50), residues: 67 sheet: 0.15 (0.25), residues: 422 loop : -1.10 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 431 TYR 0.031 0.003 TYR C 217 PHE 0.040 0.003 PHE A 213 TRP 0.028 0.003 TRP B 54 HIS 0.009 0.002 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (12124) covalent geometry : angle 0.87915 / 0.45 (16624) hydrogen bonds : bond 0.04850 / 3.22 ( 305) hydrogen bonds : angle 6.17302 / 4.35 ( 843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.6546 (pm20) cc_final: 0.6213 (pm20) REVERT: A 229 MET cc_start: 0.4637 (tpt) cc_final: 0.3748 (ttm) REVERT: A 357 MET cc_start: 0.3096 (tmt) cc_final: 0.1839 (pmm) REVERT: A 477 TYR cc_start: 0.3173 (t80) cc_final: 0.2512 (t80) REVERT: B 72 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8513 (mpp-170) REVERT: B 494 GLU cc_start: 0.6087 (tm-30) cc_final: 0.5466 (mp0) REVERT: C 47 GLN cc_start: 0.6108 (mt0) cc_final: 0.4315 (pm20) REVERT: C 148 MET cc_start: 0.8935 (ttm) cc_final: 0.8676 (ttm) REVERT: C 176 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7453 (mt-10) REVERT: C 340 GLN cc_start: 0.2684 (OUTLIER) cc_final: 0.2346 (mt0) REVERT: C 476 ARG cc_start: 0.6384 (ttp-170) cc_final: 0.5332 (ttm-80) REVERT: C 494 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: C 516 GLU cc_start: 0.8212 (mp0) cc_final: 0.7939 (mp0) outliers start: 38 outliers final: 17 residues processed: 121 average time/residue: 0.6342 time to fit residues: 82.3488 Evaluate side-chains 80 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 437 ARG Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 68 optimal weight: 0.0770 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN A 50 GLN A 214 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** C 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.249405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.182306 restraints weight = 11866.560| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 6.95 r_work: 0.3299 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 1.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12124 Z= 0.173 Angle : 0.733 18.590 16624 Z= 0.373 Chirality : 0.049 0.252 1891 Planarity : 0.007 0.175 2178 Dihedral : 5.579 38.580 1659 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.84 % Favored : 94.96 % Rotamer: Outliers : 2.44 % Allowed : 25.41 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % 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: -0.95 (0.21), residues: 1529 helix: -1.71 (0.55), residues: 66 sheet: 0.17 (0.26), residues: 420 loop : -0.93 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 152 TYR 0.016 0.002 TYR A 217 PHE 0.029 0.002 PHE B 117 TRP 0.034 0.002 TRP C 285 HIS 0.006 0.002 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (12124) covalent geometry : angle 0.73350 / 0.37 (16624) hydrogen bonds : bond 0.03681 / 2.45 ( 305) hydrogen bonds : angle 5.72627 / 4.03 ( 843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6657 (mt-10) cc_final: 0.5852 (tt0) REVERT: A 357 MET cc_start: 0.2999 (tmt) cc_final: 0.1754 (pmm) REVERT: B 72 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8347 (mpp-170) REVERT: B 436 MET cc_start: 0.3060 (mpp) cc_final: 0.2281 (ttp) REVERT: B 494 GLU cc_start: 0.6337 (tm-30) cc_final: 0.5470 (mp0) REVERT: C 47 GLN cc_start: 0.5670 (mt0) cc_final: 0.4106 (mp10) REVERT: C 106 MET cc_start: 0.9245 (mtt) cc_final: 0.8924 (mtt) REVERT: C 274 THR cc_start: 0.7748 (m) cc_final: 0.7340 (t) REVERT: C 340 GLN cc_start: 0.3146 (OUTLIER) cc_final: 0.2761 (mt0) REVERT: C 436 MET cc_start: 0.4191 (ptm) cc_final: 0.3612 (tpt) REVERT: C 476 ARG cc_start: 0.6615 (ttp-170) cc_final: 0.5181 (ttm170) REVERT: C 494 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: C 516 GLU cc_start: 0.7936 (mp0) cc_final: 0.7319 (mp0) outliers start: 31 outliers final: 12 residues processed: 108 average time/residue: 0.5716 time to fit residues: 66.4005 Evaluate side-chains 81 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 99 optimal weight: 8.9990 chunk 45 optimal weight: 0.0470 chunk 49 optimal weight: 9.9990 chunk 39 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.238442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.174807 restraints weight = 11469.652| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 5.95 r_work: 0.3256 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 1.8459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12124 Z= 0.243 Angle : 0.916 15.033 16624 Z= 0.471 Chirality : 0.056 0.296 1891 Planarity : 0.008 0.161 2178 Dihedral : 6.405 42.959 1659 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.82 % Favored : 93.98 % Rotamer: Outliers : 2.20 % Allowed : 25.10 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % 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: -1.14 (0.20), residues: 1529 helix: -1.67 (0.55), residues: 59 sheet: -0.02 (0.26), residues: 412 loop : -1.04 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 244 TYR 0.042 0.003 TYR C 217 PHE 0.028 0.003 PHE B 117 TRP 0.065 0.005 TRP B 54 HIS 0.019 0.004 HIS C 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (12124) covalent geometry : angle 0.91632 / 0.47 (16624) hydrogen bonds : bond 0.05231 / 3.56 ( 305) hydrogen bonds : angle 6.35563 / 4.41 ( 843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.410 Fit side-chains REVERT: A 176 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6102 (mt-10) REVERT: A 252 LEU cc_start: 0.7157 (tp) cc_final: 0.6669 (tm) REVERT: A 489 CYS cc_start: 0.7213 (m) cc_final: 0.6755 (m) REVERT: A 511 THR cc_start: 0.5959 (OUTLIER) cc_final: 0.5399 (p) REVERT: B 141 ILE cc_start: 0.8321 (pt) cc_final: 0.7916 (tt) REVERT: B 488 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7134 (pt0) REVERT: B 494 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6356 (mp0) REVERT: B 501 TYR cc_start: 0.6179 (t80) cc_final: 0.5572 (t80) REVERT: C 47 GLN cc_start: 0.6771 (mt0) cc_final: 0.4983 (pm20) REVERT: C 106 MET cc_start: 0.9291 (mtt) cc_final: 0.9031 (mtt) REVERT: C 148 MET cc_start: 0.9055 (ttm) cc_final: 0.8809 (ttm) REVERT: C 176 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7755 (mt-10) REVERT: C 322 ARG cc_start: 0.6824 (ttm110) cc_final: 0.6420 (ttm170) REVERT: C 340 GLN cc_start: 0.4286 (OUTLIER) cc_final: 0.2887 (mm-40) REVERT: C 373 ARG cc_start: 0.5470 (tpm170) cc_final: 0.4916 (ttp80) REVERT: C 476 ARG cc_start: 0.6843 (ttp-170) cc_final: 0.5526 (ttm170) REVERT: C 479 ASN cc_start: 0.4751 (OUTLIER) cc_final: 0.4202 (t0) REVERT: C 494 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: C 516 GLU cc_start: 0.8238 (mp0) cc_final: 0.7533 (mp0) outliers start: 28 outliers final: 13 residues processed: 135 average time/residue: 0.5529 time to fit residues: 80.4503 Evaluate side-chains 112 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 27 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 111 optimal weight: 7.9990 chunk 97 optimal weight: 30.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN B 493 ASN B 526 GLN C 261 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.239791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.178457 restraints weight = 11576.491| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 5.74 r_work: 0.3285 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 1.8550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12124 Z= 0.127 Angle : 0.688 13.261 16624 Z= 0.347 Chirality : 0.047 0.260 1891 Planarity : 0.007 0.154 2178 Dihedral : 5.575 42.668 1659 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 1.49 % Allowed : 26.20 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1529 helix: -1.19 (0.59), residues: 58 sheet: 0.15 (0.27), residues: 404 loop : -0.96 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 478 TYR 0.012 0.001 TYR C 217 PHE 0.018 0.002 PHE A 80 TRP 0.046 0.002 TRP C 285 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (12124) covalent geometry : angle 0.68807 / 0.35 (16624) hydrogen bonds : bond 0.03448 / 2.34 ( 305) hydrogen bonds : angle 5.77657 / 4.03 ( 843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6601 (mt-10) REVERT: A 357 MET cc_start: 0.3803 (tmm) cc_final: 0.2704 (pmm) REVERT: A 511 THR cc_start: 0.5961 (OUTLIER) cc_final: 0.5512 (p) REVERT: B 235 ILE cc_start: 0.6778 (mt) cc_final: 0.6086 (tp) REVERT: B 311 GLU cc_start: 0.4948 (mm-30) cc_final: 0.3857 (tt0) REVERT: B 494 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6062 (mp0) REVERT: B 501 TYR cc_start: 0.6224 (t80) cc_final: 0.5586 (t80) REVERT: B 512 ASP cc_start: 0.6244 (m-30) cc_final: 0.5949 (m-30) REVERT: B 516 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8020 (mt-10) REVERT: C 47 GLN cc_start: 0.6147 (mt0) cc_final: 0.4477 (mp10) REVERT: C 106 MET cc_start: 0.9290 (mtt) cc_final: 0.9010 (mtt) REVERT: C 176 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7460 (mt-10) REVERT: C 373 ARG cc_start: 0.5718 (tpm170) cc_final: 0.5504 (ttp80) REVERT: C 431 ARG cc_start: 0.6547 (mtp85) cc_final: 0.6338 (mtp85) REVERT: C 476 ARG cc_start: 0.6911 (ttp-170) cc_final: 0.5683 (ttm170) REVERT: C 494 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: C 516 GLU cc_start: 0.8182 (mp0) cc_final: 0.7579 (mp0) outliers start: 19 outliers final: 13 residues processed: 107 average time/residue: 0.7002 time to fit residues: 80.3754 Evaluate side-chains 100 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN B 236 GLN B 493 ASN C 340 GLN C 493 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.230027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.166931 restraints weight = 11248.784| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 5.87 r_work: 0.3195 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 1.9836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12124 Z= 0.277 Angle : 0.995 14.955 16624 Z= 0.516 Chirality : 0.060 0.382 1891 Planarity : 0.009 0.160 2178 Dihedral : 6.829 40.925 1659 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 2.28 % Allowed : 25.96 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.07 % Twisted Proline : 1.49 % Twisted General : 0.07 % 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: -1.38 (0.20), residues: 1529 helix: -1.54 (0.57), residues: 60 sheet: -0.26 (0.25), residues: 419 loop : -1.21 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 478 TYR 0.044 0.003 TYR C 217 PHE 0.049 0.004 PHE A 213 TRP 0.087 0.005 TRP B 54 HIS 0.013 0.003 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.28 (12124) covalent geometry : angle 0.99487 / 0.52 (16624) hydrogen bonds : bond 0.06094 / 4.22 ( 305) hydrogen bonds : angle 6.41564 / 4.47 ( 843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.368 Fit side-chains REVERT: A 154 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8933 (mp) REVERT: A 176 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6254 (mt-10) REVERT: A 231 ASP cc_start: 0.7302 (p0) cc_final: 0.7059 (p0) REVERT: A 238 ARG cc_start: 0.5460 (mtp180) cc_final: 0.5100 (ptp-170) REVERT: A 269 VAL cc_start: 0.8001 (m) cc_final: 0.7607 (p) REVERT: A 348 GLU cc_start: 0.0825 (OUTLIER) cc_final: 0.0298 (tp30) REVERT: A 357 MET cc_start: 0.4350 (OUTLIER) cc_final: 0.3854 (tmt) REVERT: A 511 THR cc_start: 0.5898 (OUTLIER) cc_final: 0.5593 (p) REVERT: B 21 LEU cc_start: 0.7408 (mt) cc_final: 0.6850 (pp) REVERT: B 141 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8148 (tp) REVERT: B 311 GLU cc_start: 0.5350 (mm-30) cc_final: 0.4257 (mm-30) REVERT: B 471 GLU cc_start: 0.7373 (tp30) cc_final: 0.6560 (mt-10) REVERT: B 494 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6448 (mp0) REVERT: B 516 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7971 (mt-10) REVERT: C 47 GLN cc_start: 0.6756 (mt0) cc_final: 0.4939 (pm20) REVERT: C 106 MET cc_start: 0.9300 (mtt) cc_final: 0.8988 (mtt) REVERT: C 176 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 373 ARG cc_start: 0.5852 (tpm170) cc_final: 0.5639 (ttp80) REVERT: C 476 ARG cc_start: 0.7079 (ttp-170) cc_final: 0.5948 (ttm170) REVERT: C 494 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: C 516 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7592 (mp0) outliers start: 29 outliers final: 14 residues processed: 144 average time/residue: 0.5682 time to fit residues: 88.8093 Evaluate side-chains 127 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 40.0000 chunk 129 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 3 optimal weight: 0.1980 chunk 108 optimal weight: 0.0670 chunk 140 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 overall best weight: 1.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN B 236 GLN B 263 GLN B 493 ASN C 270 HIS C 493 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.233203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.174847 restraints weight = 11381.292| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 5.30 r_work: 0.3259 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 1.9893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12124 Z= 0.124 Angle : 0.689 13.807 16624 Z= 0.347 Chirality : 0.047 0.274 1891 Planarity : 0.007 0.155 2178 Dihedral : 5.677 38.956 1659 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.58 % Favored : 95.23 % Rotamer: Outliers : 1.57 % Allowed : 26.28 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % 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: -1.03 (0.20), residues: 1529 helix: -1.21 (0.59), residues: 59 sheet: 0.04 (0.26), residues: 415 loop : -0.99 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 478 TYR 0.013 0.001 TYR B 295 PHE 0.020 0.002 PHE A 80 TRP 0.043 0.002 TRP B 54 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12124) covalent geometry : angle 0.68894 / 0.35 (16624) hydrogen bonds : bond 0.03553 / 2.42 ( 305) hydrogen bonds : angle 5.82040 / 4.07 ( 843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.07 seconds wall clock time: 81 minutes 58.24 seconds (4918.24 seconds total)