Starting phenix.real_space_refine on Tue Jul 29 23:26:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ku9_0776/07_2025/6ku9_0776.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ku9_0776/07_2025/6ku9_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_0776/07_2025/6ku9_0776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ku9_0776/07_2025/6ku9_0776.map" model { file = "/net/cci-nas-00/data/ceres_data/6ku9_0776/07_2025/6ku9_0776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ku9_0776/07_2025/6ku9_0776.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.54, per 1000 atoms: 0.64 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: 2.78 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.70 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: 4.17 Time building geometry restraints manager: 3.33 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.110 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:28.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP C 396 HIS 0.005 0.001 HIS A 102 PHE 0.016 0.002 PHE B 193 TYR 0.012 0.002 TYR C 561 ARG 0.009 0.001 ARG B 307 Details of bonding type rmsd hydrogen bonds : bond 0.15525 ( 372) hydrogen bonds : angle 6.73259 ( 1107) covalent geometry : bond 0.00524 (12102) covalent geometry : angle 0.89530 (16488) *********************** 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 : 1.384 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: 0.8290 (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: 1.5677 time to fit residues: 428.2733 Evaluate side-chains 174 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 121 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 107 HIS A 171 ASN A 483 GLN B 102 HIS B 171 ASN B 483 GLN C 102 HIS C 171 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.091872 restraints weight = 13128.753| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.47 r_work: 0.2777 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12102 Z= 0.156 Angle : 0.610 6.873 16488 Z= 0.321 Chirality : 0.047 0.239 1761 Planarity : 0.005 0.043 2142 Dihedral : 7.039 64.920 1621 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 3.47 % Allowed : 11.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.20), residues: 1437 helix: -2.15 (0.39), residues: 111 sheet: 0.14 (0.19), residues: 576 loop : -2.08 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 461 HIS 0.007 0.001 HIS C 102 PHE 0.030 0.001 PHE B 101 TYR 0.019 0.001 TYR B 561 ARG 0.006 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 372) hydrogen bonds : angle 5.48246 ( 1107) covalent geometry : bond 0.00375 (12102) covalent geometry : angle 0.60987 (16488) *********************** 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 200 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6415 (p90) REVERT: A 133 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: A 334 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7134 (mtp85) REVERT: A 360 LYS cc_start: 0.8995 (tptm) cc_final: 0.8735 (tppt) REVERT: A 388 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.7922 (mtp-110) REVERT: A 450 HIS cc_start: 0.6424 (t-90) cc_final: 0.6114 (t-90) REVERT: A 455 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7302 (mp) REVERT: A 502 HIS cc_start: 0.8439 (m-70) cc_final: 0.6378 (t70) REVERT: A 508 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6663 (p90) REVERT: A 510 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7034 (t0) REVERT: B 78 ARG cc_start: 0.8333 (mmm160) cc_final: 0.8129 (mmt90) REVERT: B 133 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: B 354 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6256 (pm20) REVERT: B 388 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7827 (mtp-110) REVERT: B 446 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7306 (p) REVERT: B 479 GLN cc_start: 0.8763 (mm110) cc_final: 0.8403 (mm-40) REVERT: B 575 ASP cc_start: 0.8817 (m-30) cc_final: 0.8500 (m-30) REVERT: C 354 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6234 (pm20) REVERT: C 388 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7587 (mtp85) REVERT: C 455 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7404 (mp) REVERT: C 581 MET cc_start: 0.9498 (ttt) cc_final: 0.9196 (ttt) REVERT: C 622 ASP cc_start: 0.8111 (m-30) cc_final: 0.7751 (m-30) outliers start: 45 outliers final: 16 residues processed: 185 average time/residue: 1.6880 time to fit residues: 338.4724 Evaluate side-chains 163 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 334 ARG 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 133 GLN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 354 GLU 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 C residue 105 VAL 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 441 THR 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 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 416 ASN B 107 HIS ** 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 = 0.3613 r_free = 0.3613 target = 0.142921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.093096 restraints weight = 13636.897| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.25 r_work: 0.2841 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12102 Z= 0.127 Angle : 0.568 6.595 16488 Z= 0.295 Chirality : 0.046 0.183 1761 Planarity : 0.005 0.040 2142 Dihedral : 6.015 47.779 1603 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 3.47 % Allowed : 12.11 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1437 helix: -1.13 (0.45), residues: 111 sheet: 0.25 (0.20), residues: 576 loop : -1.87 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 474 HIS 0.007 0.001 HIS C 80 PHE 0.010 0.001 PHE A 101 TYR 0.017 0.001 TYR B 561 ARG 0.002 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 372) hydrogen bonds : angle 5.14542 ( 1107) covalent geometry : bond 0.00298 (12102) covalent geometry : angle 0.56783 (16488) *********************** 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 189 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6621 (p-80) REVERT: A 133 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7666 (mt0) REVERT: A 170 LYS cc_start: 0.8768 (mmtm) cc_final: 0.8551 (mmtp) REVERT: A 334 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7107 (mtp85) REVERT: A 360 LYS cc_start: 0.8964 (tptm) cc_final: 0.8719 (tppt) REVERT: A 388 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7901 (mtp-110) REVERT: A 450 HIS cc_start: 0.6447 (t-90) cc_final: 0.6107 (t-90) REVERT: A 502 HIS cc_start: 0.8400 (m-70) cc_final: 0.6421 (t70) REVERT: A 508 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6575 (p90) REVERT: B 78 ARG cc_start: 0.8255 (mmm160) cc_final: 0.8042 (mmt90) REVERT: B 170 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8543 (mptm) REVERT: B 388 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7849 (mtp-110) REVERT: B 575 ASP cc_start: 0.8702 (m-30) cc_final: 0.8397 (m-30) REVERT: C 80 HIS cc_start: 0.8122 (t-90) cc_final: 0.7885 (t-90) REVERT: C 102 HIS cc_start: 0.6982 (OUTLIER) cc_final: 0.6268 (p-80) REVERT: C 170 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8387 (mttp) REVERT: C 202 GLU cc_start: 0.8162 (tt0) cc_final: 0.7531 (tm-30) REVERT: C 388 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7594 (mtp85) REVERT: C 463 ILE cc_start: 0.8559 (mt) cc_final: 0.8264 (mm) REVERT: C 581 MET cc_start: 0.9471 (ttt) cc_final: 0.9135 (ttt) REVERT: C 622 ASP cc_start: 0.8171 (m-30) cc_final: 0.7873 (m-30) outliers start: 45 outliers final: 20 residues processed: 170 average time/residue: 1.5137 time to fit residues: 278.8219 Evaluate side-chains 165 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 334 ARG 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 520 SER 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 446 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 170 LYS 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 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 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 86 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 102 HIS B 502 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.094190 restraints weight = 13514.924| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.24 r_work: 0.2863 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12102 Z= 0.110 Angle : 0.540 6.192 16488 Z= 0.279 Chirality : 0.045 0.174 1761 Planarity : 0.004 0.039 2142 Dihedral : 5.309 47.562 1590 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.62 % Allowed : 13.43 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.21), residues: 1437 helix: -0.51 (0.49), residues: 111 sheet: 0.38 (0.20), residues: 576 loop : -1.71 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 474 HIS 0.005 0.001 HIS A 80 PHE 0.034 0.001 PHE C 101 TYR 0.015 0.001 TYR B 561 ARG 0.002 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 372) hydrogen bonds : angle 4.97505 ( 1107) covalent geometry : bond 0.00256 (12102) covalent geometry : angle 0.54036 (16488) *********************** 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 184 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7673 (mt0) REVERT: A 170 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8580 (mmtp) REVERT: A 360 LYS cc_start: 0.8955 (tptm) cc_final: 0.8714 (tppt) REVERT: A 388 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.7922 (mtp-110) REVERT: A 450 HIS cc_start: 0.6433 (t-90) cc_final: 0.5986 (t-90) REVERT: A 502 HIS cc_start: 0.8402 (m-70) cc_final: 0.6483 (t70) REVERT: A 508 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.6394 (p90) REVERT: B 133 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7746 (mt0) REVERT: B 170 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8631 (mptm) REVERT: B 388 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.7783 (mtp85) REVERT: B 446 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7346 (p) REVERT: B 575 ASP cc_start: 0.8659 (m-30) cc_final: 0.8409 (m-30) REVERT: B 607 TYR cc_start: 0.7875 (m-10) cc_final: 0.7462 (m-10) REVERT: C 102 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6311 (t-90) REVERT: C 202 GLU cc_start: 0.8080 (tt0) cc_final: 0.7486 (tm-30) REVERT: C 388 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7588 (mtp85) REVERT: C 463 ILE cc_start: 0.8514 (mt) cc_final: 0.8259 (mm) REVERT: C 581 MET cc_start: 0.9476 (ttt) cc_final: 0.9127 (ttt) REVERT: C 607 TYR cc_start: 0.7894 (m-10) cc_final: 0.7240 (m-10) outliers start: 34 outliers final: 22 residues processed: 173 average time/residue: 1.5506 time to fit residues: 291.7049 Evaluate side-chains 163 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 4.776 ------------------------------------------------------------------------------- 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 248 LEU Chi-restraints excluded: chain A residue 385 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 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 510 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 B 75 ASN B 416 ASN B 502 HIS C 75 ASN C 80 HIS C 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.089627 restraints weight = 13133.663| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.55 r_work: 0.2750 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12102 Z= 0.169 Angle : 0.597 6.750 16488 Z= 0.309 Chirality : 0.047 0.167 1761 Planarity : 0.004 0.042 2142 Dihedral : 4.923 38.802 1582 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.78 % Allowed : 13.66 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1437 helix: -0.41 (0.50), residues: 111 sheet: 0.36 (0.20), residues: 576 loop : -1.63 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.007 0.001 HIS B 102 PHE 0.032 0.001 PHE A 101 TYR 0.020 0.001 TYR B 561 ARG 0.003 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 372) hydrogen bonds : angle 5.07580 ( 1107) covalent geometry : bond 0.00416 (12102) covalent geometry : angle 0.59666 (16488) *********************** 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 177 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: A 170 LYS cc_start: 0.8834 (mmtm) cc_final: 0.8618 (mmtp) REVERT: A 388 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7888 (mtp-110) REVERT: A 451 HIS cc_start: 0.7253 (p-80) cc_final: 0.6480 (p-80) REVERT: A 502 HIS cc_start: 0.8457 (m-70) cc_final: 0.6472 (t70) REVERT: A 508 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6682 (p90) REVERT: A 607 TYR cc_start: 0.7930 (m-80) cc_final: 0.7286 (m-80) REVERT: B 133 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7686 (mt0) REVERT: B 388 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7852 (mtp-110) REVERT: B 453 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: B 607 TYR cc_start: 0.7996 (m-10) cc_final: 0.7377 (m-10) REVERT: C 102 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6602 (t-90) REVERT: C 242 LEU cc_start: 0.7898 (mt) cc_final: 0.7468 (mt) REVERT: C 388 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7571 (mtp85) REVERT: C 453 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7386 (tm-30) REVERT: C 463 ILE cc_start: 0.8515 (mt) cc_final: 0.8232 (mm) REVERT: C 581 MET cc_start: 0.9430 (ttt) cc_final: 0.9126 (ttt) REVERT: C 607 TYR cc_start: 0.7935 (m-10) cc_final: 0.7448 (m-10) outliers start: 36 outliers final: 26 residues processed: 166 average time/residue: 1.2841 time to fit residues: 230.6581 Evaluate side-chains 168 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 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 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 508 PHE 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 245 ILE 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 453 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP 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 520 SER 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 101 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 B 80 HIS 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 = 0.3604 r_free = 0.3604 target = 0.142291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.092429 restraints weight = 13581.225| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.25 r_work: 0.2831 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12102 Z= 0.140 Angle : 0.566 6.454 16488 Z= 0.293 Chirality : 0.045 0.199 1761 Planarity : 0.004 0.040 2142 Dihedral : 4.734 30.363 1582 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.78 % Allowed : 14.43 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.21), residues: 1437 helix: -0.22 (0.50), residues: 111 sheet: 0.43 (0.20), residues: 576 loop : -1.55 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.007 0.001 HIS C 102 PHE 0.031 0.001 PHE A 101 TYR 0.017 0.001 TYR B 561 ARG 0.002 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 372) hydrogen bonds : angle 5.00174 ( 1107) covalent geometry : bond 0.00339 (12102) covalent geometry : angle 0.56628 (16488) *********************** 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 176 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: A 170 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8584 (mmtp) REVERT: A 388 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.7941 (mtp-110) REVERT: A 451 HIS cc_start: 0.7316 (p-80) cc_final: 0.6579 (p-80) REVERT: A 502 HIS cc_start: 0.8439 (m-70) cc_final: 0.6477 (t70) REVERT: A 607 TYR cc_start: 0.7994 (m-80) cc_final: 0.7426 (m-80) REVERT: B 133 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7746 (mt0) REVERT: B 388 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7885 (mtp-110) REVERT: B 453 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: B 479 GLN cc_start: 0.8649 (mm110) cc_final: 0.8320 (mm-40) REVERT: B 607 TYR cc_start: 0.8002 (m-10) cc_final: 0.7348 (m-10) REVERT: C 102 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6828 (t-90) REVERT: C 388 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7592 (mtp85) REVERT: C 453 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7422 (tm-30) REVERT: C 463 ILE cc_start: 0.8518 (mt) cc_final: 0.8255 (mm) REVERT: C 581 MET cc_start: 0.9420 (ttt) cc_final: 0.9118 (ttt) REVERT: C 607 TYR cc_start: 0.7934 (m-10) cc_final: 0.7503 (m-10) outliers start: 36 outliers final: 28 residues processed: 165 average time/residue: 1.3163 time to fit residues: 237.2394 Evaluate side-chains 171 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 133 GLN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 LEU 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 245 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 348 VAL 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 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 348 VAL 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 520 SER 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 140 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.092605 restraints weight = 13314.091| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.61 r_work: 0.2817 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12102 Z= 0.132 Angle : 0.569 7.321 16488 Z= 0.292 Chirality : 0.045 0.151 1761 Planarity : 0.004 0.040 2142 Dihedral : 4.609 24.207 1580 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.24 % Allowed : 14.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.21), residues: 1437 helix: -0.12 (0.50), residues: 111 sheet: 0.42 (0.20), residues: 582 loop : -1.49 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.005 0.001 HIS B 102 PHE 0.029 0.001 PHE A 101 TYR 0.016 0.001 TYR B 561 ARG 0.002 0.000 ARG C 308 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 372) hydrogen bonds : angle 4.96234 ( 1107) covalent geometry : bond 0.00320 (12102) covalent geometry : angle 0.56878 (16488) *********************** 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 180 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: A 170 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8612 (mmtp) REVERT: A 334 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7925 (mtp85) REVERT: A 388 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.7937 (mtp-110) REVERT: A 451 HIS cc_start: 0.7316 (p-80) cc_final: 0.6600 (p-80) REVERT: A 607 TYR cc_start: 0.7985 (m-80) cc_final: 0.7417 (m-80) REVERT: B 133 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7743 (mt0) REVERT: B 388 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.7884 (mtp-110) REVERT: B 453 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: B 479 GLN cc_start: 0.8670 (mm110) cc_final: 0.8334 (mm-40) REVERT: B 607 TYR cc_start: 0.8012 (m-10) cc_final: 0.7361 (m-10) REVERT: C 103 ASP cc_start: 0.8545 (p0) cc_final: 0.8174 (p0) REVERT: C 202 GLU cc_start: 0.8135 (tt0) cc_final: 0.7521 (tm-30) REVERT: C 388 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7571 (mtp85) REVERT: C 453 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7382 (tm-30) REVERT: C 463 ILE cc_start: 0.8496 (mt) cc_final: 0.8240 (mm) REVERT: C 581 MET cc_start: 0.9434 (ttt) cc_final: 0.9135 (ttt) REVERT: C 607 TYR cc_start: 0.7968 (m-10) cc_final: 0.7564 (m-10) outliers start: 42 outliers final: 26 residues processed: 166 average time/residue: 1.2700 time to fit residues: 228.4041 Evaluate side-chains 163 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 LEU 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 313 SER Chi-restraints excluded: chain B residue 348 VAL 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 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 348 VAL 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 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 74 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 484 HIS B 502 HIS C 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.092989 restraints weight = 13290.251| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.23 r_work: 0.2788 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2413 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 : 0.541 8.553 16488 Z= 0.275 Chirality : 0.044 0.157 1761 Planarity : 0.004 0.037 2142 Dihedral : 4.355 17.625 1578 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.24 % Allowed : 15.51 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1437 helix: 0.12 (0.51), residues: 111 sheet: 0.48 (0.21), residues: 561 loop : -1.32 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.003 0.001 HIS B 102 PHE 0.027 0.001 PHE A 101 TYR 0.013 0.001 TYR B 561 ARG 0.002 0.000 ARG C 385 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 372) hydrogen bonds : angle 4.81576 ( 1107) covalent geometry : bond 0.00247 (12102) covalent geometry : angle 0.54067 (16488) *********************** 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 170 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: A 388 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.7979 (mtp-110) REVERT: A 451 HIS cc_start: 0.7172 (p-80) cc_final: 0.6535 (p-80) REVERT: A 463 ILE cc_start: 0.8592 (mt) cc_final: 0.8209 (mm) REVERT: A 607 TYR cc_start: 0.8012 (m-80) cc_final: 0.7469 (m-80) REVERT: B 133 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7827 (mt0) REVERT: B 388 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.7905 (mtp-110) REVERT: B 453 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: B 479 GLN cc_start: 0.8666 (mm110) cc_final: 0.8345 (mm-40) REVERT: B 502 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.6251 (t-90) REVERT: B 607 TYR cc_start: 0.8033 (m-10) cc_final: 0.7449 (m-10) REVERT: C 102 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6879 (OUTLIER) REVERT: C 103 ASP cc_start: 0.8524 (p0) cc_final: 0.8149 (p0) REVERT: C 202 GLU cc_start: 0.8119 (tt0) cc_final: 0.7534 (tm-30) REVERT: C 242 LEU cc_start: 0.8174 (mt) cc_final: 0.7520 (mt) REVERT: C 388 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7619 (mtp85) REVERT: C 453 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7397 (tm-30) REVERT: C 463 ILE cc_start: 0.8501 (mt) cc_final: 0.8301 (mm) REVERT: C 581 MET cc_start: 0.9456 (ttt) cc_final: 0.9090 (ttt) REVERT: C 607 TYR cc_start: 0.7918 (m-10) cc_final: 0.7595 (m-10) outliers start: 29 outliers final: 22 residues processed: 159 average time/residue: 1.3124 time to fit residues: 225.8307 Evaluate side-chains 162 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 ARG Chi-restraints excluded: chain A residue 455 LEU 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 313 SER Chi-restraints excluded: chain B residue 348 VAL 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 502 HIS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 0.0980 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 415 ASN B 246 HIS C 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.090113 restraints weight = 13585.155| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.19 r_work: 0.2737 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12102 Z= 0.251 Angle : 0.677 9.441 16488 Z= 0.349 Chirality : 0.050 0.180 1761 Planarity : 0.005 0.045 2142 Dihedral : 5.009 21.025 1578 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.31 % Allowed : 15.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1437 helix: -0.41 (0.50), residues: 111 sheet: 0.34 (0.19), residues: 591 loop : -1.42 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 474 HIS 0.009 0.001 HIS B 102 PHE 0.032 0.002 PHE C 101 TYR 0.022 0.002 TYR B 561 ARG 0.007 0.001 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 372) hydrogen bonds : angle 5.20326 ( 1107) covalent geometry : bond 0.00628 (12102) covalent geometry : angle 0.67656 (16488) *********************** 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 166 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: A 388 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.7900 (mtp-110) REVERT: A 451 HIS cc_start: 0.7375 (p-80) cc_final: 0.6638 (p-80) REVERT: A 607 TYR cc_start: 0.8115 (m-80) cc_final: 0.7468 (m-80) REVERT: B 133 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7783 (mt0) REVERT: B 388 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7839 (mtp-110) REVERT: B 453 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: B 502 HIS cc_start: 0.8181 (m170) cc_final: 0.6404 (t-90) REVERT: B 607 TYR cc_start: 0.8073 (m-10) cc_final: 0.7348 (m-10) REVERT: C 103 ASP cc_start: 0.8616 (p0) cc_final: 0.8330 (p0) REVERT: C 388 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7575 (mtp85) REVERT: C 447 ASN cc_start: 0.8072 (p0) cc_final: 0.7597 (p0) REVERT: C 455 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7846 (mm) REVERT: C 463 ILE cc_start: 0.8527 (mt) cc_final: 0.8225 (mm) REVERT: C 581 MET cc_start: 0.9360 (ttt) cc_final: 0.9091 (ttt) REVERT: C 622 ASP cc_start: 0.8129 (m-30) cc_final: 0.7782 (m-30) outliers start: 30 outliers final: 25 residues processed: 157 average time/residue: 1.3027 time to fit residues: 221.1567 Evaluate side-chains 160 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 LEU 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 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 453 GLU Chi-restraints excluded: chain B residue 455 LEU 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 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 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 36 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 0.0470 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 415 ASN C 80 HIS C 102 HIS C 484 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.092504 restraints weight = 13479.595| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.26 r_work: 0.2785 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12102 Z= 0.123 Angle : 0.569 9.917 16488 Z= 0.290 Chirality : 0.045 0.150 1761 Planarity : 0.004 0.041 2142 Dihedral : 4.595 19.585 1578 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.16 % Allowed : 16.36 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1437 helix: 0.04 (0.51), residues: 111 sheet: 0.46 (0.20), residues: 582 loop : -1.38 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.005 0.001 HIS B 102 PHE 0.031 0.001 PHE C 101 TYR 0.014 0.001 TYR B 561 ARG 0.002 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 372) hydrogen bonds : angle 4.92591 ( 1107) covalent geometry : bond 0.00295 (12102) covalent geometry : angle 0.56887 (16488) ********************** 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 160 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7710 (mt0) REVERT: A 388 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.7895 (mtp-110) REVERT: A 451 HIS cc_start: 0.7250 (p-80) cc_final: 0.6501 (p-80) REVERT: A 607 TYR cc_start: 0.8001 (m-80) cc_final: 0.7473 (m-80) REVERT: B 133 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7758 (mt0) REVERT: B 388 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7840 (mtp-110) REVERT: B 453 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: B 479 GLN cc_start: 0.8659 (mm110) cc_final: 0.8311 (mm-40) REVERT: B 502 HIS cc_start: 0.8168 (m170) cc_final: 0.6262 (t-90) REVERT: B 607 TYR cc_start: 0.7996 (m-10) cc_final: 0.7322 (m-10) REVERT: C 103 ASP cc_start: 0.8470 (p0) cc_final: 0.8252 (p0) REVERT: C 242 LEU cc_start: 0.8325 (mt) cc_final: 0.7957 (tp) REVERT: C 388 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7518 (mtp85) REVERT: C 453 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7534 (tm-30) REVERT: C 455 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7632 (mm) REVERT: C 463 ILE cc_start: 0.8443 (mt) cc_final: 0.8156 (mm) REVERT: C 581 MET cc_start: 0.9421 (ttt) cc_final: 0.9080 (ttt) outliers start: 28 outliers final: 24 residues processed: 151 average time/residue: 2.0123 time to fit residues: 328.6767 Evaluate side-chains 159 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 LEU 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 313 SER Chi-restraints excluded: chain B residue 348 VAL 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 C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 241 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 60 optimal weight: 0.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 415 ASN C 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.090852 restraints weight = 13103.687| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.23 r_work: 0.2781 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12102 Z= 0.143 Angle : 0.582 9.710 16488 Z= 0.296 Chirality : 0.046 0.149 1761 Planarity : 0.004 0.041 2142 Dihedral : 4.613 19.404 1578 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.08 % Allowed : 16.44 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1437 helix: 0.00 (0.51), residues: 111 sheet: 0.34 (0.20), residues: 576 loop : -1.18 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.005 0.001 HIS A 102 PHE 0.029 0.001 PHE C 101 TYR 0.016 0.001 TYR B 561 ARG 0.002 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 372) hydrogen bonds : angle 4.91552 ( 1107) covalent geometry : bond 0.00349 (12102) covalent geometry : angle 0.58174 (16488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10050.90 seconds wall clock time: 182 minutes 27.56 seconds (10947.56 seconds total)