Starting phenix.real_space_refine on Sun Aug 24 12:36:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekr_28211/08_2025/8ekr_28211.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekr_28211/08_2025/8ekr_28211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ekr_28211/08_2025/8ekr_28211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekr_28211/08_2025/8ekr_28211.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekr_28211/08_2025/8ekr_28211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekr_28211/08_2025/8ekr_28211.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 112 5.16 5 C 12940 2.51 5 N 3288 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4893 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 591} Chain breaks: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 12, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.08, per 1000 atoms: 0.21 Number of scatterers: 19712 At special positions: 0 Unit cell: (137.97, 137.97, 113.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 4 15.00 O 3368 8.00 N 3288 7.00 C 12940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 827.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 61.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.771A pdb=" N ASN A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.574A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.247A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 471 through 492 removed outlier: 4.046A pdb=" N ALA A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.638A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 519 through 529 removed outlier: 3.617A pdb=" N VAL A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 559 removed outlier: 4.071A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 619 through 650 removed outlier: 3.568A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.770A pdb=" N ASN B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.574A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.247A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 471 through 492 removed outlier: 4.047A pdb=" N ALA B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.638A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 519 through 529 removed outlier: 3.617A pdb=" N VAL B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 559 removed outlier: 4.072A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 619 through 650 removed outlier: 3.567A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.769A pdb=" N ASN C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.573A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.246A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 470 Processing helix chain 'C' and resid 471 through 492 removed outlier: 4.046A pdb=" N ALA C 480 " --> pdb=" O PHE C 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.639A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 519 through 529 removed outlier: 3.616A pdb=" N VAL C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 559 removed outlier: 4.071A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 619 through 650 removed outlier: 3.567A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.770A pdb=" N ASN D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.574A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 4.075A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.587A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.754A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.247A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 459 through 466 removed outlier: 4.165A pdb=" N ILE D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 470 Processing helix chain 'D' and resid 471 through 492 removed outlier: 4.047A pdb=" N ALA D 480 " --> pdb=" O PHE D 476 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.637A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 Processing helix chain 'D' and resid 519 through 529 removed outlier: 3.617A pdb=" N VAL D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE D 529 " --> pdb=" O TYR D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 559 removed outlier: 4.071A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 619 through 650 removed outlier: 3.567A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 672 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 5.008A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A 700 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 5.009A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP B 700 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 330 through 335 removed outlier: 5.008A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP C 700 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 330 through 335 removed outlier: 5.009A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP D 700 " --> pdb=" O VAL D 691 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3012 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2980 1.31 - 1.44: 5712 1.44 - 1.56: 11320 1.56 - 1.69: 8 1.69 - 1.82: 172 Bond restraints: 20192 Sorted by residual: bond pdb=" C4 PEX A 801 " pdb=" O4 PEX A 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX D 801 " pdb=" O4 PEX D 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX B 801 " pdb=" O4 PEX B 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4 PEX C 801 " pdb=" O4 PEX C 801 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C14 PEX D 801 " pdb=" O6 PEX D 801 " ideal model delta sigma weight residual 1.331 1.401 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 20187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 27074 3.22 - 6.43: 278 6.43 - 9.65: 36 9.65 - 12.87: 4 12.87 - 16.08: 4 Bond angle restraints: 27396 Sorted by residual: angle pdb=" C ASN B 259 " pdb=" N SER B 260 " pdb=" CA SER B 260 " ideal model delta sigma weight residual 120.49 129.47 -8.98 1.42e+00 4.96e-01 4.00e+01 angle pdb=" C ASN A 259 " pdb=" N SER A 260 " pdb=" CA SER A 260 " ideal model delta sigma weight residual 120.49 129.45 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C ASN D 259 " pdb=" N SER D 260 " pdb=" CA SER D 260 " ideal model delta sigma weight residual 120.49 129.45 -8.96 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C ASN C 259 " pdb=" N SER C 260 " pdb=" CA SER C 260 " ideal model delta sigma weight residual 120.49 129.42 -8.93 1.42e+00 4.96e-01 3.95e+01 angle pdb=" O3 PEX D 801 " pdb=" P1 PEX D 801 " pdb=" O8 PEX D 801 " ideal model delta sigma weight residual 93.74 109.82 -16.08 3.00e+00 1.11e-01 2.87e+01 ... (remaining 27391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.88: 10940 18.88 - 37.76: 768 37.76 - 56.65: 108 56.65 - 75.53: 44 75.53 - 94.41: 16 Dihedral angle restraints: 11876 sinusoidal: 4712 harmonic: 7164 Sorted by residual: dihedral pdb=" CA PHE D 161 " pdb=" C PHE D 161 " pdb=" N TYR D 162 " pdb=" CA TYR D 162 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE C 161 " pdb=" C PHE C 161 " pdb=" N TYR C 162 " pdb=" CA TYR C 162 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE B 161 " pdb=" C PHE B 161 " pdb=" N TYR B 162 " pdb=" CA TYR B 162 " ideal model delta harmonic sigma weight residual 180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 11873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2076 0.036 - 0.072: 760 0.072 - 0.107: 221 0.107 - 0.143: 52 0.143 - 0.179: 23 Chirality restraints: 3132 Sorted by residual: chirality pdb=" CB VAL B 184 " pdb=" CA VAL B 184 " pdb=" CG1 VAL B 184 " pdb=" CG2 VAL B 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CB VAL D 184 " pdb=" CA VAL D 184 " pdb=" CG1 VAL D 184 " pdb=" CG2 VAL D 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CB VAL A 184 " pdb=" CA VAL A 184 " pdb=" CG1 VAL A 184 " pdb=" CG2 VAL A 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 3129 not shown) Planarity restraints: 3352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 725 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO D 726 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 726 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 726 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 725 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 726 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 726 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 726 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 725 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO C 726 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 726 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 726 " -0.044 5.00e-02 4.00e+02 ... (remaining 3349 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5451 2.81 - 3.33: 18085 3.33 - 3.86: 32646 3.86 - 4.38: 36887 4.38 - 4.90: 64293 Nonbonded interactions: 157362 Sorted by model distance: nonbonded pdb=" O LEU B 513 " pdb=" OG1 THR B 516 " model vdw 2.292 3.040 nonbonded pdb=" O LEU A 513 " pdb=" OG1 THR A 516 " model vdw 2.292 3.040 nonbonded pdb=" O LEU C 513 " pdb=" OG1 THR C 516 " model vdw 2.292 3.040 nonbonded pdb=" O LEU D 513 " pdb=" OG1 THR D 516 " model vdw 2.293 3.040 nonbonded pdb=" O TRP C 223 " pdb=" OG1 THR C 227 " model vdw 2.304 3.040 ... (remaining 157357 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4.540 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.004 0.074 20192 Z= 0.174 Angle : 0.804 16.085 27396 Z= 0.390 Chirality : 0.043 0.179 3132 Planarity : 0.006 0.081 3352 Dihedral : 14.011 94.410 7244 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.38 % Allowed : 0.57 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.15), residues: 2412 helix: -0.08 (0.13), residues: 1368 sheet: -0.04 (0.43), residues: 108 loop : -1.79 (0.16), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 371 TYR 0.034 0.002 TYR D 162 PHE 0.015 0.001 PHE D 75 TRP 0.012 0.001 TRP D 333 HIS 0.005 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00351 (20192) covalent geometry : angle 0.80409 (27396) hydrogen bonds : bond 0.16438 ( 1056) hydrogen bonds : angle 5.86447 ( 3012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 481 time to evaluate : 0.689 Fit side-chains REVERT: A 123 LYS cc_start: 0.8090 (tptm) cc_final: 0.7870 (tptm) REVERT: A 189 ASP cc_start: 0.7587 (t0) cc_final: 0.7268 (t0) REVERT: B 123 LYS cc_start: 0.8095 (tptm) cc_final: 0.7876 (tptm) REVERT: B 189 ASP cc_start: 0.7591 (t0) cc_final: 0.7268 (t0) REVERT: C 123 LYS cc_start: 0.8092 (tptm) cc_final: 0.7862 (tptm) REVERT: C 189 ASP cc_start: 0.7582 (t0) cc_final: 0.7267 (t0) REVERT: D 123 LYS cc_start: 0.8085 (tptm) cc_final: 0.7861 (tptm) REVERT: D 189 ASP cc_start: 0.7592 (t0) cc_final: 0.7271 (t0) outliers start: 8 outliers final: 0 residues processed: 489 average time/residue: 0.4845 time to fit residues: 272.5950 Evaluate side-chains 347 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 156 GLN A 247 ASN A 487 GLN B 148 ASN B 156 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 487 GLN C 148 ASN C 156 GLN C 247 ASN C 487 GLN D 148 ASN D 156 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 487 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.155700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.123726 restraints weight = 23681.543| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.87 r_work: 0.3199 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20192 Z= 0.131 Angle : 0.544 9.123 27396 Z= 0.273 Chirality : 0.038 0.168 3132 Planarity : 0.005 0.060 3352 Dihedral : 6.481 80.369 2784 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.35 % Allowed : 11.11 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.16), residues: 2412 helix: 1.06 (0.13), residues: 1456 sheet: 2.68 (0.52), residues: 68 loop : -1.61 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 539 TYR 0.029 0.001 TYR A 162 PHE 0.010 0.001 PHE D 75 TRP 0.007 0.001 TRP B 676 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00302 (20192) covalent geometry : angle 0.54385 (27396) hydrogen bonds : bond 0.03843 ( 1056) hydrogen bonds : angle 3.74456 ( 3012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 347 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.7987 (tptm) cc_final: 0.7787 (tptm) REVERT: A 189 ASP cc_start: 0.7803 (t0) cc_final: 0.7510 (t0) REVERT: A 240 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: A 269 HIS cc_start: 0.6734 (m90) cc_final: 0.6444 (t-90) REVERT: A 371 ARG cc_start: 0.8077 (mmt90) cc_final: 0.7157 (mmp-170) REVERT: A 388 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7740 (ttp-170) REVERT: A 433 MET cc_start: 0.7734 (tpt) cc_final: 0.7444 (tpp) REVERT: A 468 MET cc_start: 0.6568 (ppp) cc_final: 0.6148 (ppp) REVERT: A 637 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 640 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8079 (ttp) REVERT: B 189 ASP cc_start: 0.7779 (t0) cc_final: 0.7480 (t0) REVERT: B 240 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: B 269 HIS cc_start: 0.6722 (m90) cc_final: 0.6420 (t-90) REVERT: B 371 ARG cc_start: 0.8078 (mmt90) cc_final: 0.7160 (mmp-170) REVERT: B 388 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7725 (ttp-170) REVERT: B 538 LEU cc_start: 0.8110 (mm) cc_final: 0.7860 (mm) REVERT: B 539 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6262 (ptt90) REVERT: B 637 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8440 (mt) REVERT: B 640 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8056 (ttp) REVERT: C 189 ASP cc_start: 0.7768 (t0) cc_final: 0.7469 (t0) REVERT: C 240 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: C 269 HIS cc_start: 0.6730 (m90) cc_final: 0.6426 (t-90) REVERT: C 371 ARG cc_start: 0.8084 (mmt90) cc_final: 0.7167 (mmp-170) REVERT: C 388 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7730 (ttp-170) REVERT: C 538 LEU cc_start: 0.8116 (mm) cc_final: 0.7868 (mm) REVERT: C 637 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8457 (mt) REVERT: C 640 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8089 (ttp) REVERT: C 708 GLU cc_start: 0.8683 (tt0) cc_final: 0.8419 (mt-10) REVERT: D 189 ASP cc_start: 0.7787 (t0) cc_final: 0.7488 (t0) REVERT: D 240 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: D 269 HIS cc_start: 0.6713 (m90) cc_final: 0.6423 (t-90) REVERT: D 371 ARG cc_start: 0.8076 (mmt90) cc_final: 0.7166 (mmp-170) REVERT: D 388 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7731 (ttp-170) REVERT: D 538 LEU cc_start: 0.8114 (mm) cc_final: 0.7864 (mm) REVERT: D 539 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6277 (ptt90) REVERT: D 637 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8445 (mt) REVERT: D 640 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8075 (ttp) outliers start: 70 outliers final: 38 residues processed: 377 average time/residue: 0.4398 time to fit residues: 191.9768 Evaluate side-chains 383 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 327 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 242 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS B 191 HIS C 191 HIS D 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.154144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.122693 restraints weight = 23850.607| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.75 r_work: 0.3199 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20192 Z= 0.109 Angle : 0.505 8.959 27396 Z= 0.250 Chirality : 0.036 0.173 3132 Planarity : 0.004 0.049 3352 Dihedral : 6.107 78.640 2784 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.21 % Allowed : 15.23 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.17), residues: 2412 helix: 1.65 (0.13), residues: 1448 sheet: 2.62 (0.50), residues: 68 loop : -1.44 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 539 TYR 0.020 0.001 TYR C 162 PHE 0.006 0.001 PHE C 81 TRP 0.007 0.001 TRP D 333 HIS 0.005 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00251 (20192) covalent geometry : angle 0.50497 (27396) hydrogen bonds : bond 0.03378 ( 1056) hydrogen bonds : angle 3.39676 ( 3012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 337 time to evaluate : 0.588 Fit side-chains REVERT: A 123 LYS cc_start: 0.7886 (tptm) cc_final: 0.7596 (tptm) REVERT: A 189 ASP cc_start: 0.7741 (t0) cc_final: 0.7405 (t0) REVERT: A 191 HIS cc_start: 0.8226 (m170) cc_final: 0.7972 (m-70) REVERT: A 269 HIS cc_start: 0.6877 (m90) cc_final: 0.6562 (t70) REVERT: A 371 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7146 (mmp-170) REVERT: A 388 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7666 (ttp-170) REVERT: A 468 MET cc_start: 0.6618 (ppp) cc_final: 0.6367 (tmm) REVERT: A 520 GLN cc_start: 0.6800 (pm20) cc_final: 0.6456 (pm20) REVERT: A 539 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6256 (ptt90) REVERT: A 640 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8077 (ttp) REVERT: A 708 GLU cc_start: 0.8684 (tt0) cc_final: 0.8433 (mt-10) REVERT: B 189 ASP cc_start: 0.7738 (t0) cc_final: 0.7412 (t0) REVERT: B 191 HIS cc_start: 0.8226 (m170) cc_final: 0.7951 (m-70) REVERT: B 269 HIS cc_start: 0.6867 (m90) cc_final: 0.6512 (t70) REVERT: B 371 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7153 (mmp-170) REVERT: B 388 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7655 (ttp-170) REVERT: B 520 GLN cc_start: 0.6802 (pm20) cc_final: 0.6463 (pm20) REVERT: B 539 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6299 (ptt90) REVERT: B 640 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8050 (ttp) REVERT: B 708 GLU cc_start: 0.8675 (tt0) cc_final: 0.8426 (mt-10) REVERT: C 123 LYS cc_start: 0.7928 (tttt) cc_final: 0.7432 (tppp) REVERT: C 189 ASP cc_start: 0.7729 (t0) cc_final: 0.7406 (t0) REVERT: C 191 HIS cc_start: 0.8228 (m170) cc_final: 0.7953 (m-70) REVERT: C 371 ARG cc_start: 0.8052 (mmt90) cc_final: 0.7184 (mmp-170) REVERT: C 388 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7661 (ttp-170) REVERT: C 520 GLN cc_start: 0.6786 (pm20) cc_final: 0.6440 (pm20) REVERT: C 539 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6310 (ptt90) REVERT: C 640 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8086 (ttp) REVERT: D 189 ASP cc_start: 0.7733 (t0) cc_final: 0.7406 (t0) REVERT: D 191 HIS cc_start: 0.8227 (m170) cc_final: 0.7953 (m-70) REVERT: D 371 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7172 (mmp-170) REVERT: D 388 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7649 (ttp-170) REVERT: D 520 GLN cc_start: 0.6796 (pm20) cc_final: 0.6451 (pm20) REVERT: D 539 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6304 (ptt90) REVERT: D 640 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8073 (ttp) outliers start: 67 outliers final: 38 residues processed: 369 average time/residue: 0.4628 time to fit residues: 197.1504 Evaluate side-chains 366 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 316 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 88 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 104 optimal weight: 0.0570 chunk 33 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.150493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118854 restraints weight = 23819.066| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.75 r_work: 0.3199 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20192 Z= 0.139 Angle : 0.525 8.496 27396 Z= 0.263 Chirality : 0.037 0.183 3132 Planarity : 0.004 0.044 3352 Dihedral : 6.196 74.707 2784 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.41 % Allowed : 15.09 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.17), residues: 2412 helix: 1.77 (0.13), residues: 1448 sheet: 2.68 (0.49), residues: 68 loop : -1.31 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 539 TYR 0.019 0.001 TYR C 162 PHE 0.007 0.001 PHE A 199 TRP 0.007 0.001 TRP A 223 HIS 0.005 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00328 (20192) covalent geometry : angle 0.52514 (27396) hydrogen bonds : bond 0.03617 ( 1056) hydrogen bonds : angle 3.37956 ( 3012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 341 time to evaluate : 0.647 Fit side-chains REVERT: A 123 LYS cc_start: 0.7992 (tptm) cc_final: 0.7703 (tptm) REVERT: A 173 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7676 (tm-30) REVERT: A 189 ASP cc_start: 0.7811 (t0) cc_final: 0.7450 (t0) REVERT: A 221 LYS cc_start: 0.8290 (ttpt) cc_final: 0.7859 (tttm) REVERT: A 240 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: A 371 ARG cc_start: 0.8030 (mmt90) cc_final: 0.7196 (mmp-170) REVERT: A 388 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7689 (ttp-170) REVERT: A 520 GLN cc_start: 0.6868 (pm20) cc_final: 0.6524 (mp10) REVERT: A 624 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 173 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7650 (tm-30) REVERT: B 189 ASP cc_start: 0.7805 (t0) cc_final: 0.7452 (t0) REVERT: B 191 HIS cc_start: 0.8217 (m170) cc_final: 0.8009 (m-70) REVERT: B 240 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7036 (pm20) REVERT: B 371 ARG cc_start: 0.8022 (mmt90) cc_final: 0.7187 (mmp-170) REVERT: B 388 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7683 (ttp-170) REVERT: B 520 GLN cc_start: 0.6854 (pm20) cc_final: 0.6511 (mp10) REVERT: B 539 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6399 (ptt90) REVERT: B 624 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8608 (mp) REVERT: B 640 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8173 (ttp) REVERT: C 123 LYS cc_start: 0.8041 (tptt) cc_final: 0.7558 (tppp) REVERT: C 173 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 189 ASP cc_start: 0.7796 (t0) cc_final: 0.7442 (t0) REVERT: C 191 HIS cc_start: 0.8216 (m170) cc_final: 0.8002 (m-70) REVERT: C 240 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: C 371 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7203 (mmp-170) REVERT: C 388 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7934 (ttt180) REVERT: C 520 GLN cc_start: 0.6826 (pm20) cc_final: 0.6484 (mp10) REVERT: C 539 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6402 (ptt90) REVERT: C 624 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8605 (mp) REVERT: C 640 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8200 (ttp) REVERT: C 708 GLU cc_start: 0.8653 (tt0) cc_final: 0.8414 (mt-10) REVERT: D 173 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7641 (tm-30) REVERT: D 189 ASP cc_start: 0.7807 (t0) cc_final: 0.7452 (t0) REVERT: D 191 HIS cc_start: 0.8222 (m170) cc_final: 0.8010 (m-70) REVERT: D 240 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: D 371 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7202 (mmp-170) REVERT: D 388 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7675 (ttp-170) REVERT: D 469 ASP cc_start: 0.7533 (m-30) cc_final: 0.7319 (m-30) REVERT: D 520 GLN cc_start: 0.6855 (pm20) cc_final: 0.6520 (mp10) REVERT: D 539 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6383 (ptt90) REVERT: D 624 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8602 (mp) REVERT: D 640 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8175 (ttp) REVERT: D 708 GLU cc_start: 0.8633 (tt0) cc_final: 0.8383 (mt-10) outliers start: 92 outliers final: 49 residues processed: 392 average time/residue: 0.4340 time to fit residues: 198.1040 Evaluate side-chains 374 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 307 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 220 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.151219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119432 restraints weight = 23570.379| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.74 r_work: 0.3156 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20192 Z= 0.110 Angle : 0.489 8.343 27396 Z= 0.245 Chirality : 0.036 0.196 3132 Planarity : 0.004 0.040 3352 Dihedral : 6.008 74.612 2784 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.07 % Allowed : 17.10 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.17), residues: 2412 helix: 1.91 (0.13), residues: 1452 sheet: 2.93 (0.48), residues: 68 loop : -1.23 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 539 TYR 0.009 0.001 TYR A 271 PHE 0.005 0.001 PHE C 199 TRP 0.010 0.001 TRP D 223 HIS 0.004 0.001 HIS D 521 Details of bonding type rmsd covalent geometry : bond 0.00255 (20192) covalent geometry : angle 0.48860 (27396) hydrogen bonds : bond 0.03384 ( 1056) hydrogen bonds : angle 3.30787 ( 3012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 336 time to evaluate : 0.719 Fit side-chains REVERT: A 123 LYS cc_start: 0.7915 (tptm) cc_final: 0.7645 (tptm) REVERT: A 173 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 189 ASP cc_start: 0.7721 (t0) cc_final: 0.7318 (t0) REVERT: A 191 HIS cc_start: 0.8290 (m170) cc_final: 0.7988 (m-70) REVERT: A 221 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7823 (tttm) REVERT: A 371 ARG cc_start: 0.7986 (mmt90) cc_final: 0.7176 (mmp-170) REVERT: A 388 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7734 (ttp-170) REVERT: A 520 GLN cc_start: 0.6735 (pm20) cc_final: 0.6434 (mp10) REVERT: A 528 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5281 (mpt) REVERT: A 624 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8607 (mp) REVERT: A 640 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8114 (ttp) REVERT: A 708 GLU cc_start: 0.8630 (tt0) cc_final: 0.8376 (mt-10) REVERT: B 173 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 189 ASP cc_start: 0.7733 (t0) cc_final: 0.7306 (t0) REVERT: B 191 HIS cc_start: 0.8257 (m170) cc_final: 0.7953 (m-70) REVERT: B 221 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7803 (tttm) REVERT: B 371 ARG cc_start: 0.7994 (mmt90) cc_final: 0.7169 (mmp-170) REVERT: B 388 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7688 (ttp-170) REVERT: B 433 MET cc_start: 0.7693 (tpt) cc_final: 0.7383 (tpp) REVERT: B 520 GLN cc_start: 0.6739 (pm20) cc_final: 0.6432 (mp10) REVERT: B 528 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.5278 (mpt) REVERT: B 640 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8137 (ttp) REVERT: B 708 GLU cc_start: 0.8647 (tt0) cc_final: 0.8392 (mt-10) REVERT: C 123 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7518 (tppp) REVERT: C 173 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7666 (tm-30) REVERT: C 189 ASP cc_start: 0.7718 (t0) cc_final: 0.7289 (t0) REVERT: C 191 HIS cc_start: 0.8253 (m170) cc_final: 0.7948 (m-70) REVERT: C 221 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7801 (tttm) REVERT: C 371 ARG cc_start: 0.8008 (mmt90) cc_final: 0.7190 (mmp-170) REVERT: C 388 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7955 (ttt180) REVERT: C 520 GLN cc_start: 0.6707 (pm20) cc_final: 0.6391 (mp10) REVERT: C 528 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5155 (mpp) REVERT: C 624 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8625 (mp) REVERT: C 640 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8116 (ttp) REVERT: C 708 GLU cc_start: 0.8678 (tt0) cc_final: 0.8417 (mt-10) REVERT: D 173 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7657 (tm-30) REVERT: D 189 ASP cc_start: 0.7723 (t0) cc_final: 0.7280 (t0) REVERT: D 191 HIS cc_start: 0.8248 (m170) cc_final: 0.7951 (m-70) REVERT: D 221 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7813 (tttm) REVERT: D 371 ARG cc_start: 0.7995 (mmt90) cc_final: 0.7184 (mmp-170) REVERT: D 388 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7943 (ttt180) REVERT: D 520 GLN cc_start: 0.6727 (pm20) cc_final: 0.6442 (pm20) REVERT: D 528 MET cc_start: 0.5863 (OUTLIER) cc_final: 0.5274 (mpt) REVERT: D 624 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8613 (mp) REVERT: D 640 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8099 (ttp) REVERT: D 708 GLU cc_start: 0.8653 (tt0) cc_final: 0.8385 (mt-10) outliers start: 85 outliers final: 45 residues processed: 380 average time/residue: 0.5130 time to fit residues: 223.1586 Evaluate side-chains 380 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 319 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 34 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 178 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.151680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120185 restraints weight = 23460.158| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.73 r_work: 0.3164 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20192 Z= 0.104 Angle : 0.489 8.197 27396 Z= 0.246 Chirality : 0.036 0.208 3132 Planarity : 0.004 0.037 3352 Dihedral : 5.893 74.809 2784 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.93 % Allowed : 18.34 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.17), residues: 2412 helix: 1.97 (0.13), residues: 1468 sheet: 3.04 (0.47), residues: 68 loop : -1.29 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 560 TYR 0.010 0.001 TYR C 162 PHE 0.005 0.001 PHE A 199 TRP 0.013 0.001 TRP C 223 HIS 0.006 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00242 (20192) covalent geometry : angle 0.48950 (27396) hydrogen bonds : bond 0.03302 ( 1056) hydrogen bonds : angle 3.24396 ( 3012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 330 time to evaluate : 0.803 Fit side-chains REVERT: A 123 LYS cc_start: 0.7816 (tptm) cc_final: 0.7566 (tptm) REVERT: A 173 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 189 ASP cc_start: 0.7762 (t0) cc_final: 0.7334 (t0) REVERT: A 221 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7846 (tttm) REVERT: A 371 ARG cc_start: 0.7985 (mmt90) cc_final: 0.7168 (mmp-170) REVERT: A 388 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7959 (ttt180) REVERT: A 433 MET cc_start: 0.7687 (tpt) cc_final: 0.7396 (tpp) REVERT: A 520 GLN cc_start: 0.6713 (pm20) cc_final: 0.6492 (pm20) REVERT: A 528 MET cc_start: 0.5862 (OUTLIER) cc_final: 0.5268 (mpt) REVERT: A 640 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8130 (ttp) REVERT: A 708 GLU cc_start: 0.8625 (tt0) cc_final: 0.8378 (mt-10) REVERT: B 173 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 189 ASP cc_start: 0.7767 (t0) cc_final: 0.7340 (t0) REVERT: B 191 HIS cc_start: 0.8281 (m170) cc_final: 0.7959 (m-70) REVERT: B 371 ARG cc_start: 0.7982 (mmt90) cc_final: 0.7164 (mmp-170) REVERT: B 388 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7881 (mtm180) REVERT: B 433 MET cc_start: 0.7711 (tpt) cc_final: 0.7418 (tpp) REVERT: B 520 GLN cc_start: 0.6763 (pm20) cc_final: 0.6535 (pm20) REVERT: B 528 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5104 (mpp) REVERT: B 640 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8179 (ttp) REVERT: B 708 GLU cc_start: 0.8626 (tt0) cc_final: 0.8379 (mt-10) REVERT: C 123 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7473 (tppp) REVERT: C 173 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7656 (tm-30) REVERT: C 189 ASP cc_start: 0.7743 (t0) cc_final: 0.7317 (t0) REVERT: C 191 HIS cc_start: 0.8272 (m170) cc_final: 0.7949 (m-70) REVERT: C 221 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7782 (tttm) REVERT: C 371 ARG cc_start: 0.8002 (mmt90) cc_final: 0.7185 (mmp-170) REVERT: C 388 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7958 (ttt180) REVERT: C 520 GLN cc_start: 0.6706 (pm20) cc_final: 0.6479 (pm20) REVERT: C 528 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.5129 (mpp) REVERT: C 640 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8199 (ttp) REVERT: C 708 GLU cc_start: 0.8641 (tt0) cc_final: 0.8366 (mt-10) REVERT: D 173 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7670 (tm-30) REVERT: D 189 ASP cc_start: 0.7768 (t0) cc_final: 0.7342 (t0) REVERT: D 191 HIS cc_start: 0.8248 (m170) cc_final: 0.7930 (m-70) REVERT: D 371 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7169 (mmp-170) REVERT: D 388 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7892 (mtm180) REVERT: D 528 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5295 (mpt) REVERT: D 708 GLU cc_start: 0.8618 (tt0) cc_final: 0.8366 (mt-10) outliers start: 82 outliers final: 43 residues processed: 372 average time/residue: 0.4956 time to fit residues: 213.1136 Evaluate side-chains 375 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 320 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 168 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 195 optimal weight: 0.0040 chunk 149 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 HIS D 413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.151800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.120254 restraints weight = 23590.137| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.75 r_work: 0.3172 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20192 Z= 0.102 Angle : 0.489 8.035 27396 Z= 0.246 Chirality : 0.036 0.214 3132 Planarity : 0.004 0.034 3352 Dihedral : 5.812 74.845 2784 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.69 % Allowed : 18.77 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.17), residues: 2412 helix: 2.03 (0.13), residues: 1472 sheet: 2.95 (0.47), residues: 68 loop : -1.24 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 312 TYR 0.011 0.001 TYR D 162 PHE 0.006 0.001 PHE C 81 TRP 0.013 0.001 TRP D 223 HIS 0.005 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00238 (20192) covalent geometry : angle 0.48902 (27396) hydrogen bonds : bond 0.03251 ( 1056) hydrogen bonds : angle 3.19068 ( 3012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 345 time to evaluate : 0.640 Fit side-chains REVERT: A 160 GLU cc_start: 0.7999 (tp30) cc_final: 0.7132 (pt0) REVERT: A 173 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7628 (tm-30) REVERT: A 189 ASP cc_start: 0.7752 (t0) cc_final: 0.7263 (t0) REVERT: A 191 HIS cc_start: 0.8300 (m170) cc_final: 0.7832 (m-70) REVERT: A 221 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7828 (tttm) REVERT: A 371 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7134 (mmp-170) REVERT: A 388 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7952 (ttt180) REVERT: A 433 MET cc_start: 0.7681 (tpt) cc_final: 0.7389 (tpp) REVERT: A 520 GLN cc_start: 0.6638 (pm20) cc_final: 0.6420 (pm20) REVERT: A 528 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.5123 (mpp) REVERT: A 538 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7881 (mp) REVERT: A 640 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8086 (ttp) REVERT: A 708 GLU cc_start: 0.8589 (tt0) cc_final: 0.8296 (mt-10) REVERT: B 173 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 189 ASP cc_start: 0.7748 (t0) cc_final: 0.7261 (t0) REVERT: B 191 HIS cc_start: 0.8278 (m170) cc_final: 0.7812 (m-70) REVERT: B 371 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7134 (mmp-170) REVERT: B 388 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7864 (mtm180) REVERT: B 433 MET cc_start: 0.7672 (tpt) cc_final: 0.7373 (tpp) REVERT: B 520 GLN cc_start: 0.6661 (pm20) cc_final: 0.6449 (pm20) REVERT: B 528 MET cc_start: 0.5840 (OUTLIER) cc_final: 0.5103 (mpp) REVERT: B 640 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8148 (ttp) REVERT: B 708 GLU cc_start: 0.8604 (tt0) cc_final: 0.8353 (mt-10) REVERT: C 160 GLU cc_start: 0.8017 (tp30) cc_final: 0.7140 (pt0) REVERT: C 173 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 189 ASP cc_start: 0.7742 (t0) cc_final: 0.7259 (t0) REVERT: C 371 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7134 (mmp-170) REVERT: C 388 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7927 (ttt180) REVERT: C 520 GLN cc_start: 0.6639 (pm20) cc_final: 0.6424 (pm20) REVERT: C 528 MET cc_start: 0.5845 (OUTLIER) cc_final: 0.5115 (mpp) REVERT: C 708 GLU cc_start: 0.8624 (tt0) cc_final: 0.8341 (mt-10) REVERT: D 160 GLU cc_start: 0.8035 (tp30) cc_final: 0.7140 (pt0) REVERT: D 173 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7644 (tm-30) REVERT: D 189 ASP cc_start: 0.7752 (t0) cc_final: 0.7274 (t0) REVERT: D 371 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7137 (mmp-170) REVERT: D 388 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7704 (mtm-85) REVERT: D 520 GLN cc_start: 0.6631 (pm20) cc_final: 0.6416 (pm20) REVERT: D 528 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.5242 (mpt) REVERT: D 708 GLU cc_start: 0.8615 (tt0) cc_final: 0.8350 (mt-10) outliers start: 77 outliers final: 45 residues processed: 377 average time/residue: 0.4109 time to fit residues: 179.6076 Evaluate side-chains 386 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 330 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 217 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 137 optimal weight: 0.0770 chunk 193 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 195 optimal weight: 0.0070 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS B 413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.153472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.121945 restraints weight = 23491.792| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.74 r_work: 0.3186 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20192 Z= 0.096 Angle : 0.497 7.921 27396 Z= 0.247 Chirality : 0.036 0.230 3132 Planarity : 0.003 0.033 3352 Dihedral : 5.719 75.459 2784 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.97 % Allowed : 20.50 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.17), residues: 2412 helix: 2.17 (0.13), residues: 1464 sheet: 2.92 (0.47), residues: 68 loop : -1.24 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 312 TYR 0.011 0.001 TYR A 162 PHE 0.006 0.001 PHE C 81 TRP 0.015 0.001 TRP D 223 HIS 0.004 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00222 (20192) covalent geometry : angle 0.49744 (27396) hydrogen bonds : bond 0.03136 ( 1056) hydrogen bonds : angle 3.18127 ( 3012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 347 time to evaluate : 0.675 Fit side-chains REVERT: A 173 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 189 ASP cc_start: 0.7711 (t0) cc_final: 0.7196 (t0) REVERT: A 191 HIS cc_start: 0.8251 (m170) cc_final: 0.7813 (m-70) REVERT: A 371 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7126 (mmp-170) REVERT: A 388 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7930 (ttt180) REVERT: A 433 MET cc_start: 0.7659 (tpt) cc_final: 0.7366 (tpp) REVERT: A 528 MET cc_start: 0.5857 (OUTLIER) cc_final: 0.5146 (mpp) REVERT: A 538 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 640 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8068 (ttp) REVERT: A 645 MET cc_start: 0.7274 (tpp) cc_final: 0.6806 (ttm) REVERT: A 708 GLU cc_start: 0.8585 (tt0) cc_final: 0.8271 (mt-10) REVERT: B 173 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7613 (tm-30) REVERT: B 189 ASP cc_start: 0.7717 (t0) cc_final: 0.7206 (t0) REVERT: B 191 HIS cc_start: 0.8201 (m170) cc_final: 0.7778 (m-70) REVERT: B 371 ARG cc_start: 0.7969 (mmt90) cc_final: 0.7130 (mmp-170) REVERT: B 388 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7851 (mtm180) REVERT: B 433 MET cc_start: 0.7695 (tpt) cc_final: 0.7396 (tpp) REVERT: B 528 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.5127 (mpp) REVERT: B 645 MET cc_start: 0.7297 (tpp) cc_final: 0.7037 (ttp) REVERT: B 708 GLU cc_start: 0.8599 (tt0) cc_final: 0.8282 (mt-10) REVERT: C 173 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 189 ASP cc_start: 0.7707 (t0) cc_final: 0.7195 (t0) REVERT: C 191 HIS cc_start: 0.8215 (m170) cc_final: 0.7811 (m-70) REVERT: C 371 ARG cc_start: 0.7967 (mmt90) cc_final: 0.7127 (mmp-170) REVERT: C 388 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7924 (ttt180) REVERT: C 528 MET cc_start: 0.5839 (OUTLIER) cc_final: 0.5126 (mpp) REVERT: C 708 GLU cc_start: 0.8604 (tt0) cc_final: 0.8345 (mt-10) REVERT: D 173 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7653 (tm-30) REVERT: D 189 ASP cc_start: 0.7726 (t0) cc_final: 0.7221 (t0) REVERT: D 191 HIS cc_start: 0.8209 (m170) cc_final: 0.7789 (m-70) REVERT: D 371 ARG cc_start: 0.7967 (mmt90) cc_final: 0.7130 (mmp-170) REVERT: D 388 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7693 (mtm-85) REVERT: D 406 ILE cc_start: 0.8779 (mm) cc_final: 0.8517 (mt) REVERT: D 520 GLN cc_start: 0.6589 (pm20) cc_final: 0.6385 (pm20) REVERT: D 528 MET cc_start: 0.5863 (OUTLIER) cc_final: 0.5124 (mpp) REVERT: D 708 GLU cc_start: 0.8597 (tt0) cc_final: 0.8282 (mt-10) outliers start: 62 outliers final: 40 residues processed: 371 average time/residue: 0.4901 time to fit residues: 210.7061 Evaluate side-chains 387 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 337 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.146782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114307 restraints weight = 23440.205| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.85 r_work: 0.3093 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20192 Z= 0.212 Angle : 0.605 9.805 27396 Z= 0.302 Chirality : 0.042 0.239 3132 Planarity : 0.004 0.036 3352 Dihedral : 6.496 71.496 2784 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.74 % Allowed : 18.97 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.17), residues: 2412 helix: 1.72 (0.13), residues: 1472 sheet: 0.55 (0.57), residues: 88 loop : -1.14 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 175 TYR 0.015 0.002 TYR C 162 PHE 0.008 0.001 PHE D 199 TRP 0.012 0.001 TRP A 223 HIS 0.006 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00509 (20192) covalent geometry : angle 0.60531 (27396) hydrogen bonds : bond 0.04132 ( 1056) hydrogen bonds : angle 3.50270 ( 3012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 363 time to evaluate : 0.777 Fit side-chains REVERT: A 123 LYS cc_start: 0.7922 (tptm) cc_final: 0.7594 (tptm) REVERT: A 173 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 189 ASP cc_start: 0.7686 (t0) cc_final: 0.7203 (t0) REVERT: A 191 HIS cc_start: 0.8334 (m170) cc_final: 0.8014 (m-70) REVERT: A 221 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8071 (ttmm) REVERT: A 371 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7225 (mmp-170) REVERT: A 388 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7991 (ttt180) REVERT: A 406 ILE cc_start: 0.8786 (mm) cc_final: 0.8574 (mt) REVERT: A 520 GLN cc_start: 0.6858 (pm20) cc_final: 0.6479 (pm20) REVERT: A 708 GLU cc_start: 0.8679 (tt0) cc_final: 0.8424 (mt-10) REVERT: B 160 GLU cc_start: 0.8062 (tp30) cc_final: 0.7180 (pt0) REVERT: B 173 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 189 ASP cc_start: 0.7694 (t0) cc_final: 0.7216 (t0) REVERT: B 191 HIS cc_start: 0.8279 (m170) cc_final: 0.7972 (m-70) REVERT: B 221 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8055 (ttmm) REVERT: B 371 ARG cc_start: 0.8027 (mmt90) cc_final: 0.7214 (mmp-170) REVERT: B 388 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7945 (ttt180) REVERT: B 406 ILE cc_start: 0.8791 (mm) cc_final: 0.8585 (mt) REVERT: B 708 GLU cc_start: 0.8696 (tt0) cc_final: 0.8429 (mt-10) REVERT: C 123 LYS cc_start: 0.7968 (tttt) cc_final: 0.7301 (tptm) REVERT: C 173 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7722 (tm-30) REVERT: C 189 ASP cc_start: 0.7674 (t0) cc_final: 0.7201 (t0) REVERT: C 191 HIS cc_start: 0.8297 (m170) cc_final: 0.7985 (m-70) REVERT: C 221 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8050 (ttmm) REVERT: C 371 ARG cc_start: 0.8026 (mmt90) cc_final: 0.7201 (mmp-170) REVERT: C 388 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7953 (ttt180) REVERT: C 406 ILE cc_start: 0.8813 (mm) cc_final: 0.8609 (mt) REVERT: D 173 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7705 (tm-30) REVERT: D 189 ASP cc_start: 0.7694 (t0) cc_final: 0.7219 (t0) REVERT: D 191 HIS cc_start: 0.8287 (m170) cc_final: 0.7973 (m-70) REVERT: D 221 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8059 (ttmm) REVERT: D 371 ARG cc_start: 0.8017 (mmt90) cc_final: 0.7212 (mmp-170) REVERT: D 388 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7776 (mmm-85) REVERT: D 406 ILE cc_start: 0.8803 (mm) cc_final: 0.8597 (mt) REVERT: D 479 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8707 (tm-30) REVERT: D 520 GLN cc_start: 0.6861 (pm20) cc_final: 0.6489 (pm20) REVERT: D 708 GLU cc_start: 0.8692 (tt0) cc_final: 0.8423 (mt-10) outliers start: 99 outliers final: 52 residues processed: 410 average time/residue: 0.5363 time to fit residues: 252.1326 Evaluate side-chains 392 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 335 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 479 GLN Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 198 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 124 optimal weight: 0.2980 chunk 64 optimal weight: 5.9990 chunk 220 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.150369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118707 restraints weight = 23505.781| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.74 r_work: 0.3149 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20192 Z= 0.111 Angle : 0.534 10.595 27396 Z= 0.266 Chirality : 0.038 0.242 3132 Planarity : 0.004 0.034 3352 Dihedral : 6.054 71.656 2784 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.63 % Allowed : 22.27 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.17), residues: 2412 helix: 2.03 (0.13), residues: 1472 sheet: 0.64 (0.57), residues: 88 loop : -1.07 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 560 TYR 0.013 0.001 TYR B 162 PHE 0.006 0.001 PHE C 81 TRP 0.013 0.001 TRP D 223 HIS 0.005 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00261 (20192) covalent geometry : angle 0.53355 (27396) hydrogen bonds : bond 0.03412 ( 1056) hydrogen bonds : angle 3.29681 ( 3012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 351 time to evaluate : 0.756 Fit side-chains REVERT: A 189 ASP cc_start: 0.7663 (t0) cc_final: 0.7167 (t0) REVERT: A 191 HIS cc_start: 0.8258 (m170) cc_final: 0.7842 (m-70) REVERT: A 371 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7165 (mmp-170) REVERT: A 388 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7926 (ttt180) REVERT: A 520 GLN cc_start: 0.6732 (pm20) cc_final: 0.6424 (pm20) REVERT: A 528 MET cc_start: 0.5808 (mpt) cc_final: 0.5089 (mpp) REVERT: A 538 LEU cc_start: 0.8207 (mm) cc_final: 0.7901 (mp) REVERT: A 645 MET cc_start: 0.7489 (tpp) cc_final: 0.7228 (tpp) REVERT: A 708 GLU cc_start: 0.8592 (tt0) cc_final: 0.8313 (mt-10) REVERT: B 160 GLU cc_start: 0.8011 (tp30) cc_final: 0.7185 (pt0) REVERT: B 173 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 189 ASP cc_start: 0.7655 (t0) cc_final: 0.7153 (t0) REVERT: B 191 HIS cc_start: 0.8240 (m170) cc_final: 0.7873 (m-70) REVERT: B 350 SER cc_start: 0.8218 (m) cc_final: 0.7910 (p) REVERT: B 371 ARG cc_start: 0.7966 (mmt90) cc_final: 0.7159 (mmp-170) REVERT: B 388 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7921 (ttt180) REVERT: B 433 MET cc_start: 0.7716 (tpt) cc_final: 0.7428 (tpp) REVERT: B 520 GLN cc_start: 0.6731 (pm20) cc_final: 0.6524 (pm20) REVERT: B 528 MET cc_start: 0.5810 (mpt) cc_final: 0.5066 (mpp) REVERT: B 708 GLU cc_start: 0.8598 (tt0) cc_final: 0.8334 (mt-10) REVERT: C 189 ASP cc_start: 0.7639 (t0) cc_final: 0.7139 (t0) REVERT: C 191 HIS cc_start: 0.8244 (m170) cc_final: 0.7832 (m-70) REVERT: C 371 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7170 (mmp-170) REVERT: C 388 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7923 (ttt180) REVERT: C 520 GLN cc_start: 0.6710 (pm20) cc_final: 0.6399 (pm20) REVERT: C 528 MET cc_start: 0.5839 (mpt) cc_final: 0.5095 (mpp) REVERT: C 708 GLU cc_start: 0.8588 (tt0) cc_final: 0.8334 (mt-10) REVERT: D 189 ASP cc_start: 0.7646 (t0) cc_final: 0.7144 (t0) REVERT: D 191 HIS cc_start: 0.8232 (m170) cc_final: 0.7869 (m-70) REVERT: D 350 SER cc_start: 0.8236 (m) cc_final: 0.7922 (p) REVERT: D 371 ARG cc_start: 0.7991 (mmt90) cc_final: 0.7195 (mmp-170) REVERT: D 388 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7896 (ttt180) REVERT: D 406 ILE cc_start: 0.8798 (mm) cc_final: 0.8583 (mt) REVERT: D 520 GLN cc_start: 0.6697 (pm20) cc_final: 0.6494 (pm20) REVERT: D 708 GLU cc_start: 0.8616 (tt0) cc_final: 0.8345 (mt-10) outliers start: 55 outliers final: 38 residues processed: 375 average time/residue: 0.4923 time to fit residues: 213.2916 Evaluate side-chains 388 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 346 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 204 optimal weight: 0.0980 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 233 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.151632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119987 restraints weight = 23607.226| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.75 r_work: 0.3170 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20192 Z= 0.106 Angle : 0.534 10.513 27396 Z= 0.266 Chirality : 0.037 0.242 3132 Planarity : 0.004 0.034 3352 Dihedral : 5.875 73.128 2784 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.44 % Allowed : 22.51 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.17), residues: 2412 helix: 2.16 (0.13), residues: 1472 sheet: 0.60 (0.57), residues: 88 loop : -1.07 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 560 TYR 0.014 0.001 TYR A 162 PHE 0.009 0.001 PHE D 394 TRP 0.017 0.001 TRP A 223 HIS 0.004 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00245 (20192) covalent geometry : angle 0.53406 (27396) hydrogen bonds : bond 0.03268 ( 1056) hydrogen bonds : angle 3.22602 ( 3012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6311.60 seconds wall clock time: 108 minutes 13.45 seconds (6493.45 seconds total)