Starting phenix.real_space_refine on Thu Mar 5 03:05:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m49_63619/03_2026/9m49_63619.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m49_63619/03_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_63619/03_2026/9m49_63619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m49_63619/03_2026/9m49_63619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m49_63619/03_2026/9m49_63619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m49_63619/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.67, per 1000 atoms: 0.20 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: 1.46 Conformation dependent library (CDL) restraints added in 727.9 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: 2.32 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: 3.36 Time building geometry restraints manager: 1.89 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: 25594 1.22 - 2.44: 486 2.44 - 3.65: 128 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=" 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=" C GLN C 309 " pdb=" N ASP C 310 " pdb=" CA ASP C 310 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" CA LYS D 149 " pdb=" CB LYS D 149 " pdb=" CG LYS D 149 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.90e+00 angle pdb=" CA ASP C 310 " pdb=" CB ASP C 310 " pdb=" CG ASP C 310 " ideal model delta sigma weight residual 112.60 115.36 -2.76 1.00e+00 1.00e+00 7.61e+00 ... (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: 2105 0.029 - 0.058: 586 0.058 - 0.087: 213 0.087 - 0.116: 179 0.116 - 0.146: 41 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=" CA ILE F 79 " pdb=" N ILE F 79 " pdb=" C ILE F 79 " pdb=" CB ILE F 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 79 " pdb=" N ILE A 79 " pdb=" C ILE A 79 " pdb=" CB ILE A 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-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: 4.310 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.080 Find NCS groups from input model: 0.340 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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= 0.111 Angle : 0.460 6.092 26225 Z= 0.259 Chirality : 0.040 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 covalent geometry : bond 0.00227 (18909) covalent geometry : angle 0.45994 (26225) hydrogen bonds : bond 0.14103 ( 714) hydrogen bonds : angle 6.25207 ( 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 : 0.644 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: 0.6707 time to fit residues: 121.8203 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 : 0.632 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.182623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126712 restraints weight = 19470.709| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.14 r_work: 0.3096 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0602 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= 0.121 Angle : 0.457 5.211 26225 Z= 0.249 Chirality : 0.042 0.136 3124 Planarity : 0.003 0.043 2910 Dihedral : 13.359 166.822 3925 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.95 % Allowed : 16.79 % Favored : 80.26 % 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: 0.86 (0.19), residues: 1971 helix: 1.32 (0.24), residues: 507 sheet: 1.81 (0.29), residues: 329 loop : -0.11 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 138 TYR 0.010 0.001 TYR C 225 PHE 0.015 0.001 PHE F 7 TRP 0.013 0.001 TRP B 332 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00283 (18909) covalent geometry : angle 0.45726 (26225) hydrogen bonds : bond 0.03916 ( 714) hydrogen bonds : angle 5.02691 ( 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 200 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.630 Fit side-chains REVERT: A 223 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7483 (tp30) REVERT: A 232 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: A 264 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8059 (tp30) REVERT: A 311 LEU cc_start: 0.8425 (mp) cc_final: 0.8145 (mt) REVERT: A 312 SER cc_start: 0.8723 (p) cc_final: 0.8185 (m) REVERT: C 44 GLU cc_start: 0.8818 (tt0) cc_final: 0.8432 (tm-30) REVERT: C 202 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6775 (pt0) REVERT: C 223 GLU cc_start: 0.8185 (tt0) cc_final: 0.7878 (tm-30) REVERT: C 250 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8455 (mp) REVERT: E 21 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: E 149 LYS cc_start: 0.8240 (mttt) cc_final: 0.7688 (pmtt) REVERT: E 173 LYS cc_start: 0.8579 (tttp) cc_final: 0.8086 (mtmm) REVERT: E 201 GLN cc_start: 0.7726 (mp10) cc_final: 0.7350 (mp10) REVERT: F 204 LYS cc_start: 0.8730 (mttm) cc_final: 0.8351 (mtmt) REVERT: F 232 PHE cc_start: 0.4928 (OUTLIER) cc_final: 0.3306 (t80) REVERT: F 257 ARG cc_start: 0.6624 (tpt170) cc_final: 0.6341 (tpt170) REVERT: F 296 ASP cc_start: 0.8369 (t0) cc_final: 0.7966 (t0) REVERT: B 254 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7193 (mp) outliers start: 52 outliers final: 15 residues processed: 189 average time/residue: 0.6391 time to fit residues: 135.6319 Evaluate side-chains 157 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 313 VAL 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 165 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 78 ASP 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 F residue 232 PHE 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: 2.9990 chunk 18 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 GLN F 242 HIS ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN D 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.183305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128307 restraints weight = 19718.198| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.20 r_work: 0.3114 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18909 Z= 0.087 Angle : 0.416 4.976 26225 Z= 0.227 Chirality : 0.040 0.135 3124 Planarity : 0.003 0.047 2910 Dihedral : 13.102 164.792 3903 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.38 % Allowed : 17.70 % Favored : 79.92 % 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: 1.46 (0.24), residues: 507 sheet: 1.80 (0.29), residues: 327 loop : -0.09 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 138 TYR 0.008 0.001 TYR B 225 PHE 0.026 0.001 PHE F 213 TRP 0.011 0.001 TRP B 332 HIS 0.005 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00195 (18909) covalent geometry : angle 0.41603 (26225) hydrogen bonds : bond 0.03183 ( 714) hydrogen bonds : angle 4.67329 ( 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 188 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.664 Fit side-chains REVERT: A 223 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7385 (tp30) REVERT: A 232 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8456 (m-80) REVERT: A 264 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8044 (tp30) REVERT: A 311 LEU cc_start: 0.8371 (mp) cc_final: 0.8059 (mt) REVERT: A 312 SER cc_start: 0.8760 (p) cc_final: 0.8232 (m) REVERT: C 44 GLU cc_start: 0.8766 (tt0) cc_final: 0.8382 (tm-30) REVERT: C 68 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: C 202 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6748 (pt0) REVERT: C 223 GLU cc_start: 0.8205 (tt0) cc_final: 0.7886 (tm-30) REVERT: C 245 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8431 (tt) REVERT: C 264 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: E 21 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: E 149 LYS cc_start: 0.8170 (mttt) cc_final: 0.7674 (pmtt) REVERT: E 173 LYS cc_start: 0.8584 (tttp) cc_final: 0.8102 (mttm) REVERT: E 201 GLN cc_start: 0.7741 (mp10) cc_final: 0.7432 (mp10) REVERT: F 21 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: F 204 LYS cc_start: 0.8724 (mttm) cc_final: 0.8335 (mtmt) REVERT: F 232 PHE cc_start: 0.4948 (OUTLIER) cc_final: 0.3310 (t80) REVERT: F 296 ASP cc_start: 0.8382 (t0) cc_final: 0.7984 (t0) REVERT: B 244 GLN cc_start: 0.7542 (tt0) cc_final: 0.7031 (tt0) REVERT: B 254 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7151 (mp) outliers start: 42 outliers final: 15 residues processed: 182 average time/residue: 0.5779 time to fit residues: 118.4203 Evaluate side-chains 162 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 264 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR 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 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: 4.9990 chunk 207 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 GLN F 177 ASN ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.181953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126310 restraints weight = 19443.540| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.13 r_work: 0.3083 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18909 Z= 0.135 Angle : 0.459 4.825 26225 Z= 0.249 Chirality : 0.042 0.144 3124 Planarity : 0.004 0.051 2910 Dihedral : 13.129 166.837 3902 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.23 % Allowed : 17.81 % Favored : 78.96 % 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 (0.18), residues: 1971 helix: 1.31 (0.24), residues: 507 sheet: 1.63 (0.29), residues: 327 loop : -0.21 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 138 TYR 0.012 0.001 TYR C 225 PHE 0.024 0.002 PHE F 213 TRP 0.011 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00327 (18909) covalent geometry : angle 0.45930 (26225) hydrogen bonds : bond 0.03746 ( 714) hydrogen bonds : angle 4.78780 ( 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 195 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 0.613 Fit side-chains REVERT: A 223 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7394 (tp30) REVERT: A 232 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8578 (m-80) REVERT: A 264 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8089 (tp30) REVERT: A 311 LEU cc_start: 0.8456 (mp) cc_final: 0.8132 (mt) REVERT: A 312 SER cc_start: 0.8803 (p) cc_final: 0.8306 (m) REVERT: A 340 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7999 (p) REVERT: C 44 GLU cc_start: 0.8780 (tt0) cc_final: 0.8387 (tm-30) REVERT: C 68 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: C 90 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8158 (mtm-85) REVERT: C 202 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6902 (pt0) REVERT: C 223 GLU cc_start: 0.8153 (tt0) cc_final: 0.7831 (tm-30) REVERT: C 250 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8489 (mp) REVERT: E 149 LYS cc_start: 0.8310 (mttt) cc_final: 0.7732 (pmtt) REVERT: E 173 LYS cc_start: 0.8580 (tttp) cc_final: 0.8064 (mttm) REVERT: E 201 GLN cc_start: 0.7758 (mp10) cc_final: 0.7436 (mp10) REVERT: F 21 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: F 204 LYS cc_start: 0.8704 (mttm) cc_final: 0.8300 (mtmt) REVERT: F 232 PHE cc_start: 0.4915 (OUTLIER) cc_final: 0.3332 (t80) REVERT: F 296 ASP cc_start: 0.8403 (t0) cc_final: 0.8000 (t0) REVERT: B 244 GLN cc_start: 0.7591 (tt0) cc_final: 0.7012 (tt0) REVERT: B 254 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7235 (mp) outliers start: 57 outliers final: 21 residues processed: 184 average time/residue: 0.6168 time to fit residues: 127.7159 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 : 0.620 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 340 THR 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 318 VAL 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 F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 144 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 D residue 250 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 23 optimal weight: 0.2980 chunk 165 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 206 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 90 optimal weight: 0.0870 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN C 201 GLN ** F 249 HIS ** 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 = 0.4076 r_free = 0.4076 target = 0.183616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127929 restraints weight = 19470.975| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.07 r_work: 0.3099 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18909 Z= 0.090 Angle : 0.417 5.683 26225 Z= 0.227 Chirality : 0.040 0.138 3124 Planarity : 0.003 0.055 2910 Dihedral : 13.059 165.930 3902 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.33 % Allowed : 18.83 % Favored : 78.84 % 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: 0.82 (0.19), residues: 1971 helix: 1.42 (0.24), residues: 507 sheet: 1.65 (0.29), residues: 327 loop : -0.16 (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 342 PHE 0.022 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 covalent geometry : bond 0.00207 (18909) covalent geometry : angle 0.41691 (26225) hydrogen bonds : bond 0.03065 ( 714) hydrogen bonds : angle 4.59077 ( 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 184 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.598 Fit side-chains REVERT: A 223 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7360 (tp30) REVERT: A 232 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8589 (m-80) REVERT: A 264 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7933 (tm-30) REVERT: A 311 LEU cc_start: 0.8476 (mp) cc_final: 0.8160 (mt) REVERT: A 312 SER cc_start: 0.8804 (p) cc_final: 0.8307 (m) REVERT: A 340 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7924 (p) REVERT: C 44 GLU cc_start: 0.8780 (tt0) cc_final: 0.8398 (tm-30) REVERT: C 68 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: C 90 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.7841 (mtm-85) REVERT: C 202 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6771 (pt0) REVERT: C 223 GLU cc_start: 0.8174 (tt0) cc_final: 0.7859 (tm-30) REVERT: C 245 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8431 (tt) REVERT: C 250 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8399 (mp) REVERT: C 264 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: E 149 LYS cc_start: 0.8281 (mttt) cc_final: 0.7762 (pmtt) REVERT: E 173 LYS cc_start: 0.8594 (tttp) cc_final: 0.8070 (mttm) REVERT: E 201 GLN cc_start: 0.7764 (mp10) cc_final: 0.7420 (mp10) REVERT: F 21 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: F 204 LYS cc_start: 0.8723 (mttm) cc_final: 0.8314 (mtmt) REVERT: F 232 PHE cc_start: 0.4956 (OUTLIER) cc_final: 0.3345 (t80) REVERT: F 296 ASP cc_start: 0.8389 (t0) cc_final: 0.7975 (t0) REVERT: F 304 GLU cc_start: 0.6357 (tt0) cc_final: 0.6148 (tt0) REVERT: B 244 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: B 254 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7160 (mp) outliers start: 41 outliers final: 19 residues processed: 177 average time/residue: 0.6410 time to fit residues: 127.2213 Evaluate side-chains 167 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 340 THR 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 338 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR 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 244 GLN 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 Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 128 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 10 optimal weight: 0.0030 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 GLN F 177 ASN ** F 249 HIS ** 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 = 0.4060 r_free = 0.4060 target = 0.181705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123955 restraints weight = 19625.485| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.94 r_work: 0.3128 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1190 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= 0.086 Angle : 0.412 4.881 26225 Z= 0.224 Chirality : 0.040 0.136 3124 Planarity : 0.003 0.048 2910 Dihedral : 13.024 165.516 3902 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.95 % Allowed : 18.43 % Favored : 78.62 % 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: 0.86 (0.19), residues: 1971 helix: 1.45 (0.24), residues: 507 sheet: 1.68 (0.29), residues: 327 loop : -0.15 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 138 TYR 0.009 0.001 TYR C 225 PHE 0.023 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 covalent geometry : bond 0.00195 (18909) covalent geometry : angle 0.41161 (26225) hydrogen bonds : bond 0.02993 ( 714) hydrogen bonds : angle 4.52770 ( 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 193 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 0.556 Fit side-chains REVERT: A 149 LYS cc_start: 0.8038 (mmpt) cc_final: 0.7808 (mmmt) REVERT: A 223 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7307 (tp30) REVERT: A 232 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8427 (m-80) REVERT: A 264 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7777 (tp30) REVERT: A 311 LEU cc_start: 0.8240 (mp) cc_final: 0.7924 (mt) REVERT: A 312 SER cc_start: 0.8759 (p) cc_final: 0.8302 (m) REVERT: A 340 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7861 (p) REVERT: C 44 GLU cc_start: 0.8705 (tt0) cc_final: 0.8236 (tm-30) REVERT: C 46 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8420 (mmmt) REVERT: C 68 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: C 90 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8026 (mtm-85) REVERT: C 202 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6555 (pt0) REVERT: C 223 GLU cc_start: 0.8078 (tt0) cc_final: 0.7677 (tm-30) REVERT: C 245 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8296 (tt) REVERT: C 250 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8246 (mp) REVERT: C 264 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: E 149 LYS cc_start: 0.8190 (mttt) cc_final: 0.7632 (pmtt) REVERT: E 173 LYS cc_start: 0.8532 (tttp) cc_final: 0.7926 (mttm) REVERT: E 187 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: E 201 GLN cc_start: 0.7686 (mp10) cc_final: 0.7323 (mp10) REVERT: F 21 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: F 204 LYS cc_start: 0.8732 (mttm) cc_final: 0.8307 (mtmt) REVERT: F 232 PHE cc_start: 0.4896 (OUTLIER) cc_final: 0.3307 (t80) REVERT: F 296 ASP cc_start: 0.8315 (t0) cc_final: 0.7852 (t0) REVERT: B 244 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6770 (tt0) REVERT: B 254 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6911 (mp) outliers start: 52 outliers final: 24 residues processed: 185 average time/residue: 0.6006 time to fit residues: 125.0296 Evaluate side-chains 174 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 243 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR 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 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 E residue 96 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR 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 66 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 244 GLN 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 Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 35 optimal weight: 0.6980 chunk 206 optimal weight: 9.9990 chunk 113 optimal weight: 0.0770 chunk 105 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 200 optimal weight: 0.1980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 GLN F 177 ASN ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4065 r_free = 0.4065 target = 0.182273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124731 restraints weight = 19872.099| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.94 r_work: 0.3141 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1278 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= 0.082 Angle : 0.408 5.549 26225 Z= 0.222 Chirality : 0.040 0.135 3124 Planarity : 0.003 0.043 2910 Dihedral : 12.985 165.153 3902 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.61 % Allowed : 18.66 % 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: 0.88 (0.19), residues: 1971 helix: 1.48 (0.24), residues: 507 sheet: 1.73 (0.29), residues: 322 loop : -0.13 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 138 TYR 0.008 0.001 TYR B 225 PHE 0.023 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 covalent geometry : bond 0.00185 (18909) covalent geometry : angle 0.40828 (26225) hydrogen bonds : bond 0.02841 ( 714) hydrogen bonds : angle 4.47745 ( 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 192 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.677 Fit side-chains REVERT: A 223 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7303 (tp30) REVERT: A 232 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: A 264 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7785 (tp30) REVERT: A 311 LEU cc_start: 0.8272 (mp) cc_final: 0.7952 (mt) REVERT: A 312 SER cc_start: 0.8765 (p) cc_final: 0.8313 (m) REVERT: A 340 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7828 (p) REVERT: C 44 GLU cc_start: 0.8682 (tt0) cc_final: 0.8199 (tm-30) REVERT: C 68 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: C 90 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8016 (mtm-85) REVERT: C 202 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6473 (pt0) REVERT: C 223 GLU cc_start: 0.8034 (tt0) cc_final: 0.7672 (tm-30) REVERT: C 245 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8285 (tt) REVERT: C 250 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8417 (mm) REVERT: E 21 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: E 149 LYS cc_start: 0.8155 (mttt) cc_final: 0.7623 (pmtt) REVERT: E 173 LYS cc_start: 0.8531 (tttp) cc_final: 0.7925 (mttm) REVERT: E 201 GLN cc_start: 0.7685 (mp10) cc_final: 0.7319 (mp10) REVERT: E 284 GLN cc_start: 0.6435 (tp40) cc_final: 0.6220 (mm110) REVERT: F 21 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: F 204 LYS cc_start: 0.8732 (mttm) cc_final: 0.8301 (mtmt) REVERT: F 296 ASP cc_start: 0.8314 (t0) cc_final: 0.7865 (t0) REVERT: B 244 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6837 (tt0) REVERT: B 254 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6931 (mp) outliers start: 46 outliers final: 23 residues processed: 181 average time/residue: 0.5962 time to fit residues: 121.7768 Evaluate side-chains 170 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 340 THR 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 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 166 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR 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 236 VAL Chi-restraints excluded: chain F residue 250 LEU 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 244 GLN 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 D residue 166 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: 2.9990 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: C 201 GLN F 177 ASN ** 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 = 0.4054 r_free = 0.4054 target = 0.181129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123394 restraints weight = 19769.510| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.97 r_work: 0.3117 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1303 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= 0.105 Angle : 0.434 5.962 26225 Z= 0.235 Chirality : 0.041 0.137 3124 Planarity : 0.003 0.062 2910 Dihedral : 13.003 166.629 3902 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.38 % Allowed : 19.00 % Favored : 78.62 % 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: 1.40 (0.24), residues: 507 sheet: 1.66 (0.29), residues: 322 loop : -0.18 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 138 TYR 0.010 0.001 TYR C 225 PHE 0.027 0.001 PHE F 213 TRP 0.008 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00250 (18909) covalent geometry : angle 0.43412 (26225) hydrogen bonds : bond 0.03220 ( 714) hydrogen bonds : angle 4.56821 ( 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 181 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.595 Fit side-chains REVERT: A 223 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7311 (tp30) REVERT: A 232 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: A 264 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7852 (tp30) REVERT: A 311 LEU cc_start: 0.8249 (mp) cc_final: 0.7930 (mt) REVERT: A 312 SER cc_start: 0.8760 (p) cc_final: 0.8331 (m) REVERT: A 340 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7845 (p) REVERT: C 44 GLU cc_start: 0.8707 (tt0) cc_final: 0.8232 (tm-30) REVERT: C 46 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8393 (mmmt) REVERT: C 68 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: C 90 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8093 (mtm-85) REVERT: C 202 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6609 (pt0) REVERT: C 223 GLU cc_start: 0.7995 (tt0) cc_final: 0.7620 (tm-30) REVERT: C 245 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8339 (tt) REVERT: C 250 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8301 (mp) REVERT: E 149 LYS cc_start: 0.8171 (mttt) cc_final: 0.7615 (pmtt) REVERT: E 173 LYS cc_start: 0.8510 (tttp) cc_final: 0.7905 (mttm) REVERT: E 187 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: E 201 GLN cc_start: 0.7670 (mp10) cc_final: 0.7305 (mp10) REVERT: E 284 GLN cc_start: 0.6615 (tp40) cc_final: 0.6374 (mm110) REVERT: F 21 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: F 204 LYS cc_start: 0.8722 (mttm) cc_final: 0.8290 (mtmt) REVERT: F 296 ASP cc_start: 0.8326 (t0) cc_final: 0.7850 (t0) REVERT: B 173 LYS cc_start: 0.8833 (mttt) cc_final: 0.8581 (mtpp) REVERT: B 191 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7804 (mp0) REVERT: B 244 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: B 254 LEU cc_start: 0.7170 (mm) cc_final: 0.6888 (mp) outliers start: 42 outliers final: 24 residues processed: 173 average time/residue: 0.6097 time to fit residues: 118.4462 Evaluate side-chains 169 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 340 THR 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 98 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU 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 127 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR 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 236 VAL Chi-restraints excluded: chain F residue 250 LEU 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 244 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain D residue 166 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: 0.9980 chunk 36 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN C 201 GLN F 177 ASN ** F 249 HIS ** 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 = 0.4044 r_free = 0.4044 target = 0.180215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122251 restraints weight = 19667.729| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.00 r_work: 0.3105 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18909 Z= 0.126 Angle : 0.464 6.305 26225 Z= 0.250 Chirality : 0.042 0.140 3124 Planarity : 0.004 0.062 2910 Dihedral : 13.028 167.440 3900 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.38 % Allowed : 19.23 % Favored : 78.39 % 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: 0.66 (0.19), residues: 1971 helix: 1.27 (0.24), residues: 508 sheet: 1.55 (0.29), residues: 322 loop : -0.25 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 138 TYR 0.011 0.001 TYR A 342 PHE 0.027 0.002 PHE F 213 TRP 0.009 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00304 (18909) covalent geometry : angle 0.46401 (26225) hydrogen bonds : bond 0.03559 ( 714) hydrogen bonds : angle 4.67719 ( 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 178 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.681 Fit side-chains REVERT: A 223 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7318 (tp30) REVERT: A 232 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: A 264 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7825 (tp30) REVERT: A 311 LEU cc_start: 0.8262 (mp) cc_final: 0.7933 (mt) REVERT: A 312 SER cc_start: 0.8744 (p) cc_final: 0.8332 (m) REVERT: A 340 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7844 (p) REVERT: C 44 GLU cc_start: 0.8699 (tt0) cc_final: 0.8203 (tm-30) REVERT: C 46 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8351 (mmmt) REVERT: C 68 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: C 90 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8485 (mtm-85) REVERT: C 202 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6696 (pt0) REVERT: C 223 GLU cc_start: 0.8003 (tt0) cc_final: 0.7651 (tm-30) REVERT: C 245 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8369 (tt) REVERT: C 250 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8349 (mp) REVERT: E 149 LYS cc_start: 0.8205 (mttt) cc_final: 0.7599 (pmtt) REVERT: E 173 LYS cc_start: 0.8518 (tttp) cc_final: 0.7934 (mttm) REVERT: E 187 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: E 201 GLN cc_start: 0.7685 (mp10) cc_final: 0.7319 (mp10) REVERT: E 284 GLN cc_start: 0.6638 (tp40) cc_final: 0.6409 (mm110) REVERT: F 21 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: F 204 LYS cc_start: 0.8712 (mttm) cc_final: 0.8271 (mtmt) REVERT: F 232 PHE cc_start: 0.4824 (OUTLIER) cc_final: 0.3208 (t80) REVERT: F 296 ASP cc_start: 0.8372 (t0) cc_final: 0.7885 (t0) REVERT: B 173 LYS cc_start: 0.8817 (mttt) cc_final: 0.8559 (mtpp) REVERT: B 191 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7828 (mp0) REVERT: B 244 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: B 254 LEU cc_start: 0.7302 (mm) cc_final: 0.7023 (mp) outliers start: 42 outliers final: 26 residues processed: 171 average time/residue: 0.6025 time to fit residues: 115.7674 Evaluate side-chains 171 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 264 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR 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 98 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 LEU 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 127 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR 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 66 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 11 optimal weight: 0.0870 chunk 204 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 145 optimal weight: 20.0000 chunk 67 optimal weight: 0.4980 chunk 168 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 0.0050 chunk 176 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 GLN F 177 ASN ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4066 r_free = 0.4066 target = 0.182317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124758 restraints weight = 19844.880| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.94 r_work: 0.3139 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1447 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= 0.081 Angle : 0.413 6.615 26225 Z= 0.224 Chirality : 0.040 0.137 3124 Planarity : 0.003 0.056 2910 Dihedral : 12.964 165.823 3900 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.04 % Allowed : 19.68 % Favored : 78.28 % 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: 0.83 (0.19), residues: 1971 helix: 1.45 (0.24), residues: 507 sheet: 1.63 (0.29), residues: 327 loop : -0.16 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 138 TYR 0.007 0.001 TYR C 225 PHE 0.028 0.001 PHE F 213 TRP 0.008 0.001 TRP A 332 HIS 0.004 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00179 (18909) covalent geometry : angle 0.41321 (26225) hydrogen bonds : bond 0.02830 ( 714) hydrogen bonds : angle 4.47218 ( 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 182 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.653 Fit side-chains REVERT: A 149 LYS cc_start: 0.8038 (mmpt) cc_final: 0.7820 (mmmt) REVERT: A 223 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7283 (tp30) REVERT: A 264 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7713 (tp30) REVERT: A 311 LEU cc_start: 0.8116 (mp) cc_final: 0.7808 (mt) REVERT: A 312 SER cc_start: 0.8756 (p) cc_final: 0.8316 (m) REVERT: A 340 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7771 (p) REVERT: C 44 GLU cc_start: 0.8655 (tt0) cc_final: 0.8142 (tm-30) REVERT: C 68 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: C 90 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8367 (mtm-85) REVERT: C 202 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6451 (pt0) REVERT: C 223 GLU cc_start: 0.7993 (tt0) cc_final: 0.7615 (tm-30) REVERT: C 245 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8237 (tt) REVERT: C 250 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8350 (mm) REVERT: E 149 LYS cc_start: 0.8119 (mttt) cc_final: 0.7608 (pmtt) REVERT: E 173 LYS cc_start: 0.8513 (tttp) cc_final: 0.7881 (mttm) REVERT: E 187 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7611 (mt0) REVERT: E 201 GLN cc_start: 0.7644 (mp10) cc_final: 0.7277 (mp10) REVERT: E 284 GLN cc_start: 0.6580 (tp40) cc_final: 0.6333 (mm110) REVERT: F 21 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: F 204 LYS cc_start: 0.8719 (mttm) cc_final: 0.8285 (mtmt) REVERT: F 232 PHE cc_start: 0.4763 (OUTLIER) cc_final: 0.3155 (t80) REVERT: F 296 ASP cc_start: 0.8320 (t0) cc_final: 0.7843 (t0) REVERT: B 173 LYS cc_start: 0.8816 (mttt) cc_final: 0.8546 (mtpp) REVERT: B 191 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7802 (mp0) REVERT: B 244 GLN cc_start: 0.7268 (tt0) cc_final: 0.6807 (tt0) REVERT: B 254 LEU cc_start: 0.7131 (mm) cc_final: 0.6849 (mp) REVERT: D 104 MET cc_start: 0.7950 (mmt) cc_final: 0.7679 (mmm) outliers start: 36 outliers final: 24 residues processed: 174 average time/residue: 0.5661 time to fit residues: 111.6966 Evaluate side-chains 173 residues out of total 1763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 264 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 THR 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 318 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 166 THR Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 47 THR 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 66 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 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: 8.9990 chunk 142 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 GLN F 177 ASN ** 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 = 0.4059 r_free = 0.4059 target = 0.181636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124893 restraints weight = 19854.531| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.04 r_work: 0.3113 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1462 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= 0.096 Angle : 0.435 8.220 26225 Z= 0.233 Chirality : 0.040 0.138 3124 Planarity : 0.003 0.057 2910 Dihedral : 12.955 166.431 3900 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.27 % Allowed : 19.51 % Favored : 78.22 % 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: 1.44 (0.24), residues: 507 sheet: 1.64 (0.29), residues: 322 loop : -0.18 (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 0.028 0.001 PHE F 213 TRP 0.008 0.001 TRP E 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00225 (18909) covalent geometry : angle 0.43543 (26225) hydrogen bonds : bond 0.03101 ( 714) hydrogen bonds : angle 4.51286 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7304.81 seconds wall clock time: 125 minutes 0.63 seconds (7500.63 seconds total)