Starting phenix.real_space_refine on Tue Jun 17 12:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekr_28211/06_2025/8ekr_28211.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekr_28211/06_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_28211/06_2025/8ekr_28211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekr_28211/06_2025/8ekr_28211.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekr_28211/06_2025/8ekr_28211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekr_28211/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.13, 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: 4.43 Conformation dependent library (CDL) restraints added in 2.3 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: 1.72 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: 5.79 Time building geometry restraints manager: 5.30 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: 0.13 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: 6.010 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: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 42.020 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.460 ------------------------------------------------------------------------------- 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 : 2.223 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: 1.0694 time to fit residues: 601.8792 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 : 2.150 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128005 restraints weight = 23604.801| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.73 r_work: 0.3250 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.7807 (t0) cc_final: 0.7533 (t0) REVERT: A 269 HIS cc_start: 0.6678 (m90) cc_final: 0.6440 (t-90) REVERT: A 371 ARG cc_start: 0.8037 (mmt90) cc_final: 0.7119 (mmp-170) REVERT: A 388 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7678 (tpp-160) REVERT: A 433 MET cc_start: 0.7704 (tpt) cc_final: 0.7409 (tpp) REVERT: A 468 MET cc_start: 0.6548 (ppp) cc_final: 0.6128 (tmm) REVERT: A 520 GLN cc_start: 0.6820 (pm20) cc_final: 0.6493 (pm20) REVERT: A 637 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8424 (mt) REVERT: A 640 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8015 (ttp) REVERT: A 708 GLU cc_start: 0.8644 (tt0) cc_final: 0.8406 (mt-10) REVERT: B 123 LYS cc_start: 0.7960 (tptm) cc_final: 0.7615 (tptm) REVERT: B 189 ASP cc_start: 0.7796 (t0) cc_final: 0.7494 (t0) REVERT: B 269 HIS cc_start: 0.6657 (m90) cc_final: 0.6419 (t-90) REVERT: B 327 SER cc_start: 0.8923 (m) cc_final: 0.8722 (t) REVERT: B 371 ARG cc_start: 0.8042 (mmt90) cc_final: 0.7114 (mmp-170) REVERT: B 388 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7660 (tpp-160) REVERT: B 538 LEU cc_start: 0.8075 (mm) cc_final: 0.7819 (mm) REVERT: B 637 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8422 (mt) REVERT: B 640 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8004 (ttp) REVERT: B 708 GLU cc_start: 0.8643 (tt0) cc_final: 0.8397 (mt-10) REVERT: C 189 ASP cc_start: 0.7783 (t0) cc_final: 0.7511 (t0) REVERT: C 269 HIS cc_start: 0.6650 (m90) cc_final: 0.6422 (t-90) REVERT: C 371 ARG cc_start: 0.8040 (mmt90) cc_final: 0.7120 (mmp-170) REVERT: C 388 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7656 (tpp-160) REVERT: C 468 MET cc_start: 0.7172 (tmm) cc_final: 0.6855 (tmm) REVERT: C 538 LEU cc_start: 0.8083 (mm) cc_final: 0.7828 (mm) REVERT: C 637 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8421 (mt) REVERT: C 640 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8026 (ttp) REVERT: C 708 GLU cc_start: 0.8638 (tt0) cc_final: 0.8367 (mt-10) REVERT: D 123 LYS cc_start: 0.7965 (tptm) cc_final: 0.7621 (tptm) REVERT: D 189 ASP cc_start: 0.7795 (t0) cc_final: 0.7497 (t0) REVERT: D 269 HIS cc_start: 0.6657 (m90) cc_final: 0.6424 (t-90) REVERT: D 371 ARG cc_start: 0.8032 (mmt90) cc_final: 0.7117 (mmp-170) REVERT: D 388 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7650 (tpp-160) REVERT: D 468 MET cc_start: 0.7147 (tmm) cc_final: 0.6815 (tmm) REVERT: D 538 LEU cc_start: 0.8070 (mm) cc_final: 0.7814 (mm) REVERT: D 637 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8418 (mt) REVERT: D 640 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8006 (ttp) REVERT: D 708 GLU cc_start: 0.8624 (tt0) cc_final: 0.8381 (mt-10) outliers start: 62 outliers final: 36 residues processed: 369 average time/residue: 1.0500 time to fit residues: 447.7742 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 : 2.086 ------------------------------------------------------------------------------- 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: 2.9990 chunk 66 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.153114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.120773 restraints weight = 23566.486| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.86 r_work: 0.3229 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2070 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= 0.120 Angle : 0.523 8.902 27396 Z= 0.259 Chirality : 0.037 0.180 3132 Planarity : 0.004 0.049 3352 Dihedral : 6.157 78.341 2784 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.16 % Allowed : 14.70 % Favored : 82.14 % 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: 0.95 (0.17), residues: 2412 helix: 1.78 (0.14), residues: 1412 sheet: 2.63 (0.49), residues: 68 loop : -1.41 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 676 HIS 0.006 0.001 HIS A 165 PHE 0.006 0.001 PHE C 407 TYR 0.023 0.001 TYR A 162 ARG 0.005 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 1056) hydrogen bonds : angle 3.42260 ( 3012) covalent geometry : bond 0.00280 (20192) covalent geometry : angle 0.52300 (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 408 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 342 time to evaluate : 2.334 Fit side-chains REVERT: A 189 ASP cc_start: 0.7740 (t0) cc_final: 0.7430 (t0) REVERT: A 191 HIS cc_start: 0.8210 (m170) cc_final: 0.8009 (m-70) REVERT: A 371 ARG cc_start: 0.8074 (mmt90) cc_final: 0.7233 (mmp-170) REVERT: A 388 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7700 (ttp-170) REVERT: A 520 GLN cc_start: 0.6918 (pm20) cc_final: 0.6682 (pm20) REVERT: A 539 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6367 (ptt90) REVERT: A 637 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8471 (mt) REVERT: A 640 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8137 (ttp) REVERT: B 123 LYS cc_start: 0.7942 (tptm) cc_final: 0.7696 (tptm) REVERT: B 189 ASP cc_start: 0.7792 (t0) cc_final: 0.7498 (t0) REVERT: B 191 HIS cc_start: 0.8232 (m170) cc_final: 0.7962 (m-70) REVERT: B 269 HIS cc_start: 0.6926 (m90) cc_final: 0.6573 (t70) REVERT: B 371 ARG cc_start: 0.8074 (mmt90) cc_final: 0.7235 (mmp-170) REVERT: B 388 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7717 (ttp-170) REVERT: B 520 GLN cc_start: 0.6902 (pm20) cc_final: 0.6557 (pm20) REVERT: B 539 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6420 (ptt90) REVERT: B 637 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8475 (mt) REVERT: B 640 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8111 (ttp) REVERT: C 189 ASP cc_start: 0.7759 (t0) cc_final: 0.7436 (t0) REVERT: C 191 HIS cc_start: 0.8204 (m170) cc_final: 0.7960 (m-70) REVERT: C 371 ARG cc_start: 0.8075 (mmt90) cc_final: 0.7240 (mmp-170) REVERT: C 388 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7965 (ttt180) REVERT: C 468 MET cc_start: 0.7145 (tmm) cc_final: 0.6752 (tmm) REVERT: C 520 GLN cc_start: 0.6902 (pm20) cc_final: 0.6556 (pm20) REVERT: C 539 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6427 (ptt90) REVERT: C 637 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8495 (mt) REVERT: C 640 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8141 (ttp) REVERT: D 123 LYS cc_start: 0.7949 (tptm) cc_final: 0.7706 (tptm) REVERT: D 189 ASP cc_start: 0.7787 (t0) cc_final: 0.7496 (t0) REVERT: D 191 HIS cc_start: 0.8244 (m170) cc_final: 0.7982 (m-70) REVERT: D 371 ARG cc_start: 0.8069 (mmt90) cc_final: 0.7235 (mmp-170) REVERT: D 388 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7688 (ttp-170) REVERT: D 468 MET cc_start: 0.7150 (tmm) cc_final: 0.6792 (tmm) REVERT: D 520 GLN cc_start: 0.6893 (pm20) cc_final: 0.6540 (pm20) REVERT: D 538 LEU cc_start: 0.8149 (mm) cc_final: 0.7868 (mm) REVERT: D 539 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6421 (ptt90) REVERT: D 637 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8490 (mt) REVERT: D 640 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8152 (ttp) outliers start: 66 outliers final: 42 residues processed: 377 average time/residue: 1.1713 time to fit residues: 511.0204 Evaluate side-chains 381 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 323 time to evaluate : 1.969 ------------------------------------------------------------------------------- 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: 6.9990 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.149154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.117535 restraints weight = 23555.903| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.73 r_work: 0.3116 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2607 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= 0.174 Angle : 0.563 8.489 27396 Z= 0.283 Chirality : 0.039 0.186 3132 Planarity : 0.004 0.044 3352 Dihedral : 6.480 71.736 2784 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.55 % Allowed : 15.37 % Favored : 80.08 % 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: 0.84 (0.17), residues: 2412 helix: 1.62 (0.13), residues: 1456 sheet: 0.76 (0.57), residues: 88 loop : -1.35 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 509 HIS 0.007 0.001 HIS D 165 PHE 0.008 0.001 PHE D 199 TYR 0.022 0.002 TYR B 162 ARG 0.006 0.001 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 1056) hydrogen bonds : angle 3.50058 ( 3012) covalent geometry : bond 0.00413 (20192) covalent geometry : angle 0.56333 (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 447 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 352 time to evaluate : 2.086 Fit side-chains REVERT: A 173 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 189 ASP cc_start: 0.7763 (t0) cc_final: 0.7355 (t0) REVERT: A 221 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7915 (tttm) REVERT: A 240 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: A 371 ARG cc_start: 0.8055 (mmt90) cc_final: 0.7202 (mmp-170) REVERT: A 388 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7676 (tpp-160) REVERT: A 539 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6215 (ppt90) REVERT: A 624 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8652 (mp) REVERT: A 708 GLU cc_start: 0.8709 (tt0) cc_final: 0.8468 (mt-10) REVERT: B 123 LYS cc_start: 0.7952 (tptm) cc_final: 0.7656 (tptm) REVERT: B 173 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 189 ASP cc_start: 0.7712 (t0) cc_final: 0.7336 (t0) REVERT: B 191 HIS cc_start: 0.8272 (m170) cc_final: 0.8047 (m-70) REVERT: B 221 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7838 (tttm) REVERT: B 240 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7151 (pm20) REVERT: B 371 ARG cc_start: 0.8037 (mmt90) cc_final: 0.7174 (mmp-170) REVERT: B 388 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7668 (tpp-160) REVERT: B 520 GLN cc_start: 0.6860 (pm20) cc_final: 0.6522 (mp10) REVERT: B 539 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6248 (ppt90) REVERT: B 624 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8661 (mp) REVERT: B 708 GLU cc_start: 0.8710 (tt0) cc_final: 0.8469 (mt-10) REVERT: C 173 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 189 ASP cc_start: 0.7763 (t0) cc_final: 0.7353 (t0) REVERT: C 191 HIS cc_start: 0.8217 (m170) cc_final: 0.7972 (m-70) REVERT: C 221 LYS cc_start: 0.8335 (ttpt) cc_final: 0.7877 (tttm) REVERT: C 240 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7141 (pm20) REVERT: C 371 ARG cc_start: 0.8056 (mmt90) cc_final: 0.7200 (mmp-170) REVERT: C 388 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7663 (tpp-160) REVERT: C 520 GLN cc_start: 0.6839 (pm20) cc_final: 0.6497 (mp10) REVERT: C 539 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6228 (ppt90) REVERT: C 624 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8659 (mp) REVERT: C 708 GLU cc_start: 0.8703 (tt0) cc_final: 0.8462 (mt-10) REVERT: D 123 LYS cc_start: 0.7938 (tptm) cc_final: 0.7646 (tptm) REVERT: D 173 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7649 (tm-30) REVERT: D 189 ASP cc_start: 0.7728 (t0) cc_final: 0.7351 (t0) REVERT: D 191 HIS cc_start: 0.8267 (m170) cc_final: 0.8050 (m-70) REVERT: D 221 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7860 (tttm) REVERT: D 240 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: D 371 ARG cc_start: 0.8046 (mmt90) cc_final: 0.7209 (mmp-170) REVERT: D 388 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7661 (tpp-160) REVERT: D 520 GLN cc_start: 0.6867 (pm20) cc_final: 0.6521 (mp10) REVERT: D 624 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8655 (mp) outliers start: 95 outliers final: 46 residues processed: 415 average time/residue: 1.0136 time to fit residues: 487.7641 Evaluate side-chains 388 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 327 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain C residue 727 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 160 optimal weight: 0.0040 chunk 192 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 212 optimal weight: 0.4980 chunk 239 optimal weight: 0.0050 chunk 68 optimal weight: 1.9990 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.152834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.121093 restraints weight = 23470.190| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.75 r_work: 0.3175 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2595 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= 0.095 Angle : 0.483 8.354 27396 Z= 0.241 Chirality : 0.036 0.193 3132 Planarity : 0.004 0.039 3352 Dihedral : 5.908 75.324 2784 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.78 % Allowed : 18.97 % Favored : 78.26 % 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: 1.30 (0.17), residues: 2412 helix: 1.98 (0.14), residues: 1452 sheet: 3.15 (0.49), residues: 68 loop : -1.27 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 223 HIS 0.005 0.001 HIS C 521 PHE 0.006 0.001 PHE D 407 TYR 0.010 0.001 TYR B 271 ARG 0.005 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 1056) hydrogen bonds : angle 3.29552 ( 3012) covalent geometry : bond 0.00213 (20192) covalent geometry : angle 0.48266 (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 409 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 351 time to evaluate : 2.295 Fit side-chains REVERT: A 173 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 189 ASP cc_start: 0.7725 (t0) cc_final: 0.7268 (t0) REVERT: A 191 HIS cc_start: 0.8270 (m170) cc_final: 0.7943 (m-70) REVERT: A 319 PHE cc_start: 0.8063 (m-80) cc_final: 0.7703 (m-10) REVERT: A 371 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7112 (mmp-170) REVERT: A 388 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7929 (ttt180) REVERT: A 528 MET cc_start: 0.5726 (mpt) cc_final: 0.5054 (mpp) REVERT: A 708 GLU cc_start: 0.8622 (tt0) cc_final: 0.8329 (mt-10) REVERT: B 123 LYS cc_start: 0.7808 (tptm) cc_final: 0.7558 (tptm) REVERT: B 173 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 189 ASP cc_start: 0.7707 (t0) cc_final: 0.7267 (t0) REVERT: B 191 HIS cc_start: 0.8325 (m170) cc_final: 0.7993 (m-70) REVERT: B 371 ARG cc_start: 0.7976 (mmt90) cc_final: 0.7128 (mmp-170) REVERT: B 388 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7762 (mtm180) REVERT: B 433 MET cc_start: 0.7698 (tpt) cc_final: 0.7401 (tpp) REVERT: B 520 GLN cc_start: 0.6706 (pm20) cc_final: 0.6461 (pm20) REVERT: B 528 MET cc_start: 0.5722 (mpt) cc_final: 0.5027 (mpp) REVERT: B 640 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8073 (ttp) REVERT: B 708 GLU cc_start: 0.8633 (tt0) cc_final: 0.8295 (mt-10) REVERT: C 173 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7694 (tm-30) REVERT: C 189 ASP cc_start: 0.7663 (t0) cc_final: 0.7206 (t0) REVERT: C 371 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7129 (mmp-170) REVERT: C 388 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7764 (mtm180) REVERT: C 520 GLN cc_start: 0.6647 (pm20) cc_final: 0.6401 (pm20) REVERT: C 528 MET cc_start: 0.5711 (mpt) cc_final: 0.5038 (mpp) REVERT: C 708 GLU cc_start: 0.8620 (tt0) cc_final: 0.8315 (mt-10) REVERT: D 123 LYS cc_start: 0.7785 (tptm) cc_final: 0.7561 (tptm) REVERT: D 173 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7648 (tm-30) REVERT: D 189 ASP cc_start: 0.7694 (t0) cc_final: 0.7251 (t0) REVERT: D 191 HIS cc_start: 0.8301 (m170) cc_final: 0.7981 (m-70) REVERT: D 371 ARG cc_start: 0.7962 (mmt90) cc_final: 0.7116 (mmp-170) REVERT: D 388 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7860 (mtm180) REVERT: D 433 MET cc_start: 0.7679 (tpt) cc_final: 0.7382 (tpp) REVERT: D 520 GLN cc_start: 0.6713 (pm20) cc_final: 0.6470 (pm20) REVERT: D 528 MET cc_start: 0.5755 (mpt) cc_final: 0.5058 (mpp) REVERT: D 708 GLU cc_start: 0.8607 (tt0) cc_final: 0.8279 (mt-10) outliers start: 58 outliers final: 28 residues processed: 386 average time/residue: 1.1367 time to fit residues: 502.8200 Evaluate side-chains 358 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 325 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET 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 555 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET 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 555 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 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 162 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 70 optimal weight: 0.0270 chunk 152 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 655 ASN D 655 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.151833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120237 restraints weight = 23378.655| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.73 r_work: 0.3158 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2691 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= 0.109 Angle : 0.510 8.126 27396 Z= 0.254 Chirality : 0.037 0.203 3132 Planarity : 0.004 0.036 3352 Dihedral : 5.900 74.524 2784 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.50 % Allowed : 19.44 % Favored : 77.06 % 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: 1.32 (0.17), residues: 2412 helix: 1.97 (0.13), residues: 1472 sheet: 3.15 (0.47), residues: 68 loop : -1.31 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 223 HIS 0.005 0.001 HIS A 521 PHE 0.005 0.001 PHE C 199 TYR 0.009 0.001 TYR D 271 ARG 0.003 0.000 ARG C 560 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 1056) hydrogen bonds : angle 3.27881 ( 3012) covalent geometry : bond 0.00256 (20192) covalent geometry : angle 0.51020 (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 416 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 343 time to evaluate : 2.180 Fit side-chains REVERT: A 160 GLU cc_start: 0.7990 (tp30) cc_final: 0.7111 (pt0) REVERT: A 173 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 189 ASP cc_start: 0.7667 (t0) cc_final: 0.7193 (t0) REVERT: A 191 HIS cc_start: 0.8272 (m170) cc_final: 0.7847 (m-70) REVERT: A 371 ARG cc_start: 0.8007 (mmt90) cc_final: 0.7179 (mmp-170) REVERT: A 388 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7705 (mtm-85) REVERT: A 433 MET cc_start: 0.7775 (tpt) cc_final: 0.7494 (tpp) REVERT: A 528 MET cc_start: 0.5799 (mpt) cc_final: 0.5115 (mpp) REVERT: A 708 GLU cc_start: 0.8632 (tt0) cc_final: 0.8355 (mt-10) REVERT: B 123 LYS cc_start: 0.7818 (tptm) cc_final: 0.7589 (tptm) REVERT: B 160 GLU cc_start: 0.7962 (tp30) cc_final: 0.7111 (pt0) REVERT: B 173 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 189 ASP cc_start: 0.7684 (t0) cc_final: 0.7241 (t0) REVERT: B 191 HIS cc_start: 0.8294 (m170) cc_final: 0.7947 (m-70) REVERT: B 371 ARG cc_start: 0.7990 (mmt90) cc_final: 0.7169 (mmp-170) REVERT: B 388 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7876 (mtm180) REVERT: B 433 MET cc_start: 0.7700 (tpt) cc_final: 0.7402 (tpp) REVERT: B 520 GLN cc_start: 0.6750 (pm20) cc_final: 0.6522 (pm20) REVERT: B 528 MET cc_start: 0.5759 (mpt) cc_final: 0.5090 (mpp) REVERT: B 640 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8100 (ttp) REVERT: B 708 GLU cc_start: 0.8627 (tt0) cc_final: 0.8351 (mt-10) REVERT: C 160 GLU cc_start: 0.7955 (tp30) cc_final: 0.7095 (pt0) REVERT: C 173 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7651 (tm-30) REVERT: C 189 ASP cc_start: 0.7678 (t0) cc_final: 0.7210 (t0) REVERT: C 371 ARG cc_start: 0.7991 (mmt90) cc_final: 0.7173 (mmp-170) REVERT: C 388 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7827 (mtp180) REVERT: C 520 GLN cc_start: 0.6712 (pm20) cc_final: 0.6472 (pm20) REVERT: C 528 MET cc_start: 0.5831 (mpt) cc_final: 0.5135 (mpp) REVERT: C 708 GLU cc_start: 0.8620 (tt0) cc_final: 0.8344 (mt-10) REVERT: D 123 LYS cc_start: 0.7824 (tptm) cc_final: 0.7589 (tptm) REVERT: D 160 GLU cc_start: 0.7976 (tp30) cc_final: 0.7125 (pt0) REVERT: D 173 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7656 (tm-30) REVERT: D 189 ASP cc_start: 0.7731 (t0) cc_final: 0.7283 (t0) REVERT: D 191 HIS cc_start: 0.8295 (m170) cc_final: 0.7971 (m-70) REVERT: D 371 ARG cc_start: 0.7999 (mmt90) cc_final: 0.7180 (mmp-170) REVERT: D 388 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7872 (mtm180) REVERT: D 528 MET cc_start: 0.5801 (mpt) cc_final: 0.5110 (mpp) REVERT: D 708 GLU cc_start: 0.8570 (tt0) cc_final: 0.8273 (mt-10) outliers start: 73 outliers final: 38 residues processed: 382 average time/residue: 1.0516 time to fit residues: 466.4342 Evaluate side-chains 376 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 333 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 40 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 131 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 213 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 chunk 239 optimal weight: 0.0060 chunk 197 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 HIS B 413 HIS C 413 HIS D 413 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.122900 restraints weight = 23356.878| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.75 r_work: 0.3200 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2753 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= 0.091 Angle : 0.488 8.109 27396 Z= 0.242 Chirality : 0.036 0.218 3132 Planarity : 0.003 0.033 3352 Dihedral : 5.663 76.641 2784 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.54 % Allowed : 21.26 % Favored : 76.20 % 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: 1.56 (0.17), residues: 2412 helix: 2.20 (0.13), residues: 1464 sheet: 3.21 (0.47), residues: 68 loop : -1.27 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 223 HIS 0.005 0.001 HIS A 521 PHE 0.006 0.001 PHE C 407 TYR 0.009 0.001 TYR C 271 ARG 0.002 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 1056) hydrogen bonds : angle 3.15549 ( 3012) covalent geometry : bond 0.00205 (20192) covalent geometry : angle 0.48793 (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 407 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 354 time to evaluate : 3.181 Fit side-chains REVERT: A 173 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 189 ASP cc_start: 0.7712 (t0) cc_final: 0.7189 (t0) REVERT: A 191 HIS cc_start: 0.8213 (m170) cc_final: 0.7836 (m-70) REVERT: A 312 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8301 (ttp80) REVERT: A 371 ARG cc_start: 0.7949 (mmt90) cc_final: 0.7083 (mmp-170) REVERT: A 388 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7906 (ttt180) REVERT: A 394 PHE cc_start: 0.8313 (m-80) cc_final: 0.8097 (m-80) REVERT: A 433 MET cc_start: 0.7705 (tpt) cc_final: 0.7420 (tpp) REVERT: A 528 MET cc_start: 0.5786 (mpt) cc_final: 0.5097 (mpp) REVERT: A 645 MET cc_start: 0.7403 (tpp) cc_final: 0.7081 (ttp) REVERT: A 708 GLU cc_start: 0.8595 (tt0) cc_final: 0.8275 (mt-10) REVERT: B 173 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B 189 ASP cc_start: 0.7719 (t0) cc_final: 0.7204 (t0) REVERT: B 191 HIS cc_start: 0.8226 (m170) cc_final: 0.7820 (m-70) REVERT: B 371 ARG cc_start: 0.7958 (mmt90) cc_final: 0.7099 (mmp-170) REVERT: B 388 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7851 (mtm180) REVERT: B 394 PHE cc_start: 0.8314 (m-80) cc_final: 0.8095 (m-80) REVERT: B 433 MET cc_start: 0.7688 (tpt) cc_final: 0.7393 (tpp) REVERT: B 528 MET cc_start: 0.5788 (mpt) cc_final: 0.5061 (mpp) REVERT: B 708 GLU cc_start: 0.8602 (tt0) cc_final: 0.8284 (mt-10) REVERT: C 173 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 189 ASP cc_start: 0.7660 (t0) cc_final: 0.7173 (t0) REVERT: C 191 HIS cc_start: 0.8194 (m170) cc_final: 0.7821 (m-70) REVERT: C 371 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7109 (mmp-170) REVERT: C 388 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7909 (ttt180) REVERT: C 394 PHE cc_start: 0.8322 (m-80) cc_final: 0.8094 (m-80) REVERT: C 528 MET cc_start: 0.5841 (mpt) cc_final: 0.5139 (mpp) REVERT: C 708 GLU cc_start: 0.8589 (tt0) cc_final: 0.8276 (mt-10) REVERT: D 160 GLU cc_start: 0.7984 (tp30) cc_final: 0.7050 (pt0) REVERT: D 173 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7598 (tm-30) REVERT: D 189 ASP cc_start: 0.7666 (t0) cc_final: 0.7183 (t0) REVERT: D 191 HIS cc_start: 0.8215 (m170) cc_final: 0.7839 (m-70) REVERT: D 312 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8308 (ttp80) REVERT: D 371 ARG cc_start: 0.7945 (mmt90) cc_final: 0.7085 (mmp-170) REVERT: D 388 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7897 (ttt180) REVERT: D 520 GLN cc_start: 0.6616 (pm20) cc_final: 0.6395 (pm20) REVERT: D 528 MET cc_start: 0.5797 (mpt) cc_final: 0.5070 (mpp) REVERT: D 645 MET cc_start: 0.7374 (tpp) cc_final: 0.7014 (ttp) outliers start: 53 outliers final: 30 residues processed: 385 average time/residue: 1.3083 time to fit residues: 586.2488 Evaluate side-chains 378 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 522 THR Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 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 555 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: 4.9990 chunk 50 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 218 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 655 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.147603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.115064 restraints weight = 23561.545| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.87 r_work: 0.3150 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3052 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= 0.172 Angle : 0.573 8.995 27396 Z= 0.285 Chirality : 0.040 0.227 3132 Planarity : 0.004 0.035 3352 Dihedral : 6.255 70.516 2784 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.74 % Allowed : 20.45 % Favored : 75.81 % 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: 1.30 (0.17), residues: 2412 helix: 1.96 (0.13), residues: 1456 sheet: 0.58 (0.56), residues: 88 loop : -1.06 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 223 HIS 0.005 0.001 HIS A 521 PHE 0.013 0.001 PHE D 394 TYR 0.011 0.001 TYR B 525 ARG 0.003 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1056) hydrogen bonds : angle 3.41010 ( 3012) covalent geometry : bond 0.00412 (20192) covalent geometry : angle 0.57314 (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 416 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 338 time to evaluate : 1.936 Fit side-chains REVERT: A 173 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7675 (tm-30) REVERT: A 189 ASP cc_start: 0.7717 (t0) cc_final: 0.7216 (t0) REVERT: A 191 HIS cc_start: 0.8283 (m170) cc_final: 0.7962 (m-70) REVERT: A 371 ARG cc_start: 0.8018 (mmt90) cc_final: 0.7205 (mmp-170) REVERT: A 388 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7787 (mmm-85) REVERT: A 433 MET cc_start: 0.7726 (tpt) cc_final: 0.7439 (tpp) REVERT: A 538 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8015 (mp) REVERT: B 123 LYS cc_start: 0.7938 (tptm) cc_final: 0.7630 (tptm) REVERT: B 173 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 189 ASP cc_start: 0.7715 (t0) cc_final: 0.7198 (t0) REVERT: B 371 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7215 (mmp-170) REVERT: B 388 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7765 (mmm-85) REVERT: B 433 MET cc_start: 0.7660 (tpt) cc_final: 0.7360 (tpp) REVERT: B 520 GLN cc_start: 0.6815 (pm20) cc_final: 0.6473 (pm20) REVERT: C 173 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7677 (tm-30) REVERT: C 189 ASP cc_start: 0.7647 (t0) cc_final: 0.7150 (t0) REVERT: C 191 HIS cc_start: 0.8275 (m170) cc_final: 0.7831 (m-70) REVERT: C 371 ARG cc_start: 0.8017 (mmt90) cc_final: 0.7206 (mmp-170) REVERT: C 388 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7772 (mmm-85) REVERT: C 406 ILE cc_start: 0.8778 (mm) cc_final: 0.8567 (mt) REVERT: C 433 MET cc_start: 0.7694 (tpt) cc_final: 0.7404 (tpp) REVERT: C 479 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8684 (tm130) REVERT: C 520 GLN cc_start: 0.6798 (pm20) cc_final: 0.6455 (pm20) REVERT: D 123 LYS cc_start: 0.7946 (tptm) cc_final: 0.7651 (tptm) REVERT: D 173 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7672 (tm-30) REVERT: D 189 ASP cc_start: 0.7654 (t0) cc_final: 0.7161 (t0) REVERT: D 191 HIS cc_start: 0.8270 (m170) cc_final: 0.7844 (m-70) REVERT: D 371 ARG cc_start: 0.8017 (mmt90) cc_final: 0.7206 (mmp-170) REVERT: D 388 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7764 (mmm-85) REVERT: D 406 ILE cc_start: 0.8766 (mm) cc_final: 0.8556 (mt) REVERT: D 479 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: D 520 GLN cc_start: 0.6855 (pm20) cc_final: 0.6568 (pm20) outliers start: 78 outliers final: 46 residues processed: 377 average time/residue: 1.0750 time to fit residues: 466.9849 Evaluate side-chains 376 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 323 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 538 LEU 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 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 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 479 GLN Chi-restraints excluded: chain C residue 522 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 127 ASN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 479 GLN Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain D residue 727 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 185 optimal weight: 9.9990 chunk 112 optimal weight: 0.4980 chunk 125 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 184 optimal weight: 0.0170 chunk 203 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.150465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118790 restraints weight = 23463.683| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.75 r_work: 0.3148 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20192 Z= 0.109 Angle : 0.524 9.688 27396 Z= 0.261 Chirality : 0.038 0.236 3132 Planarity : 0.004 0.034 3352 Dihedral : 5.960 72.550 2784 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.59 % Allowed : 22.61 % 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: 1.48 (0.17), residues: 2412 helix: 2.11 (0.13), residues: 1472 sheet: 0.59 (0.57), residues: 88 loop : -1.06 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.004 0.001 HIS B 521 PHE 0.006 0.001 PHE A 407 TYR 0.009 0.001 TYR D 271 ARG 0.003 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 1056) hydrogen bonds : angle 3.25200 ( 3012) covalent geometry : bond 0.00255 (20192) covalent geometry : angle 0.52405 (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 413 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 359 time to evaluate : 2.004 Fit side-chains REVERT: A 173 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 189 ASP cc_start: 0.7663 (t0) cc_final: 0.7121 (t0) REVERT: A 191 HIS cc_start: 0.8212 (m170) cc_final: 0.7818 (m-70) REVERT: A 371 ARG cc_start: 0.7935 (mmt90) cc_final: 0.7094 (mmp-170) REVERT: A 388 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7649 (mtm-85) REVERT: A 406 ILE cc_start: 0.8729 (mm) cc_final: 0.8513 (mt) REVERT: A 433 MET cc_start: 0.7734 (tpt) cc_final: 0.7450 (tpp) REVERT: A 528 MET cc_start: 0.5916 (mpt) cc_final: 0.5158 (mpp) REVERT: A 538 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7896 (mp) REVERT: A 708 GLU cc_start: 0.8595 (tt0) cc_final: 0.8300 (mt-10) REVERT: B 173 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 189 ASP cc_start: 0.7663 (t0) cc_final: 0.7126 (t0) REVERT: B 191 HIS cc_start: 0.8242 (m170) cc_final: 0.7868 (m-70) REVERT: B 371 ARG cc_start: 0.7970 (mmt90) cc_final: 0.7144 (mmp-170) REVERT: B 388 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7591 (mtm-85) REVERT: B 406 ILE cc_start: 0.8754 (mm) cc_final: 0.8524 (mt) REVERT: B 433 MET cc_start: 0.7695 (tpt) cc_final: 0.7399 (tpp) REVERT: B 520 GLN cc_start: 0.6666 (pm20) cc_final: 0.6457 (pm20) REVERT: B 708 GLU cc_start: 0.8573 (tt0) cc_final: 0.8292 (mt-10) REVERT: C 173 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7648 (tm-30) REVERT: C 189 ASP cc_start: 0.7614 (t0) cc_final: 0.7075 (t0) REVERT: C 191 HIS cc_start: 0.8201 (m170) cc_final: 0.7840 (m-70) REVERT: C 371 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7142 (mmp-170) REVERT: C 388 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7653 (mtm-85) REVERT: C 406 ILE cc_start: 0.8723 (mm) cc_final: 0.8500 (mt) REVERT: C 520 GLN cc_start: 0.6667 (pm20) cc_final: 0.6334 (pm20) REVERT: D 123 LYS cc_start: 0.7758 (tptm) cc_final: 0.7471 (tptm) REVERT: D 173 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7638 (tm-30) REVERT: D 189 ASP cc_start: 0.7625 (t0) cc_final: 0.7093 (t0) REVERT: D 191 HIS cc_start: 0.8225 (m170) cc_final: 0.7885 (m-70) REVERT: D 371 ARG cc_start: 0.7933 (mmt90) cc_final: 0.7098 (mmp-170) REVERT: D 388 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7621 (mtm-85) REVERT: D 406 ILE cc_start: 0.8738 (mm) cc_final: 0.8525 (mt) REVERT: D 520 GLN cc_start: 0.6629 (pm20) cc_final: 0.6421 (pm20) outliers start: 54 outliers final: 35 residues processed: 383 average time/residue: 1.0393 time to fit residues: 461.8028 Evaluate side-chains 389 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 349 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU 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 522 THR Chi-restraints excluded: chain C residue 709 GLU 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 522 THR 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: 0.7980 chunk 164 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.150055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.118536 restraints weight = 23324.541| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.73 r_work: 0.3150 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20192 Z= 0.125 Angle : 0.548 10.357 27396 Z= 0.271 Chirality : 0.038 0.243 3132 Planarity : 0.004 0.034 3352 Dihedral : 6.011 71.685 2784 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.35 % Allowed : 23.18 % Favored : 74.47 % 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: 1.45 (0.17), residues: 2412 helix: 2.10 (0.13), residues: 1472 sheet: 0.53 (0.57), residues: 88 loop : -1.07 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 223 HIS 0.004 0.001 HIS B 521 PHE 0.006 0.001 PHE A 199 TYR 0.010 0.001 TYR C 403 ARG 0.002 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 1056) hydrogen bonds : angle 3.28365 ( 3012) covalent geometry : bond 0.00299 (20192) covalent geometry : angle 0.54838 (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 395 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 346 time to evaluate : 1.964 Fit side-chains REVERT: A 160 GLU cc_start: 0.8122 (tp30) cc_final: 0.7258 (pt0) REVERT: A 173 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7651 (tm-30) REVERT: A 189 ASP cc_start: 0.7663 (t0) cc_final: 0.7151 (t0) REVERT: A 191 HIS cc_start: 0.8237 (m170) cc_final: 0.7879 (m-70) REVERT: A 371 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7180 (mmp-170) REVERT: A 388 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7632 (mtm-85) REVERT: A 433 MET cc_start: 0.7720 (tpt) cc_final: 0.7441 (tpp) REVERT: A 538 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 645 MET cc_start: 0.7228 (tpp) cc_final: 0.6862 (ttp) REVERT: A 708 GLU cc_start: 0.8599 (tt0) cc_final: 0.8308 (mt-10) REVERT: B 123 LYS cc_start: 0.7839 (tptm) cc_final: 0.7529 (tptm) REVERT: B 173 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7687 (tm-30) REVERT: B 189 ASP cc_start: 0.7664 (t0) cc_final: 0.7152 (t0) REVERT: B 191 HIS cc_start: 0.8217 (m170) cc_final: 0.7873 (m-70) REVERT: B 371 ARG cc_start: 0.8019 (mmt90) cc_final: 0.7214 (mmp-170) REVERT: B 388 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7622 (mtm-85) REVERT: B 433 MET cc_start: 0.7685 (tpt) cc_final: 0.7400 (tpp) REVERT: B 520 GLN cc_start: 0.6779 (pm20) cc_final: 0.6553 (pm20) REVERT: B 645 MET cc_start: 0.7568 (tmm) cc_final: 0.7050 (mtm) REVERT: B 708 GLU cc_start: 0.8600 (tt0) cc_final: 0.8309 (mt-10) REVERT: C 173 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7643 (tm-30) REVERT: C 189 ASP cc_start: 0.7624 (t0) cc_final: 0.7112 (t0) REVERT: C 191 HIS cc_start: 0.8224 (m170) cc_final: 0.7846 (m-70) REVERT: C 371 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7210 (mmp-170) REVERT: C 388 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7675 (mtm-85) REVERT: C 406 ILE cc_start: 0.8812 (mm) cc_final: 0.8593 (mt) REVERT: C 520 GLN cc_start: 0.6731 (pm20) cc_final: 0.6378 (pm20) REVERT: D 123 LYS cc_start: 0.7832 (tptm) cc_final: 0.7550 (tptm) REVERT: D 173 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7649 (tm-30) REVERT: D 189 ASP cc_start: 0.7663 (t0) cc_final: 0.7126 (t0) REVERT: D 191 HIS cc_start: 0.8242 (m170) cc_final: 0.7909 (m-70) REVERT: D 371 ARG cc_start: 0.7988 (mmt90) cc_final: 0.7189 (mmp-170) REVERT: D 388 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7757 (mmm-85) REVERT: D 520 GLN cc_start: 0.6713 (pm20) cc_final: 0.6487 (pm20) outliers start: 49 outliers final: 40 residues processed: 366 average time/residue: 1.0280 time to fit residues: 435.6510 Evaluate side-chains 388 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 343 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 388 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 727 SER 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 522 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 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 522 THR Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 147 optimal weight: 0.7980 chunk 212 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 127 optimal weight: 0.0170 chunk 74 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.151542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.119197 restraints weight = 23489.093| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.88 r_work: 0.3188 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.003 0.036 20192 Z= 0.107 Angle : 0.529 10.382 27396 Z= 0.261 Chirality : 0.037 0.242 3132 Planarity : 0.004 0.034 3352 Dihedral : 5.876 72.862 2784 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.68 % Allowed : 22.89 % Favored : 74.43 % 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: 1.58 (0.17), residues: 2412 helix: 2.20 (0.13), residues: 1472 sheet: 0.54 (0.57), residues: 88 loop : -1.03 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 223 HIS 0.004 0.001 HIS B 521 PHE 0.006 0.001 PHE D 407 TYR 0.009 0.001 TYR D 271 ARG 0.002 0.000 ARG D 560 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 1056) hydrogen bonds : angle 3.21783 ( 3012) covalent geometry : bond 0.00251 (20192) covalent geometry : angle 0.52866 (27396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16570.37 seconds wall clock time: 292 minutes 35.26 seconds (17555.26 seconds total)