Starting phenix.real_space_refine on Tue May 20 12:02:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekr_28211/05_2025/8ekr_28211.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekr_28211/05_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_28211/05_2025/8ekr_28211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekr_28211/05_2025/8ekr_28211.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekr_28211/05_2025/8ekr_28211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekr_28211/05_2025/8ekr_28211.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3} 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: C, B, D Time building chain proxies: 12.30, per 1000 atoms: 0.62 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: 5.39 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.06 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: 6.77 Time building geometry restraints manager: 6.27 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 46.660 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (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 TRP 0.012 0.001 TRP D 333 HIS 0.005 0.001 HIS D 169 PHE 0.015 0.001 PHE D 75 TYR 0.034 0.002 TYR D 162 ARG 0.010 0.001 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.16438 ( 1056) hydrogen bonds : angle 5.86447 ( 3012) covalent geometry : bond 0.00351 (20192) covalent geometry : angle 0.80409 (27396) *********************** 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 : 2.229 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: 1.0999 time to fit residues: 616.3537 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 : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 0.0020 chunk 221 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 247 ASN 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.158740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127995 restraints weight = 23604.801| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.73 r_work: 0.3258 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20192 Z= 0.109 Angle : 0.524 9.222 27396 Z= 0.261 Chirality : 0.037 0.168 3132 Planarity : 0.004 0.058 3352 Dihedral : 6.452 84.031 2784 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.97 % Allowed : 11.16 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2412 helix: 1.14 (0.13), residues: 1456 sheet: 2.55 (0.50), residues: 68 loop : -1.63 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 333 HIS 0.004 0.001 HIS D 521 PHE 0.009 0.001 PHE D 75 TYR 0.027 0.001 TYR B 162 ARG 0.006 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1056) hydrogen bonds : angle 3.68552 ( 3012) covalent geometry : bond 0.00246 (20192) covalent geometry : angle 0.52352 (27396) *********************** 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 409 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 347 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.7810 (t0) cc_final: 0.7548 (t0) REVERT: A 269 HIS cc_start: 0.6698 (m90) cc_final: 0.6477 (t-90) REVERT: A 371 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7162 (mmp-170) REVERT: A 388 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7695 (tpp-160) REVERT: A 433 MET cc_start: 0.7719 (tpt) cc_final: 0.7428 (tpp) REVERT: A 468 MET cc_start: 0.6538 (ppp) cc_final: 0.6129 (tmm) REVERT: A 520 GLN cc_start: 0.6868 (pm20) cc_final: 0.6541 (pm20) REVERT: A 637 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 640 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8040 (ttp) REVERT: A 708 GLU cc_start: 0.8641 (tt0) cc_final: 0.8413 (mt-10) REVERT: B 123 LYS cc_start: 0.7997 (tptm) cc_final: 0.7652 (tptm) REVERT: B 189 ASP cc_start: 0.7802 (t0) cc_final: 0.7511 (t0) REVERT: B 269 HIS cc_start: 0.6681 (m90) cc_final: 0.6457 (t-90) REVERT: B 371 ARG cc_start: 0.8066 (mmt90) cc_final: 0.7158 (mmp-170) REVERT: B 388 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7678 (tpp-160) REVERT: B 538 LEU cc_start: 0.8103 (mm) cc_final: 0.7847 (mm) REVERT: B 637 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8446 (mt) REVERT: B 640 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8027 (ttp) REVERT: B 708 GLU cc_start: 0.8640 (tt0) cc_final: 0.8404 (mt-10) REVERT: C 189 ASP cc_start: 0.7790 (t0) cc_final: 0.7529 (t0) REVERT: C 269 HIS cc_start: 0.6673 (m90) cc_final: 0.6462 (t-90) REVERT: C 371 ARG cc_start: 0.8064 (mmt90) cc_final: 0.7164 (mmp-170) REVERT: C 388 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7677 (tpp-160) REVERT: C 468 MET cc_start: 0.7161 (tmm) cc_final: 0.6850 (tmm) REVERT: C 538 LEU cc_start: 0.8111 (mm) cc_final: 0.7856 (mm) REVERT: C 637 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8446 (mt) REVERT: C 640 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8048 (ttp) REVERT: C 708 GLU cc_start: 0.8636 (tt0) cc_final: 0.8377 (mt-10) REVERT: D 123 LYS cc_start: 0.8000 (tptm) cc_final: 0.7657 (tptm) REVERT: D 189 ASP cc_start: 0.7800 (t0) cc_final: 0.7513 (t0) REVERT: D 269 HIS cc_start: 0.6681 (m90) cc_final: 0.6464 (t-90) REVERT: D 371 ARG cc_start: 0.8055 (mmt90) cc_final: 0.7160 (mmp-170) REVERT: D 388 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7670 (tpp-160) REVERT: D 468 MET cc_start: 0.7136 (tmm) cc_final: 0.6809 (tmm) REVERT: D 538 LEU cc_start: 0.8099 (mm) cc_final: 0.7842 (mm) REVERT: D 637 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (mt) REVERT: D 640 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8032 (ttp) REVERT: D 708 GLU cc_start: 0.8622 (tt0) cc_final: 0.8389 (mt-10) outliers start: 62 outliers final: 36 residues processed: 369 average time/residue: 1.0740 time to fit residues: 455.7203 Evaluate side-chains 373 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 325 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR 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 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 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 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 59 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 191 HIS A 487 GLN B 191 HIS C 191 HIS D 191 HIS D 487 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.152974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.120595 restraints weight = 23546.561| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.86 r_work: 0.3218 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20192 Z= 0.127 Angle : 0.530 8.929 27396 Z= 0.263 Chirality : 0.037 0.178 3132 Planarity : 0.004 0.049 3352 Dihedral : 6.199 77.703 2784 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.21 % Allowed : 14.94 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2412 helix: 1.76 (0.14), residues: 1412 sheet: 2.61 (0.49), residues: 68 loop : -1.41 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 676 HIS 0.007 0.001 HIS D 165 PHE 0.007 0.001 PHE C 407 TYR 0.024 0.001 TYR A 162 ARG 0.005 0.001 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1056) hydrogen bonds : angle 3.43823 ( 3012) covalent geometry : bond 0.00297 (20192) covalent geometry : angle 0.53048 (27396) *********************** 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 412 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 345 time to evaluate : 2.065 Fit side-chains REVERT: A 189 ASP cc_start: 0.7745 (t0) cc_final: 0.7424 (t0) REVERT: A 191 HIS cc_start: 0.8212 (m170) cc_final: 0.8005 (m-70) REVERT: A 371 ARG cc_start: 0.8056 (mmt90) cc_final: 0.7213 (mmp-170) REVERT: A 388 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7696 (ttp-170) REVERT: A 468 MET cc_start: 0.6623 (ppp) cc_final: 0.6224 (tmm) REVERT: A 520 GLN cc_start: 0.6903 (pm20) cc_final: 0.6644 (mp10) REVERT: A 539 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6340 (ptt90) REVERT: A 637 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8471 (mt) REVERT: B 123 LYS cc_start: 0.7942 (tptm) cc_final: 0.7683 (tptm) REVERT: B 189 ASP cc_start: 0.7774 (t0) cc_final: 0.7466 (t0) REVERT: B 191 HIS cc_start: 0.8230 (m170) cc_final: 0.7958 (m-70) REVERT: B 269 HIS cc_start: 0.6927 (m90) cc_final: 0.6603 (t-90) REVERT: B 371 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7224 (mmp-170) REVERT: B 388 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7704 (ttp-170) REVERT: B 520 GLN cc_start: 0.6905 (pm20) cc_final: 0.6561 (pm20) REVERT: B 539 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6363 (ptt90) REVERT: B 637 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8462 (mt) REVERT: B 640 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8119 (ttp) REVERT: C 189 ASP cc_start: 0.7741 (t0) cc_final: 0.7415 (t0) REVERT: C 191 HIS cc_start: 0.8201 (m170) cc_final: 0.7963 (m-70) REVERT: C 371 ARG cc_start: 0.8079 (mmt90) cc_final: 0.7243 (mmp-170) REVERT: C 388 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7706 (ttp-170) REVERT: C 468 MET cc_start: 0.7157 (tmm) cc_final: 0.6752 (tmm) REVERT: C 520 GLN cc_start: 0.6888 (pm20) cc_final: 0.6541 (pm20) REVERT: C 539 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6360 (ptt90) REVERT: C 637 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8481 (mt) REVERT: C 640 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8133 (ttp) REVERT: D 123 LYS cc_start: 0.7938 (tptm) cc_final: 0.7680 (tptm) REVERT: D 189 ASP cc_start: 0.7777 (t0) cc_final: 0.7473 (t0) REVERT: D 191 HIS cc_start: 0.8222 (m170) cc_final: 0.7962 (m-70) REVERT: D 371 ARG cc_start: 0.8054 (mmt90) cc_final: 0.7220 (mmp-170) REVERT: D 388 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7690 (ttp-170) REVERT: D 468 MET cc_start: 0.7164 (tmm) cc_final: 0.6803 (tmm) REVERT: D 520 GLN cc_start: 0.6908 (pm20) cc_final: 0.6557 (pm20) REVERT: D 538 LEU cc_start: 0.8134 (mm) cc_final: 0.7850 (mm) REVERT: D 539 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6340 (ptt90) REVERT: D 637 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8485 (mt) outliers start: 67 outliers final: 44 residues processed: 380 average time/residue: 1.1005 time to fit residues: 481.3858 Evaluate side-chains 378 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 320 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 105 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 44 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.153707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121973 restraints weight = 23538.596| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.75 r_work: 0.3188 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20192 Z= 0.102 Angle : 0.489 8.500 27396 Z= 0.244 Chirality : 0.036 0.187 3132 Planarity : 0.004 0.041 3352 Dihedral : 5.965 77.145 2784 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.64 % Allowed : 16.04 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2412 helix: 1.86 (0.13), residues: 1452 sheet: 2.66 (0.49), residues: 68 loop : -1.37 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 223 HIS 0.004 0.001 HIS D 521 PHE 0.004 0.001 PHE A 199 TYR 0.015 0.001 TYR C 162 ARG 0.005 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 1056) hydrogen bonds : angle 3.31743 ( 3012) covalent geometry : bond 0.00236 (20192) covalent geometry : angle 0.48915 (27396) *********************** 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 413 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 337 time to evaluate : 2.246 Fit side-chains REVERT: A 189 ASP cc_start: 0.7787 (t0) cc_final: 0.7364 (t0) REVERT: A 191 HIS cc_start: 0.8195 (m170) cc_final: 0.7953 (m-70) REVERT: A 371 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7122 (mmp-170) REVERT: A 388 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7920 (ttt180) REVERT: A 528 MET cc_start: 0.5797 (OUTLIER) cc_final: 0.5217 (mpt) REVERT: A 624 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 640 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8118 (ttp) REVERT: A 708 GLU cc_start: 0.8651 (tt0) cc_final: 0.8398 (mt-10) REVERT: B 123 LYS cc_start: 0.7846 (tptm) cc_final: 0.7621 (tptm) REVERT: B 173 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 189 ASP cc_start: 0.7733 (t0) cc_final: 0.7369 (t0) REVERT: B 191 HIS cc_start: 0.8243 (m170) cc_final: 0.7976 (m-70) REVERT: B 371 ARG cc_start: 0.7974 (mmt90) cc_final: 0.7108 (mmp-170) REVERT: B 388 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7908 (ttt180) REVERT: B 520 GLN cc_start: 0.6718 (pm20) cc_final: 0.6396 (pm20) REVERT: B 528 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.5183 (mpt) REVERT: B 624 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8529 (mp) REVERT: B 637 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 640 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8131 (ttp) REVERT: B 708 GLU cc_start: 0.8661 (tt0) cc_final: 0.8424 (mt-10) REVERT: C 173 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 189 ASP cc_start: 0.7731 (t0) cc_final: 0.7312 (t0) REVERT: C 191 HIS cc_start: 0.8197 (m170) cc_final: 0.7914 (m-70) REVERT: C 319 PHE cc_start: 0.8028 (m-80) cc_final: 0.7822 (m-10) REVERT: C 371 ARG cc_start: 0.7997 (mmt90) cc_final: 0.7121 (mmp-170) REVERT: C 388 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7922 (ttt180) REVERT: C 433 MET cc_start: 0.7670 (tpt) cc_final: 0.7356 (tpp) REVERT: C 520 GLN cc_start: 0.6694 (pm20) cc_final: 0.6348 (mp10) REVERT: C 528 MET cc_start: 0.5778 (OUTLIER) cc_final: 0.5197 (mpt) REVERT: C 539 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6324 (ptt90) REVERT: C 624 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8533 (mp) REVERT: C 637 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8433 (mt) REVERT: C 640 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8106 (ttp) REVERT: C 708 GLU cc_start: 0.8635 (tt0) cc_final: 0.8342 (mt-10) REVERT: D 123 LYS cc_start: 0.7839 (tptm) cc_final: 0.7608 (tptm) REVERT: D 173 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7604 (tm-30) REVERT: D 189 ASP cc_start: 0.7736 (t0) cc_final: 0.7367 (t0) REVERT: D 191 HIS cc_start: 0.8232 (m170) cc_final: 0.7976 (m-70) REVERT: D 371 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7131 (mmp-170) REVERT: D 388 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7913 (ttt180) REVERT: D 520 GLN cc_start: 0.6731 (pm20) cc_final: 0.6397 (mp10) REVERT: D 528 MET cc_start: 0.5788 (OUTLIER) cc_final: 0.5203 (mpt) REVERT: D 624 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 640 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8116 (ttp) REVERT: D 708 GLU cc_start: 0.8635 (tt0) cc_final: 0.8346 (mt-10) outliers start: 76 outliers final: 42 residues processed: 373 average time/residue: 1.1480 time to fit residues: 489.5918 Evaluate side-chains 363 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 302 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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 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 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 624 LEU 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 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 522 THR Chi-restraints excluded: chain C residue 528 MET 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 637 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 522 THR Chi-restraints excluded: chain D residue 528 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 160 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.151158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119398 restraints weight = 23588.504| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.75 r_work: 0.3154 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20192 Z= 0.115 Angle : 0.497 8.355 27396 Z= 0.248 Chirality : 0.037 0.196 3132 Planarity : 0.004 0.037 3352 Dihedral : 5.958 75.614 2784 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.59 % Allowed : 17.00 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.17), residues: 2412 helix: 1.92 (0.13), residues: 1456 sheet: 3.03 (0.47), residues: 68 loop : -1.21 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.005 0.001 HIS A 521 PHE 0.006 0.001 PHE A 199 TYR 0.016 0.001 TYR C 162 ARG 0.005 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 1056) hydrogen bonds : angle 3.31968 ( 3012) covalent geometry : bond 0.00269 (20192) covalent geometry : angle 0.49732 (27396) *********************** 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 405 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 330 time to evaluate : 2.163 Fit side-chains REVERT: A 173 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 189 ASP cc_start: 0.7723 (t0) cc_final: 0.7237 (t0) REVERT: A 191 HIS cc_start: 0.8281 (m170) cc_final: 0.7983 (m-70) REVERT: A 371 ARG cc_start: 0.7960 (mmt90) cc_final: 0.7071 (mmp-170) REVERT: A 388 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7930 (ttt180) REVERT: A 433 MET cc_start: 0.7668 (tpt) cc_final: 0.7365 (tpp) REVERT: A 528 MET cc_start: 0.5854 (OUTLIER) cc_final: 0.5234 (mpt) REVERT: A 624 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 640 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8152 (ttp) REVERT: B 123 LYS cc_start: 0.7809 (tptm) cc_final: 0.7578 (tptm) REVERT: B 173 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 189 ASP cc_start: 0.7748 (t0) cc_final: 0.7321 (t0) REVERT: B 191 HIS cc_start: 0.8277 (m170) cc_final: 0.7948 (m-70) REVERT: B 371 ARG cc_start: 0.7958 (mmt90) cc_final: 0.7075 (mmp-170) REVERT: B 388 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7874 (mtm180) REVERT: B 433 MET cc_start: 0.7737 (tpt) cc_final: 0.7429 (tpp) REVERT: B 520 GLN cc_start: 0.6696 (pm20) cc_final: 0.6422 (pm20) REVERT: B 528 MET cc_start: 0.5909 (OUTLIER) cc_final: 0.5261 (mpt) REVERT: B 624 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8568 (mp) REVERT: B 637 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8427 (mt) REVERT: B 640 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8128 (ttp) REVERT: C 173 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 189 ASP cc_start: 0.7720 (t0) cc_final: 0.7252 (t0) REVERT: C 191 HIS cc_start: 0.8265 (m170) cc_final: 0.7920 (m-70) REVERT: C 371 ARG cc_start: 0.7995 (mmt90) cc_final: 0.7110 (mmp-170) REVERT: C 388 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7942 (ttt180) REVERT: C 520 GLN cc_start: 0.6629 (pm20) cc_final: 0.6349 (pm20) REVERT: C 528 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5194 (mpt) REVERT: C 539 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6341 (ptt90) REVERT: C 624 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8555 (mp) REVERT: C 637 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8432 (mt) REVERT: C 640 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8141 (ttp) REVERT: C 708 GLU cc_start: 0.8678 (tt0) cc_final: 0.8415 (mt-10) REVERT: D 123 LYS cc_start: 0.7792 (tptm) cc_final: 0.7555 (tptm) REVERT: D 173 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7645 (tm-30) REVERT: D 189 ASP cc_start: 0.7745 (t0) cc_final: 0.7314 (t0) REVERT: D 191 HIS cc_start: 0.8277 (m170) cc_final: 0.7970 (m-70) REVERT: D 371 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7087 (mmp-170) REVERT: D 388 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7929 (ttt180) REVERT: D 520 GLN cc_start: 0.6661 (pm20) cc_final: 0.6377 (pm20) REVERT: D 624 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8557 (mp) REVERT: D 640 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8150 (ttp) REVERT: D 708 GLU cc_start: 0.8667 (tt0) cc_final: 0.8401 (mt-10) outliers start: 75 outliers final: 43 residues processed: 370 average time/residue: 1.0953 time to fit residues: 466.2500 Evaluate side-chains 374 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 313 time to evaluate : 2.148 ------------------------------------------------------------------------------- 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 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 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 624 LEU 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 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 522 THR Chi-restraints excluded: chain C residue 528 MET 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 637 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 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 162 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 HIS C 413 HIS D 413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.150698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118989 restraints weight = 23458.098| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.74 r_work: 0.3144 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20192 Z= 0.119 Angle : 0.506 8.184 27396 Z= 0.253 Chirality : 0.037 0.207 3132 Planarity : 0.004 0.036 3352 Dihedral : 5.969 74.074 2784 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.17 % Allowed : 18.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2412 helix: 1.93 (0.13), residues: 1468 sheet: 1.02 (0.57), residues: 88 loop : -1.17 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.005 0.001 HIS A 521 PHE 0.006 0.001 PHE C 199 TYR 0.009 0.001 TYR B 271 ARG 0.005 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 1056) hydrogen bonds : angle 3.31093 ( 3012) covalent geometry : bond 0.00279 (20192) covalent geometry : angle 0.50552 (27396) *********************** 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 419 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 332 time to evaluate : 2.166 Fit side-chains REVERT: A 173 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 189 ASP cc_start: 0.7713 (t0) cc_final: 0.7240 (t0) REVERT: A 191 HIS cc_start: 0.8266 (m170) cc_final: 0.7956 (m-70) REVERT: A 221 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7827 (tttm) REVERT: A 371 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7114 (mmp-170) REVERT: A 388 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7940 (ttt180) REVERT: A 433 MET cc_start: 0.7674 (tpt) cc_final: 0.7378 (tpp) REVERT: A 528 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5161 (mpp) REVERT: A 624 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8595 (mp) REVERT: A 708 GLU cc_start: 0.8616 (tt0) cc_final: 0.8345 (mt-10) REVERT: B 123 LYS cc_start: 0.7800 (tptm) cc_final: 0.7567 (tptm) REVERT: B 173 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 189 ASP cc_start: 0.7750 (t0) cc_final: 0.7300 (t0) REVERT: B 191 HIS cc_start: 0.8300 (m170) cc_final: 0.7972 (m-70) REVERT: B 221 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7863 (tttm) REVERT: B 371 ARG cc_start: 0.7952 (mmt90) cc_final: 0.7118 (mmp-170) REVERT: B 388 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7857 (mtm180) REVERT: B 433 MET cc_start: 0.7702 (tpt) cc_final: 0.7397 (tpp) REVERT: B 520 GLN cc_start: 0.6770 (pm20) cc_final: 0.6550 (pm20) REVERT: B 624 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8604 (mp) REVERT: B 637 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8430 (mt) REVERT: B 640 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8156 (ttp) REVERT: B 708 GLU cc_start: 0.8637 (tt0) cc_final: 0.8366 (mt-10) REVERT: C 173 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7656 (tm-30) REVERT: C 189 ASP cc_start: 0.7685 (t0) cc_final: 0.7196 (t0) REVERT: C 221 LYS cc_start: 0.8280 (ttpt) cc_final: 0.7825 (tttm) REVERT: C 371 ARG cc_start: 0.7985 (mmt90) cc_final: 0.7151 (mmp-170) REVERT: C 388 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7931 (ttt180) REVERT: C 520 GLN cc_start: 0.6699 (pm20) cc_final: 0.6467 (pm20) REVERT: C 528 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.5142 (mpp) REVERT: C 624 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8605 (mp) REVERT: C 637 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8435 (mt) REVERT: C 640 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8135 (ttp) REVERT: C 708 GLU cc_start: 0.8671 (tt0) cc_final: 0.8396 (mt-10) REVERT: D 123 LYS cc_start: 0.7800 (tptm) cc_final: 0.7569 (tptm) REVERT: D 173 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7628 (tm-30) REVERT: D 189 ASP cc_start: 0.7711 (t0) cc_final: 0.7261 (t0) REVERT: D 191 HIS cc_start: 0.8293 (m170) cc_final: 0.7972 (m-70) REVERT: D 221 LYS cc_start: 0.8312 (ttpt) cc_final: 0.7849 (tttm) REVERT: D 371 ARG cc_start: 0.7953 (mmt90) cc_final: 0.7120 (mmp-170) REVERT: D 388 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7878 (mtm180) REVERT: D 528 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5247 (mpt) REVERT: D 624 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8592 (mp) REVERT: D 708 GLU cc_start: 0.8658 (tt0) cc_final: 0.8359 (mt-10) outliers start: 87 outliers final: 49 residues processed: 384 average time/residue: 1.1335 time to fit residues: 498.0169 Evaluate side-chains 379 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 315 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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 555 LEU Chi-restraints excluded: chain A residue 624 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 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 555 LEU Chi-restraints excluded: chain B residue 624 LEU 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 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 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 528 MET Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 624 LEU 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 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 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 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 40 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 191 optimal weight: 0.1980 chunk 68 optimal weight: 7.9990 chunk 213 optimal weight: 0.0570 chunk 108 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.152902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.121481 restraints weight = 23345.164| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.73 r_work: 0.3177 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2642 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= 0.097 Angle : 0.499 9.120 27396 Z= 0.248 Chirality : 0.037 0.217 3132 Planarity : 0.003 0.033 3352 Dihedral : 5.794 75.074 2784 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.92 % Allowed : 19.78 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.17), residues: 2412 helix: 2.07 (0.13), residues: 1468 sheet: 3.13 (0.48), residues: 68 loop : -1.24 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.005 0.001 HIS B 521 PHE 0.006 0.001 PHE A 407 TYR 0.009 0.001 TYR A 271 ARG 0.003 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 1056) hydrogen bonds : angle 3.22843 ( 3012) covalent geometry : bond 0.00223 (20192) covalent geometry : angle 0.49937 (27396) *********************** 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 417 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 356 time to evaluate : 2.350 Fit side-chains REVERT: A 162 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 173 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 189 ASP cc_start: 0.7750 (t0) cc_final: 0.7258 (t0) REVERT: A 191 HIS cc_start: 0.8254 (m170) cc_final: 0.7809 (m-70) REVERT: A 371 ARG cc_start: 0.7970 (mmt90) cc_final: 0.7143 (mmp-170) REVERT: A 388 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7959 (ttt180) REVERT: A 433 MET cc_start: 0.7705 (tpt) cc_final: 0.7414 (tpp) REVERT: A 528 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.5184 (mpp) REVERT: A 538 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 640 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8183 (ttp) REVERT: A 708 GLU cc_start: 0.8590 (tt0) cc_final: 0.8314 (mt-10) REVERT: B 162 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7932 (t80) REVERT: B 173 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7647 (tm-30) REVERT: B 189 ASP cc_start: 0.7739 (t0) cc_final: 0.7251 (t0) REVERT: B 191 HIS cc_start: 0.8277 (m170) cc_final: 0.7827 (m-70) REVERT: B 371 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7145 (mmp-170) REVERT: B 388 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7889 (mtm180) REVERT: B 433 MET cc_start: 0.7706 (tpt) cc_final: 0.7417 (tpp) REVERT: B 520 GLN cc_start: 0.6683 (pm20) cc_final: 0.6471 (pm20) REVERT: B 528 MET cc_start: 0.5769 (mpt) cc_final: 0.5064 (mpp) REVERT: B 708 GLU cc_start: 0.8611 (tt0) cc_final: 0.8311 (mt-10) REVERT: C 162 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.7913 (t80) REVERT: C 173 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 189 ASP cc_start: 0.7709 (t0) cc_final: 0.7221 (t0) REVERT: C 191 HIS cc_start: 0.8229 (m170) cc_final: 0.7777 (m-70) REVERT: C 371 ARG cc_start: 0.7974 (mmt90) cc_final: 0.7156 (mmp-170) REVERT: C 388 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7915 (ttt180) REVERT: C 520 GLN cc_start: 0.6655 (pm20) cc_final: 0.6441 (pm20) REVERT: C 528 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5168 (mpp) REVERT: C 637 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8464 (mt) REVERT: C 708 GLU cc_start: 0.8616 (tt0) cc_final: 0.8363 (mt-10) REVERT: D 173 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7654 (tm-30) REVERT: D 189 ASP cc_start: 0.7678 (t0) cc_final: 0.7199 (t0) REVERT: D 191 HIS cc_start: 0.8255 (m170) cc_final: 0.7816 (m-70) REVERT: D 371 ARG cc_start: 0.7972 (mmt90) cc_final: 0.7164 (mmp-170) REVERT: D 388 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7921 (ttt180) REVERT: D 520 GLN cc_start: 0.6671 (pm20) cc_final: 0.6432 (pm20) REVERT: D 528 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.5154 (mpp) REVERT: D 708 GLU cc_start: 0.8608 (tt0) cc_final: 0.8282 (mt-10) outliers start: 61 outliers final: 31 residues processed: 380 average time/residue: 1.0218 time to fit residues: 449.4714 Evaluate side-chains 380 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 336 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TYR 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 162 TYR 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 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 162 TYR 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 637 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 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 528 MET Chi-restraints excluded: chain D residue 538 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 78 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.148149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.115697 restraints weight = 23555.049| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.86 r_work: 0.3098 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20192 Z= 0.160 Angle : 0.557 9.093 27396 Z= 0.278 Chirality : 0.039 0.226 3132 Planarity : 0.004 0.035 3352 Dihedral : 6.216 70.626 2784 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.12 % Allowed : 19.49 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2412 helix: 1.88 (0.13), residues: 1472 sheet: 0.70 (0.56), residues: 88 loop : -1.16 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 223 HIS 0.005 0.001 HIS A 521 PHE 0.009 0.001 PHE C 161 TYR 0.011 0.001 TYR B 525 ARG 0.004 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 1056) hydrogen bonds : angle 3.39817 ( 3012) covalent geometry : bond 0.00383 (20192) covalent geometry : angle 0.55748 (27396) *********************** 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 419 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 333 time to evaluate : 2.147 Fit side-chains REVERT: A 173 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 189 ASP cc_start: 0.7704 (t0) cc_final: 0.7204 (t0) REVERT: A 191 HIS cc_start: 0.8291 (m170) cc_final: 0.7980 (m-70) REVERT: A 221 LYS cc_start: 0.8402 (ttpt) cc_final: 0.8066 (ttmm) REVERT: A 371 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7177 (mmp-170) REVERT: A 388 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7814 (mmm-85) REVERT: A 406 ILE cc_start: 0.8779 (mm) cc_final: 0.8568 (mt) REVERT: A 433 MET cc_start: 0.7706 (tpt) cc_final: 0.7418 (tpp) REVERT: A 528 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5565 (mmm) REVERT: A 538 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7977 (mp) REVERT: A 645 MET cc_start: 0.7374 (tpp) cc_final: 0.7033 (ttp) REVERT: A 708 GLU cc_start: 0.8694 (tt0) cc_final: 0.8449 (mt-10) REVERT: B 123 LYS cc_start: 0.7867 (tptm) cc_final: 0.7580 (tptm) REVERT: B 173 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 189 ASP cc_start: 0.7743 (t0) cc_final: 0.7262 (t0) REVERT: B 191 HIS cc_start: 0.8306 (m170) cc_final: 0.7975 (m-70) REVERT: B 221 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8050 (ttmm) REVERT: B 371 ARG cc_start: 0.8008 (mmt90) cc_final: 0.7171 (mmp-170) REVERT: B 388 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7777 (mmm-85) REVERT: B 406 ILE cc_start: 0.8783 (mm) cc_final: 0.8574 (mt) REVERT: B 433 MET cc_start: 0.7716 (tpt) cc_final: 0.7423 (tpp) REVERT: B 645 MET cc_start: 0.7355 (tpp) cc_final: 0.7079 (ttp) REVERT: B 708 GLU cc_start: 0.8699 (tt0) cc_final: 0.8448 (mt-10) REVERT: C 160 GLU cc_start: 0.8016 (tp30) cc_final: 0.7168 (pt0) REVERT: C 173 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 189 ASP cc_start: 0.7683 (t0) cc_final: 0.7182 (t0) REVERT: C 191 HIS cc_start: 0.8261 (m170) cc_final: 0.7913 (m-70) REVERT: C 221 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8056 (ttmm) REVERT: C 371 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7174 (mmp-170) REVERT: C 388 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7854 (mtp180) REVERT: C 406 ILE cc_start: 0.8783 (mm) cc_final: 0.8575 (mt) REVERT: C 520 GLN cc_start: 0.6734 (pm20) cc_final: 0.6522 (pm20) REVERT: D 123 LYS cc_start: 0.7845 (tptm) cc_final: 0.7571 (tptm) REVERT: D 160 GLU cc_start: 0.7977 (tp30) cc_final: 0.7101 (pt0) REVERT: D 173 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7688 (tm-30) REVERT: D 189 ASP cc_start: 0.7645 (t0) cc_final: 0.7161 (t0) REVERT: D 221 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8043 (ttmm) REVERT: D 371 ARG cc_start: 0.8009 (mmt90) cc_final: 0.7193 (mmp-170) REVERT: D 388 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7783 (mmm-85) REVERT: D 406 ILE cc_start: 0.8783 (mm) cc_final: 0.8569 (mt) REVERT: D 520 GLN cc_start: 0.6807 (pm20) cc_final: 0.6540 (pm20) REVERT: D 645 MET cc_start: 0.7345 (tpp) cc_final: 0.7115 (ttp) outliers start: 86 outliers final: 46 residues processed: 372 average time/residue: 1.0831 time to fit residues: 462.7376 Evaluate side-chains 378 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 326 time to evaluate : 2.065 ------------------------------------------------------------------------------- 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 486 SER 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 640 MET 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 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 709 GLU 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 538 LEU 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 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 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 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 185 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.147557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115348 restraints weight = 23523.344| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.86 r_work: 0.3137 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20192 Z= 0.157 Angle : 0.561 9.825 27396 Z= 0.280 Chirality : 0.039 0.237 3132 Planarity : 0.004 0.036 3352 Dihedral : 6.320 69.164 2784 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.78 % Allowed : 20.59 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2412 helix: 1.86 (0.13), residues: 1472 sheet: 0.55 (0.57), residues: 88 loop : -1.13 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 223 HIS 0.005 0.001 HIS B 521 PHE 0.008 0.001 PHE C 199 TYR 0.011 0.001 TYR D 403 ARG 0.003 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 1056) hydrogen bonds : angle 3.40258 ( 3012) covalent geometry : bond 0.00377 (20192) covalent geometry : angle 0.56125 (27396) *********************** 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 420 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 341 time to evaluate : 2.007 Fit side-chains REVERT: A 160 GLU cc_start: 0.8017 (tp30) cc_final: 0.7152 (pt0) REVERT: A 173 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7671 (tm-30) REVERT: A 189 ASP cc_start: 0.7696 (t0) cc_final: 0.7193 (t0) REVERT: A 191 HIS cc_start: 0.8286 (m170) cc_final: 0.7985 (m-70) REVERT: A 221 LYS cc_start: 0.8384 (ttpt) cc_final: 0.8057 (ttmm) REVERT: A 371 ARG cc_start: 0.8017 (mmt90) cc_final: 0.7195 (mmp-170) REVERT: A 388 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7785 (mmm-85) REVERT: A 406 ILE cc_start: 0.8775 (mm) cc_final: 0.8558 (mt) REVERT: A 433 MET cc_start: 0.7729 (tpt) cc_final: 0.7447 (tpp) REVERT: A 528 MET cc_start: 0.5924 (OUTLIER) cc_final: 0.5212 (mpp) REVERT: A 538 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7987 (mp) REVERT: A 708 GLU cc_start: 0.8636 (tt0) cc_final: 0.8387 (mt-10) REVERT: B 123 LYS cc_start: 0.7824 (tptm) cc_final: 0.7520 (tptm) REVERT: B 160 GLU cc_start: 0.8041 (tp30) cc_final: 0.7173 (pt0) REVERT: B 173 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7687 (tm-30) REVERT: B 189 ASP cc_start: 0.7673 (t0) cc_final: 0.7173 (t0) REVERT: B 221 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8053 (ttmm) REVERT: B 371 ARG cc_start: 0.8018 (mmt90) cc_final: 0.7198 (mmp-170) REVERT: B 388 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7762 (mmm-85) REVERT: B 406 ILE cc_start: 0.8785 (mm) cc_final: 0.8570 (mt) REVERT: B 433 MET cc_start: 0.7724 (tpt) cc_final: 0.7436 (tpp) REVERT: B 520 GLN cc_start: 0.6764 (pm20) cc_final: 0.6531 (pm20) REVERT: B 708 GLU cc_start: 0.8644 (tt0) cc_final: 0.8394 (mt-10) REVERT: C 173 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7685 (tm-30) REVERT: C 189 ASP cc_start: 0.7693 (t0) cc_final: 0.7183 (t0) REVERT: C 191 HIS cc_start: 0.8289 (m170) cc_final: 0.7862 (m-70) REVERT: C 221 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8047 (ttmm) REVERT: C 371 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7187 (mmp-170) REVERT: C 388 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7775 (mmm-85) REVERT: C 406 ILE cc_start: 0.8778 (mm) cc_final: 0.8565 (mt) REVERT: C 520 GLN cc_start: 0.6718 (pm20) cc_final: 0.6511 (pm20) REVERT: C 708 GLU cc_start: 0.8617 (tt0) cc_final: 0.8340 (mt-10) REVERT: D 123 LYS cc_start: 0.7824 (tptm) cc_final: 0.7527 (tptm) REVERT: D 173 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7671 (tm-30) REVERT: D 189 ASP cc_start: 0.7647 (t0) cc_final: 0.7150 (t0) REVERT: D 221 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8052 (ttmm) REVERT: D 371 ARG cc_start: 0.8007 (mmt90) cc_final: 0.7201 (mmp-170) REVERT: D 388 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7760 (mmm-85) REVERT: D 406 ILE cc_start: 0.8768 (mm) cc_final: 0.8553 (mt) REVERT: D 520 GLN cc_start: 0.6785 (pm20) cc_final: 0.6559 (pm20) REVERT: D 708 GLU cc_start: 0.8616 (tt0) cc_final: 0.8335 (mt-10) outliers start: 79 outliers final: 52 residues processed: 376 average time/residue: 1.0867 time to fit residues: 469.8857 Evaluate side-chains 395 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 2.143 ------------------------------------------------------------------------------- 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 486 SER 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 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 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 494 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 538 LEU 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 494 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 555 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 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 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 642 ILE 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 223 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 182 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.147414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.114986 restraints weight = 23379.851| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.85 r_work: 0.3148 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20192 Z= 0.169 Angle : 0.585 10.242 27396 Z= 0.292 Chirality : 0.040 0.237 3132 Planarity : 0.004 0.036 3352 Dihedral : 6.403 70.123 2784 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.21 % Allowed : 21.98 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2412 helix: 1.84 (0.13), residues: 1472 sheet: 0.47 (0.57), residues: 88 loop : -1.18 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 223 HIS 0.005 0.001 HIS C 251 PHE 0.008 0.001 PHE A 199 TYR 0.012 0.001 TYR D 403 ARG 0.003 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 1056) hydrogen bonds : angle 3.41978 ( 3012) covalent geometry : bond 0.00403 (20192) covalent geometry : angle 0.58459 (27396) ********************** 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 405 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 2.695 Fit side-chains REVERT: A 173 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 189 ASP cc_start: 0.7653 (t0) cc_final: 0.7146 (t0) REVERT: A 191 HIS cc_start: 0.8296 (m170) cc_final: 0.7998 (m-70) REVERT: A 221 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8060 (ttmm) REVERT: A 371 ARG cc_start: 0.8016 (mmt90) cc_final: 0.7192 (mmp-170) REVERT: A 388 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7797 (mmm-85) REVERT: A 433 MET cc_start: 0.7724 (tpt) cc_final: 0.7442 (tpp) REVERT: A 528 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5290 (mpt) REVERT: A 538 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7996 (mp) REVERT: A 708 GLU cc_start: 0.8652 (tt0) cc_final: 0.8400 (mt-10) REVERT: B 123 LYS cc_start: 0.7892 (tptm) cc_final: 0.7567 (tptm) REVERT: B 173 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7679 (tm-30) REVERT: B 189 ASP cc_start: 0.7633 (t0) cc_final: 0.7126 (t0) REVERT: B 191 HIS cc_start: 0.8320 (m170) cc_final: 0.7971 (m-70) REVERT: B 221 LYS cc_start: 0.8385 (ttpt) cc_final: 0.8058 (ttmm) REVERT: B 371 ARG cc_start: 0.8010 (mmt90) cc_final: 0.7185 (mmp-170) REVERT: B 388 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7769 (mmm-85) REVERT: B 433 MET cc_start: 0.7722 (tpt) cc_final: 0.7437 (tpp) REVERT: B 520 GLN cc_start: 0.6839 (pm20) cc_final: 0.6596 (pm20) REVERT: B 708 GLU cc_start: 0.8629 (tt0) cc_final: 0.8377 (mt-10) REVERT: C 173 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7689 (tm-30) REVERT: C 189 ASP cc_start: 0.7641 (t0) cc_final: 0.7136 (t0) REVERT: C 191 HIS cc_start: 0.8271 (m170) cc_final: 0.7859 (m-70) REVERT: C 221 LYS cc_start: 0.8396 (ttpt) cc_final: 0.8070 (ttmm) REVERT: C 371 ARG cc_start: 0.8027 (mmt90) cc_final: 0.7205 (mmp-170) REVERT: C 388 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7775 (mmm-85) REVERT: C 406 ILE cc_start: 0.8773 (mm) cc_final: 0.8566 (mt) REVERT: C 520 GLN cc_start: 0.6730 (pm20) cc_final: 0.6518 (pm20) REVERT: C 708 GLU cc_start: 0.8631 (tt0) cc_final: 0.8369 (mt-10) REVERT: D 123 LYS cc_start: 0.7888 (tptm) cc_final: 0.7567 (tptm) REVERT: D 173 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7685 (tm-30) REVERT: D 189 ASP cc_start: 0.7647 (t0) cc_final: 0.7138 (t0) REVERT: D 191 HIS cc_start: 0.8282 (m170) cc_final: 0.7870 (m-70) REVERT: D 221 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8067 (ttmm) REVERT: D 371 ARG cc_start: 0.7999 (mmt90) cc_final: 0.7194 (mmp-170) REVERT: D 388 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7766 (mmm-85) REVERT: D 406 ILE cc_start: 0.8770 (mm) cc_final: 0.8532 (mt) REVERT: D 520 GLN cc_start: 0.6794 (pm20) cc_final: 0.6563 (pm20) REVERT: D 708 GLU cc_start: 0.8626 (tt0) cc_final: 0.8353 (mt-10) outliers start: 67 outliers final: 56 residues processed: 368 average time/residue: 1.2766 time to fit residues: 540.2715 Evaluate side-chains 398 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 336 time to evaluate : 2.191 ------------------------------------------------------------------------------- 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 486 SER 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 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 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 494 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 538 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 494 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 555 LEU 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 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 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 147 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 127 optimal weight: 0.0170 chunk 74 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN B 200 GLN C 200 GLN D 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.151807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119768 restraints weight = 23524.898| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.86 r_work: 0.3156 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20192 Z= 0.104 Angle : 0.529 10.053 27396 Z= 0.263 Chirality : 0.037 0.240 3132 Planarity : 0.004 0.034 3352 Dihedral : 5.953 71.875 2784 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.20 % Allowed : 23.04 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.17), residues: 2412 helix: 2.15 (0.13), residues: 1468 sheet: 0.56 (0.57), residues: 88 loop : -1.14 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 223 HIS 0.005 0.001 HIS B 521 PHE 0.013 0.001 PHE C 394 TYR 0.008 0.001 TYR D 271 ARG 0.003 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 1056) hydrogen bonds : angle 3.24006 ( 3012) covalent geometry : bond 0.00241 (20192) covalent geometry : angle 0.52851 (27396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13595.06 seconds wall clock time: 235 minutes 11.61 seconds (14111.61 seconds total)