Starting phenix.real_space_refine on Mon Dec 30 03:05:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gn5_34155/12_2024/8gn5_34155.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gn5_34155/12_2024/8gn5_34155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gn5_34155/12_2024/8gn5_34155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gn5_34155/12_2024/8gn5_34155.map" model { file = "/net/cci-nas-00/data/ceres_data/8gn5_34155/12_2024/8gn5_34155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gn5_34155/12_2024/8gn5_34155.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 7588 2.51 5 N 2108 2.21 5 O 2348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376} Chain breaks: 1 Chain: "B" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376} Chain breaks: 1 Chain: "C" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376} Chain breaks: 1 Chain: "D" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 376} Chain breaks: 1 Time building chain proxies: 7.48, per 1000 atoms: 0.62 Number of scatterers: 12096 At special positions: 0 Unit cell: (137.747, 103.96, 166.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2348 8.00 N 2108 7.00 C 7588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.8 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 28 sheets defined 22.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 7 through 24 removed outlier: 4.066A pdb=" N LEU A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 30 removed outlier: 3.522A pdb=" N ALA A 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 removed outlier: 4.258A pdb=" N ARG A 95 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 127 removed outlier: 4.797A pdb=" N ARG A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 removed outlier: 4.152A pdb=" N ASP A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N MET A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 4.397A pdb=" N LYS A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.511A pdb=" N ALA A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'B' and resid 8 through 22 removed outlier: 4.516A pdb=" N ASP B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.600A pdb=" N ARG B 95 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 127 removed outlier: 4.278A pdb=" N ARG B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 104 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 removed outlier: 4.410A pdb=" N ASP B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N MET B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.563A pdb=" N LYS B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'C' and resid 7 through 23 removed outlier: 4.080A pdb=" N LEU C 11 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 18 " --> pdb=" O ASP C 14 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 21 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 91 through 95 removed outlier: 4.148A pdb=" N ARG C 95 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 127 removed outlier: 4.676A pdb=" N ARG C 102 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 104 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.805A pdb=" N ASP C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N MET C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 178 removed outlier: 3.951A pdb=" N LYS C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'D' and resid 7 through 24 removed outlier: 4.181A pdb=" N LEU D 11 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 28 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 96 through 127 removed outlier: 4.412A pdb=" N ARG D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 104 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 157 removed outlier: 4.041A pdb=" N ASP D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.786A pdb=" N LYS D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.909A pdb=" N ALA D 326 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.827A pdb=" N LYS A 31 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A 360 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 414 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 removed outlier: 4.622A pdb=" N GLN A 58 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN B 84 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY B 403 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 89 removed outlier: 4.125A pdb=" N GLY A 403 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN A 389 " --> pdb=" O TRP A 410 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.352A pdb=" N LEU A 129 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A 425 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 131 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 351 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA7, first strand: chain 'A' and resid 257 through 260 removed outlier: 3.706A pdb=" N ARG A 299 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR A 309 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 297 " --> pdb=" O THR A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 281 removed outlier: 5.382A pdb=" N PHE A 280 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.600A pdb=" N ILE B 361 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 50 Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 132 removed outlier: 6.521A pdb=" N LEU B 129 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU B 425 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 131 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN B 351 " --> pdb=" O GLY B 424 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 352 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 241 through 243 Processing sheet with id=AB4, first strand: chain 'B' and resid 257 through 260 removed outlier: 3.795A pdb=" N ARG B 299 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR B 309 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL B 297 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 279 through 281 removed outlier: 5.520A pdb=" N PHE B 280 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.784A pdb=" N LYS C 31 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.200A pdb=" N LEU C 73 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 83 through 89 removed outlier: 3.601A pdb=" N GLY C 403 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN C 389 " --> pdb=" O TRP C 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 129 through 132 removed outlier: 6.407A pdb=" N LEU C 129 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU C 425 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 131 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LEU C 212 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR C 168 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AC2, first strand: chain 'C' and resid 257 through 260 removed outlier: 3.695A pdb=" N ARG C 299 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C 309 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL C 297 " --> pdb=" O THR C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 279 through 281 removed outlier: 5.102A pdb=" N PHE C 280 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 31 through 33 Processing sheet with id=AC5, first strand: chain 'D' and resid 46 through 51 removed outlier: 4.180A pdb=" N LEU D 73 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 83 through 89 removed outlier: 3.589A pdb=" N GLY D 403 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 402 " --> pdb=" O ASP D 397 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN D 389 " --> pdb=" O TRP D 410 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 377 " --> pdb=" O THR D 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 129 through 132 removed outlier: 6.401A pdb=" N LEU D 129 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU D 425 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE D 131 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC9, first strand: chain 'D' and resid 257 through 260 removed outlier: 3.704A pdb=" N ARG D 299 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR D 309 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL D 297 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 279 through 281 removed outlier: 5.613A pdb=" N PHE D 280 " --> pdb=" O LEU D 289 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1011 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: 3.77 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3853 1.34 - 1.46: 1717 1.46 - 1.58: 6653 1.58 - 1.71: 1 1.71 - 1.83: 100 Bond restraints: 12324 Sorted by residual: bond pdb=" CA ARG B 109 " pdb=" C ARG B 109 " ideal model delta sigma weight residual 1.524 1.585 -0.061 1.27e-02 6.20e+03 2.32e+01 bond pdb=" CA ARG A 406 " pdb=" C ARG A 406 " ideal model delta sigma weight residual 1.522 1.567 -0.045 1.14e-02 7.69e+03 1.59e+01 bond pdb=" CA ARG A 162 " pdb=" C ARG A 162 " ideal model delta sigma weight residual 1.531 1.580 -0.049 1.39e-02 5.18e+03 1.25e+01 bond pdb=" CA ARG B 162 " pdb=" C ARG B 162 " ideal model delta sigma weight residual 1.521 1.564 -0.043 1.23e-02 6.61e+03 1.24e+01 bond pdb=" CA ARG A 417 " pdb=" C ARG A 417 " ideal model delta sigma weight residual 1.524 1.566 -0.042 1.26e-02 6.30e+03 1.12e+01 ... (remaining 12319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11621 1.81 - 3.62: 4370 3.62 - 5.43: 690 5.43 - 7.23: 79 7.23 - 9.04: 8 Bond angle restraints: 16768 Sorted by residual: angle pdb=" N ARG B 90 " pdb=" CA ARG B 90 " pdb=" C ARG B 90 " ideal model delta sigma weight residual 110.33 101.78 8.55 1.29e+00 6.01e-01 4.39e+01 angle pdb=" CA ASP A 253 " pdb=" CB ASP A 253 " pdb=" CG ASP A 253 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.00e+00 1.00e+00 4.08e+01 angle pdb=" CA PHE C 256 " pdb=" CB PHE C 256 " pdb=" CG PHE C 256 " ideal model delta sigma weight residual 113.80 119.79 -5.99 1.00e+00 1.00e+00 3.58e+01 angle pdb=" N ARG A 90 " pdb=" CA ARG A 90 " pdb=" C ARG A 90 " ideal model delta sigma weight residual 110.41 103.08 7.33 1.23e+00 6.61e-01 3.55e+01 angle pdb=" CA ASP B 347 " pdb=" CB ASP B 347 " pdb=" CG ASP B 347 " ideal model delta sigma weight residual 112.60 118.23 -5.63 1.00e+00 1.00e+00 3.17e+01 ... (remaining 16763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6854 17.87 - 35.75: 487 35.75 - 53.62: 65 53.62 - 71.49: 23 71.49 - 89.36: 11 Dihedral angle restraints: 7440 sinusoidal: 2868 harmonic: 4572 Sorted by residual: dihedral pdb=" CA ASN C 84 " pdb=" C ASN C 84 " pdb=" N ASP C 85 " pdb=" CA ASP C 85 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ASN B 84 " pdb=" C ASN B 84 " pdb=" N ASP B 85 " pdb=" CA ASP B 85 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ALA C 151 " pdb=" C ALA C 151 " pdb=" N GLU C 152 " pdb=" CA GLU C 152 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 7437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1029 0.069 - 0.138: 636 0.138 - 0.208: 203 0.208 - 0.277: 53 0.277 - 0.346: 19 Chirality restraints: 1940 Sorted by residual: chirality pdb=" CA THR C 221 " pdb=" N THR C 221 " pdb=" C THR C 221 " pdb=" CB THR C 221 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA THR A 260 " pdb=" N THR A 260 " pdb=" C THR A 260 " pdb=" CB THR A 260 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA THR A 221 " pdb=" N THR A 221 " pdb=" C THR A 221 " pdb=" CB THR A 221 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1937 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 410 " 0.132 2.00e-02 2.50e+03 6.92e-02 1.20e+02 pdb=" CG TRP B 410 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 410 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 410 " -0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP B 410 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP B 410 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 410 " -0.107 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 410 " 0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 410 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP B 410 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 410 " 0.126 2.00e-02 2.50e+03 6.00e-02 9.01e+01 pdb=" CG TRP A 410 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 410 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 410 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 410 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP A 410 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 410 " -0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 410 " 0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 410 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 410 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 410 " 0.114 2.00e-02 2.50e+03 5.66e-02 8.00e+01 pdb=" CG TRP C 410 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 410 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP C 410 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP C 410 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP C 410 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 410 " -0.063 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 410 " 0.076 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 410 " -0.035 2.00e-02 2.50e+03 pdb=" CH2 TRP C 410 " 0.050 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 523 2.75 - 3.29: 12244 3.29 - 3.83: 15994 3.83 - 4.36: 19935 4.36 - 4.90: 33011 Nonbonded interactions: 81707 Sorted by model distance: nonbonded pdb=" OE2 GLU B 52 " pdb=" NH1 ARG B 417 " model vdw 2.215 3.120 nonbonded pdb=" N ARG B 90 " pdb=" O ARG B 90 " model vdw 2.446 2.496 nonbonded pdb=" N ARG C 90 " pdb=" O ARG C 90 " model vdw 2.497 2.496 nonbonded pdb=" OE2 GLU B 15 " pdb=" NH1 ARG B 101 " model vdw 2.504 3.120 nonbonded pdb=" NH2 ARG A 162 " pdb=" O ASP A 356 " model vdw 2.507 3.120 ... (remaining 81702 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.060 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.012 0.061 12324 Z= 0.754 Angle : 1.811 9.043 16768 Z= 1.214 Chirality : 0.097 0.346 1940 Planarity : 0.012 0.097 2200 Dihedral : 13.402 89.362 4472 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.29 (0.19), residues: 1568 helix: -1.84 (0.27), residues: 250 sheet: -0.04 (0.26), residues: 344 loop : -0.87 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.132 0.022 TRP B 410 HIS 0.009 0.002 HIS B 287 PHE 0.101 0.014 PHE D 280 TYR 0.103 0.022 TYR A 175 ARG 0.007 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 680 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.9395 (p) cc_final: 0.9092 (t) REVERT: A 66 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7827 (mtmm) REVERT: A 93 ASP cc_start: 0.8780 (m-30) cc_final: 0.8415 (m-30) REVERT: A 121 ASN cc_start: 0.9135 (t0) cc_final: 0.8730 (t0) REVERT: A 169 PHE cc_start: 0.9110 (m-80) cc_final: 0.8835 (m-10) REVERT: A 216 LYS cc_start: 0.9274 (mmtt) cc_final: 0.8946 (mmtt) REVERT: A 284 MET cc_start: 0.8832 (mmt) cc_final: 0.8409 (mmt) REVERT: A 291 GLN cc_start: 0.8961 (pm20) cc_final: 0.8633 (pm20) REVERT: A 311 LYS cc_start: 0.9423 (tttt) cc_final: 0.8892 (tttp) REVERT: A 317 ASP cc_start: 0.8293 (t0) cc_final: 0.7451 (t0) REVERT: A 319 SER cc_start: 0.8898 (m) cc_final: 0.8556 (p) REVERT: A 321 SER cc_start: 0.8526 (t) cc_final: 0.8080 (t) REVERT: A 331 ASN cc_start: 0.8957 (t0) cc_final: 0.8599 (t0) REVERT: A 336 ASP cc_start: 0.9144 (t0) cc_final: 0.8944 (t70) REVERT: A 349 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.8068 (tpt-90) REVERT: A 356 ASP cc_start: 0.8799 (t0) cc_final: 0.8530 (t0) REVERT: A 357 ASP cc_start: 0.8637 (m-30) cc_final: 0.8187 (m-30) REVERT: A 359 ILE cc_start: 0.9279 (mt) cc_final: 0.8969 (mm) REVERT: B 45 ASN cc_start: 0.8674 (t0) cc_final: 0.8275 (t0) REVERT: B 48 TRP cc_start: 0.9173 (m100) cc_final: 0.8693 (m100) REVERT: B 135 ASP cc_start: 0.7792 (m-30) cc_final: 0.7560 (m-30) REVERT: B 180 TYR cc_start: 0.7959 (m-80) cc_final: 0.6696 (m-80) REVERT: B 213 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7644 (mtm-85) REVERT: B 230 VAL cc_start: 0.9173 (t) cc_final: 0.8887 (p) REVERT: B 249 LYS cc_start: 0.8410 (mtmt) cc_final: 0.8099 (mtpp) REVERT: B 284 MET cc_start: 0.8858 (mmm) cc_final: 0.8406 (mmt) REVERT: C 63 LEU cc_start: 0.7966 (mt) cc_final: 0.7729 (mp) REVERT: C 126 MET cc_start: 0.8437 (ttm) cc_final: 0.8090 (ttm) REVERT: C 143 ASP cc_start: 0.8340 (t70) cc_final: 0.8048 (t0) REVERT: C 145 TRP cc_start: 0.9426 (t60) cc_final: 0.9041 (t60) REVERT: C 279 LYS cc_start: 0.7771 (mttp) cc_final: 0.7156 (mmmt) REVERT: C 346 LYS cc_start: 0.8580 (tttt) cc_final: 0.8293 (ttmm) REVERT: C 359 ILE cc_start: 0.9236 (mt) cc_final: 0.8910 (mm) REVERT: C 389 ASN cc_start: 0.9165 (m-40) cc_final: 0.8481 (m110) REVERT: D 18 GLU cc_start: 0.8118 (tt0) cc_final: 0.7590 (mm-30) REVERT: D 42 ARG cc_start: 0.7543 (mmt180) cc_final: 0.7187 (mmt180) REVERT: D 96 ASP cc_start: 0.8308 (t0) cc_final: 0.7903 (t0) REVERT: D 116 GLU cc_start: 0.8181 (tt0) cc_final: 0.7980 (tt0) REVERT: D 126 MET cc_start: 0.8074 (ttm) cc_final: 0.7691 (ttp) REVERT: D 173 GLN cc_start: 0.7473 (tt0) cc_final: 0.7049 (tm-30) REVERT: D 216 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8624 (mmmt) REVERT: D 243 LEU cc_start: 0.8338 (mt) cc_final: 0.8073 (mt) REVERT: D 253 ASP cc_start: 0.7502 (t0) cc_final: 0.7103 (t0) REVERT: D 279 LYS cc_start: 0.8322 (mttt) cc_final: 0.7809 (mmtt) REVERT: D 292 ASP cc_start: 0.9191 (p0) cc_final: 0.8529 (p0) REVERT: D 349 ARG cc_start: 0.8869 (ttm-80) cc_final: 0.8509 (mtp-110) REVERT: D 362 VAL cc_start: 0.9547 (t) cc_final: 0.9152 (m) REVERT: D 377 LYS cc_start: 0.8951 (tppt) cc_final: 0.8691 (tptt) outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.2590 time to fit residues: 243.9693 Evaluate side-chains 515 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 chunk 141 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS A 370 HIS A 389 ASN A 428 GLN B 74 ASN B 84 ASN B 369 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12324 Z= 0.249 Angle : 0.655 6.759 16768 Z= 0.364 Chirality : 0.045 0.199 1940 Planarity : 0.004 0.039 2200 Dihedral : 6.676 49.110 1680 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.20), residues: 1568 helix: -0.98 (0.29), residues: 264 sheet: 0.20 (0.24), residues: 428 loop : -0.87 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 241 HIS 0.005 0.001 HIS D 287 PHE 0.016 0.002 PHE B 147 TYR 0.012 0.002 TYR A 411 ARG 0.005 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8871 (tttm) cc_final: 0.8441 (tttm) REVERT: A 46 THR cc_start: 0.9143 (p) cc_final: 0.8939 (p) REVERT: A 90 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7510 (mmm-85) REVERT: A 121 ASN cc_start: 0.9003 (t0) cc_final: 0.8655 (t0) REVERT: A 213 ARG cc_start: 0.8011 (ptt180) cc_final: 0.7480 (ptt180) REVERT: A 216 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8999 (mmtt) REVERT: A 284 MET cc_start: 0.8694 (mmt) cc_final: 0.8217 (mmt) REVERT: A 311 LYS cc_start: 0.9402 (tttt) cc_final: 0.8877 (tttm) REVERT: A 317 ASP cc_start: 0.8441 (t0) cc_final: 0.8007 (t0) REVERT: A 356 ASP cc_start: 0.8971 (t0) cc_final: 0.7899 (t0) REVERT: A 359 ILE cc_start: 0.9304 (mt) cc_final: 0.9051 (mm) REVERT: A 362 VAL cc_start: 0.9294 (t) cc_final: 0.9026 (m) REVERT: A 385 ASP cc_start: 0.9226 (p0) cc_final: 0.9023 (p0) REVERT: B 48 TRP cc_start: 0.9101 (m100) cc_final: 0.8709 (m100) REVERT: B 83 ASP cc_start: 0.9230 (t0) cc_final: 0.8692 (t0) REVERT: B 164 MET cc_start: 0.8156 (tpp) cc_final: 0.7524 (tpp) REVERT: B 249 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8162 (mtpt) REVERT: B 268 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8602 (mtpt) REVERT: B 289 LEU cc_start: 0.8810 (mm) cc_final: 0.8416 (mm) REVERT: C 40 MET cc_start: 0.8460 (ttm) cc_final: 0.8101 (ttt) REVERT: C 48 TRP cc_start: 0.9108 (m100) cc_final: 0.8870 (m100) REVERT: C 63 LEU cc_start: 0.8038 (mt) cc_final: 0.7823 (mp) REVERT: C 75 VAL cc_start: 0.8933 (t) cc_final: 0.8634 (t) REVERT: C 81 GLU cc_start: 0.7880 (mp0) cc_final: 0.7674 (mp0) REVERT: C 97 GLU cc_start: 0.8242 (tt0) cc_final: 0.7912 (tt0) REVERT: C 143 ASP cc_start: 0.7974 (t70) cc_final: 0.7412 (t0) REVERT: C 145 TRP cc_start: 0.9393 (t60) cc_final: 0.9137 (t60) REVERT: C 234 GLN cc_start: 0.8689 (mt0) cc_final: 0.8211 (mp-120) REVERT: C 241 TRP cc_start: 0.8333 (m100) cc_final: 0.8112 (m100) REVERT: C 279 LYS cc_start: 0.7908 (mttp) cc_final: 0.7697 (mmmt) REVERT: C 284 MET cc_start: 0.9412 (mmp) cc_final: 0.9126 (mmt) REVERT: C 344 ASN cc_start: 0.8131 (t0) cc_final: 0.7920 (t0) REVERT: C 359 ILE cc_start: 0.9251 (mt) cc_final: 0.8930 (mm) REVERT: C 389 ASN cc_start: 0.9208 (m-40) cc_final: 0.8290 (m110) REVERT: C 397 ASP cc_start: 0.7930 (t70) cc_final: 0.7628 (t70) REVERT: D 42 ARG cc_start: 0.7574 (mmt180) cc_final: 0.7318 (mmt180) REVERT: D 44 SER cc_start: 0.8776 (t) cc_final: 0.8407 (p) REVERT: D 85 ASP cc_start: 0.8897 (t0) cc_final: 0.8550 (t0) REVERT: D 118 LYS cc_start: 0.8885 (tppt) cc_final: 0.8298 (ttmt) REVERT: D 126 MET cc_start: 0.7931 (ttm) cc_final: 0.7724 (mtm) REVERT: D 163 ASP cc_start: 0.8446 (t0) cc_final: 0.8121 (t0) REVERT: D 173 GLN cc_start: 0.7902 (tt0) cc_final: 0.7247 (tm-30) REVERT: D 174 ASP cc_start: 0.8638 (m-30) cc_final: 0.8426 (m-30) REVERT: D 216 LYS cc_start: 0.9269 (mmtt) cc_final: 0.8680 (mmmt) REVERT: D 241 TRP cc_start: 0.7574 (m100) cc_final: 0.7156 (m100) REVERT: D 243 LEU cc_start: 0.8219 (mt) cc_final: 0.7956 (mt) REVERT: D 253 ASP cc_start: 0.7639 (t0) cc_final: 0.7427 (t0) REVERT: D 279 LYS cc_start: 0.8190 (mttt) cc_final: 0.7856 (mmmt) REVERT: D 292 ASP cc_start: 0.9225 (p0) cc_final: 0.8608 (p0) REVERT: D 338 MET cc_start: 0.7078 (mmt) cc_final: 0.6727 (mmm) REVERT: D 349 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8530 (mtt-85) REVERT: D 357 ASP cc_start: 0.8665 (t70) cc_final: 0.8248 (t70) REVERT: D 371 GLU cc_start: 0.8861 (pp20) cc_final: 0.8249 (pp20) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.2238 time to fit residues: 181.9706 Evaluate side-chains 479 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.0870 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 0.0470 chunk 48 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 370 HIS B 389 ASN C 88 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN D 74 ASN D 305 HIS D 364 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12324 Z= 0.185 Angle : 0.575 7.794 16768 Z= 0.311 Chirality : 0.043 0.184 1940 Planarity : 0.004 0.049 2200 Dihedral : 5.676 51.275 1680 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.68 (0.20), residues: 1568 helix: -0.49 (0.29), residues: 276 sheet: 0.32 (0.25), residues: 420 loop : -0.80 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 354 HIS 0.003 0.001 HIS D 287 PHE 0.015 0.002 PHE B 170 TYR 0.024 0.002 TYR D 100 ARG 0.007 0.001 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7574 (mmm-85) REVERT: A 121 ASN cc_start: 0.8951 (t0) cc_final: 0.8611 (t0) REVERT: A 213 ARG cc_start: 0.7938 (ptt180) cc_final: 0.7635 (ptt180) REVERT: A 284 MET cc_start: 0.8681 (mmt) cc_final: 0.8288 (mmt) REVERT: A 311 LYS cc_start: 0.9430 (tttt) cc_final: 0.8947 (tttm) REVERT: A 317 ASP cc_start: 0.8352 (t0) cc_final: 0.8011 (t0) REVERT: B 48 TRP cc_start: 0.9095 (m100) cc_final: 0.8685 (m100) REVERT: B 249 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8224 (mtpp) REVERT: B 268 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8609 (mtpt) REVERT: B 289 LEU cc_start: 0.8885 (mm) cc_final: 0.8348 (mm) REVERT: B 338 MET cc_start: 0.8608 (mmm) cc_final: 0.7829 (tpp) REVERT: B 349 ARG cc_start: 0.8813 (ttm-80) cc_final: 0.8505 (ttt-90) REVERT: B 361 ILE cc_start: 0.9427 (mt) cc_final: 0.9199 (mm) REVERT: C 40 MET cc_start: 0.8137 (ttm) cc_final: 0.7639 (ttt) REVERT: C 71 LEU cc_start: 0.8517 (tp) cc_final: 0.8157 (tt) REVERT: C 81 GLU cc_start: 0.7896 (mp0) cc_final: 0.7672 (mp0) REVERT: C 88 GLN cc_start: 0.7798 (pt0) cc_final: 0.7542 (pt0) REVERT: C 145 TRP cc_start: 0.9318 (t60) cc_final: 0.9113 (t60) REVERT: C 159 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7799 (mt-10) REVERT: C 279 LYS cc_start: 0.7972 (mttp) cc_final: 0.7433 (mmmt) REVERT: C 357 ASP cc_start: 0.8581 (t0) cc_final: 0.8372 (t0) REVERT: C 359 ILE cc_start: 0.9174 (mt) cc_final: 0.8870 (mm) REVERT: C 376 MET cc_start: 0.7087 (ttm) cc_final: 0.6883 (ttm) REVERT: C 389 ASN cc_start: 0.9230 (m-40) cc_final: 0.8777 (m-40) REVERT: D 42 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7085 (mmt180) REVERT: D 44 SER cc_start: 0.8598 (t) cc_final: 0.8298 (p) REVERT: D 71 LEU cc_start: 0.7450 (tp) cc_final: 0.7212 (tp) REVERT: D 85 ASP cc_start: 0.8659 (t0) cc_final: 0.8376 (t0) REVERT: D 118 LYS cc_start: 0.8889 (tppt) cc_final: 0.8322 (ttmm) REVERT: D 133 SER cc_start: 0.8297 (m) cc_final: 0.7946 (p) REVERT: D 216 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8239 (mmmt) REVERT: D 234 GLN cc_start: 0.7868 (mp10) cc_final: 0.7594 (mp10) REVERT: D 241 TRP cc_start: 0.7700 (m100) cc_final: 0.7429 (m100) REVERT: D 243 LEU cc_start: 0.8368 (mt) cc_final: 0.8067 (mm) REVERT: D 279 LYS cc_start: 0.8166 (mttt) cc_final: 0.7804 (mmmt) REVERT: D 292 ASP cc_start: 0.9211 (p0) cc_final: 0.8621 (p0) REVERT: D 338 MET cc_start: 0.7120 (mmt) cc_final: 0.6740 (mmm) REVERT: D 349 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8498 (ttm-80) REVERT: D 357 ASP cc_start: 0.8516 (t70) cc_final: 0.8017 (t70) REVERT: D 371 GLU cc_start: 0.8847 (pp20) cc_final: 0.8493 (pp20) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.2216 time to fit residues: 175.5739 Evaluate side-chains 480 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 9.9990 chunk 106 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 overall best weight: 2.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 74 ASN C 161 ASN C 251 ASN D 74 ASN D 364 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12324 Z= 0.194 Angle : 0.565 8.982 16768 Z= 0.302 Chirality : 0.043 0.193 1940 Planarity : 0.004 0.045 2200 Dihedral : 5.302 48.899 1680 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.53 (0.20), residues: 1568 helix: -0.17 (0.30), residues: 270 sheet: 0.35 (0.25), residues: 422 loop : -0.73 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 354 HIS 0.003 0.001 HIS D 287 PHE 0.023 0.001 PHE B 86 TYR 0.015 0.001 TYR C 100 ARG 0.007 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8483 (ttpp) REVERT: A 121 ASN cc_start: 0.8904 (t0) cc_final: 0.8603 (t0) REVERT: A 164 MET cc_start: 0.7206 (mpp) cc_final: 0.6951 (mmm) REVERT: A 284 MET cc_start: 0.8704 (mmt) cc_final: 0.8329 (mmt) REVERT: A 311 LYS cc_start: 0.9486 (tttt) cc_final: 0.8992 (tttm) REVERT: A 317 ASP cc_start: 0.8302 (t0) cc_final: 0.8030 (t0) REVERT: B 15 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7971 (mm-30) REVERT: B 48 TRP cc_start: 0.9114 (m100) cc_final: 0.8715 (m100) REVERT: B 73 LEU cc_start: 0.9206 (mt) cc_final: 0.8971 (mt) REVERT: B 249 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8209 (mtpp) REVERT: B 268 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8606 (mtpt) REVERT: B 361 ILE cc_start: 0.9438 (mt) cc_final: 0.9174 (mm) REVERT: C 71 LEU cc_start: 0.8522 (tp) cc_final: 0.8072 (tt) REVERT: C 81 GLU cc_start: 0.7884 (mp0) cc_final: 0.7681 (mp0) REVERT: C 217 LEU cc_start: 0.8985 (mt) cc_final: 0.8761 (mt) REVERT: C 279 LYS cc_start: 0.7871 (mttp) cc_final: 0.7371 (mmmt) REVERT: C 327 TYR cc_start: 0.8612 (m-80) cc_final: 0.8088 (m-10) REVERT: C 344 ASN cc_start: 0.8087 (t0) cc_final: 0.7828 (t0) REVERT: C 359 ILE cc_start: 0.9247 (mt) cc_final: 0.8939 (mm) REVERT: C 361 ILE cc_start: 0.9478 (mt) cc_final: 0.9206 (mm) REVERT: C 376 MET cc_start: 0.7062 (ttm) cc_final: 0.6858 (ttm) REVERT: C 389 ASN cc_start: 0.9199 (m-40) cc_final: 0.8655 (m110) REVERT: D 42 ARG cc_start: 0.7453 (mmt180) cc_final: 0.7063 (mmt180) REVERT: D 44 SER cc_start: 0.8633 (t) cc_final: 0.8326 (p) REVERT: D 72 GLU cc_start: 0.7831 (tt0) cc_final: 0.7615 (tt0) REVERT: D 116 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8155 (tm-30) REVERT: D 118 LYS cc_start: 0.8884 (tppt) cc_final: 0.8317 (ttmm) REVERT: D 133 SER cc_start: 0.8329 (m) cc_final: 0.8006 (p) REVERT: D 241 TRP cc_start: 0.7826 (m100) cc_final: 0.7535 (m100) REVERT: D 242 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7067 (tm-30) REVERT: D 243 LEU cc_start: 0.8457 (mt) cc_final: 0.8040 (mm) REVERT: D 279 LYS cc_start: 0.8078 (mttt) cc_final: 0.7781 (mmmt) REVERT: D 292 ASP cc_start: 0.9202 (p0) cc_final: 0.8539 (p0) REVERT: D 338 MET cc_start: 0.7156 (mmt) cc_final: 0.6770 (mmm) REVERT: D 349 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.8422 (tpp-160) REVERT: D 357 ASP cc_start: 0.8554 (t70) cc_final: 0.8048 (t70) REVERT: D 370 HIS cc_start: 0.8854 (m-70) cc_final: 0.8464 (m90) REVERT: D 371 GLU cc_start: 0.8947 (pp20) cc_final: 0.8373 (pp20) REVERT: D 376 MET cc_start: 0.8464 (ttm) cc_final: 0.8229 (ttm) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.2211 time to fit residues: 172.2604 Evaluate side-chains 487 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 2 optimal weight: 0.0570 chunk 112 optimal weight: 0.4980 chunk 62 optimal weight: 30.0000 chunk 128 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN B 74 ASN B 428 GLN C 88 GLN C 251 ASN C 414 ASN D 324 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12324 Z= 0.172 Angle : 0.545 6.778 16768 Z= 0.292 Chirality : 0.042 0.201 1940 Planarity : 0.004 0.045 2200 Dihedral : 5.089 48.736 1680 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.54 (0.20), residues: 1568 helix: -0.08 (0.30), residues: 276 sheet: 0.24 (0.25), residues: 432 loop : -0.72 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 410 HIS 0.003 0.001 HIS D 287 PHE 0.021 0.001 PHE B 156 TYR 0.014 0.001 TYR C 100 ARG 0.006 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8859 (t0) cc_final: 0.8539 (t0) REVERT: A 164 MET cc_start: 0.6748 (mpp) cc_final: 0.6462 (mpp) REVERT: A 284 MET cc_start: 0.8479 (mmt) cc_final: 0.8221 (mmt) REVERT: A 311 LYS cc_start: 0.9505 (tttt) cc_final: 0.9022 (tttm) REVERT: A 317 ASP cc_start: 0.8335 (t0) cc_final: 0.8096 (t0) REVERT: B 15 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7990 (mm-30) REVERT: B 48 TRP cc_start: 0.9042 (m100) cc_final: 0.8739 (m100) REVERT: B 118 LYS cc_start: 0.9191 (tppp) cc_final: 0.8923 (ttpt) REVERT: B 164 MET cc_start: 0.7907 (mmm) cc_final: 0.7065 (tpp) REVERT: B 268 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8617 (mtpt) REVERT: B 289 LEU cc_start: 0.8728 (mm) cc_final: 0.8255 (mm) REVERT: B 361 ILE cc_start: 0.9397 (mt) cc_final: 0.9169 (mm) REVERT: B 376 MET cc_start: 0.7584 (ttm) cc_final: 0.7365 (ttm) REVERT: C 71 LEU cc_start: 0.8504 (tp) cc_final: 0.8078 (tt) REVERT: C 217 LEU cc_start: 0.8932 (mt) cc_final: 0.8702 (mt) REVERT: C 234 GLN cc_start: 0.8805 (mt0) cc_final: 0.8421 (mp-120) REVERT: C 279 LYS cc_start: 0.7960 (mttp) cc_final: 0.7446 (mmmt) REVERT: C 327 TYR cc_start: 0.8567 (m-80) cc_final: 0.8071 (m-10) REVERT: C 338 MET cc_start: 0.7503 (mmt) cc_final: 0.6992 (mmt) REVERT: C 344 ASN cc_start: 0.8103 (t0) cc_final: 0.7654 (t0) REVERT: C 359 ILE cc_start: 0.9207 (mt) cc_final: 0.8906 (mm) REVERT: C 389 ASN cc_start: 0.9323 (m-40) cc_final: 0.8686 (m110) REVERT: D 42 ARG cc_start: 0.7447 (mmt180) cc_final: 0.7021 (mmt180) REVERT: D 44 SER cc_start: 0.8612 (t) cc_final: 0.8310 (p) REVERT: D 66 LYS cc_start: 0.7223 (mmtm) cc_final: 0.6670 (tppt) REVERT: D 116 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8161 (tm-30) REVERT: D 118 LYS cc_start: 0.8853 (tppt) cc_final: 0.8269 (ttmm) REVERT: D 133 SER cc_start: 0.8249 (m) cc_final: 0.7926 (p) REVERT: D 241 TRP cc_start: 0.7830 (m100) cc_final: 0.7546 (m100) REVERT: D 242 GLN cc_start: 0.7434 (tm-30) cc_final: 0.6674 (tm-30) REVERT: D 243 LEU cc_start: 0.8513 (mt) cc_final: 0.8004 (mm) REVERT: D 279 LYS cc_start: 0.8063 (mttt) cc_final: 0.7784 (mmmt) REVERT: D 292 ASP cc_start: 0.9193 (p0) cc_final: 0.8502 (p0) REVERT: D 324 GLN cc_start: 0.8768 (mt0) cc_final: 0.8342 (mp10) REVERT: D 338 MET cc_start: 0.7117 (mmt) cc_final: 0.6695 (mmm) REVERT: D 349 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8260 (ttt90) REVERT: D 370 HIS cc_start: 0.8849 (m-70) cc_final: 0.8430 (m90) REVERT: D 371 GLU cc_start: 0.8975 (pp20) cc_final: 0.8487 (pp20) REVERT: D 407 ILE cc_start: 0.7935 (pt) cc_final: 0.7614 (mt) outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 0.2207 time to fit residues: 179.3369 Evaluate side-chains 491 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN B 74 ASN B 428 GLN C 88 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN D 74 ASN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12324 Z= 0.175 Angle : 0.549 7.035 16768 Z= 0.291 Chirality : 0.042 0.205 1940 Planarity : 0.004 0.047 2200 Dihedral : 4.960 48.818 1680 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.46 (0.21), residues: 1568 helix: 0.19 (0.31), residues: 264 sheet: 0.31 (0.25), residues: 428 loop : -0.74 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 410 HIS 0.003 0.001 HIS D 287 PHE 0.015 0.001 PHE B 86 TYR 0.014 0.001 TYR C 100 ARG 0.006 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 553 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8855 (t0) cc_final: 0.8531 (t0) REVERT: A 126 MET cc_start: 0.8886 (ttp) cc_final: 0.8637 (ttm) REVERT: A 164 MET cc_start: 0.6548 (mpp) cc_final: 0.6135 (mpp) REVERT: A 249 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7839 (mtpt) REVERT: A 311 LYS cc_start: 0.9503 (tttt) cc_final: 0.9024 (tttm) REVERT: A 317 ASP cc_start: 0.8359 (t0) cc_final: 0.8126 (t0) REVERT: A 385 ASP cc_start: 0.9449 (p0) cc_final: 0.8993 (p0) REVERT: B 15 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 48 TRP cc_start: 0.9050 (m100) cc_final: 0.8793 (m100) REVERT: B 75 VAL cc_start: 0.9529 (m) cc_final: 0.9239 (p) REVERT: B 164 MET cc_start: 0.7950 (mmm) cc_final: 0.7214 (tpp) REVERT: B 175 TYR cc_start: 0.9132 (t80) cc_final: 0.8893 (t80) REVERT: B 268 LYS cc_start: 0.8919 (mtpt) cc_final: 0.8603 (mtpt) REVERT: B 289 LEU cc_start: 0.8669 (mm) cc_final: 0.8328 (mm) REVERT: B 361 ILE cc_start: 0.9447 (mt) cc_final: 0.9221 (mm) REVERT: B 376 MET cc_start: 0.7574 (ttm) cc_final: 0.7342 (ttm) REVERT: C 71 LEU cc_start: 0.8469 (tp) cc_final: 0.8042 (tt) REVERT: C 81 GLU cc_start: 0.7932 (mp0) cc_final: 0.7728 (mp0) REVERT: C 217 LEU cc_start: 0.8936 (mt) cc_final: 0.8671 (mt) REVERT: C 234 GLN cc_start: 0.8761 (mt0) cc_final: 0.8075 (mp10) REVERT: C 279 LYS cc_start: 0.7891 (mttp) cc_final: 0.7485 (mmmt) REVERT: C 327 TYR cc_start: 0.8614 (m-80) cc_final: 0.8058 (m-10) REVERT: C 338 MET cc_start: 0.7582 (mmt) cc_final: 0.7004 (mmt) REVERT: C 344 ASN cc_start: 0.8284 (t0) cc_final: 0.7812 (t0) REVERT: C 359 ILE cc_start: 0.9282 (mt) cc_final: 0.9006 (mm) REVERT: C 389 ASN cc_start: 0.9236 (m-40) cc_final: 0.8536 (m110) REVERT: D 42 ARG cc_start: 0.7504 (mmt180) cc_final: 0.7069 (mmt180) REVERT: D 44 SER cc_start: 0.8495 (t) cc_final: 0.8157 (p) REVERT: D 66 LYS cc_start: 0.7249 (mmtm) cc_final: 0.6676 (tppt) REVERT: D 116 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8216 (tm-30) REVERT: D 118 LYS cc_start: 0.8885 (tppt) cc_final: 0.8235 (ttmt) REVERT: D 216 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8890 (mmtt) REVERT: D 234 GLN cc_start: 0.7651 (mp10) cc_final: 0.7272 (mp10) REVERT: D 241 TRP cc_start: 0.7810 (m100) cc_final: 0.7542 (m100) REVERT: D 242 GLN cc_start: 0.7422 (tm-30) cc_final: 0.6933 (tm-30) REVERT: D 243 LEU cc_start: 0.8582 (mt) cc_final: 0.8258 (mm) REVERT: D 279 LYS cc_start: 0.7961 (mttt) cc_final: 0.7494 (mmmt) REVERT: D 292 ASP cc_start: 0.9189 (p0) cc_final: 0.8383 (p0) REVERT: D 338 MET cc_start: 0.7210 (mmt) cc_final: 0.6796 (mmm) REVERT: D 349 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8280 (ttt90) REVERT: D 370 HIS cc_start: 0.8857 (m-70) cc_final: 0.8402 (m90) REVERT: D 371 GLU cc_start: 0.8948 (pp20) cc_final: 0.8423 (pp20) REVERT: D 376 MET cc_start: 0.8451 (ttm) cc_final: 0.8225 (tpt) REVERT: D 407 ILE cc_start: 0.7956 (pt) cc_final: 0.7637 (mt) outliers start: 0 outliers final: 0 residues processed: 553 average time/residue: 0.2247 time to fit residues: 181.7102 Evaluate side-chains 506 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 0.0770 chunk 85 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 overall best weight: 3.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN A 242 GLN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN D 324 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12324 Z= 0.222 Angle : 0.578 11.508 16768 Z= 0.306 Chirality : 0.043 0.209 1940 Planarity : 0.004 0.055 2200 Dihedral : 5.070 47.893 1680 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.50 (0.21), residues: 1568 helix: 0.19 (0.31), residues: 270 sheet: 0.45 (0.26), residues: 414 loop : -0.87 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 410 HIS 0.003 0.001 HIS B 370 PHE 0.031 0.002 PHE B 156 TYR 0.017 0.002 TYR D 100 ARG 0.007 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 28 GLN cc_start: 0.9269 (tt0) cc_final: 0.8942 (tt0) REVERT: A 121 ASN cc_start: 0.8878 (t0) cc_final: 0.8579 (t0) REVERT: A 164 MET cc_start: 0.6508 (mpp) cc_final: 0.6102 (mpp) REVERT: A 311 LYS cc_start: 0.9514 (tttt) cc_final: 0.9044 (tttm) REVERT: A 317 ASP cc_start: 0.8419 (t0) cc_final: 0.8219 (t0) REVERT: A 385 ASP cc_start: 0.9516 (p0) cc_final: 0.9152 (p0) REVERT: B 15 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7894 (mm-30) REVERT: B 48 TRP cc_start: 0.9090 (m100) cc_final: 0.8805 (m100) REVERT: B 75 VAL cc_start: 0.9561 (m) cc_final: 0.9290 (p) REVERT: B 162 ARG cc_start: 0.8928 (tpp80) cc_final: 0.8711 (mmt-90) REVERT: B 164 MET cc_start: 0.7935 (mmm) cc_final: 0.7441 (tpp) REVERT: B 175 TYR cc_start: 0.9103 (t80) cc_final: 0.8878 (t80) REVERT: B 268 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8622 (mtpt) REVERT: B 320 LEU cc_start: 0.9253 (mp) cc_final: 0.9051 (mp) REVERT: B 361 ILE cc_start: 0.9423 (mt) cc_final: 0.9185 (mm) REVERT: B 376 MET cc_start: 0.7648 (ttm) cc_final: 0.7350 (ttm) REVERT: C 79 MET cc_start: 0.8517 (ptm) cc_final: 0.8303 (ptm) REVERT: C 81 GLU cc_start: 0.7925 (mp0) cc_final: 0.7686 (mp0) REVERT: C 152 GLU cc_start: 0.8819 (tp30) cc_final: 0.8405 (tp30) REVERT: C 155 MET cc_start: 0.8914 (ttp) cc_final: 0.8694 (ttp) REVERT: C 234 GLN cc_start: 0.8728 (mt0) cc_final: 0.8028 (mp10) REVERT: C 279 LYS cc_start: 0.8038 (mttp) cc_final: 0.7529 (mmmt) REVERT: C 327 TYR cc_start: 0.8655 (m-80) cc_final: 0.8266 (m-10) REVERT: C 344 ASN cc_start: 0.8261 (t0) cc_final: 0.8055 (t0) REVERT: C 359 ILE cc_start: 0.9304 (mt) cc_final: 0.9008 (mm) REVERT: C 389 ASN cc_start: 0.9203 (m-40) cc_final: 0.8413 (m110) REVERT: C 397 ASP cc_start: 0.8256 (t0) cc_final: 0.7947 (t70) REVERT: C 401 LEU cc_start: 0.8224 (mp) cc_final: 0.7977 (mp) REVERT: D 42 ARG cc_start: 0.7517 (mmt180) cc_final: 0.7070 (mmt180) REVERT: D 44 SER cc_start: 0.8533 (t) cc_final: 0.8207 (p) REVERT: D 66 LYS cc_start: 0.7288 (mmtm) cc_final: 0.6717 (tppt) REVERT: D 116 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8151 (tm-30) REVERT: D 118 LYS cc_start: 0.8830 (tppt) cc_final: 0.8274 (ttmt) REVERT: D 241 TRP cc_start: 0.7849 (m100) cc_final: 0.7511 (m100) REVERT: D 242 GLN cc_start: 0.7511 (tm-30) cc_final: 0.6966 (tm-30) REVERT: D 243 LEU cc_start: 0.8618 (mt) cc_final: 0.8278 (mm) REVERT: D 292 ASP cc_start: 0.9193 (p0) cc_final: 0.8511 (p0) REVERT: D 324 GLN cc_start: 0.8702 (mt0) cc_final: 0.8300 (mp10) REVERT: D 370 HIS cc_start: 0.8848 (m-70) cc_final: 0.8381 (m90) REVERT: D 371 GLU cc_start: 0.8968 (pp20) cc_final: 0.8397 (pp20) REVERT: D 382 SER cc_start: 0.8236 (p) cc_final: 0.8011 (p) outliers start: 0 outliers final: 0 residues processed: 537 average time/residue: 0.2294 time to fit residues: 180.9654 Evaluate side-chains 486 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 136 optimal weight: 40.0000 chunk 144 optimal weight: 8.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 84 ASN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 389 ASN C 88 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 395 GLN D 7 GLN D 74 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12324 Z= 0.302 Angle : 0.629 9.973 16768 Z= 0.334 Chirality : 0.044 0.220 1940 Planarity : 0.004 0.058 2200 Dihedral : 5.420 47.924 1680 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.59 (0.21), residues: 1568 helix: 0.10 (0.31), residues: 268 sheet: 0.38 (0.26), residues: 408 loop : -0.92 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 410 HIS 0.004 0.001 HIS B 287 PHE 0.021 0.002 PHE C 169 TYR 0.016 0.002 TYR D 100 ARG 0.006 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 28 GLN cc_start: 0.9261 (tt0) cc_final: 0.8954 (tt0) REVERT: A 46 THR cc_start: 0.9317 (p) cc_final: 0.9089 (t) REVERT: A 121 ASN cc_start: 0.8922 (t0) cc_final: 0.8630 (t0) REVERT: A 164 MET cc_start: 0.6615 (mpp) cc_final: 0.6398 (mpp) REVERT: A 311 LYS cc_start: 0.9460 (tttt) cc_final: 0.8973 (tttm) REVERT: A 385 ASP cc_start: 0.9505 (p0) cc_final: 0.9155 (p0) REVERT: B 15 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8094 (mm-30) REVERT: B 164 MET cc_start: 0.8021 (mmm) cc_final: 0.7494 (tpp) REVERT: B 268 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8608 (mtpt) REVERT: B 289 LEU cc_start: 0.8798 (mm) cc_final: 0.8449 (mm) REVERT: B 361 ILE cc_start: 0.9419 (mt) cc_final: 0.9178 (mm) REVERT: B 376 MET cc_start: 0.7781 (ttm) cc_final: 0.7465 (ttm) REVERT: C 81 GLU cc_start: 0.7959 (mp0) cc_final: 0.7725 (mp0) REVERT: C 152 GLU cc_start: 0.8897 (tp30) cc_final: 0.8446 (tp30) REVERT: C 155 MET cc_start: 0.9022 (ttp) cc_final: 0.8794 (ttp) REVERT: C 159 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7746 (mt-10) REVERT: C 234 GLN cc_start: 0.8740 (mt0) cc_final: 0.8057 (mp10) REVERT: C 279 LYS cc_start: 0.8047 (mttp) cc_final: 0.7549 (mmmt) REVERT: C 327 TYR cc_start: 0.8679 (m-80) cc_final: 0.8383 (m-10) REVERT: C 338 MET cc_start: 0.7780 (mmt) cc_final: 0.7351 (mmt) REVERT: C 344 ASN cc_start: 0.8440 (t0) cc_final: 0.8021 (t0) REVERT: C 359 ILE cc_start: 0.9314 (mt) cc_final: 0.9001 (mm) REVERT: C 389 ASN cc_start: 0.9183 (m-40) cc_final: 0.8881 (m110) REVERT: C 397 ASP cc_start: 0.8322 (t0) cc_final: 0.8096 (t70) REVERT: D 42 ARG cc_start: 0.7545 (mmt180) cc_final: 0.7061 (mmt180) REVERT: D 44 SER cc_start: 0.8415 (t) cc_final: 0.8027 (p) REVERT: D 66 LYS cc_start: 0.7441 (mmtm) cc_final: 0.6859 (tppt) REVERT: D 118 LYS cc_start: 0.8827 (tppt) cc_final: 0.8281 (ttmm) REVERT: D 216 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8359 (mmtt) REVERT: D 242 GLN cc_start: 0.7506 (tm-30) cc_final: 0.6882 (tm-30) REVERT: D 243 LEU cc_start: 0.8531 (mt) cc_final: 0.8147 (mm) REVERT: D 279 LYS cc_start: 0.7956 (mttm) cc_final: 0.7731 (mmtt) REVERT: D 292 ASP cc_start: 0.9220 (p0) cc_final: 0.8481 (p0) REVERT: D 349 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8094 (ttt90) REVERT: D 370 HIS cc_start: 0.8874 (m-70) cc_final: 0.8399 (m90) REVERT: D 371 GLU cc_start: 0.8975 (pp20) cc_final: 0.8406 (pp20) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.2165 time to fit residues: 171.8105 Evaluate side-chains 491 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 0.0470 chunk 110 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 92 optimal weight: 0.0040 overall best weight: 2.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 242 GLN B 74 ASN ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN C 84 ASN C 161 ASN D 84 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 GLN D 364 GLN D 428 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12324 Z= 0.175 Angle : 0.571 10.620 16768 Z= 0.300 Chirality : 0.043 0.229 1940 Planarity : 0.004 0.054 2200 Dihedral : 5.051 53.726 1680 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.15 % Allowed : 0.77 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.49 (0.21), residues: 1568 helix: 0.39 (0.31), residues: 264 sheet: 0.38 (0.26), residues: 414 loop : -0.88 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 410 HIS 0.004 0.001 HIS D 287 PHE 0.015 0.001 PHE B 86 TYR 0.021 0.001 TYR B 175 ARG 0.005 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 532 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8584 (pm20) cc_final: 0.7940 (pm20) REVERT: A 121 ASN cc_start: 0.8853 (t0) cc_final: 0.8557 (t0) REVERT: A 164 MET cc_start: 0.6627 (mpp) cc_final: 0.6392 (mpp) REVERT: A 249 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7436 (mtpt) REVERT: A 311 LYS cc_start: 0.9508 (tttt) cc_final: 0.9053 (tttm) REVERT: A 385 ASP cc_start: 0.9512 (p0) cc_final: 0.9266 (p0) REVERT: B 15 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7995 (mm-30) REVERT: B 162 ARG cc_start: 0.8721 (mmt-90) cc_final: 0.8491 (tpp80) REVERT: B 164 MET cc_start: 0.7907 (mmm) cc_final: 0.7441 (tpp) REVERT: B 234 GLN cc_start: 0.8986 (mt0) cc_final: 0.8379 (mp10) REVERT: B 268 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8572 (mtpt) REVERT: B 361 ILE cc_start: 0.9403 (mt) cc_final: 0.9159 (mm) REVERT: B 376 MET cc_start: 0.7168 (ttm) cc_final: 0.6898 (ttm) REVERT: C 143 ASP cc_start: 0.8157 (t0) cc_final: 0.7952 (t0) REVERT: C 152 GLU cc_start: 0.8885 (tp30) cc_final: 0.8382 (tp30) REVERT: C 159 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7647 (mt-10) REVERT: C 234 GLN cc_start: 0.8729 (mt0) cc_final: 0.8060 (mp10) REVERT: C 279 LYS cc_start: 0.8006 (mttp) cc_final: 0.7540 (mmmt) REVERT: C 338 MET cc_start: 0.7759 (mmt) cc_final: 0.7397 (mmt) REVERT: C 344 ASN cc_start: 0.8375 (t0) cc_final: 0.8016 (t0) REVERT: C 359 ILE cc_start: 0.9289 (mt) cc_final: 0.8975 (mm) REVERT: C 389 ASN cc_start: 0.9234 (m-40) cc_final: 0.8429 (m110) REVERT: C 397 ASP cc_start: 0.8215 (t0) cc_final: 0.7921 (t70) REVERT: D 42 ARG cc_start: 0.7368 (mmt180) cc_final: 0.6901 (mmt180) REVERT: D 44 SER cc_start: 0.8346 (t) cc_final: 0.8008 (p) REVERT: D 66 LYS cc_start: 0.7360 (mmtm) cc_final: 0.6788 (tppt) REVERT: D 77 VAL cc_start: 0.8828 (t) cc_final: 0.8317 (m) REVERT: D 116 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8093 (tm-30) REVERT: D 118 LYS cc_start: 0.8828 (tppt) cc_final: 0.8255 (ttmm) REVERT: D 133 SER cc_start: 0.8225 (m) cc_final: 0.7846 (p) REVERT: D 216 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8375 (mmtt) REVERT: D 241 TRP cc_start: 0.7737 (m100) cc_final: 0.7205 (m100) REVERT: D 242 GLN cc_start: 0.7426 (tm-30) cc_final: 0.6811 (tm-30) REVERT: D 243 LEU cc_start: 0.8471 (mt) cc_final: 0.8156 (mm) REVERT: D 279 LYS cc_start: 0.7850 (mttm) cc_final: 0.7506 (mmmt) REVERT: D 292 ASP cc_start: 0.9236 (p0) cc_final: 0.8515 (p0) REVERT: D 349 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8061 (ttt90) REVERT: D 370 HIS cc_start: 0.8865 (m-70) cc_final: 0.8365 (m90) REVERT: D 371 GLU cc_start: 0.8944 (pp20) cc_final: 0.8413 (pp20) outliers start: 2 outliers final: 2 residues processed: 533 average time/residue: 0.2105 time to fit residues: 165.0151 Evaluate side-chains 487 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 485 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 0.1980 chunk 143 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 98 optimal weight: 0.0970 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 242 GLN A 395 GLN B 74 ASN B 364 GLN C 88 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 84 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12324 Z= 0.151 Angle : 0.564 10.176 16768 Z= 0.294 Chirality : 0.043 0.230 1940 Planarity : 0.004 0.054 2200 Dihedral : 4.825 54.620 1680 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.08 % Allowed : 0.38 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.43 (0.21), residues: 1568 helix: 0.59 (0.31), residues: 264 sheet: 0.28 (0.26), residues: 420 loop : -0.83 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 410 HIS 0.004 0.001 HIS D 287 PHE 0.014 0.001 PHE C 86 TYR 0.029 0.001 TYR D 100 ARG 0.009 0.000 ARG C 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 544 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8596 (pm20) cc_final: 0.7965 (pm20) REVERT: A 109 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8292 (ttm170) REVERT: A 121 ASN cc_start: 0.8782 (t0) cc_final: 0.7255 (t0) REVERT: A 125 GLU cc_start: 0.7833 (mt-10) cc_final: 0.6859 (mt-10) REVERT: A 164 MET cc_start: 0.6594 (mpp) cc_final: 0.6375 (mpp) REVERT: A 249 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7464 (mtpt) REVERT: A 311 LYS cc_start: 0.9501 (tttt) cc_final: 0.9043 (tttm) REVERT: A 385 ASP cc_start: 0.9530 (p0) cc_final: 0.9286 (p0) REVERT: B 15 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7860 (mm-30) REVERT: B 28 GLN cc_start: 0.9438 (mm-40) cc_final: 0.9056 (mm110) REVERT: B 154 ILE cc_start: 0.8463 (tp) cc_final: 0.8259 (tp) REVERT: B 162 ARG cc_start: 0.8745 (mmt-90) cc_final: 0.8453 (tpp80) REVERT: B 164 MET cc_start: 0.7852 (mmm) cc_final: 0.7398 (tpp) REVERT: B 234 GLN cc_start: 0.8980 (mt0) cc_final: 0.8064 (mp10) REVERT: B 268 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8614 (mtpt) REVERT: B 291 GLN cc_start: 0.7882 (pm20) cc_final: 0.7652 (pm20) REVERT: B 361 ILE cc_start: 0.9375 (mt) cc_final: 0.9130 (mm) REVERT: B 376 MET cc_start: 0.7171 (ttm) cc_final: 0.6862 (ttm) REVERT: B 417 ARG cc_start: 0.9452 (mtm-85) cc_final: 0.9206 (mtm180) REVERT: C 71 LEU cc_start: 0.8479 (tp) cc_final: 0.8182 (tt) REVERT: C 81 GLU cc_start: 0.7974 (mp0) cc_final: 0.7685 (mp0) REVERT: C 143 ASP cc_start: 0.8169 (t0) cc_final: 0.7944 (t0) REVERT: C 152 GLU cc_start: 0.8858 (tp30) cc_final: 0.8343 (tp30) REVERT: C 159 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7588 (mt-10) REVERT: C 161 ASN cc_start: 0.8605 (p0) cc_final: 0.8333 (p0) REVERT: C 234 GLN cc_start: 0.8704 (mt0) cc_final: 0.8099 (mp10) REVERT: C 279 LYS cc_start: 0.7999 (mttp) cc_final: 0.7679 (mmtt) REVERT: C 338 MET cc_start: 0.7727 (mmt) cc_final: 0.7389 (mmt) REVERT: C 344 ASN cc_start: 0.8262 (t0) cc_final: 0.7973 (t0) REVERT: C 359 ILE cc_start: 0.9296 (mt) cc_final: 0.9014 (mm) REVERT: C 389 ASN cc_start: 0.9205 (m-40) cc_final: 0.7903 (m110) REVERT: C 397 ASP cc_start: 0.8012 (t0) cc_final: 0.7623 (t0) REVERT: D 42 ARG cc_start: 0.7370 (mmt180) cc_final: 0.6907 (mmt180) REVERT: D 44 SER cc_start: 0.8298 (t) cc_final: 0.7984 (p) REVERT: D 66 LYS cc_start: 0.7308 (mmtm) cc_final: 0.6707 (tppt) REVERT: D 77 VAL cc_start: 0.8821 (t) cc_final: 0.8445 (p) REVERT: D 116 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7989 (tm-30) REVERT: D 118 LYS cc_start: 0.8827 (tppt) cc_final: 0.8231 (ttmm) REVERT: D 175 TYR cc_start: 0.9015 (t80) cc_final: 0.8784 (t80) REVERT: D 241 TRP cc_start: 0.7894 (m100) cc_final: 0.7497 (m100) REVERT: D 242 GLN cc_start: 0.7335 (tm-30) cc_final: 0.6746 (tm-30) REVERT: D 243 LEU cc_start: 0.8469 (mt) cc_final: 0.8214 (mm) REVERT: D 279 LYS cc_start: 0.7733 (mttm) cc_final: 0.7523 (mmmt) REVERT: D 292 ASP cc_start: 0.9251 (p0) cc_final: 0.8542 (p0) REVERT: D 338 MET cc_start: 0.7352 (mmt) cc_final: 0.6985 (mmm) REVERT: D 349 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8054 (ttt90) REVERT: D 370 HIS cc_start: 0.8872 (m-70) cc_final: 0.8437 (m90) REVERT: D 371 GLU cc_start: 0.8946 (pp20) cc_final: 0.8424 (pp20) REVERT: D 382 SER cc_start: 0.8134 (p) cc_final: 0.7927 (p) REVERT: D 385 ASP cc_start: 0.8057 (t0) cc_final: 0.7630 (t0) REVERT: D 407 ILE cc_start: 0.7887 (pt) cc_final: 0.7591 (mt) outliers start: 1 outliers final: 1 residues processed: 544 average time/residue: 0.2185 time to fit residues: 174.6735 Evaluate side-chains 492 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 491 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 395 GLN B 74 ASN C 84 ASN C 88 GLN C 395 GLN D 7 GLN D 74 ASN D 84 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.125884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.106999 restraints weight = 18551.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.110369 restraints weight = 9968.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.112609 restraints weight = 6345.896| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12324 Z= 0.198 Angle : 0.589 11.377 16768 Z= 0.305 Chirality : 0.043 0.230 1940 Planarity : 0.004 0.056 2200 Dihedral : 4.895 53.162 1680 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.48 (0.20), residues: 1568 helix: 0.42 (0.31), residues: 266 sheet: 0.30 (0.25), residues: 420 loop : -0.85 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 410 HIS 0.003 0.001 HIS D 287 PHE 0.018 0.001 PHE C 86 TYR 0.027 0.002 TYR B 100 ARG 0.009 0.000 ARG C 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3357.40 seconds wall clock time: 61 minutes 36.60 seconds (3696.60 seconds total)