Starting phenix.real_space_refine on Tue Jun 10 15:19:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ean_47837/06_2025/9ean_47837.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ean_47837/06_2025/9ean_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ean_47837/06_2025/9ean_47837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ean_47837/06_2025/9ean_47837.map" model { file = "/net/cci-nas-00/data/ceres_data/9ean_47837/06_2025/9ean_47837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ean_47837/06_2025/9ean_47837.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.98, per 1000 atoms: 0.85 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: 2.56 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.36 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: 3.79 Time building geometry restraints manager: 3.15 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: 31.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.130 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0238 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (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 TRP 0.015 0.002 TRP B 102 HIS 0.007 0.003 HIS B 270 PHE 0.022 0.003 PHE A 289 TYR 0.032 0.003 TYR C 217 ARG 0.007 0.001 ARG B 152 Details of bonding type rmsd hydrogen bonds : bond 0.17408 ( 305) hydrogen bonds : angle 7.57402 ( 843) covalent geometry : bond 0.00576 (12124) covalent geometry : angle 0.84297 (16624) *********************** 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 : 1.169 Fit side-chains 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: 1.0393 time to fit residues: 144.5690 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 : 1.165 ------------------------------------------------------------------------------- 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 128 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 340 GLN B 409 ASN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.238738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.190198 restraints weight = 11855.072| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 1.35 r_work: 0.3703 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0364 moved from start: 0.2074 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= 0.131 Angle : 0.648 10.928 16624 Z= 0.325 Chirality : 0.045 0.204 1891 Planarity : 0.006 0.141 2178 Dihedral : 6.115 75.963 1681 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.66 % Favored : 96.08 % Rotamer: Outliers : 3.30 % Allowed : 25.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1529 helix: -1.30 (0.58), residues: 58 sheet: 0.18 (0.23), residues: 448 loop : -0.69 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 460 HIS 0.011 0.001 HIS B 270 PHE 0.021 0.001 PHE C 80 TYR 0.015 0.001 TYR B 99 ARG 0.004 0.001 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 305) hydrogen bonds : angle 5.93967 ( 843) covalent geometry : bond 0.00287 (12124) covalent geometry : angle 0.64813 (16624) *********************** 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 99 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 57 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.1815 (mtp) cc_final: 0.1350 (mpp) REVERT: A 335 LEU cc_start: 0.3379 (OUTLIER) cc_final: 0.3038 (mm) REVERT: A 350 LEU cc_start: 0.1998 (OUTLIER) cc_final: 0.1673 (tp) REVERT: A 357 MET cc_start: 0.3027 (OUTLIER) cc_final: 0.1463 (ptp) REVERT: B 436 MET cc_start: 0.3422 (ttp) cc_final: 0.2509 (mtm) outliers start: 42 outliers final: 16 residues processed: 92 average time/residue: 1.0928 time to fit residues: 114.2343 Evaluate side-chains 62 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 270 HIS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 463 SER 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 310 ILE 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 179 MET Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 214 ASN 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 147 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 6 optimal weight: 0.3980 chunk 136 optimal weight: 8.9990 chunk 28 optimal weight: 50.0000 chunk 109 optimal weight: 0.0980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN A 265 GLN A 312 GLN A 340 GLN A 409 ASN A 464 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 73 ASN B 173 GLN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 455 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.301051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.278586 restraints weight = 15870.392| |-----------------------------------------------------------------------------| r_work (start): 0.4859 rms_B_bonded: 1.18 r_work: 0.4645 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4507 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 moved from start: 0.9712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.141 12124 Z= 0.401 Angle : 1.345 28.469 16624 Z= 0.692 Chirality : 0.066 0.411 1891 Planarity : 0.012 0.203 2178 Dihedral : 8.414 58.143 1664 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.98 % Favored : 91.76 % Rotamer: Outliers : 6.69 % Allowed : 22.42 % Favored : 70.89 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 3.73 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.19), residues: 1529 helix: -2.68 (0.53), residues: 52 sheet: -0.26 (0.25), residues: 413 loop : -1.77 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.005 TRP C 169 HIS 0.027 0.005 HIS A 170 PHE 0.055 0.005 PHE B 117 TYR 0.056 0.004 TYR B 99 ARG 0.011 0.002 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.07143 ( 305) hydrogen bonds : angle 8.58433 ( 843) covalent geometry : bond 0.00878 (12124) covalent geometry : angle 1.34537 (16624) *********************** 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 193 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 108 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.5148 (OUTLIER) cc_final: 0.4798 (ptp) REVERT: A 109 GLN cc_start: 0.4276 (OUTLIER) cc_final: 0.3859 (mt0) REVERT: A 263 GLN cc_start: 0.1737 (OUTLIER) cc_final: 0.1236 (mt0) REVERT: A 312 GLN cc_start: 0.3261 (OUTLIER) cc_final: 0.1901 (pm20) REVERT: A 338 GLU cc_start: 0.1460 (OUTLIER) cc_final: 0.0228 (pp20) REVERT: A 357 MET cc_start: 0.3210 (OUTLIER) cc_final: 0.1140 (mpp) REVERT: A 398 ILE cc_start: 0.0858 (OUTLIER) cc_final: 0.0338 (mp) REVERT: A 508 THR cc_start: 0.4311 (OUTLIER) cc_final: 0.3922 (m) REVERT: B 28 GLN cc_start: 0.2969 (mp10) cc_final: 0.2737 (mm-40) REVERT: B 229 MET cc_start: 0.3226 (OUTLIER) cc_final: 0.2673 (pmm) REVERT: B 357 MET cc_start: 0.3846 (mpt) cc_final: 0.3529 (mpt) REVERT: B 436 MET cc_start: 0.4345 (ttp) cc_final: 0.1714 (mtm) REVERT: C 202 SER cc_start: 0.7720 (OUTLIER) cc_final: 0.7176 (m) REVERT: C 342 GLU cc_start: 0.4592 (OUTLIER) cc_final: 0.2037 (mp0) REVERT: C 405 ILE cc_start: 0.5933 (OUTLIER) cc_final: 0.5707 (pt) REVERT: C 516 GLU cc_start: 0.3933 (OUTLIER) cc_final: 0.3723 (mm-30) outliers start: 85 outliers final: 20 residues processed: 177 average time/residue: 1.5127 time to fit residues: 297.1441 Evaluate side-chains 95 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 167 VAL 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 338 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 516 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 97 optimal weight: 20.0000 chunk 128 optimal weight: 40.0000 chunk 56 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 137 optimal weight: 40.0000 chunk 72 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 84 optimal weight: 0.0010 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 242 HIS A 312 GLN A 340 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN B 242 HIS ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN C 146 HIS C 265 GLN C 270 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.288505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.256319 restraints weight = 14593.713| |-----------------------------------------------------------------------------| r_work (start): 0.4666 rms_B_bonded: 1.27 r_work: 0.4376 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.4221 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 1.0058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12124 Z= 0.133 Angle : 0.699 14.295 16624 Z= 0.350 Chirality : 0.047 0.222 1891 Planarity : 0.007 0.162 2178 Dihedral : 5.978 55.625 1660 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.58 % Favored : 95.23 % Rotamer: Outliers : 2.91 % Allowed : 26.36 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.20), residues: 1529 helix: -1.68 (0.55), residues: 64 sheet: 0.19 (0.24), residues: 425 loop : -1.27 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 54 HIS 0.010 0.002 HIS C 146 PHE 0.023 0.002 PHE C 80 TYR 0.019 0.001 TYR C 99 ARG 0.010 0.001 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 305) hydrogen bonds : angle 6.25213 ( 843) covalent geometry : bond 0.00291 (12124) covalent geometry : angle 0.69861 (16624) *********************** 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 114 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6919 (mtm110) REVERT: A 312 GLN cc_start: 0.2635 (OUTLIER) cc_final: 0.1985 (pm20) REVERT: A 338 GLU cc_start: 0.1868 (OUTLIER) cc_final: 0.0713 (pp20) REVERT: A 357 MET cc_start: 0.3142 (OUTLIER) cc_final: 0.1257 (pmm) REVERT: B 229 MET cc_start: 0.4360 (OUTLIER) cc_final: 0.3877 (tpp) REVERT: B 311 GLU cc_start: 0.3763 (mm-30) cc_final: 0.2970 (mm-30) REVERT: B 357 MET cc_start: 0.4046 (mpt) cc_final: 0.3663 (mpp) REVERT: C 98 MET cc_start: 0.5646 (OUTLIER) cc_final: 0.5411 (mtp) REVERT: C 342 GLU cc_start: 0.4585 (OUTLIER) cc_final: 0.1664 (mm-30) REVERT: C 357 MET cc_start: 0.4141 (tpt) cc_final: 0.3870 (mmm) outliers start: 37 outliers final: 11 residues processed: 103 average time/residue: 1.2410 time to fit residues: 140.1646 Evaluate side-chains 77 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 373 ARG Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 386 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN B 270 HIS ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.276293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.247861 restraints weight = 12848.634| |-----------------------------------------------------------------------------| r_work (start): 0.4602 rms_B_bonded: 1.29 r_work: 0.4284 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4222 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 1.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12124 Z= 0.205 Angle : 0.835 19.364 16624 Z= 0.423 Chirality : 0.050 0.266 1891 Planarity : 0.007 0.172 2178 Dihedral : 6.244 54.976 1660 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.08 % Favored : 93.72 % Rotamer: Outliers : 4.33 % Allowed : 24.55 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.20), residues: 1529 helix: -0.74 (0.59), residues: 51 sheet: -0.07 (0.24), residues: 444 loop : -1.20 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 54 HIS 0.010 0.003 HIS A 146 PHE 0.037 0.002 PHE B 117 TYR 0.030 0.002 TYR C 99 ARG 0.020 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 305) hydrogen bonds : angle 6.04202 ( 843) covalent geometry : bond 0.00462 (12124) covalent geometry : angle 0.83459 (16624) *********************** 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 134 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 79 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 106 MET cc_start: 0.8495 (mtp) cc_final: 0.8236 (mtp) REVERT: A 166 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8368 (ptm-80) REVERT: A 357 MET cc_start: 0.2337 (OUTLIER) cc_final: 0.0830 (pmm) REVERT: B 98 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7732 (mtt) REVERT: B 225 THR cc_start: 0.3858 (OUTLIER) cc_final: 0.3640 (p) REVERT: C 47 GLN cc_start: 0.6046 (mt0) cc_final: 0.4875 (pm20) REVERT: C 357 MET cc_start: 0.2932 (tpt) cc_final: 0.2580 (mmm) outliers start: 55 outliers final: 15 residues processed: 122 average time/residue: 1.2822 time to fit residues: 169.7443 Evaluate side-chains 77 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 66 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 386 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 127 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 56 optimal weight: 0.4980 chunk 149 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 30.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN B 484 GLN B 526 GLN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.261959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.206021 restraints weight = 12247.690| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 5.56 r_work: 0.3491 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 1.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12124 Z= 0.190 Angle : 0.790 18.297 16624 Z= 0.397 Chirality : 0.049 0.210 1891 Planarity : 0.007 0.169 2178 Dihedral : 5.899 46.720 1660 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.10 % Favored : 94.70 % Rotamer: Outliers : 3.23 % Allowed : 25.33 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.20), residues: 1529 helix: -1.63 (0.53), residues: 65 sheet: 0.09 (0.25), residues: 412 loop : -1.13 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 54 HIS 0.008 0.002 HIS C 146 PHE 0.046 0.003 PHE A 59 TYR 0.024 0.002 TYR A 217 ARG 0.009 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 305) hydrogen bonds : angle 5.98129 ( 843) covalent geometry : bond 0.00435 (12124) covalent geometry : angle 0.79009 (16624) *********************** 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 118 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 1.287 Fit side-chains REVERT: A 223 GLU cc_start: 0.5727 (pm20) cc_final: 0.5429 (pm20) REVERT: A 357 MET cc_start: 0.3155 (OUTLIER) cc_final: 0.1344 (pmm) REVERT: B 98 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7856 (mtt) REVERT: B 436 MET cc_start: 0.4076 (tmm) cc_final: 0.1207 (mtm) REVERT: B 494 GLU cc_start: 0.5678 (tm-30) cc_final: 0.4717 (mp0) REVERT: C 47 GLN cc_start: 0.6040 (mt0) cc_final: 0.4499 (pm20) REVERT: C 174 ASP cc_start: 0.7724 (p0) cc_final: 0.7499 (m-30) REVERT: C 340 GLN cc_start: 0.2316 (OUTLIER) cc_final: 0.2040 (mt0) REVERT: C 357 MET cc_start: 0.4108 (tpt) cc_final: 0.3693 (mmm) REVERT: C 436 MET cc_start: 0.4356 (ptm) cc_final: 0.3623 (tpt) REVERT: C 494 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6912 (mp0) outliers start: 41 outliers final: 10 residues processed: 110 average time/residue: 1.4391 time to fit residues: 172.5377 Evaluate side-chains 74 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 357 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 225 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 374 VAL Chi-restraints excluded: chain C residue 386 LEU 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 7 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 173 GLN A 214 ASN ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN C 236 GLN 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 = 0.4579 r_free = 0.4579 target = 0.243861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.173524 restraints weight = 11633.653| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 7.38 r_work: 0.3260 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 1.7623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12124 Z= 0.268 Angle : 0.972 15.581 16624 Z= 0.503 Chirality : 0.057 0.284 1891 Planarity : 0.009 0.162 2178 Dihedral : 6.899 52.577 1660 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.89 % Favored : 93.92 % Rotamer: Outliers : 3.46 % Allowed : 24.94 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1529 helix: -1.03 (0.64), residues: 52 sheet: -0.15 (0.25), residues: 409 loop : -1.25 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP C 285 HIS 0.013 0.003 HIS B 242 PHE 0.069 0.004 PHE B 117 TYR 0.037 0.003 TYR C 99 ARG 0.012 0.002 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.05293 ( 305) hydrogen bonds : angle 6.44002 ( 843) covalent geometry : bond 0.00615 (12124) covalent geometry : angle 0.97172 (16624) *********************** 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 158 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 1.575 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.6614 (pm20) cc_final: 0.6395 (pm20) REVERT: A 292 GLU cc_start: 0.2050 (OUTLIER) cc_final: 0.1626 (pm20) REVERT: A 357 MET cc_start: 0.2716 (OUTLIER) cc_final: 0.1488 (pmm) REVERT: A 511 THR cc_start: 0.4928 (OUTLIER) cc_final: 0.4648 (p) REVERT: B 27 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.5321 (pp20) REVERT: B 197 GLU cc_start: 0.6631 (tt0) cc_final: 0.6204 (tm-30) REVERT: B 353 THR cc_start: -0.0605 (OUTLIER) cc_final: -0.1008 (p) REVERT: B 471 GLU cc_start: 0.6610 (tp30) cc_final: 0.6198 (tp30) REVERT: B 494 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6659 (mp0) REVERT: C 47 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.4734 (pm20) REVERT: C 270 HIS cc_start: 0.8129 (m170) cc_final: 0.7783 (m-70) REVERT: C 322 ARG cc_start: 0.6618 (ttm110) cc_final: 0.5549 (ttm170) REVERT: C 373 ARG cc_start: 0.5355 (tpm170) cc_final: 0.4712 (ttp80) REVERT: C 436 MET cc_start: 0.4050 (ptm) cc_final: 0.3784 (ptm) REVERT: C 450 ASP cc_start: 0.6553 (m-30) cc_final: 0.6270 (m-30) REVERT: C 476 ARG cc_start: 0.6831 (ttp-170) cc_final: 0.5572 (ttm-80) REVERT: C 488 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6795 (mt-10) REVERT: C 494 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: C 516 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7699 (mp0) outliers start: 44 outliers final: 18 residues processed: 146 average time/residue: 1.8629 time to fit residues: 292.0338 Evaluate side-chains 116 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 214 ASN Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 516 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 0.0370 chunk 51 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 20 optimal weight: 0.0570 chunk 138 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 112 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN C 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.247743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.184011 restraints weight = 11945.498| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 6.66 r_work: 0.3355 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 1.7593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12124 Z= 0.105 Angle : 0.629 12.088 16624 Z= 0.314 Chirality : 0.046 0.248 1891 Planarity : 0.006 0.147 2178 Dihedral : 5.548 47.531 1660 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.38 % Favored : 95.42 % Rotamer: Outliers : 2.36 % Allowed : 26.44 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1529 helix: -1.07 (0.60), residues: 59 sheet: -0.08 (0.24), residues: 434 loop : -0.91 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 285 HIS 0.005 0.001 HIS B 242 PHE 0.021 0.001 PHE A 80 TYR 0.010 0.001 TYR C 328 ARG 0.010 0.001 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 305) hydrogen bonds : angle 5.69603 ( 843) covalent geometry : bond 0.00230 (12124) covalent geometry : angle 0.62877 (16624) *********************** 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 131 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 3.507 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.6823 (pm20) cc_final: 0.6519 (pm20) REVERT: A 292 GLU cc_start: 0.2052 (OUTLIER) cc_final: 0.1738 (pm20) REVERT: A 357 MET cc_start: 0.2817 (OUTLIER) cc_final: 0.1680 (pmm) REVERT: A 488 GLU cc_start: 0.6226 (pt0) cc_final: 0.5990 (pp20) REVERT: A 511 THR cc_start: 0.5286 (OUTLIER) cc_final: 0.4940 (p) REVERT: B 353 THR cc_start: -0.0883 (OUTLIER) cc_final: -0.1270 (p) REVERT: B 471 GLU cc_start: 0.5770 (tp30) cc_final: 0.5512 (tp30) REVERT: B 494 GLU cc_start: 0.6691 (tm-30) cc_final: 0.6265 (mp0) REVERT: C 47 GLN cc_start: 0.4996 (mt0) cc_final: 0.4049 (pt0) REVERT: C 322 ARG cc_start: 0.6727 (ttm110) cc_final: 0.5904 (ttm170) REVERT: C 373 ARG cc_start: 0.5296 (tpm170) cc_final: 0.4939 (ttp80) REVERT: C 450 ASP cc_start: 0.6218 (m-30) cc_final: 0.5817 (m-30) REVERT: C 476 ARG cc_start: 0.6767 (ttp-170) cc_final: 0.6548 (ttp-170) REVERT: C 488 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6044 (mp0) REVERT: C 494 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8067 (mp0) outliers start: 30 outliers final: 11 residues processed: 121 average time/residue: 2.0910 time to fit residues: 273.8737 Evaluate side-chains 109 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 2.191 ------------------------------------------------------------------------------- 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 292 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 225 THR 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 386 LEU Chi-restraints excluded: chain C residue 414 VAL 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 6 optimal weight: 10.0000 chunk 52 optimal weight: 0.0870 chunk 114 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 118 optimal weight: 0.2980 chunk 59 optimal weight: 6.9990 chunk 50 optimal weight: 0.0040 chunk 33 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 493 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.247596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.191736 restraints weight = 11926.870| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 5.32 r_work: 0.3411 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 1.7648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12124 Z= 0.098 Angle : 0.601 11.041 16624 Z= 0.298 Chirality : 0.045 0.234 1891 Planarity : 0.006 0.143 2178 Dihedral : 4.986 45.180 1659 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.71 % Favored : 95.09 % Rotamer: Outliers : 1.57 % Allowed : 27.14 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1529 helix: -0.85 (0.61), residues: 59 sheet: 0.06 (0.25), residues: 431 loop : -0.81 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 285 HIS 0.006 0.001 HIS B 242 PHE 0.019 0.001 PHE A 59 TYR 0.013 0.001 TYR C 317 ARG 0.011 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.02801 ( 305) hydrogen bonds : angle 5.36661 ( 843) covalent geometry : bond 0.00220 (12124) covalent geometry : angle 0.60057 (16624) *********************** 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 119 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7182 (m-30) cc_final: 0.6887 (t0) REVERT: A 176 GLU cc_start: 0.6461 (mt-10) cc_final: 0.5146 (tt0) REVERT: A 223 GLU cc_start: 0.6991 (pm20) cc_final: 0.6757 (pm20) REVERT: A 292 GLU cc_start: 0.2070 (OUTLIER) cc_final: 0.1749 (pm20) REVERT: A 357 MET cc_start: 0.2979 (OUTLIER) cc_final: 0.1732 (pmm) REVERT: A 461 PHE cc_start: 0.3284 (m-10) cc_final: 0.2960 (m-80) REVERT: A 511 THR cc_start: 0.5619 (OUTLIER) cc_final: 0.5186 (p) REVERT: A 526 GLN cc_start: 0.7074 (tp-100) cc_final: 0.6789 (mm-40) REVERT: B 494 GLU cc_start: 0.6563 (tm-30) cc_final: 0.6026 (mp0) REVERT: C 47 GLN cc_start: 0.5175 (mt0) cc_final: 0.4337 (pt0) REVERT: C 322 ARG cc_start: 0.6951 (ttm110) cc_final: 0.6387 (ttm170) REVERT: C 373 ARG cc_start: 0.5529 (tpm170) cc_final: 0.5197 (ttp80) REVERT: C 450 ASP cc_start: 0.6215 (m-30) cc_final: 0.5905 (m-30) REVERT: C 476 ARG cc_start: 0.6853 (ttp-170) cc_final: 0.6307 (ttp-170) REVERT: C 478 ARG cc_start: 0.5983 (ptp-110) cc_final: 0.5721 (mtm110) REVERT: C 488 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6006 (mp0) REVERT: C 494 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: C 516 GLU cc_start: 0.8175 (mp0) cc_final: 0.7634 (mp0) outliers start: 20 outliers final: 11 residues processed: 115 average time/residue: 1.4532 time to fit residues: 179.9511 Evaluate side-chains 109 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 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 83 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 214 ASN A 265 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN B 493 ASN C 493 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.239776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.180600 restraints weight = 11476.451| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 5.51 r_work: 0.3277 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 1.8407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12124 Z= 0.152 Angle : 0.720 12.084 16624 Z= 0.364 Chirality : 0.049 0.231 1891 Planarity : 0.007 0.146 2178 Dihedral : 5.589 47.376 1659 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 1.89 % Allowed : 26.91 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1529 helix: -0.74 (0.65), residues: 52 sheet: 0.03 (0.25), residues: 435 loop : -0.92 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP B 54 HIS 0.009 0.002 HIS A 146 PHE 0.046 0.002 PHE A 59 TYR 0.031 0.002 TYR A 496 ARG 0.011 0.001 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 305) hydrogen bonds : angle 5.74846 ( 843) covalent geometry : bond 0.00341 (12124) covalent geometry : angle 0.71985 (16624) ********************** 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 120 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.208 Fit side-chains REVERT: A 173 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7597 (mp-120) REVERT: A 176 GLU cc_start: 0.6577 (mt-10) cc_final: 0.5353 (tt0) REVERT: A 223 GLU cc_start: 0.6923 (pm20) cc_final: 0.6678 (pm20) REVERT: A 231 ASP cc_start: 0.6818 (p0) cc_final: 0.6562 (p0) REVERT: A 238 ARG cc_start: 0.5216 (mtp180) cc_final: 0.4933 (ptp-170) REVERT: A 292 GLU cc_start: 0.1940 (OUTLIER) cc_final: 0.1638 (pm20) REVERT: A 357 MET cc_start: 0.2740 (OUTLIER) cc_final: 0.1959 (pmm) REVERT: A 461 PHE cc_start: 0.3755 (m-10) cc_final: 0.3485 (m-80) REVERT: A 511 THR cc_start: 0.5644 (OUTLIER) cc_final: 0.5369 (p) REVERT: A 526 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7291 (mm-40) REVERT: B 436 MET cc_start: 0.4898 (tmm) cc_final: 0.4207 (tmm) REVERT: B 494 GLU cc_start: 0.6619 (tm-30) cc_final: 0.6208 (mp0) REVERT: B 501 TYR cc_start: 0.6164 (t80) cc_final: 0.5615 (t80) REVERT: C 47 GLN cc_start: 0.5966 (mt0) cc_final: 0.4395 (pt0) REVERT: C 322 ARG cc_start: 0.6562 (ttm110) cc_final: 0.5736 (ttm170) REVERT: C 373 ARG cc_start: 0.6109 (tpm170) cc_final: 0.5754 (ttp80) REVERT: C 450 ASP cc_start: 0.6506 (m-30) cc_final: 0.6152 (m-30) REVERT: C 476 ARG cc_start: 0.6784 (ttp-170) cc_final: 0.6245 (ttp-170) REVERT: C 488 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6135 (mp0) REVERT: C 494 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: C 516 GLU cc_start: 0.8107 (mp0) cc_final: 0.7493 (mp0) outliers start: 24 outliers final: 11 residues processed: 113 average time/residue: 1.3882 time to fit residues: 169.4590 Evaluate side-chains 107 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 386 LEU 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 142 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 23 optimal weight: 0.0170 chunk 10 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 270 HIS A 526 GLN B 479 ASN B 493 ASN C 493 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.236587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.174821 restraints weight = 11447.495| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 5.98 r_work: 0.3267 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 1.8986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12124 Z= 0.162 Angle : 0.724 11.807 16624 Z= 0.370 Chirality : 0.049 0.253 1891 Planarity : 0.007 0.146 2178 Dihedral : 5.548 46.605 1659 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.62 % Favored : 94.24 % Rotamer: Outliers : 1.97 % Allowed : 27.07 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1529 helix: -0.78 (0.62), residues: 52 sheet: -0.01 (0.24), residues: 431 loop : -0.92 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 54 HIS 0.009 0.002 HIS C 146 PHE 0.038 0.002 PHE A 59 TYR 0.031 0.002 TYR A 496 ARG 0.012 0.001 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 305) hydrogen bonds : angle 5.65649 ( 843) covalent geometry : bond 0.00361 (12124) covalent geometry : angle 0.72420 (16624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12658.17 seconds wall clock time: 224 minutes 14.38 seconds (13454.38 seconds total)