Starting phenix.real_space_refine on Fri Aug 7 01:48:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m49_63619/08_2026/9m49_63619.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m49_63619/08_2026/9m49_63619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m49_63619/08_2026/9m49_63619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m49_63619/08_2026/9m49_63619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m49_63619/08_2026/9m49_63619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m49_63619/08_2026/9m49_63619.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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: 6 Type Number sf(0) Gaussians Co 2 6.85 5 P 124 5.49 5 S 56 5.16 5 C 11250 2.51 5 N 2993 2.21 5 O 3862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18287 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain: "C" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "E" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "F" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2714 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "G" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna3p': 30} Chain: "H" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna3p': 30} Chain: "I" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna3p': 30} Chain: "J" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 654 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna3p': 30} Chain: "B" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2705 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "D" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2091 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 2 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CO': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.24, per 1000 atoms: 0.23 Number of scatterers: 18287 At special positions: 0 Unit cell: (120.12, 136.92, 132.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Co 2 26.99 S 56 16.00 P 124 15.00 O 3862 8.00 N 2993 7.00 C 11250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 730.7 milliseconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3724 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 43 sheets defined 26.4% alpha, 22.0% beta 60 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 298 through 308 removed outlier: 3.715A pdb=" N SER C 308 " --> pdb=" O GLU C 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 76 Processing helix chain 'E' and resid 129 through 137 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 298 through 310 removed outlier: 4.327A pdb=" N ASP E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 298 through 309 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 250 through 261 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.632A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.291A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.287A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 266 removed outlier: 5.271A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 322 removed outlier: 7.387A pdb=" N SER A 328 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET A 330 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 341 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 24 through 27 removed outlier: 6.694A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.296A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 99 removed outlier: 8.238A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AB4, first strand: chain 'C' and resid 263 through 266 removed outlier: 5.298A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP C 282 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N SER C 288 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.427A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.596A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.287A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.287A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.312A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AC3, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.984A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 315 through 322 Processing sheet with id=AC5, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.679A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.254A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS F 180 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AC8, first strand: chain 'F' and resid 98 through 99 removed outlier: 8.292A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AD1, first strand: chain 'F' and resid 264 through 266 removed outlier: 6.510A pdb=" N LYS F 276 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER F 293 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR F 278 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL F 291 " --> pdb=" O TYR F 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 315 through 322 removed outlier: 8.442A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.693A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.265A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AD6, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.443A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD8, first strand: chain 'B' and resid 264 through 266 removed outlier: 4.878A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 315 through 322 Processing sheet with id=AE1, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.536A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.298A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AE4, first strand: chain 'D' and resid 98 through 99 removed outlier: 8.371A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AE6, first strand: chain 'D' and resid 263 through 266 removed outlier: 4.562A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASP D 282 " --> pdb=" O SER D 288 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N SER D 288 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 319 through 322 591 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 264 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4494 1.33 - 1.45: 4118 1.45 - 1.57: 9970 1.57 - 1.69: 244 1.69 - 1.81: 83 Bond restraints: 18909 Sorted by residual: bond pdb=" CA ASP C 310 " pdb=" CB ASP C 310 " ideal model delta sigma weight residual 1.530 1.555 -0.025 1.69e-02 3.50e+03 2.19e+00 bond pdb=" N THR A 340 " pdb=" CA THR A 340 " ideal model delta sigma weight residual 1.455 1.472 -0.018 1.26e-02 6.30e+03 1.94e+00 bond pdb=" C THR A 340 " pdb=" O THR A 340 " ideal model delta sigma weight residual 1.234 1.250 -0.016 1.22e-02 6.72e+03 1.71e+00 bond pdb=" CB ASP C 310 " pdb=" CG ASP C 310 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CB LYS D 149 " pdb=" CG LYS D 149 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.16e+00 ... (remaining 18904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 25221 1.22 - 2.44: 726 2.44 - 3.65: 261 3.65 - 4.87: 12 4.87 - 6.09: 5 Bond angle restraints: 26225 Sorted by residual: angle pdb=" N ILE B 107 " pdb=" CA ILE B 107 " pdb=" C ILE B 107 " ideal model delta sigma weight residual 112.96 108.24 4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" O5' C J 29 " pdb=" C5' C J 29 " pdb=" C4' C J 29 " ideal model delta sigma weight residual 109.40 112.21 -2.81 8.00e-01 1.56e+00 1.24e+01 angle pdb=" C1' U G 18 " pdb=" N1 U G 18 " pdb=" C2 U G 18 " ideal model delta sigma weight residual 117.70 121.83 -4.13 1.20e+00 6.94e-01 1.19e+01 angle pdb=" CA THR A 340 " pdb=" CB THR A 340 " pdb=" OG1 THR A 340 " ideal model delta sigma weight residual 109.60 104.66 4.94 1.50e+00 4.44e-01 1.09e+01 angle pdb=" O5' A I 20 " pdb=" C5' A I 20 " pdb=" C4' A I 20 " ideal model delta sigma weight residual 109.40 112.01 -2.61 8.00e-01 1.56e+00 1.07e+01 ... (remaining 26220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.45: 10831 33.45 - 66.91: 499 66.91 - 100.36: 34 100.36 - 133.81: 0 133.81 - 167.26: 1 Dihedral angle restraints: 11365 sinusoidal: 5599 harmonic: 5766 Sorted by residual: dihedral pdb=" O4' U G 18 " pdb=" C1' U G 18 " pdb=" N1 U G 18 " pdb=" C2 U G 18 " ideal model delta sinusoidal sigma weight residual 200.00 32.74 167.26 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" CA THR A 192 " pdb=" C THR A 192 " pdb=" N TYR A 193 " pdb=" CA TYR A 193 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA THR B 192 " pdb=" C THR B 192 " pdb=" N TYR B 193 " pdb=" CA TYR B 193 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 11362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1965 0.029 - 0.058: 595 0.058 - 0.087: 218 0.087 - 0.116: 182 0.116 - 0.146: 164 Chirality restraints: 3124 Sorted by residual: chirality pdb=" CA ASP C 310 " pdb=" N ASP C 310 " pdb=" C ASP C 310 " pdb=" CB ASP C 310 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" C2' U G 14 " pdb=" C3' U G 14 " pdb=" O2' U G 14 " pdb=" C1' U G 14 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C2' A J 31 " pdb=" C3' A J 31 " pdb=" O2' A J 31 " pdb=" C1' A J 31 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 3121 not shown) Planarity restraints: 2910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 117 " 0.039 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO B 118 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 310 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C ASP C 310 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP C 310 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU C 311 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 261 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 262 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.018 5.00e-02 4.00e+02 ... (remaining 2907 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 83 2.60 - 3.17: 14003 3.17 - 3.75: 28270 3.75 - 4.32: 40755 4.32 - 4.90: 64953 Nonbonded interactions: 148064 Sorted by model distance: nonbonded pdb=" O2' U I 18 " pdb="CO CO I 101 " model vdw 2.024 2.220 nonbonded pdb=" O GLU F 304 " pdb=" OG SER F 308 " model vdw 2.224 3.040 nonbonded pdb=" OE1 GLU A 339 " pdb=" O2' A G 19 " model vdw 2.279 3.040 nonbonded pdb=" N GLU D 326 " pdb=" OE1 GLU D 326 " model vdw 2.286 3.120 nonbonded pdb=" OD1 ASN E 45 " pdb=" OG1 THR E 47 " model vdw 2.295 3.040 ... (remaining 148059 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' and (resid 1 through 20 or resid 22 through 344)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 20 or resid 22 through 344)) selection = (chain 'E' and (resid 1 through 20 or resid 22 through 344)) selection = (chain 'F' and (resid 1 through 20 or resid 22 through 344)) } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.170 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.620 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.002 0.032 18909 Z= 0.126 Angle : 0.539 6.092 26225 Z= 0.358 Chirality : 0.048 0.146 3124 Planarity : 0.003 0.060 2910 Dihedral : 16.701 167.263 7641 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.19 % Allowed : 18.43 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1971 helix: 1.35 (0.24), residues: 508 sheet: 1.64 (0.28), residues: 356 loop : -0.02 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 138 TYR 0.008 0.001 TYR B 225 PHE 0.020 0.001 PHE F 302 TRP 0.007 0.001 TRP A 332 HIS 0.002 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (18909) covalent geometry : angle 0.53858 / 0.36 (26225) hydrogen bonds : bond 0.14103 / 9.36 ( 714) hydrogen bonds : angle 6.25207 / 4.39 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.655 Fit side-chains REVERT: A 223 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7254 (tp30) REVERT: A 232 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: A 264 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7589 (tp30) REVERT: A 311 LEU cc_start: 0.7961 (mp) cc_final: 0.7701 (mt) REVERT: A 340 THR cc_start: 0.6596 (OUTLIER) cc_final: 0.6344 (p) REVERT: C 44 GLU cc_start: 0.8540 (tt0) cc_final: 0.8026 (tm-30) REVERT: C 68 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: C 202 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6295 (pt0) REVERT: C 204 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8346 (mttp) REVERT: C 223 GLU cc_start: 0.8045 (tt0) cc_final: 0.7719 (tm-30) REVERT: C 245 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8154 (tt) REVERT: C 319 LYS cc_start: 0.8689 (mttp) cc_final: 0.8468 (mttt) REVERT: E 149 LYS cc_start: 0.8293 (mttt) cc_final: 0.7737 (pmtt) REVERT: E 173 LYS cc_start: 0.8619 (tttp) cc_final: 0.8266 (mtmm) REVERT: E 201 GLN cc_start: 0.7758 (mp10) cc_final: 0.7438 (mp10) REVERT: E 284 GLN cc_start: 0.6580 (tp40) cc_final: 0.6189 (mm110) REVERT: F 204 LYS cc_start: 0.8719 (mttm) cc_final: 0.8357 (mtmt) REVERT: F 296 ASP cc_start: 0.8256 (t0) cc_final: 0.7764 (t0) REVERT: B 254 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7250 (mp) REVERT: B 317 VAL cc_start: 0.6895 (t) cc_final: 0.6637 (p) outliers start: 21 outliers final: 12 residues processed: 163 average time/residue: 0.6669 time to fit residues: 121.5914 Evaluate side-chains 161 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 165 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0570 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0270 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.182616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126574 restraints weight = 19477.870| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.16 r_work: 0.3083 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.0474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18909 Z= 0.124 Angle : 0.456 5.859 26225 Z= 0.255 Chirality : 0.042 0.141 3124 Planarity : 0.003 0.042 2910 Dihedral : 13.375 165.640 3925 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.89 % Allowed : 16.73 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.19), residues: 1971 helix: 1.32 (0.24), residues: 507 sheet: 1.76 (0.28), residues: 332 loop : -0.08 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 138 TYR 0.011 0.001 TYR B 342 PHE 0.015 0.001 PHE F 7 TRP 0.011 0.001 TRP B 332 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (18909) covalent geometry : angle 0.45557 / 0.26 (26225) hydrogen bonds : bond 0.04444 / 2.90 ( 714) hydrogen bonds : angle 5.20893 / 3.65 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7463 (tp30) REVERT: A 232 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: A 264 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8058 (tp30) REVERT: A 311 LEU cc_start: 0.8412 (mp) cc_final: 0.8123 (mt) REVERT: A 312 SER cc_start: 0.8705 (p) cc_final: 0.8164 (m) REVERT: C 44 GLU cc_start: 0.8801 (tt0) cc_final: 0.8435 (tm-30) REVERT: C 202 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6752 (pt0) REVERT: C 223 GLU cc_start: 0.8196 (tt0) cc_final: 0.7881 (tm-30) REVERT: C 245 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8482 (tt) REVERT: C 250 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8417 (mp) REVERT: C 264 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: C 319 LYS cc_start: 0.8937 (mttp) cc_final: 0.8728 (mttt) REVERT: E 21 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: E 149 LYS cc_start: 0.8290 (mttt) cc_final: 0.7730 (pmtt) REVERT: E 173 LYS cc_start: 0.8580 (tttp) cc_final: 0.8093 (mttm) REVERT: E 201 GLN cc_start: 0.7757 (mp10) cc_final: 0.7385 (mp10) REVERT: F 204 LYS cc_start: 0.8734 (mttm) cc_final: 0.8364 (mtmt) REVERT: F 296 ASP cc_start: 0.8371 (t0) cc_final: 0.8002 (t0) REVERT: B 254 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7170 (mp) REVERT: B 317 VAL cc_start: 0.6789 (t) cc_final: 0.6558 (p) outliers start: 51 outliers final: 15 residues processed: 187 average time/residue: 0.6226 time to fit residues: 131.0961 Evaluate side-chains 164 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 189 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 186 optimal weight: 0.0870 chunk 123 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 177 ASN B 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128240 restraints weight = 19733.031| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.28 r_work: 0.3108 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18909 Z= 0.088 Angle : 0.409 5.222 26225 Z= 0.229 Chirality : 0.040 0.133 3124 Planarity : 0.003 0.049 2910 Dihedral : 13.174 162.556 3907 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.27 % Allowed : 17.58 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.19), residues: 1971 helix: 1.41 (0.24), residues: 507 sheet: 1.79 (0.29), residues: 327 loop : -0.08 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.008 0.001 TYR C 225 PHE 0.021 0.001 PHE F 213 TRP 0.012 0.001 TRP B 332 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (18909) covalent geometry : angle 0.40873 / 0.23 (26225) hydrogen bonds : bond 0.03608 / 2.36 ( 714) hydrogen bonds : angle 4.85895 / 3.40 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.818 Fit side-chains REVERT: A 223 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7472 (tp30) REVERT: A 232 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: A 264 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8131 (tp30) REVERT: A 311 LEU cc_start: 0.8503 (mp) cc_final: 0.8195 (mt) REVERT: A 312 SER cc_start: 0.8723 (p) cc_final: 0.8181 (m) REVERT: C 44 GLU cc_start: 0.8775 (tt0) cc_final: 0.8430 (tm-30) REVERT: C 202 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6843 (pt0) REVERT: C 223 GLU cc_start: 0.8249 (tt0) cc_final: 0.7946 (tm-30) REVERT: C 250 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8416 (mp) REVERT: E 21 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: E 149 LYS cc_start: 0.8229 (mttt) cc_final: 0.7759 (pmtt) REVERT: E 173 LYS cc_start: 0.8593 (tttp) cc_final: 0.8173 (mttm) REVERT: E 201 GLN cc_start: 0.7803 (mp10) cc_final: 0.7405 (mp10) REVERT: E 284 GLN cc_start: 0.6807 (tp40) cc_final: 0.6580 (mm110) REVERT: F 21 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: F 204 LYS cc_start: 0.8714 (mttm) cc_final: 0.8360 (mtmt) REVERT: F 232 PHE cc_start: 0.4996 (OUTLIER) cc_final: 0.3359 (t80) REVERT: F 296 ASP cc_start: 0.8376 (t0) cc_final: 0.8033 (t0) REVERT: B 254 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7324 (mp) outliers start: 40 outliers final: 16 residues processed: 177 average time/residue: 0.6099 time to fit residues: 121.7368 Evaluate side-chains 155 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 66 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.180693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124558 restraints weight = 19430.650| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.16 r_work: 0.3065 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18909 Z= 0.176 Angle : 0.503 5.623 26225 Z= 0.275 Chirality : 0.044 0.149 3124 Planarity : 0.004 0.047 2910 Dihedral : 13.257 166.006 3903 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.74 % Allowed : 16.85 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1971 helix: 1.13 (0.24), residues: 508 sheet: 1.60 (0.29), residues: 319 loop : -0.32 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.014 0.001 TYR A 342 PHE 0.023 0.002 PHE F 213 TRP 0.013 0.002 TRP A 332 HIS 0.008 0.001 HIS F 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (18909) covalent geometry : angle 0.50268 / 0.28 (26225) hydrogen bonds : bond 0.04505 / 2.94 ( 714) hydrogen bonds : angle 5.03373 / 3.53 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 132 time to evaluate : 0.683 Fit side-chains REVERT: A 223 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7485 (tp30) REVERT: A 232 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: A 264 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8092 (tp30) REVERT: A 311 LEU cc_start: 0.8503 (mp) cc_final: 0.8210 (mt) REVERT: A 312 SER cc_start: 0.8774 (p) cc_final: 0.8242 (m) REVERT: C 44 GLU cc_start: 0.8817 (tt0) cc_final: 0.8432 (tm-30) REVERT: C 68 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: C 90 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8211 (mtm-85) REVERT: C 202 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6923 (pt0) REVERT: C 223 GLU cc_start: 0.8147 (tt0) cc_final: 0.7824 (tm-30) REVERT: C 250 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8553 (mp) REVERT: C 264 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: E 149 LYS cc_start: 0.8324 (mttt) cc_final: 0.7683 (pmtt) REVERT: E 173 LYS cc_start: 0.8583 (tttp) cc_final: 0.8067 (mttm) REVERT: E 201 GLN cc_start: 0.7739 (mp10) cc_final: 0.7429 (mp10) REVERT: E 284 GLN cc_start: 0.6761 (tp40) cc_final: 0.6468 (mm110) REVERT: E 321 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7908 (m) REVERT: F 21 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: F 204 LYS cc_start: 0.8712 (mttm) cc_final: 0.8322 (mtmt) REVERT: F 232 PHE cc_start: 0.4899 (OUTLIER) cc_final: 0.3295 (t80) REVERT: F 296 ASP cc_start: 0.8416 (t0) cc_final: 0.8023 (t0) REVERT: B 254 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7243 (mp) REVERT: D 104 MET cc_start: 0.8441 (mmm) cc_final: 0.8199 (mmt) outliers start: 66 outliers final: 25 residues processed: 187 average time/residue: 0.5921 time to fit residues: 125.2703 Evaluate side-chains 165 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain D residue 166 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 23 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 116 optimal weight: 0.0670 chunk 163 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 206 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 188 GLN F 242 HIS B 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.181737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126220 restraints weight = 19524.120| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.16 r_work: 0.3090 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18909 Z= 0.100 Angle : 0.421 4.920 26225 Z= 0.236 Chirality : 0.041 0.138 3124 Planarity : 0.003 0.056 2910 Dihedral : 13.180 163.861 3902 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.61 % Allowed : 18.04 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 1971 helix: 1.30 (0.24), residues: 507 sheet: 1.57 (0.29), residues: 327 loop : -0.26 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.011 0.001 TYR C 342 PHE 0.023 0.001 PHE F 213 TRP 0.011 0.001 TRP A 332 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (18909) covalent geometry : angle 0.42098 / 0.24 (26225) hydrogen bonds : bond 0.03544 / 2.32 ( 714) hydrogen bonds : angle 4.79437 / 3.35 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.688 Fit side-chains REVERT: A 223 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7431 (tp30) REVERT: A 232 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: A 264 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7886 (tm-30) REVERT: A 311 LEU cc_start: 0.8464 (mp) cc_final: 0.8160 (mt) REVERT: A 312 SER cc_start: 0.8765 (p) cc_final: 0.8233 (m) REVERT: C 44 GLU cc_start: 0.8801 (tt0) cc_final: 0.8406 (tm-30) REVERT: C 46 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8511 (mmmt) REVERT: C 68 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: C 90 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8177 (mtm-85) REVERT: C 202 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6764 (pt0) REVERT: C 223 GLU cc_start: 0.8179 (tt0) cc_final: 0.7860 (tm-30) REVERT: C 245 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8443 (tt) REVERT: C 250 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8456 (mp) REVERT: E 149 LYS cc_start: 0.8288 (mttt) cc_final: 0.7717 (pmtt) REVERT: E 173 LYS cc_start: 0.8595 (tttp) cc_final: 0.8072 (mttm) REVERT: E 201 GLN cc_start: 0.7758 (mp10) cc_final: 0.7426 (mp10) REVERT: E 284 GLN cc_start: 0.6763 (tp40) cc_final: 0.6462 (mm110) REVERT: E 328 SER cc_start: 0.6740 (OUTLIER) cc_final: 0.6030 (p) REVERT: F 21 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: F 187 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7083 (mp10) REVERT: F 204 LYS cc_start: 0.8720 (mttm) cc_final: 0.8339 (mtmt) REVERT: F 232 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.3304 (t80) REVERT: F 296 ASP cc_start: 0.8395 (t0) cc_final: 0.7981 (t0) REVERT: B 244 GLN cc_start: 0.7551 (tt0) cc_final: 0.7088 (tt0) REVERT: B 254 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7131 (mp) REVERT: D 104 MET cc_start: 0.8453 (mmm) cc_final: 0.8197 (mmt) outliers start: 46 outliers final: 19 residues processed: 177 average time/residue: 0.5670 time to fit residues: 113.4908 Evaluate side-chains 160 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain D residue 250 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 128 optimal weight: 0.0870 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 10 optimal weight: 0.0060 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 187 GLN C 201 GLN F 188 GLN D 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128103 restraints weight = 19402.750| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.13 r_work: 0.3126 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18909 Z= 0.080 Angle : 0.396 4.962 26225 Z= 0.222 Chirality : 0.040 0.132 3124 Planarity : 0.003 0.046 2910 Dihedral : 13.094 160.574 3902 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 18.77 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1971 helix: 1.41 (0.24), residues: 507 sheet: 1.63 (0.29), residues: 327 loop : -0.18 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.009 0.001 TYR E 193 PHE 0.023 0.001 PHE F 213 TRP 0.010 0.001 TRP B 332 HIS 0.004 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.08 (18909) covalent geometry : angle 0.39638 / 0.22 (26225) hydrogen bonds : bond 0.03118 / 2.04 ( 714) hydrogen bonds : angle 4.61738 / 3.23 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.566 Fit side-chains REVERT: A 223 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7361 (tp30) REVERT: A 232 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: A 264 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7866 (tm-30) REVERT: A 311 LEU cc_start: 0.8459 (mp) cc_final: 0.8158 (mt) REVERT: A 312 SER cc_start: 0.8773 (p) cc_final: 0.8252 (m) REVERT: C 44 GLU cc_start: 0.8771 (tt0) cc_final: 0.8385 (tm-30) REVERT: C 68 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: C 202 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6712 (pt0) REVERT: C 223 GLU cc_start: 0.8203 (tt0) cc_final: 0.7876 (tm-30) REVERT: C 245 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8409 (tt) REVERT: C 250 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8372 (mp) REVERT: E 149 LYS cc_start: 0.8192 (mttt) cc_final: 0.7716 (pmtt) REVERT: E 173 LYS cc_start: 0.8597 (tttp) cc_final: 0.8090 (mttm) REVERT: E 187 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: E 201 GLN cc_start: 0.7770 (mp10) cc_final: 0.7420 (mp10) REVERT: E 284 GLN cc_start: 0.6770 (tp40) cc_final: 0.6461 (mm110) REVERT: E 328 SER cc_start: 0.6633 (OUTLIER) cc_final: 0.6005 (p) REVERT: F 21 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: F 187 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7141 (mp10) REVERT: F 204 LYS cc_start: 0.8701 (mttm) cc_final: 0.8319 (mtmt) REVERT: F 232 PHE cc_start: 0.4941 (OUTLIER) cc_final: 0.3341 (t80) REVERT: F 296 ASP cc_start: 0.8408 (t0) cc_final: 0.8007 (t0) REVERT: B 244 GLN cc_start: 0.7581 (tt0) cc_final: 0.7117 (tt0) REVERT: B 254 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7142 (mp) REVERT: D 104 MET cc_start: 0.8450 (mmm) cc_final: 0.8193 (mmt) outliers start: 41 outliers final: 20 residues processed: 181 average time/residue: 0.5848 time to fit residues: 119.8773 Evaluate side-chains 166 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain D residue 250 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 35 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 200 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 177 ASN F 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.181978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126376 restraints weight = 19574.227| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.13 r_work: 0.3097 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18909 Z= 0.112 Angle : 0.420 5.180 26225 Z= 0.233 Chirality : 0.041 0.138 3124 Planarity : 0.003 0.043 2910 Dihedral : 13.094 161.990 3902 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.44 % Allowed : 18.83 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1971 helix: 1.36 (0.24), residues: 507 sheet: 1.60 (0.29), residues: 322 loop : -0.22 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 198 TYR 0.010 0.001 TYR C 225 PHE 0.024 0.001 PHE F 213 TRP 0.008 0.001 TRP B 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (18909) covalent geometry : angle 0.41990 / 0.23 (26225) hydrogen bonds : bond 0.03422 / 2.23 ( 714) hydrogen bonds : angle 4.66010 / 3.26 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.664 Fit side-chains REVERT: A 223 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7367 (tp30) REVERT: A 232 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8546 (m-80) REVERT: A 264 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8030 (tp30) REVERT: A 311 LEU cc_start: 0.8453 (mp) cc_final: 0.8149 (mt) REVERT: A 312 SER cc_start: 0.8803 (p) cc_final: 0.8292 (m) REVERT: C 44 GLU cc_start: 0.8796 (tt0) cc_final: 0.8405 (tm-30) REVERT: C 68 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: C 90 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.7866 (mtm-85) REVERT: C 202 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6802 (pt0) REVERT: C 223 GLU cc_start: 0.8177 (tt0) cc_final: 0.7858 (tm-30) REVERT: C 245 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8472 (tt) REVERT: C 250 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8445 (mp) REVERT: E 21 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: E 149 LYS cc_start: 0.8229 (mttt) cc_final: 0.7698 (pmtt) REVERT: E 173 LYS cc_start: 0.8587 (tttp) cc_final: 0.8064 (mttm) REVERT: E 201 GLN cc_start: 0.7761 (mp10) cc_final: 0.7401 (mp10) REVERT: E 284 GLN cc_start: 0.6743 (tp40) cc_final: 0.6391 (mm110) REVERT: E 328 SER cc_start: 0.6626 (OUTLIER) cc_final: 0.6018 (p) REVERT: F 21 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: F 187 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7112 (mp10) REVERT: F 204 LYS cc_start: 0.8705 (mttm) cc_final: 0.8319 (mtmt) REVERT: F 232 PHE cc_start: 0.4874 (OUTLIER) cc_final: 0.3295 (t80) REVERT: F 296 ASP cc_start: 0.8420 (t0) cc_final: 0.8026 (t0) REVERT: B 244 GLN cc_start: 0.7567 (tt0) cc_final: 0.7099 (tt0) REVERT: B 254 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7168 (mp) REVERT: D 104 MET cc_start: 0.8462 (mmm) cc_final: 0.8198 (mmt) outliers start: 43 outliers final: 24 residues processed: 171 average time/residue: 0.5442 time to fit residues: 105.4068 Evaluate side-chains 168 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain D residue 250 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.182127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126435 restraints weight = 19455.219| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.23 r_work: 0.3085 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18909 Z= 0.103 Angle : 0.415 4.787 26225 Z= 0.231 Chirality : 0.041 0.141 3124 Planarity : 0.003 0.063 2910 Dihedral : 13.084 162.163 3902 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.44 % Allowed : 19.00 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1971 helix: 1.36 (0.24), residues: 507 sheet: 1.55 (0.29), residues: 322 loop : -0.21 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 138 TYR 0.009 0.001 TYR F 193 PHE 0.026 0.001 PHE F 213 TRP 0.009 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (18909) covalent geometry : angle 0.41466 / 0.23 (26225) hydrogen bonds : bond 0.03349 / 2.19 ( 714) hydrogen bonds : angle 4.65588 / 3.26 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.708 Fit side-chains REVERT: A 223 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7371 (tp30) REVERT: A 232 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8599 (m-80) REVERT: A 264 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8016 (tp30) REVERT: A 311 LEU cc_start: 0.8411 (mp) cc_final: 0.8096 (mt) REVERT: A 312 SER cc_start: 0.8809 (p) cc_final: 0.8307 (m) REVERT: C 44 GLU cc_start: 0.8792 (tt0) cc_final: 0.8414 (tm-30) REVERT: C 68 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: C 90 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.7954 (mtm-85) REVERT: C 202 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6792 (pt0) REVERT: C 223 GLU cc_start: 0.8172 (tt0) cc_final: 0.7850 (tm-30) REVERT: C 245 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8463 (tt) REVERT: C 250 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8455 (mp) REVERT: C 264 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: E 149 LYS cc_start: 0.8188 (mttt) cc_final: 0.7670 (pmtt) REVERT: E 173 LYS cc_start: 0.8590 (tttp) cc_final: 0.8057 (mttm) REVERT: E 201 GLN cc_start: 0.7743 (mp10) cc_final: 0.7386 (mp10) REVERT: E 284 GLN cc_start: 0.6754 (tp40) cc_final: 0.6395 (mm110) REVERT: E 328 SER cc_start: 0.6582 (OUTLIER) cc_final: 0.6021 (p) REVERT: F 21 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: F 187 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7138 (mp10) REVERT: F 204 LYS cc_start: 0.8704 (mttm) cc_final: 0.8316 (mtmt) REVERT: F 232 PHE cc_start: 0.4915 (OUTLIER) cc_final: 0.3310 (t80) REVERT: F 296 ASP cc_start: 0.8434 (t0) cc_final: 0.8011 (t0) REVERT: B 254 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7158 (mp) REVERT: D 104 MET cc_start: 0.8459 (mmm) cc_final: 0.8195 (mmt) outliers start: 43 outliers final: 25 residues processed: 169 average time/residue: 0.6163 time to fit residues: 117.3262 Evaluate side-chains 168 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain D residue 250 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 157 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 133 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 177 ASN F 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.128014 restraints weight = 19395.558| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.23 r_work: 0.3086 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18909 Z= 0.090 Angle : 0.408 6.299 26225 Z= 0.227 Chirality : 0.040 0.150 3124 Planarity : 0.003 0.060 2910 Dihedral : 13.065 161.706 3902 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.67 % Rotamer: Outliers : 2.44 % Allowed : 19.12 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1971 helix: 1.40 (0.24), residues: 507 sheet: 1.54 (0.29), residues: 322 loop : -0.20 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 138 TYR 0.009 0.001 TYR C 225 PHE 0.026 0.001 PHE F 213 TRP 0.009 0.001 TRP B 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (18909) covalent geometry : angle 0.40764 / 0.23 (26225) hydrogen bonds : bond 0.03202 / 2.10 ( 714) hydrogen bonds : angle 4.61096 / 3.22 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.703 Fit side-chains REVERT: A 223 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7378 (tp30) REVERT: A 232 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: A 264 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: A 311 LEU cc_start: 0.8418 (mp) cc_final: 0.8113 (mt) REVERT: A 312 SER cc_start: 0.8802 (p) cc_final: 0.8303 (m) REVERT: A 340 THR cc_start: 0.8190 (p) cc_final: 0.7959 (p) REVERT: C 44 GLU cc_start: 0.8798 (tt0) cc_final: 0.8422 (tm-30) REVERT: C 68 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: C 90 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8042 (mtm-85) REVERT: C 202 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6775 (pt0) REVERT: C 223 GLU cc_start: 0.8175 (tt0) cc_final: 0.7853 (tm-30) REVERT: C 245 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8450 (tt) REVERT: C 250 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8430 (mp) REVERT: C 264 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: E 149 LYS cc_start: 0.8180 (mttt) cc_final: 0.7716 (pmtt) REVERT: E 173 LYS cc_start: 0.8594 (tttp) cc_final: 0.8064 (mttm) REVERT: E 201 GLN cc_start: 0.7730 (mp10) cc_final: 0.7364 (mp10) REVERT: E 284 GLN cc_start: 0.6768 (tp40) cc_final: 0.6432 (mm110) REVERT: F 21 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: F 187 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7152 (mp10) REVERT: F 204 LYS cc_start: 0.8699 (mttm) cc_final: 0.8312 (mtmt) REVERT: F 232 PHE cc_start: 0.4878 (OUTLIER) cc_final: 0.3298 (t80) REVERT: F 296 ASP cc_start: 0.8426 (t0) cc_final: 0.8011 (t0) REVERT: B 254 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7173 (mp) REVERT: D 104 MET cc_start: 0.8456 (mmm) cc_final: 0.8194 (mmt) outliers start: 43 outliers final: 26 residues processed: 169 average time/residue: 0.5476 time to fit residues: 104.6131 Evaluate side-chains 170 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain D residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 11 optimal weight: 0.0000 chunk 204 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 145 optimal weight: 40.0000 chunk 67 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 78 optimal weight: 0.2980 chunk 176 optimal weight: 9.9990 chunk 10 optimal weight: 0.0270 chunk 31 optimal weight: 0.0570 overall best weight: 0.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 188 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.184648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130785 restraints weight = 19600.363| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.28 r_work: 0.3136 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.042 18909 Z= 0.072 Angle : 0.388 6.502 26225 Z= 0.216 Chirality : 0.039 0.133 3124 Planarity : 0.003 0.056 2910 Dihedral : 12.987 157.752 3902 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.76 % Allowed : 19.68 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1971 helix: 1.53 (0.25), residues: 507 sheet: 1.62 (0.29), residues: 327 loop : -0.11 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 138 TYR 0.008 0.001 TYR B 225 PHE 0.025 0.001 PHE F 213 TRP 0.009 0.001 TRP B 332 HIS 0.004 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00149 / 0.07 (18909) covalent geometry : angle 0.38766 / 0.22 (26225) hydrogen bonds : bond 0.02683 / 1.77 ( 714) hydrogen bonds : angle 4.45302 / 3.12 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.579 Fit side-chains REVERT: A 223 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7306 (tp30) REVERT: A 232 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: A 264 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7757 (tm-30) REVERT: A 311 LEU cc_start: 0.8439 (mp) cc_final: 0.8161 (mt) REVERT: A 312 SER cc_start: 0.8799 (p) cc_final: 0.8303 (m) REVERT: C 44 GLU cc_start: 0.8783 (tt0) cc_final: 0.8392 (tm-30) REVERT: C 202 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6573 (pt0) REVERT: C 223 GLU cc_start: 0.8170 (tt0) cc_final: 0.7831 (tm-30) REVERT: C 245 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8385 (tt) REVERT: E 138 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7324 (ttt90) REVERT: E 149 LYS cc_start: 0.8153 (mttt) cc_final: 0.7727 (pmtt) REVERT: E 173 LYS cc_start: 0.8614 (tttp) cc_final: 0.8091 (mttm) REVERT: E 201 GLN cc_start: 0.7730 (mp10) cc_final: 0.7356 (mp10) REVERT: E 284 GLN cc_start: 0.6746 (tp40) cc_final: 0.6432 (mm110) REVERT: E 328 SER cc_start: 0.6565 (OUTLIER) cc_final: 0.6081 (p) REVERT: F 21 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: F 187 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7155 (mp10) REVERT: F 204 LYS cc_start: 0.8699 (mttm) cc_final: 0.8315 (mtmt) REVERT: F 232 PHE cc_start: 0.4932 (OUTLIER) cc_final: 0.3334 (t80) REVERT: F 296 ASP cc_start: 0.8395 (t0) cc_final: 0.8015 (t0) REVERT: B 191 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7933 (mp0) REVERT: B 244 GLN cc_start: 0.7457 (tt0) cc_final: 0.7022 (tt0) REVERT: B 254 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7157 (mp) REVERT: D 104 MET cc_start: 0.8443 (mmm) cc_final: 0.8188 (mmt) outliers start: 31 outliers final: 16 residues processed: 174 average time/residue: 0.5489 time to fit residues: 107.8809 Evaluate side-chains 159 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain D residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 110 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 142 optimal weight: 40.0000 chunk 158 optimal weight: 0.4980 chunk 3 optimal weight: 0.0170 chunk 93 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 70 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 201 GLN F 177 ASN F 188 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.184040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.129575 restraints weight = 19576.869| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.29 r_work: 0.3134 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18909 Z= 0.080 Angle : 0.399 6.909 26225 Z= 0.220 Chirality : 0.040 0.136 3124 Planarity : 0.003 0.056 2910 Dihedral : 12.963 158.100 3902 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.25 % Allowed : 20.70 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.19), residues: 1971 helix: 1.57 (0.24), residues: 507 sheet: 1.64 (0.29), residues: 327 loop : -0.10 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.009 0.001 TYR F 193 PHE 0.027 0.001 PHE F 213 TRP 0.008 0.001 TRP B 332 HIS 0.004 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.08 (18909) covalent geometry : angle 0.39940 / 0.22 (26225) hydrogen bonds : bond 0.02854 / 1.88 ( 714) hydrogen bonds : angle 4.45116 / 3.12 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6846.54 seconds wall clock time: 117 minutes 20.32 seconds (7040.32 seconds total)