Starting phenix.real_space_refine on Wed May 14 12:17:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ean_47837/05_2025/9ean_47837.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ean_47837/05_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_47837/05_2025/9ean_47837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ean_47837/05_2025/9ean_47837.map" model { file = "/net/cci-nas-00/data/ceres_data/9ean_47837/05_2025/9ean_47837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ean_47837/05_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-5687/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: 9.70, per 1000 atoms: 0.82 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: 2.65 Conformation dependent library (CDL) restraints added in 1.7 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: 1.48 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: 4.28 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: 17.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.500 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.910 ------------------------------------------------------------------------------- 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 : 1.192 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: 1.0082 time to fit residues: 139.5673 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 : 1.145 ------------------------------------------------------------------------------- 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 = 0.190205 restraints weight = 11855.072| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 1.35 r_work: 0.3702 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.15 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 : 1.104 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.1817 (mtp) cc_final: 0.1347 (mpp) REVERT: A 335 LEU cc_start: 0.3377 (OUTLIER) cc_final: 0.3041 (mm) REVERT: A 350 LEU cc_start: 0.2001 (OUTLIER) cc_final: 0.1678 (tp) REVERT: A 357 MET cc_start: 0.3020 (OUTLIER) cc_final: 0.1458 (ptp) REVERT: B 436 MET cc_start: 0.3416 (ttp) cc_final: 0.2513 (mtm) outliers start: 42 outliers final: 16 residues processed: 92 average time/residue: 0.8776 time to fit residues: 91.2856 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 : 1.139 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 28 optimal weight: 50.0000 chunk 109 optimal weight: 0.6980 overall best weight: 3.8786 ------------------------------------------------------------------------------- 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 409 ASN A 464 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 73 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 340 GLN B 455 GLN C 146 HIS C 175 GLN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN 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 = 0.5027 r_free = 0.5027 target = 0.299972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.276741 restraints weight = 15799.770| |-----------------------------------------------------------------------------| r_work (start): 0.4843 rms_B_bonded: 1.34 r_work: 0.4606 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4491 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.9669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.162 12124 Z= 0.421 Angle : 1.314 34.550 16624 Z= 0.676 Chirality : 0.068 0.415 1891 Planarity : 0.011 0.219 2178 Dihedral : 8.323 55.285 1664 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.72 % Favored : 92.09 % Rotamer: Outliers : 6.61 % Allowed : 22.74 % Favored : 70.65 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 2.24 % 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: -1.87 (0.19), residues: 1529 helix: -2.48 (0.55), residues: 52 sheet: -0.03 (0.26), residues: 389 loop : -1.77 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP A 245 HIS 0.069 0.011 HIS C 270 PHE 0.059 0.005 PHE B 117 TYR 0.067 0.005 TYR B 99 ARG 0.013 0.002 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.06835 ( 305) hydrogen bonds : angle 8.31014 ( 843) covalent geometry : bond 0.00957 (12124) covalent geometry : angle 1.31420 (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 187 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 103 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.5400 (OUTLIER) cc_final: 0.4955 (ptp) REVERT: A 100 THR cc_start: 0.7632 (t) cc_final: 0.7411 (t) REVERT: A 109 GLN cc_start: 0.4302 (OUTLIER) cc_final: 0.3816 (mt0) REVERT: A 263 GLN cc_start: 0.1755 (OUTLIER) cc_final: 0.1239 (mt0) REVERT: A 312 GLN cc_start: 0.3434 (OUTLIER) cc_final: 0.2010 (pm20) REVERT: A 357 MET cc_start: 0.2918 (OUTLIER) cc_final: 0.0931 (mpp) REVERT: A 398 ILE cc_start: 0.0846 (OUTLIER) cc_final: 0.0425 (mp) REVERT: A 508 THR cc_start: 0.4400 (OUTLIER) cc_final: 0.4039 (m) REVERT: B 28 GLN cc_start: 0.2954 (mp10) cc_final: 0.2706 (mm-40) REVERT: B 229 MET cc_start: 0.2829 (OUTLIER) cc_final: 0.2447 (pmm) REVERT: B 436 MET cc_start: 0.4435 (ttp) cc_final: 0.1757 (mtm) REVERT: C 165 ARG cc_start: 0.7771 (ptt-90) cc_final: 0.7037 (ptp90) outliers start: 84 outliers final: 23 residues processed: 172 average time/residue: 1.1722 time to fit residues: 219.9036 Evaluate side-chains 91 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 196 ASP Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 340 GLN 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 A residue 511 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 98 MET 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 225 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 374 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 97 optimal weight: 1.9990 chunk 128 optimal weight: 40.0000 chunk 56 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 72 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 409 ASN A 469 GLN B 73 ASN B 242 HIS B 270 HIS ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN C 73 ASN C 270 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.286938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.257435 restraints weight = 14486.378| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 1.36 r_work: 0.4380 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 1.0070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12124 Z= 0.130 Angle : 0.703 17.831 16624 Z= 0.344 Chirality : 0.046 0.182 1891 Planarity : 0.007 0.177 2178 Dihedral : 5.788 54.607 1660 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.32 % Favored : 95.49 % Rotamer: Outliers : 2.91 % Allowed : 26.75 % 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: -1.23 (0.20), residues: 1529 helix: -1.70 (0.57), residues: 70 sheet: 0.18 (0.24), residues: 424 loop : -1.25 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 54 HIS 0.008 0.002 HIS C 146 PHE 0.025 0.001 PHE C 80 TYR 0.029 0.001 TYR A 186 ARG 0.010 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 305) hydrogen bonds : angle 6.06119 ( 843) covalent geometry : bond 0.00284 (12124) covalent geometry : angle 0.70290 (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 113 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.7470 (mtp) cc_final: 0.7024 (mtp) REVERT: A 166 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7142 (mtm110) REVERT: A 357 MET cc_start: 0.2721 (OUTLIER) cc_final: 0.1020 (pmm) REVERT: B 179 MET cc_start: 0.6047 (ttp) cc_final: 0.5827 (ttp) REVERT: B 311 GLU cc_start: 0.3863 (mm-30) cc_final: 0.3290 (mm-30) REVERT: B 436 MET cc_start: 0.3512 (ttp) cc_final: 0.2585 (mtm) REVERT: C 106 MET cc_start: 0.6660 (mtt) cc_final: 0.6351 (mmm) REVERT: C 342 GLU cc_start: 0.3752 (OUTLIER) cc_final: 0.1402 (pt0) REVERT: C 450 ASP cc_start: 0.3824 (m-30) cc_final: 0.3017 (t0) outliers start: 37 outliers final: 11 residues processed: 104 average time/residue: 1.0347 time to fit residues: 118.8401 Evaluate side-chains 69 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 511 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 218 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 30 optimal weight: 0.0970 chunk 141 optimal weight: 0.0020 chunk 81 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 50 optimal weight: 0.0060 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.283342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.250854 restraints weight = 14302.777| |-----------------------------------------------------------------------------| r_work (start): 0.4628 rms_B_bonded: 1.30 r_work: 0.4311 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 moved from start: 1.0452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12124 Z= 0.099 Angle : 0.619 19.876 16624 Z= 0.296 Chirality : 0.044 0.213 1891 Planarity : 0.006 0.177 2178 Dihedral : 5.123 59.204 1660 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.04 % Favored : 94.77 % Rotamer: Outliers : 2.91 % Allowed : 26.28 % Favored : 70.81 % 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: -0.81 (0.21), residues: 1529 helix: -0.87 (0.64), residues: 64 sheet: 0.37 (0.25), residues: 425 loop : -0.95 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 54 HIS 0.004 0.001 HIS C 146 PHE 0.018 0.001 PHE C 80 TYR 0.010 0.001 TYR C 130 ARG 0.010 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.02880 ( 305) hydrogen bonds : angle 5.40104 ( 843) covalent geometry : bond 0.00226 (12124) covalent geometry : angle 0.61893 (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 99 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.5514 (t70) cc_final: 0.5193 (t0) REVERT: A 106 MET cc_start: 0.7861 (mtp) cc_final: 0.7385 (mtp) REVERT: A 166 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7277 (mtm110) REVERT: A 357 MET cc_start: 0.2614 (OUTLIER) cc_final: 0.1397 (pmm) REVERT: B 106 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6446 (tpp) REVERT: B 179 MET cc_start: 0.6350 (ttp) cc_final: 0.6141 (ttp) REVERT: B 229 MET cc_start: 0.3635 (tpp) cc_final: 0.3131 (pmm) REVERT: B 436 MET cc_start: 0.3309 (ttp) cc_final: 0.2497 (mtm) REVERT: C 47 GLN cc_start: 0.4983 (mt0) cc_final: 0.4592 (pm20) REVERT: C 106 MET cc_start: 0.7130 (mtt) cc_final: 0.6914 (mmm) REVERT: C 450 ASP cc_start: 0.3856 (m-30) cc_final: 0.3076 (t0) outliers start: 37 outliers final: 14 residues processed: 93 average time/residue: 0.9924 time to fit residues: 102.8438 Evaluate side-chains 71 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 511 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 524 LEU 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: 0.6980 chunk 146 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN B 73 ASN C 173 GLN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.274094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.244215 restraints weight = 12933.227| |-----------------------------------------------------------------------------| r_work (start): 0.4576 rms_B_bonded: 1.43 r_work: 0.4264 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4212 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 1.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 12124 Z= 0.177 Angle : 0.775 22.217 16624 Z= 0.388 Chirality : 0.050 0.245 1891 Planarity : 0.007 0.181 2178 Dihedral : 5.882 53.244 1660 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.21 % Favored : 93.59 % Rotamer: Outliers : 3.38 % Allowed : 25.81 % Favored : 70.81 % 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: -1.12 (0.20), residues: 1529 helix: -0.72 (0.60), residues: 58 sheet: -0.07 (0.25), residues: 420 loop : -1.07 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 285 HIS 0.005 0.002 HIS B 242 PHE 0.024 0.002 PHE B 117 TYR 0.025 0.002 TYR B 217 ARG 0.008 0.001 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 305) hydrogen bonds : angle 6.07993 ( 843) covalent geometry : bond 0.00394 (12124) covalent geometry : angle 0.77528 (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 123 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.2699 (OUTLIER) cc_final: 0.1227 (pmm) REVERT: B 98 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7578 (mtt) REVERT: B 436 MET cc_start: 0.3363 (ttp) cc_final: 0.2560 (mtm) REVERT: C 47 GLN cc_start: 0.5911 (mt0) cc_final: 0.4786 (pm20) REVERT: C 98 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7098 (mtt) REVERT: C 436 MET cc_start: 0.3932 (ptm) cc_final: 0.3730 (tpt) outliers start: 43 outliers final: 16 residues processed: 112 average time/residue: 1.3226 time to fit residues: 162.1520 Evaluate side-chains 82 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR 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 98 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 450 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 134 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 50 GLN A 173 GLN A 214 ASN A 526 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.261570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.200336 restraints weight = 12356.808| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 6.44 r_work: 0.3462 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 1.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 12124 Z= 0.203 Angle : 0.766 18.742 16624 Z= 0.386 Chirality : 0.048 0.174 1891 Planarity : 0.007 0.170 2178 Dihedral : 5.707 48.203 1660 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.30 % Favored : 94.51 % Rotamer: Outliers : 2.68 % Allowed : 26.44 % Favored : 70.89 % 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: -1.07 (0.20), residues: 1529 helix: -1.54 (0.53), residues: 65 sheet: 0.02 (0.25), residues: 413 loop : -1.00 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 54 HIS 0.005 0.002 HIS A 94 PHE 0.072 0.003 PHE A 59 TYR 0.019 0.002 TYR C 217 ARG 0.010 0.001 ARG A 476 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 305) hydrogen bonds : angle 5.84015 ( 843) covalent geometry : bond 0.00431 (12124) covalent geometry : angle 0.76615 (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 107 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 2.119 Fit side-chains REVERT: A 27 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7423 (pt0) REVERT: A 148 MET cc_start: 0.8451 (mmp) cc_final: 0.8222 (tpp) REVERT: A 229 MET cc_start: 0.4222 (tpt) cc_final: 0.2569 (ttm) REVERT: A 357 MET cc_start: 0.3169 (OUTLIER) cc_final: 0.1209 (pmm) REVERT: B 98 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7833 (mtt) REVERT: B 436 MET cc_start: 0.4579 (ttp) cc_final: 0.1504 (mtm) REVERT: B 494 GLU cc_start: 0.5681 (tm-30) cc_final: 0.4679 (mp0) REVERT: C 47 GLN cc_start: 0.6292 (mt0) cc_final: 0.4541 (pm20) REVERT: C 98 MET cc_start: 0.7821 (mtp) cc_final: 0.7517 (mtt) REVERT: C 476 ARG cc_start: 0.5916 (ttp-170) cc_final: 0.5342 (ttp80) REVERT: C 494 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7058 (mp0) outliers start: 34 outliers final: 13 residues processed: 104 average time/residue: 1.4033 time to fit residues: 157.4790 Evaluate side-chains 75 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR 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 357 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 28 optimal weight: 40.0000 chunk 112 optimal weight: 0.0670 chunk 126 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- 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 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 173 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN C 340 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.245628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.174200 restraints weight = 11763.117| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 7.81 r_work: 0.3286 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 1.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12124 Z= 0.228 Angle : 0.898 14.277 16624 Z= 0.463 Chirality : 0.055 0.296 1891 Planarity : 0.008 0.157 2178 Dihedral : 6.440 47.154 1660 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.76 % Favored : 94.11 % Rotamer: Outliers : 3.07 % Allowed : 26.51 % Favored : 70.42 % 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: -1.45 (0.58), residues: 59 sheet: -0.08 (0.25), residues: 428 loop : -1.08 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP C 285 HIS 0.009 0.002 HIS A 94 PHE 0.086 0.004 PHE B 117 TYR 0.031 0.003 TYR C 217 ARG 0.008 0.001 ARG C 228 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 305) hydrogen bonds : angle 6.31688 ( 843) covalent geometry : bond 0.00506 (12124) covalent geometry : angle 0.89808 (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 161 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 1.221 Fit side-chains REVERT: A 107 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8665 (mm-30) REVERT: A 148 MET cc_start: 0.8971 (mmt) cc_final: 0.8726 (tpp) REVERT: A 229 MET cc_start: 0.5705 (tpt) cc_final: 0.5472 (tpt) REVERT: A 357 MET cc_start: 0.2823 (OUTLIER) cc_final: 0.1317 (pmm) REVERT: A 488 GLU cc_start: 0.6555 (pt0) cc_final: 0.6087 (pp20) REVERT: B 27 GLU cc_start: 0.5597 (OUTLIER) cc_final: 0.5382 (pp20) REVERT: B 30 VAL cc_start: 0.6328 (t) cc_final: 0.6082 (p) REVERT: B 98 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8052 (mtt) REVERT: B 133 LYS cc_start: 0.7508 (ttmt) cc_final: 0.7231 (mttm) REVERT: B 436 MET cc_start: 0.4604 (ttp) cc_final: 0.1099 (mtp) REVERT: B 471 GLU cc_start: 0.6276 (tp30) cc_final: 0.5783 (tp30) REVERT: B 494 GLU cc_start: 0.6559 (tm-30) cc_final: 0.6113 (mp0) REVERT: C 47 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.4787 (pm20) REVERT: C 98 MET cc_start: 0.7878 (mtp) cc_final: 0.7536 (mtt) REVERT: C 176 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7545 (mt-10) REVERT: C 322 ARG cc_start: 0.6524 (ttm110) cc_final: 0.5487 (ttm170) REVERT: C 340 GLN cc_start: 0.3294 (OUTLIER) cc_final: 0.2722 (mm-40) REVERT: C 436 MET cc_start: 0.4273 (ptm) cc_final: 0.4004 (ptm) REVERT: C 450 ASP cc_start: 0.6235 (m-30) cc_final: 0.5985 (m-30) REVERT: C 476 ARG cc_start: 0.6611 (ttp-170) cc_final: 0.5982 (ttp-170) REVERT: C 478 ARG cc_start: 0.5810 (ptp-110) cc_final: 0.5551 (mtm110) REVERT: C 488 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6622 (mt-10) REVERT: C 494 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: C 516 GLU cc_start: 0.8324 (mp0) cc_final: 0.7725 (mp0) outliers start: 39 outliers final: 11 residues processed: 150 average time/residue: 1.4459 time to fit residues: 232.4053 Evaluate side-chains 113 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 386 LEU 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: 0.8980 chunk 114 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 173 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN C 236 GLN C 261 ASN C 263 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.242971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.171023 restraints weight = 11719.464| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 8.08 r_work: 0.3255 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 1.7640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12124 Z= 0.147 Angle : 0.716 13.038 16624 Z= 0.359 Chirality : 0.048 0.275 1891 Planarity : 0.007 0.152 2178 Dihedral : 5.554 43.827 1659 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 1.81 % Allowed : 28.48 % Favored : 69.71 % 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: -1.19 (0.60), residues: 54 sheet: -0.08 (0.24), residues: 441 loop : -0.86 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 54 HIS 0.004 0.002 HIS C 270 PHE 0.040 0.002 PHE A 59 TYR 0.021 0.002 TYR C 317 ARG 0.008 0.001 ARG C 268 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 305) hydrogen bonds : angle 5.89015 ( 843) covalent geometry : bond 0.00337 (12124) covalent geometry : angle 0.71593 (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: 23 poor density : 96 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.3058 (OUTLIER) cc_final: 0.1736 (pmm) REVERT: A 488 GLU cc_start: 0.6649 (pt0) cc_final: 0.6134 (pp20) REVERT: B 54 TRP cc_start: 0.7668 (t60) cc_final: 0.7158 (m100) REVERT: B 223 GLU cc_start: 0.5965 (tt0) cc_final: 0.5692 (tp30) REVERT: B 224 ARG cc_start: 0.5145 (mmm-85) cc_final: 0.4923 (ttm170) REVERT: B 436 MET cc_start: 0.4640 (ttp) cc_final: 0.1198 (mtp) REVERT: B 471 GLU cc_start: 0.5879 (tp30) cc_final: 0.5545 (tp30) REVERT: B 494 GLU cc_start: 0.6321 (tm-30) cc_final: 0.5565 (mp0) REVERT: C 47 GLN cc_start: 0.6125 (mt0) cc_final: 0.4377 (pt0) REVERT: C 50 GLN cc_start: 0.9080 (mm110) cc_final: 0.8754 (mt0) REVERT: C 98 MET cc_start: 0.7961 (mtp) cc_final: 0.7688 (mtt) REVERT: C 322 ARG cc_start: 0.6901 (ttm110) cc_final: 0.6365 (ttm170) REVERT: C 340 GLN cc_start: 0.3680 (OUTLIER) cc_final: 0.3007 (mm-40) REVERT: C 357 MET cc_start: 0.5127 (mmt) cc_final: 0.4636 (mmm) REVERT: C 450 ASP cc_start: 0.6182 (m-30) cc_final: 0.5862 (m-30) REVERT: C 476 ARG cc_start: 0.6499 (ttp-170) cc_final: 0.5901 (ttp-170) REVERT: C 494 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: C 516 GLU cc_start: 0.8189 (mp0) cc_final: 0.7350 (mp0) outliers start: 23 outliers final: 7 residues processed: 114 average time/residue: 1.5629 time to fit residues: 190.4444 Evaluate side-chains 100 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 B residue 352 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 386 LEU 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: 8.9990 chunk 127 optimal weight: 6.9990 chunk 66 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 265 GLN ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN B 73 ASN ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 493 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.242547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.179226 restraints weight = 11666.833| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 6.24 r_work: 0.3319 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 1.8191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12124 Z= 0.135 Angle : 0.692 13.784 16624 Z= 0.346 Chirality : 0.047 0.231 1891 Planarity : 0.007 0.149 2178 Dihedral : 5.251 44.157 1659 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 1.18 % Allowed : 28.95 % Favored : 69.87 % 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: -0.82 (0.21), residues: 1529 helix: -0.81 (0.62), residues: 52 sheet: -0.01 (0.24), residues: 443 loop : -0.79 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 54 HIS 0.004 0.001 HIS B 242 PHE 0.036 0.002 PHE A 59 TYR 0.017 0.001 TYR C 217 ARG 0.011 0.001 ARG C 437 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 305) hydrogen bonds : angle 5.68347 ( 843) covalent geometry : bond 0.00300 (12124) covalent geometry : angle 0.69218 (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 114 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7445 (m-30) cc_final: 0.7110 (t0) REVERT: A 176 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6018 (mt-10) REVERT: A 231 ASP cc_start: 0.7012 (p0) cc_final: 0.6768 (p0) REVERT: A 357 MET cc_start: 0.2673 (OUTLIER) cc_final: 0.1607 (pmm) REVERT: A 457 PHE cc_start: 0.5819 (m-80) cc_final: 0.5391 (m-80) REVERT: A 461 PHE cc_start: 0.3845 (m-80) cc_final: 0.3463 (m-80) REVERT: A 516 GLU cc_start: 0.6653 (pm20) cc_final: 0.6434 (mp0) REVERT: B 54 TRP cc_start: 0.7740 (OUTLIER) cc_final: 0.6075 (m100) REVERT: B 184 MET cc_start: 0.9152 (ttm) cc_final: 0.8902 (ttm) REVERT: B 357 MET cc_start: 0.4860 (mpt) cc_final: 0.4530 (mpp) REVERT: B 471 GLU cc_start: 0.6051 (tp30) cc_final: 0.5738 (tp30) REVERT: B 494 GLU cc_start: 0.6189 (tm-30) cc_final: 0.5482 (mp0) REVERT: C 47 GLN cc_start: 0.6360 (mt0) cc_final: 0.4785 (pt0) REVERT: C 50 GLN cc_start: 0.9071 (mm110) cc_final: 0.8769 (mt0) REVERT: C 98 MET cc_start: 0.7912 (mtp) cc_final: 0.7689 (mtt) REVERT: C 282 SER cc_start: 0.7432 (t) cc_final: 0.6823 (p) REVERT: C 322 ARG cc_start: 0.6785 (ttm110) cc_final: 0.6407 (ttm170) REVERT: C 340 GLN cc_start: 0.3715 (OUTLIER) cc_final: 0.2900 (mm-40) REVERT: C 450 ASP cc_start: 0.6342 (m-30) cc_final: 0.6041 (m-30) REVERT: C 476 ARG cc_start: 0.6579 (ttp-170) cc_final: 0.6217 (ttp-170) REVERT: C 494 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: C 516 GLU cc_start: 0.8123 (mp0) cc_final: 0.7599 (mp0) outliers start: 15 outliers final: 5 residues processed: 110 average time/residue: 1.4337 time to fit residues: 169.9504 Evaluate side-chains 104 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 54 TRP 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 340 GLN Chi-restraints excluded: chain C residue 386 LEU 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: 20.0000 chunk 129 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN C 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.236088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.175071 restraints weight = 11447.061| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 5.75 r_work: 0.3266 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 1.8994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12124 Z= 0.175 Angle : 0.796 17.160 16624 Z= 0.401 Chirality : 0.051 0.286 1891 Planarity : 0.008 0.149 2178 Dihedral : 5.821 45.010 1659 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.10 % Favored : 94.77 % Rotamer: Outliers : 1.18 % Allowed : 28.95 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.96 (0.20), residues: 1529 helix: -0.85 (0.62), residues: 52 sheet: -0.03 (0.24), residues: 427 loop : -0.92 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP B 54 HIS 0.006 0.002 HIS B 94 PHE 0.050 0.002 PHE A 59 TYR 0.030 0.002 TYR C 317 ARG 0.015 0.001 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.04351 ( 305) hydrogen bonds : angle 5.99432 ( 843) covalent geometry : bond 0.00393 (12124) covalent geometry : angle 0.79573 (16624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11364.36 seconds wall clock time: 196 minutes 17.24 seconds (11777.24 seconds total)