Starting phenix.real_space_refine on Wed Mar 4 07:19:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ku9_0776/03_2026/6ku9_0776.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ku9_0776/03_2026/6ku9_0776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ku9_0776/03_2026/6ku9_0776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ku9_0776/03_2026/6ku9_0776.map" model { file = "/net/cci-nas-00/data/ceres_data/6ku9_0776/03_2026/6ku9_0776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ku9_0776/03_2026/6ku9_0776.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 45 5.16 5 C 7548 2.51 5 N 2022 2.21 5 O 2124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11739 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "B" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "C" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Time building chain proxies: 2.88, per 1000 atoms: 0.25 Number of scatterers: 11739 At special positions: 0 Unit cell: (97.099, 92.735, 108.009, 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 45 16.00 O 2124 8.00 N 2022 7.00 C 7548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 607.1 milliseconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 30 sheets defined 10.5% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.815A pdb=" N LYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 474 through 477 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.816A pdb=" N LYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 Processing helix chain 'B' and resid 474 through 477 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.815A pdb=" N LYS C 213 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 Processing helix chain 'C' and resid 474 through 477 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 560 through 566 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU A 407 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU A 110 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN A 409 " --> pdb=" O HIS A 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS A 108 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU A 411 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY A 106 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR A 413 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET A 104 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 415 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU A 407 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU A 110 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN A 409 " --> pdb=" O HIS A 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS A 108 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU A 411 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY A 106 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR A 413 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET A 104 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 415 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 101 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 345 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.983A pdb=" N ASP A 201 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 195 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 158 removed outlier: 6.252A pdb=" N SER A 387 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER A 521 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG A 389 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER A 523 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE A 391 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 176 through 179 Processing sheet with id=AA7, first strand: chain 'A' and resid 234 through 241 removed outlier: 5.438A pdb=" N ASN A 309 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG A 307 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 23.103A pdb=" N ARG A 308 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 18.677A pdb=" N CYS B 314 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 12.478A pdb=" N VAL A 310 " --> pdb=" O TYR B 312 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N TYR B 312 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR A 312 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG B 307 " --> pdb=" O PRO B 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASN B 309 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 234 through 241 removed outlier: 5.438A pdb=" N ASN A 309 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG A 307 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR C 312 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N TYR A 312 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 12.488A pdb=" N VAL C 310 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 18.685A pdb=" N CYS A 314 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 23.112A pdb=" N ARG C 308 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG C 307 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASN C 309 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 234 through 241 removed outlier: 5.437A pdb=" N ASN B 309 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG B 307 " --> pdb=" O PRO B 240 " (cutoff:3.500A) removed outlier: 23.097A pdb=" N ARG B 308 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 18.671A pdb=" N CYS C 314 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 12.473A pdb=" N VAL B 310 " --> pdb=" O TYR C 312 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N TYR C 312 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 312 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG C 307 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASN C 309 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AB2, first strand: chain 'A' and resid 439 through 446 removed outlier: 4.197A pdb=" N TYR A 465 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 451 through 455 removed outlier: 3.852A pdb=" N ASN A 539 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 528 through 534 Processing sheet with id=AB5, first strand: chain 'B' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU B 407 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU B 110 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN B 409 " --> pdb=" O HIS B 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS B 108 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU B 411 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY B 106 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR B 413 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET B 104 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN B 415 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU B 407 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU B 110 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN B 409 " --> pdb=" O HIS B 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS B 108 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU B 411 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY B 106 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR B 413 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET B 104 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN B 415 " --> pdb=" O HIS B 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 101 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 345 " --> pdb=" O PHE B 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 89 through 93 removed outlier: 3.984A pdb=" N ASP B 201 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 195 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'B' and resid 153 through 158 removed outlier: 6.252A pdb=" N SER B 387 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N SER B 521 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG B 389 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER B 523 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE B 391 " --> pdb=" O SER B 523 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 176 through 179 Processing sheet with id=AC2, first strand: chain 'B' and resid 245 through 246 Processing sheet with id=AC3, first strand: chain 'B' and resid 439 through 446 removed outlier: 4.197A pdb=" N TYR B 465 " --> pdb=" O SER B 628 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 451 through 455 removed outlier: 3.852A pdb=" N ASN B 539 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU C 407 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU C 110 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN C 409 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS C 108 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU C 411 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY C 106 " --> pdb=" O GLU C 411 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR C 413 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET C 104 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN C 415 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU C 407 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU C 110 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN C 409 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS C 108 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU C 411 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY C 106 " --> pdb=" O GLU C 411 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR C 413 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET C 104 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN C 415 " --> pdb=" O HIS C 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C 101 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE C 345 " --> pdb=" O PHE C 101 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 89 through 93 removed outlier: 3.983A pdb=" N ASP C 201 " --> pdb=" O PHE C 193 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL C 195 " --> pdb=" O SER C 199 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER C 199 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AC9, first strand: chain 'C' and resid 153 through 158 removed outlier: 6.251A pdb=" N SER C 387 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER C 521 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG C 389 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER C 523 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 391 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 176 through 179 Processing sheet with id=AD2, first strand: chain 'C' and resid 439 through 446 removed outlier: 4.198A pdb=" N TYR C 465 " --> pdb=" O SER C 628 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 451 through 455 removed outlier: 3.851A pdb=" N ASN C 539 " --> pdb=" O ASP C 611 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1107 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: 2.16 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3749 1.34 - 1.46: 2705 1.46 - 1.58: 5579 1.58 - 1.70: 0 1.70 - 1.81: 69 Bond restraints: 12102 Sorted by residual: bond pdb=" CB GLU B 453 " pdb=" CG GLU B 453 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.32e+00 bond pdb=" CB GLU A 453 " pdb=" CG GLU A 453 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.29e+00 bond pdb=" CB GLU C 453 " pdb=" CG GLU C 453 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.25e+00 bond pdb=" C GLY A 129 " pdb=" O GLY A 129 " ideal model delta sigma weight residual 1.236 1.222 0.015 1.09e-02 8.42e+03 1.77e+00 bond pdb=" N CYS C 243 " pdb=" CA CYS C 243 " ideal model delta sigma weight residual 1.462 1.478 -0.017 1.31e-02 5.83e+03 1.63e+00 ... (remaining 12097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 15952 2.23 - 4.46: 459 4.46 - 6.69: 49 6.69 - 8.92: 19 8.92 - 11.15: 9 Bond angle restraints: 16488 Sorted by residual: angle pdb=" N GLY C 129 " pdb=" CA GLY C 129 " pdb=" C GLY C 129 " ideal model delta sigma weight residual 112.13 118.99 -6.86 1.34e+00 5.57e-01 2.62e+01 angle pdb=" CA GLU B 453 " pdb=" CB GLU B 453 " pdb=" CG GLU B 453 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA GLU C 453 " pdb=" CB GLU C 453 " pdb=" CG GLU C 453 " ideal model delta sigma weight residual 114.10 123.79 -9.69 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA GLU A 453 " pdb=" CB GLU A 453 " pdb=" CG GLU A 453 " ideal model delta sigma weight residual 114.10 123.76 -9.66 2.00e+00 2.50e-01 2.33e+01 angle pdb=" N GLY A 129 " pdb=" CA GLY A 129 " pdb=" C GLY A 129 " ideal model delta sigma weight residual 112.13 118.12 -5.99 1.34e+00 5.57e-01 2.00e+01 ... (remaining 16483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 6283 15.95 - 31.90: 575 31.90 - 47.85: 161 47.85 - 63.80: 60 63.80 - 79.75: 10 Dihedral angle restraints: 7089 sinusoidal: 2856 harmonic: 4233 Sorted by residual: dihedral pdb=" CA ASN A 449 " pdb=" C ASN A 449 " pdb=" N HIS A 450 " pdb=" CA HIS A 450 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ASN C 449 " pdb=" C ASN C 449 " pdb=" N HIS C 450 " pdb=" CA HIS C 450 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASN B 449 " pdb=" C ASN B 449 " pdb=" N HIS B 450 " pdb=" CA HIS B 450 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 7086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1350 0.058 - 0.116: 305 0.116 - 0.174: 91 0.174 - 0.232: 7 0.232 - 0.290: 8 Chirality restraints: 1761 Sorted by residual: chirality pdb=" CA PHE C 508 " pdb=" N PHE C 508 " pdb=" C PHE C 508 " pdb=" CB PHE C 508 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE C 350 " pdb=" CA ILE C 350 " pdb=" CG1 ILE C 350 " pdb=" CG2 ILE C 350 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA HIS C 102 " pdb=" N HIS C 102 " pdb=" C HIS C 102 " pdb=" CB HIS C 102 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1758 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 450 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C HIS B 450 " 0.056 2.00e-02 2.50e+03 pdb=" O HIS B 450 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS B 451 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 450 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C HIS A 450 " 0.056 2.00e-02 2.50e+03 pdb=" O HIS A 450 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS A 451 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 450 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C HIS C 450 " -0.056 2.00e-02 2.50e+03 pdb=" O HIS C 450 " 0.021 2.00e-02 2.50e+03 pdb=" N HIS C 451 " 0.019 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2415 2.79 - 3.31: 9314 3.31 - 3.84: 19286 3.84 - 4.37: 23653 4.37 - 4.90: 40420 Nonbonded interactions: 95088 Sorted by model distance: nonbonded pdb=" O SER A 555 " pdb=" OG SER A 559 " model vdw 2.258 3.040 nonbonded pdb=" O SER C 555 " pdb=" OG SER C 559 " model vdw 2.258 3.040 nonbonded pdb=" O SER B 555 " pdb=" OG SER B 559 " model vdw 2.259 3.040 nonbonded pdb=" O PHE A 508 " pdb=" N ASP A 510 " model vdw 2.282 3.120 nonbonded pdb=" OE2 GLU C 185 " pdb=" OH TYR C 224 " model vdw 2.313 3.040 ... (remaining 95083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 : 0.005 0.059 12102 Z= 0.240 Angle : 0.895 11.152 16488 Z= 0.502 Chirality : 0.056 0.290 1761 Planarity : 0.008 0.064 2142 Dihedral : 14.504 79.753 4371 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.54 % Favored : 93.11 % Rotamer: Outliers : 5.48 % Allowed : 6.10 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.19), residues: 1437 helix: -3.17 (0.36), residues: 93 sheet: -0.20 (0.19), residues: 567 loop : -2.53 (0.18), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 307 TYR 0.012 0.002 TYR C 561 PHE 0.016 0.002 PHE B 193 TRP 0.009 0.001 TRP C 396 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00524 (12102) covalent geometry : angle 0.89530 (16488) hydrogen bonds : bond 0.15525 ( 372) hydrogen bonds : angle 6.73259 ( 1107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 202 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8208 (m) REVERT: A 388 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7940 (mtp-110) REVERT: A 394 LYS cc_start: 0.8628 (tppp) cc_final: 0.8375 (tptt) REVERT: A 455 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7535 (mt) REVERT: A 510 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7153 (t0) REVERT: B 354 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6340 (pm20) REVERT: B 387 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 388 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7830 (mtp-110) REVERT: B 538 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8291 (ttpp) REVERT: B 575 ASP cc_start: 0.7981 (m-30) cc_final: 0.7771 (m-30) REVERT: C 80 HIS cc_start: 0.8103 (t-170) cc_final: 0.7539 (t-90) REVERT: C 313 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8934 (t) REVERT: C 354 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6298 (pm20) REVERT: C 387 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8780 (p) REVERT: C 388 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7648 (mtp85) REVERT: C 455 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7619 (mt) REVERT: C 581 MET cc_start: 0.9184 (ttt) cc_final: 0.8766 (ttt) REVERT: C 593 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.5880 (tt0) REVERT: C 622 ASP cc_start: 0.7342 (m-30) cc_final: 0.6968 (m-30) outliers start: 71 outliers final: 13 residues processed: 254 average time/residue: 0.6362 time to fit residues: 173.6467 Evaluate side-chains 175 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 593 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 102 HIS A 171 ASN B 102 HIS B 171 ASN B 483 GLN C 102 HIS C 171 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.095866 restraints weight = 13400.329| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.24 r_work: 0.2792 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12102 Z= 0.105 Angle : 0.561 6.408 16488 Z= 0.293 Chirality : 0.045 0.216 1761 Planarity : 0.005 0.043 2142 Dihedral : 6.894 67.586 1621 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 3.01 % Allowed : 11.65 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1437 helix: -0.97 (0.54), residues: 72 sheet: 0.32 (0.20), residues: 528 loop : -1.91 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 385 TYR 0.015 0.001 TYR B 561 PHE 0.029 0.001 PHE B 101 TRP 0.008 0.001 TRP B 474 HIS 0.006 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00237 (12102) covalent geometry : angle 0.56056 (16488) hydrogen bonds : bond 0.03518 ( 372) hydrogen bonds : angle 5.37398 ( 1107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7702 (mt0) REVERT: A 360 LYS cc_start: 0.8948 (tptm) cc_final: 0.8690 (tppt) REVERT: A 388 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.7890 (mtp-110) REVERT: A 394 LYS cc_start: 0.8963 (tppp) cc_final: 0.8607 (tptt) REVERT: A 450 HIS cc_start: 0.6216 (t-90) cc_final: 0.5960 (t-90) REVERT: A 455 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7291 (OUTLIER) REVERT: A 508 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6692 (p90) REVERT: A 510 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.7016 (t0) REVERT: B 479 GLN cc_start: 0.8704 (mm110) cc_final: 0.8323 (mm-40) REVERT: B 575 ASP cc_start: 0.8807 (m-30) cc_final: 0.8520 (m-30) REVERT: C 354 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6183 (pm20) REVERT: C 360 LYS cc_start: 0.8965 (tptm) cc_final: 0.8756 (tptp) REVERT: C 388 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.6733 (mmt180) REVERT: C 455 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7392 (mp) REVERT: C 463 ILE cc_start: 0.8571 (mt) cc_final: 0.8258 (mm) REVERT: C 502 HIS cc_start: 0.8199 (m-70) cc_final: 0.6294 (t-90) REVERT: C 581 MET cc_start: 0.9564 (ttt) cc_final: 0.9193 (ttt) outliers start: 39 outliers final: 14 residues processed: 183 average time/residue: 0.6331 time to fit residues: 124.7207 Evaluate side-chains 155 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 101 optimal weight: 0.0970 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 107 HIS A 196 ASN B 196 ASN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS C 80 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.095240 restraints weight = 13596.975| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.21 r_work: 0.2866 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12102 Z= 0.116 Angle : 0.553 6.493 16488 Z= 0.287 Chirality : 0.045 0.179 1761 Planarity : 0.004 0.037 2142 Dihedral : 5.748 47.829 1600 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 3.09 % Allowed : 12.27 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1437 helix: -0.64 (0.50), residues: 93 sheet: 0.45 (0.21), residues: 528 loop : -1.72 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 385 TYR 0.018 0.001 TYR B 561 PHE 0.009 0.001 PHE C 161 TRP 0.007 0.001 TRP C 461 HIS 0.008 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00268 (12102) covalent geometry : angle 0.55277 (16488) hydrogen bonds : bond 0.03421 ( 372) hydrogen bonds : angle 5.03059 ( 1107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7701 (mt0) REVERT: A 170 LYS cc_start: 0.8792 (mmtm) cc_final: 0.8577 (mmtp) REVERT: A 360 LYS cc_start: 0.8974 (tptm) cc_final: 0.8724 (tppt) REVERT: A 388 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7960 (mtp-110) REVERT: A 450 HIS cc_start: 0.6380 (t-90) cc_final: 0.6107 (t-90) REVERT: A 502 HIS cc_start: 0.8513 (m170) cc_final: 0.6565 (t70) REVERT: A 508 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.6647 (p90) REVERT: B 170 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8582 (mptm) REVERT: B 446 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7433 (p) REVERT: B 575 ASP cc_start: 0.8710 (m-30) cc_final: 0.8397 (m-30) REVERT: C 202 GLU cc_start: 0.8162 (tt0) cc_final: 0.7505 (tm-30) REVERT: C 388 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7621 (mtp85) REVERT: C 463 ILE cc_start: 0.8556 (mt) cc_final: 0.8277 (mm) REVERT: C 581 MET cc_start: 0.9508 (ttt) cc_final: 0.9138 (ttt) REVERT: C 622 ASP cc_start: 0.8104 (m-30) cc_final: 0.7828 (m-30) outliers start: 40 outliers final: 23 residues processed: 175 average time/residue: 0.6384 time to fit residues: 120.2529 Evaluate side-chains 161 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 80 HIS ** A 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 483 GLN B 80 HIS B 102 HIS B 107 HIS C 75 ASN C 80 HIS C 102 HIS C 416 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.090299 restraints weight = 13654.112| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.25 r_work: 0.2718 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12102 Z= 0.216 Angle : 0.642 7.263 16488 Z= 0.334 Chirality : 0.048 0.202 1761 Planarity : 0.005 0.045 2142 Dihedral : 5.694 47.278 1590 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.63 % Allowed : 13.04 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.20), residues: 1437 helix: -0.87 (0.47), residues: 111 sheet: 0.25 (0.19), residues: 576 loop : -1.74 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 308 TYR 0.022 0.002 TYR B 561 PHE 0.033 0.002 PHE C 101 TRP 0.008 0.001 TRP C 461 HIS 0.011 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00535 (12102) covalent geometry : angle 0.64223 (16488) hydrogen bonds : bond 0.04165 ( 372) hydrogen bonds : angle 5.25409 ( 1107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: A 170 LYS cc_start: 0.8799 (mmtm) cc_final: 0.8587 (mmtp) REVERT: A 334 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7890 (mtp85) REVERT: A 388 ARG cc_start: 0.8330 (mtm-85) cc_final: 0.7852 (mtp-110) REVERT: A 451 HIS cc_start: 0.7277 (p-80) cc_final: 0.6467 (p-80) REVERT: A 508 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.6460 (p90) REVERT: B 133 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7635 (mt0) REVERT: B 388 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7753 (mtp-110) REVERT: B 453 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: C 102 HIS cc_start: 0.6700 (OUTLIER) cc_final: 0.6432 (t70) REVERT: C 388 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7549 (mtp85) REVERT: C 463 ILE cc_start: 0.8510 (mt) cc_final: 0.8184 (mm) REVERT: C 581 MET cc_start: 0.9385 (ttt) cc_final: 0.9102 (ttt) REVERT: C 607 TYR cc_start: 0.7908 (m-80) cc_final: 0.6839 (m-10) REVERT: C 622 ASP cc_start: 0.8154 (m-30) cc_final: 0.7893 (m-30) outliers start: 47 outliers final: 27 residues processed: 165 average time/residue: 0.6845 time to fit residues: 121.2380 Evaluate side-chains 167 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 118 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 102 HIS B 502 HIS C 102 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.091119 restraints weight = 13661.934| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.22 r_work: 0.2795 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12102 Z= 0.180 Angle : 0.605 6.830 16488 Z= 0.314 Chirality : 0.047 0.182 1761 Planarity : 0.005 0.044 2142 Dihedral : 5.236 43.237 1584 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.16 % Allowed : 14.43 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.20), residues: 1437 helix: -0.65 (0.48), residues: 111 sheet: 0.25 (0.19), residues: 576 loop : -1.65 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.020 0.001 TYR B 561 PHE 0.035 0.002 PHE A 101 TRP 0.009 0.001 TRP A 474 HIS 0.011 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00442 (12102) covalent geometry : angle 0.60526 (16488) hydrogen bonds : bond 0.03798 ( 372) hydrogen bonds : angle 5.11570 ( 1107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 101 PHE cc_start: 0.8506 (p90) cc_final: 0.8240 (p90) REVERT: A 133 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: A 170 LYS cc_start: 0.8812 (mmtm) cc_final: 0.8596 (mmtp) REVERT: A 334 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7874 (mtp85) REVERT: A 388 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.7926 (mtp-110) REVERT: A 451 HIS cc_start: 0.7361 (p-80) cc_final: 0.6563 (p-80) REVERT: A 502 HIS cc_start: 0.8516 (m170) cc_final: 0.6567 (t70) REVERT: A 508 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6633 (p90) REVERT: A 607 TYR cc_start: 0.7940 (m-80) cc_final: 0.7469 (m-80) REVERT: B 133 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: B 388 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.7851 (mtp-110) REVERT: B 479 GLN cc_start: 0.8703 (mm110) cc_final: 0.8388 (mm-40) REVERT: C 388 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7618 (mtp85) REVERT: C 453 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7060 (tm-30) REVERT: C 463 ILE cc_start: 0.8555 (mt) cc_final: 0.8248 (mm) REVERT: C 581 MET cc_start: 0.9403 (ttt) cc_final: 0.9065 (ttt) REVERT: C 607 TYR cc_start: 0.7914 (m-80) cc_final: 0.7567 (m-80) REVERT: C 622 ASP cc_start: 0.8149 (m-30) cc_final: 0.7881 (m-30) outliers start: 41 outliers final: 27 residues processed: 163 average time/residue: 0.6665 time to fit residues: 116.9364 Evaluate side-chains 162 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 102 HIS B 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.090339 restraints weight = 13588.336| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.26 r_work: 0.2795 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12102 Z= 0.182 Angle : 0.608 7.274 16488 Z= 0.313 Chirality : 0.047 0.155 1761 Planarity : 0.005 0.045 2142 Dihedral : 5.154 41.713 1584 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.32 % Allowed : 14.12 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.21), residues: 1437 helix: -0.51 (0.49), residues: 111 sheet: 0.32 (0.19), residues: 576 loop : -1.57 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 385 TYR 0.019 0.001 TYR B 561 PHE 0.032 0.002 PHE C 101 TRP 0.009 0.001 TRP A 474 HIS 0.007 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00449 (12102) covalent geometry : angle 0.60831 (16488) hydrogen bonds : bond 0.03795 ( 372) hydrogen bonds : angle 5.08041 ( 1107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 133 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: A 170 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8561 (mmtp) REVERT: A 388 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.7901 (mtp-110) REVERT: A 451 HIS cc_start: 0.7368 (p-80) cc_final: 0.6570 (p-80) REVERT: A 502 HIS cc_start: 0.8488 (m170) cc_final: 0.6526 (t70) REVERT: A 607 TYR cc_start: 0.7931 (m-80) cc_final: 0.7421 (m-80) REVERT: B 133 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7698 (mt0) REVERT: B 388 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.7831 (mtp-110) REVERT: B 479 GLN cc_start: 0.8695 (mm110) cc_final: 0.8350 (mm-40) REVERT: B 607 TYR cc_start: 0.8002 (m-10) cc_final: 0.7719 (m-10) REVERT: C 388 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7557 (mtp85) REVERT: C 453 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7222 (tm-30) REVERT: C 463 ILE cc_start: 0.8523 (mt) cc_final: 0.8209 (mm) REVERT: C 581 MET cc_start: 0.9409 (ttt) cc_final: 0.9071 (ttt) REVERT: C 607 TYR cc_start: 0.7933 (m-80) cc_final: 0.7698 (m-10) REVERT: C 622 ASP cc_start: 0.8142 (m-30) cc_final: 0.7870 (m-30) outliers start: 43 outliers final: 30 residues processed: 157 average time/residue: 0.6424 time to fit residues: 108.6857 Evaluate side-chains 164 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS B 502 HIS C 102 HIS C 484 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.093843 restraints weight = 13543.708| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.20 r_work: 0.2776 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12102 Z= 0.122 Angle : 0.556 8.789 16488 Z= 0.284 Chirality : 0.045 0.145 1761 Planarity : 0.004 0.041 2142 Dihedral : 4.766 43.165 1582 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.55 % Allowed : 15.12 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1437 helix: -0.14 (0.50), residues: 111 sheet: 0.36 (0.20), residues: 561 loop : -1.39 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 385 TYR 0.015 0.001 TYR B 561 PHE 0.034 0.001 PHE A 101 TRP 0.009 0.001 TRP A 474 HIS 0.006 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00292 (12102) covalent geometry : angle 0.55593 (16488) hydrogen bonds : bond 0.03225 ( 372) hydrogen bonds : angle 4.87744 ( 1107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7732 (mt0) REVERT: A 334 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7337 (mtm110) REVERT: A 388 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.7919 (mtp-110) REVERT: A 451 HIS cc_start: 0.7309 (p-80) cc_final: 0.6607 (p-80) REVERT: A 502 HIS cc_start: 0.8479 (m170) cc_final: 0.6513 (t70) REVERT: A 607 TYR cc_start: 0.7909 (m-80) cc_final: 0.7624 (m-80) REVERT: B 133 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7758 (mt0) REVERT: B 388 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.7886 (mtp-110) REVERT: B 607 TYR cc_start: 0.7963 (m-10) cc_final: 0.7496 (m-80) REVERT: C 202 GLU cc_start: 0.8203 (tt0) cc_final: 0.7490 (tm-30) REVERT: C 388 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7561 (mtp85) REVERT: C 453 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7273 (tm-30) REVERT: C 463 ILE cc_start: 0.8505 (mt) cc_final: 0.8229 (mm) REVERT: C 581 MET cc_start: 0.9428 (ttt) cc_final: 0.9082 (ttt) outliers start: 33 outliers final: 25 residues processed: 155 average time/residue: 0.6483 time to fit residues: 108.1927 Evaluate side-chains 155 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 18 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.093422 restraints weight = 13495.275| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.25 r_work: 0.2784 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12102 Z= 0.116 Angle : 0.557 9.225 16488 Z= 0.282 Chirality : 0.045 0.144 1761 Planarity : 0.004 0.041 2142 Dihedral : 4.496 18.371 1578 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.39 % Allowed : 15.43 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1437 helix: 0.03 (0.51), residues: 111 sheet: 0.43 (0.20), residues: 561 loop : -1.31 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 385 TYR 0.019 0.001 TYR C 607 PHE 0.031 0.001 PHE A 101 TRP 0.009 0.001 TRP B 474 HIS 0.009 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00279 (12102) covalent geometry : angle 0.55700 (16488) hydrogen bonds : bond 0.03137 ( 372) hydrogen bonds : angle 4.83191 ( 1107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.472 Fit side-chains REVERT: A 133 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: A 334 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7290 (mtm110) REVERT: A 388 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.7897 (mtp-110) REVERT: A 451 HIS cc_start: 0.7237 (p-80) cc_final: 0.6581 (p-80) REVERT: A 607 TYR cc_start: 0.7939 (m-80) cc_final: 0.7662 (m-80) REVERT: B 133 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7741 (mt0) REVERT: B 388 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7845 (mtp-110) REVERT: B 479 GLN cc_start: 0.8684 (mm110) cc_final: 0.8353 (mm-40) REVERT: B 502 HIS cc_start: 0.8163 (m170) cc_final: 0.6147 (t-90) REVERT: B 607 TYR cc_start: 0.7959 (m-10) cc_final: 0.7637 (m-10) REVERT: C 202 GLU cc_start: 0.8202 (tt0) cc_final: 0.7472 (tm-30) REVERT: C 388 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7525 (mtp85) REVERT: C 453 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7692 (tm-30) REVERT: C 463 ILE cc_start: 0.8454 (mt) cc_final: 0.8161 (mm) REVERT: C 581 MET cc_start: 0.9441 (ttt) cc_final: 0.9080 (ttt) outliers start: 31 outliers final: 23 residues processed: 154 average time/residue: 0.6793 time to fit residues: 112.4832 Evaluate side-chains 157 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS B 246 HIS B 502 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.089886 restraints weight = 13608.809| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.25 r_work: 0.2788 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12102 Z= 0.233 Angle : 0.654 9.347 16488 Z= 0.335 Chirality : 0.049 0.173 1761 Planarity : 0.005 0.045 2142 Dihedral : 5.008 20.973 1578 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.62 % Allowed : 15.59 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.21), residues: 1437 helix: -0.40 (0.49), residues: 111 sheet: 0.45 (0.20), residues: 576 loop : -1.47 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 308 TYR 0.022 0.002 TYR B 561 PHE 0.032 0.002 PHE A 101 TRP 0.010 0.001 TRP B 474 HIS 0.011 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00583 (12102) covalent geometry : angle 0.65354 (16488) hydrogen bonds : bond 0.04097 ( 372) hydrogen bonds : angle 5.11312 ( 1107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.423 Fit side-chains REVERT: A 133 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: A 388 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.7912 (mtp-110) REVERT: A 451 HIS cc_start: 0.7351 (p-80) cc_final: 0.6568 (p-80) REVERT: A 453 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 607 TYR cc_start: 0.8023 (m-80) cc_final: 0.7693 (m-80) REVERT: B 133 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7753 (mt0) REVERT: B 388 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7866 (mtp-110) REVERT: B 479 GLN cc_start: 0.8716 (mm110) cc_final: 0.8393 (mm-40) REVERT: B 502 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.6362 (t-90) REVERT: B 607 TYR cc_start: 0.8080 (m-10) cc_final: 0.7739 (m-10) REVERT: C 388 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7562 (mtp85) REVERT: C 447 ASN cc_start: 0.8077 (p0) cc_final: 0.7589 (p0) REVERT: C 453 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7649 (tm-30) REVERT: C 454 LYS cc_start: 0.7864 (mmtm) cc_final: 0.7625 (mttp) REVERT: C 463 ILE cc_start: 0.8549 (mt) cc_final: 0.8201 (mm) REVERT: C 581 MET cc_start: 0.9365 (ttt) cc_final: 0.9090 (ttt) outliers start: 34 outliers final: 28 residues processed: 157 average time/residue: 0.6513 time to fit residues: 110.0341 Evaluate side-chains 165 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 97 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS B 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.095061 restraints weight = 13601.640| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.51 r_work: 0.2737 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12102 Z= 0.122 Angle : 0.571 9.296 16488 Z= 0.290 Chirality : 0.045 0.145 1761 Planarity : 0.004 0.041 2142 Dihedral : 4.653 18.980 1578 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.08 % Allowed : 16.36 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.21), residues: 1437 helix: 0.05 (0.51), residues: 111 sheet: 0.43 (0.20), residues: 561 loop : -1.28 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 385 TYR 0.015 0.001 TYR B 561 PHE 0.029 0.001 PHE A 101 TRP 0.010 0.001 TRP A 474 HIS 0.012 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00293 (12102) covalent geometry : angle 0.57058 (16488) hydrogen bonds : bond 0.03210 ( 372) hydrogen bonds : angle 4.90340 ( 1107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.452 Fit side-chains REVERT: A 133 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7709 (mt0) REVERT: A 388 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.7916 (mtp-110) REVERT: A 451 HIS cc_start: 0.7269 (p-80) cc_final: 0.6545 (p-80) REVERT: A 607 TYR cc_start: 0.7964 (m-80) cc_final: 0.7673 (m-80) REVERT: B 133 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7756 (mt0) REVERT: B 388 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.7888 (mtp-110) REVERT: B 479 GLN cc_start: 0.8705 (mm110) cc_final: 0.8360 (mm-40) REVERT: B 502 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.6278 (t-90) REVERT: B 607 TYR cc_start: 0.7953 (m-10) cc_final: 0.7485 (m-80) REVERT: C 202 GLU cc_start: 0.8263 (tt0) cc_final: 0.7530 (tm-30) REVERT: C 388 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7542 (mtp85) REVERT: C 447 ASN cc_start: 0.8089 (p0) cc_final: 0.7546 (p0) REVERT: C 453 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7793 (tm-30) REVERT: C 463 ILE cc_start: 0.8502 (mt) cc_final: 0.8215 (mm) REVERT: C 581 MET cc_start: 0.9423 (ttt) cc_final: 0.9116 (ttt) outliers start: 27 outliers final: 23 residues processed: 147 average time/residue: 0.6791 time to fit residues: 107.4217 Evaluate side-chains 154 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 484 HIS B 502 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.094901 restraints weight = 13465.433| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.20 r_work: 0.2784 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12102 Z= 0.106 Angle : 0.549 9.088 16488 Z= 0.278 Chirality : 0.044 0.145 1761 Planarity : 0.004 0.040 2142 Dihedral : 4.462 17.723 1578 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.93 % Allowed : 16.36 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1437 helix: 0.22 (0.52), residues: 111 sheet: 0.50 (0.20), residues: 561 loop : -1.23 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 385 TYR 0.014 0.001 TYR B 561 PHE 0.027 0.001 PHE A 101 TRP 0.008 0.001 TRP B 474 HIS 0.010 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00252 (12102) covalent geometry : angle 0.54917 (16488) hydrogen bonds : bond 0.03019 ( 372) hydrogen bonds : angle 4.79206 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4591.56 seconds wall clock time: 78 minutes 58.29 seconds (4738.29 seconds total)