Starting phenix.real_space_refine on Fri Jul 3 17:58:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8op1_17035/07_2026/8op1_17035.cif Found real_map, /net/cci-nas-00/data/ceres_data/8op1_17035/07_2026/8op1_17035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8op1_17035/07_2026/8op1_17035.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8op1_17035/07_2026/8op1_17035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8op1_17035/07_2026/8op1_17035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8op1_17035/07_2026/8op1_17035.map" model { file = "/net/cci-nas-00/data/ceres_data/8op1_17035/07_2026/8op1_17035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8op1_17035/07_2026/8op1_17035.cif" } resolution = 3.5 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 80 5.16 5 C 9630 2.51 5 N 2655 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15415 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "C" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "H" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "D" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "I" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "E" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Time building chain proxies: 3.25, per 1000 atoms: 0.21 Number of scatterers: 15415 At special positions: 0 Unit cell: (178.62, 117.935, 117.935, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 35 15.00 O 3015 8.00 N 2655 7.00 C 9630 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: 1.08 Conformation dependent library (CDL) restraints added in 789.9 milliseconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 13 sheets defined 68.0% alpha, 4.8% beta 0 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 54 Processing helix chain 'A' and resid 58 through 61 removed outlier: 4.168A pdb=" N PHE A 61 " --> pdb=" O ASN A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 62 through 75 Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 121 through 143 Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.563A pdb=" N ARG A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.097A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.764A pdb=" N ARG A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.825A pdb=" N GLY A 299 " --> pdb=" O GLY A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 3.755A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 311 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 313 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.806A pdb=" N GLU A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.529A pdb=" N VAL B 6 " --> pdb=" O LEU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 61 through 75 removed outlier: 4.044A pdb=" N ILE B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 120 through 143 removed outlier: 3.535A pdb=" N GLN B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.645A pdb=" N ARG B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 216 through 231 removed outlier: 4.175A pdb=" N ILE B 220 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.622A pdb=" N ASN B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 removed outlier: 4.173A pdb=" N ARG B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.553A pdb=" N LEU B 272 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 296 through 300 removed outlier: 4.094A pdb=" N GLY B 299 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 4.010A pdb=" N SER B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 311 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.630A pdb=" N GLU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 4.143A pdb=" N ALA B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 54 removed outlier: 3.523A pdb=" N THR C 54 " --> pdb=" O MET C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.604A pdb=" N GLN C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 171 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 216 through 231 removed outlier: 4.076A pdb=" N ILE C 220 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.727A pdb=" N ARG C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 274 through 295 removed outlier: 4.006A pdb=" N GLU C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLN C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 317 through 331 Processing helix chain 'C' and resid 343 through 360 removed outlier: 4.101A pdb=" N GLU C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 58 through 60 No H-bonds generated for 'chain 'D' and resid 58 through 60' Processing helix chain 'D' and resid 61 through 75 removed outlier: 3.903A pdb=" N ILE D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 87 Processing helix chain 'D' and resid 120 through 143 Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.584A pdb=" N ARG D 150 " --> pdb=" O PRO D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 197 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.884A pdb=" N ASP D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.926A pdb=" N ARG D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.634A pdb=" N LEU D 272 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 296 through 300 removed outlier: 4.150A pdb=" N GLY D 299 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 4.341A pdb=" N SER D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 311 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 313 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 331 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.611A pdb=" N GLU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 379 Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 40 through 54 Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 76 through 86 Processing helix chain 'E' and resid 120 through 143 removed outlier: 3.825A pdb=" N GLN E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.725A pdb=" N ARG E 150 " --> pdb=" O PRO E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 171 Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 217 through 231 removed outlier: 4.316A pdb=" N ASP E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.909A pdb=" N ARG E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 273 removed outlier: 3.572A pdb=" N LEU E 272 " --> pdb=" O ASN E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 280 through 295 Processing helix chain 'E' and resid 296 through 299 removed outlier: 3.786A pdb=" N GLY E 299 " --> pdb=" O GLY E 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 296 through 299' Processing helix chain 'E' and resid 306 through 313 removed outlier: 4.159A pdb=" N SER E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU E 311 " --> pdb=" O LYS E 308 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER E 313 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 331 Processing helix chain 'E' and resid 343 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 7.222A pdb=" N ARG A 27 " --> pdb=" O HIS A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.626A pdb=" N ILE A 33 " --> pdb=" O ASN A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 104 removed outlier: 3.648A pdb=" N PHE A 111 " --> pdb=" O HIS A 100 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 102 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 109 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 28 removed outlier: 7.071A pdb=" N ARG B 27 " --> pdb=" O HIS B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 34 removed outlier: 6.972A pdb=" N ILE B 33 " --> pdb=" O ASN B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 104 removed outlier: 4.200A pdb=" N ASP B 96 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 27 through 28 removed outlier: 7.165A pdb=" N ARG C 27 " --> pdb=" O HIS C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.599A pdb=" N ASN C 93 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 104 removed outlier: 3.532A pdb=" N GLN C 102 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 109 " --> pdb=" O GLN C 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 33 through 34 removed outlier: 6.554A pdb=" N ILE D 33 " --> pdb=" O ASN D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 97 through 104 removed outlier: 3.747A pdb=" N HIS D 100 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 111 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 33 through 34 removed outlier: 6.438A pdb=" N ILE E 33 " --> pdb=" O ASN E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 104 removed outlier: 3.525A pdb=" N PHE E 111 " --> pdb=" O HIS E 100 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN E 102 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET E 109 " --> pdb=" O GLN E 102 " (cutoff:3.500A) 851 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5025 1.34 - 1.46: 3297 1.46 - 1.58: 7188 1.58 - 1.70: 65 1.70 - 1.82: 145 Bond restraints: 15720 Sorted by residual: bond pdb=" C ILE C 270 " pdb=" N MET C 271 " ideal model delta sigma weight residual 1.335 1.305 0.030 1.39e-02 5.18e+03 4.55e+00 bond pdb=" CA MET C 271 " pdb=" C MET C 271 " ideal model delta sigma weight residual 1.524 1.493 0.030 1.59e-02 3.96e+03 3.61e+00 bond pdb=" CA SER A 231 " pdb=" C SER A 231 " ideal model delta sigma weight residual 1.522 1.494 0.027 1.72e-02 3.38e+03 2.51e+00 bond pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 1.464 1.444 0.019 1.25e-02 6.40e+03 2.39e+00 bond pdb=" CA MET B 271 " pdb=" C MET B 271 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.80e-02 3.09e+03 2.12e+00 ... (remaining 15715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 20678 1.84 - 3.69: 543 3.69 - 5.53: 76 5.53 - 7.37: 14 7.37 - 9.22: 4 Bond angle restraints: 21315 Sorted by residual: angle pdb=" C GLU C 55 " pdb=" N ASP C 56 " pdb=" CA ASP C 56 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N VAL D 267 " pdb=" CA VAL D 267 " pdb=" C VAL D 267 " ideal model delta sigma weight residual 112.98 108.60 4.38 1.25e+00 6.40e-01 1.23e+01 angle pdb=" N ILE E 378 " pdb=" CA ILE E 378 " pdb=" C ILE E 378 " ideal model delta sigma weight residual 113.42 109.41 4.01 1.17e+00 7.31e-01 1.18e+01 angle pdb=" N VAL C 267 " pdb=" CA VAL C 267 " pdb=" C VAL C 267 " ideal model delta sigma weight residual 113.07 108.63 4.44 1.36e+00 5.41e-01 1.06e+01 angle pdb=" N GLY C 296 " pdb=" CA GLY C 296 " pdb=" C GLY C 296 " ideal model delta sigma weight residual 112.50 116.23 -3.73 1.16e+00 7.43e-01 1.03e+01 ... (remaining 21310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 8454 17.60 - 35.19: 821 35.19 - 52.79: 140 52.79 - 70.39: 27 70.39 - 87.98: 18 Dihedral angle restraints: 9460 sinusoidal: 4025 harmonic: 5435 Sorted by residual: dihedral pdb=" CA ILE A 303 " pdb=" C ILE A 303 " pdb=" N LEU A 304 " pdb=" CA LEU A 304 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ILE B 303 " pdb=" C ILE B 303 " pdb=" N LEU B 304 " pdb=" CA LEU B 304 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ILE C 303 " pdb=" C ILE C 303 " pdb=" N LEU C 304 " pdb=" CA LEU C 304 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 9457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1811 0.049 - 0.098: 539 0.098 - 0.147: 92 0.147 - 0.196: 7 0.196 - 0.245: 1 Chirality restraints: 2450 Sorted by residual: chirality pdb=" CB THR C 35 " pdb=" CA THR C 35 " pdb=" OG1 THR C 35 " pdb=" CG2 THR C 35 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA MET B 142 " pdb=" N MET B 142 " pdb=" C MET B 142 " pdb=" CB MET B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA MET C 271 " pdb=" N MET C 271 " pdb=" C MET C 271 " pdb=" CB MET C 271 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.84e-01 ... (remaining 2447 not shown) Planarity restraints: 2620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 306 " 0.055 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO C 307 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 216 " 0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 217 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 306 " -0.034 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 307 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " -0.028 5.00e-02 4.00e+02 ... (remaining 2617 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 514 2.70 - 3.25: 16106 3.25 - 3.80: 24655 3.80 - 4.35: 31316 4.35 - 4.90: 52085 Nonbonded interactions: 124676 Sorted by model distance: nonbonded pdb=" OH TYR B 69 " pdb=" NH2 ARG B 73 " model vdw 2.154 3.120 nonbonded pdb=" OH TYR D 337 " pdb=" OP2 C I1004 " model vdw 2.160 3.040 nonbonded pdb=" O ASP B 31 " pdb=" NZ LYS B 91 " model vdw 2.162 3.120 nonbonded pdb=" OG SER E 32 " pdb=" O LYS E 91 " model vdw 2.163 3.040 nonbonded pdb=" OH TYR E 135 " pdb=" NH1 ARG E 150 " model vdw 2.184 3.120 ... (remaining 124671 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.300 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.190 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.006 0.062 15720 Z= 0.271 Angle : 0.747 9.217 21315 Z= 0.420 Chirality : 0.046 0.245 2450 Planarity : 0.004 0.081 2620 Dihedral : 14.308 87.981 5990 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.39 (0.19), residues: 1880 helix: 0.18 (0.15), residues: 1138 sheet: 1.49 (0.56), residues: 76 loop : -1.09 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 76 TYR 0.031 0.002 TYR D 301 PHE 0.014 0.002 PHE A 226 TRP 0.004 0.001 TRP E 260 HIS 0.010 0.002 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 (15720) covalent geometry : angle 0.74652 / 0.42 (21315) hydrogen bonds : bond 0.13089 / 9.15 ( 851) hydrogen bonds : angle 6.06503 / 4.30 ( 2460) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.560 Fit side-chains REVERT: A 50 MET cc_start: 0.8339 (mpp) cc_final: 0.8074 (mpp) REVERT: B 12 LEU cc_start: 0.8915 (tp) cc_final: 0.8483 (tp) REVERT: B 50 MET cc_start: 0.6837 (mpp) cc_final: 0.6388 (mpp) REVERT: C 67 MET cc_start: 0.8532 (mmm) cc_final: 0.7725 (mmt) REVERT: D 138 MET cc_start: 0.7424 (mtp) cc_final: 0.6628 (tmm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0983 time to fit residues: 28.3394 Evaluate side-chains 146 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN B 126 ASN C 45 ASN C 89 HIS C 151 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN E 43 HIS ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.186285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154026 restraints weight = 22039.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153339 restraints weight = 22804.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.154938 restraints weight = 18144.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.155525 restraints weight = 13439.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.155535 restraints weight = 12747.106| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15720 Z= 0.131 Angle : 0.543 6.905 21315 Z= 0.288 Chirality : 0.041 0.202 2450 Planarity : 0.004 0.041 2620 Dihedral : 5.796 54.230 2450 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.76 % Allowed : 8.63 % Favored : 90.60 % 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: 0.35 (0.19), residues: 1880 helix: 0.82 (0.15), residues: 1157 sheet: 2.03 (0.63), residues: 68 loop : -0.96 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 73 TYR 0.015 0.001 TYR A 210 PHE 0.015 0.001 PHE E 219 TRP 0.002 0.000 TRP C 260 HIS 0.006 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15720) covalent geometry : angle 0.54345 / 0.29 (21315) hydrogen bonds : bond 0.03977 / 2.75 ( 851) hydrogen bonds : angle 4.31547 / 3.02 ( 2460) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.436 Fit side-chains REVERT: A 50 MET cc_start: 0.8360 (mpp) cc_final: 0.8134 (mpp) REVERT: B 50 MET cc_start: 0.6926 (mpp) cc_final: 0.6475 (mpp) REVERT: B 175 ASP cc_start: 0.7044 (m-30) cc_final: 0.6561 (t0) REVERT: C 71 MET cc_start: 0.6261 (ptm) cc_final: 0.6047 (ptm) REVERT: C 80 ILE cc_start: 0.6838 (mm) cc_final: 0.6559 (tp) REVERT: C 257 MET cc_start: 0.8458 (mmm) cc_final: 0.8085 (mmt) REVERT: C 337 TYR cc_start: 0.7315 (t80) cc_final: 0.7009 (t80) REVERT: D 138 MET cc_start: 0.7638 (mtp) cc_final: 0.6475 (tmm) outliers start: 12 outliers final: 9 residues processed: 187 average time/residue: 0.1048 time to fit residues: 30.3471 Evaluate side-chains 162 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 201 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 104 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 126 ASN C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.191241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153336 restraints weight = 23092.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.154862 restraints weight = 19794.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155861 restraints weight = 15470.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.156149 restraints weight = 11195.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.156259 restraints weight = 10762.162| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15720 Z= 0.145 Angle : 0.533 7.756 21315 Z= 0.279 Chirality : 0.041 0.176 2450 Planarity : 0.003 0.033 2620 Dihedral : 5.641 59.023 2450 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.65 % Allowed : 11.62 % Favored : 86.73 % 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: 0.55 (0.19), residues: 1880 helix: 0.99 (0.15), residues: 1160 sheet: 1.96 (0.63), residues: 68 loop : -0.88 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 73 TYR 0.012 0.001 TYR C 353 PHE 0.012 0.001 PHE D 226 TRP 0.002 0.000 TRP D 260 HIS 0.014 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (15720) covalent geometry : angle 0.53313 / 0.28 (21315) hydrogen bonds : bond 0.03870 / 2.67 ( 851) hydrogen bonds : angle 4.16205 / 2.91 ( 2460) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: B 50 MET cc_start: 0.6734 (mpp) cc_final: 0.6368 (mtt) REVERT: B 67 MET cc_start: 0.7639 (tpp) cc_final: 0.7419 (mmm) REVERT: B 88 TYR cc_start: 0.8066 (m-80) cc_final: 0.7341 (m-80) REVERT: B 256 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7929 (m) REVERT: C 80 ILE cc_start: 0.6880 (mm) cc_final: 0.6460 (tp) REVERT: C 126 ASN cc_start: 0.8236 (m-40) cc_final: 0.7865 (t0) REVERT: D 27 ARG cc_start: 0.2985 (OUTLIER) cc_final: 0.1879 (mmp-170) REVERT: D 138 MET cc_start: 0.7763 (mtp) cc_final: 0.6443 (tmm) REVERT: D 142 MET cc_start: 0.5848 (ppp) cc_final: 0.5640 (ppp) REVERT: E 12 LEU cc_start: 0.8654 (tt) cc_final: 0.8345 (tp) outliers start: 26 outliers final: 16 residues processed: 186 average time/residue: 0.1018 time to fit residues: 29.7068 Evaluate side-chains 171 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 180 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN B 126 ASN C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** 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 = 0.4318 r_free = 0.4318 target = 0.191843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.153746 restraints weight = 22937.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.154815 restraints weight = 19978.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155854 restraints weight = 15219.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156574 restraints weight = 10903.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.156681 restraints weight = 10050.598| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15720 Z= 0.132 Angle : 0.511 8.197 21315 Z= 0.268 Chirality : 0.040 0.159 2450 Planarity : 0.003 0.032 2620 Dihedral : 5.631 59.107 2450 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.22 % Allowed : 12.70 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1880 helix: 1.11 (0.15), residues: 1163 sheet: 1.96 (0.62), residues: 68 loop : -0.75 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 73 TYR 0.026 0.001 TYR B 353 PHE 0.011 0.001 PHE D 226 TRP 0.002 0.000 TRP D 260 HIS 0.013 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (15720) covalent geometry : angle 0.51091 / 0.27 (21315) hydrogen bonds : bond 0.03668 / 2.53 ( 851) hydrogen bonds : angle 4.06441 / 2.86 ( 2460) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.589 Fit side-chains REVERT: A 50 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7815 (mpt) REVERT: B 50 MET cc_start: 0.6681 (mpp) cc_final: 0.6351 (mtt) REVERT: B 88 TYR cc_start: 0.8058 (m-80) cc_final: 0.7461 (m-80) REVERT: B 175 ASP cc_start: 0.7122 (m-30) cc_final: 0.6829 (t0) REVERT: B 256 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7900 (m) REVERT: C 67 MET cc_start: 0.8520 (mmm) cc_final: 0.7770 (mmt) REVERT: C 80 ILE cc_start: 0.6852 (mm) cc_final: 0.6519 (tp) REVERT: C 126 ASN cc_start: 0.8297 (m-40) cc_final: 0.7944 (t0) REVERT: C 201 LEU cc_start: 0.6877 (mp) cc_final: 0.6538 (tp) REVERT: C 257 MET cc_start: 0.8467 (mmm) cc_final: 0.8066 (mmt) REVERT: D 27 ARG cc_start: 0.3066 (OUTLIER) cc_final: 0.1846 (mmp-170) REVERT: D 138 MET cc_start: 0.7779 (mtp) cc_final: 0.6351 (tmm) REVERT: E 12 LEU cc_start: 0.8583 (tt) cc_final: 0.8264 (tp) outliers start: 35 outliers final: 24 residues processed: 190 average time/residue: 0.1036 time to fit residues: 30.6484 Evaluate side-chains 183 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 40 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 ASN B 43 HIS C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.191382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153467 restraints weight = 22951.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.154495 restraints weight = 19208.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155791 restraints weight = 15679.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155967 restraints weight = 11131.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.156187 restraints weight = 10905.294| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15720 Z= 0.142 Angle : 0.519 8.804 21315 Z= 0.270 Chirality : 0.040 0.148 2450 Planarity : 0.003 0.033 2620 Dihedral : 5.645 59.913 2450 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.35 % Allowed : 13.08 % Favored : 84.57 % 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: 0.77 (0.19), residues: 1880 helix: 1.11 (0.15), residues: 1163 sheet: 1.92 (0.61), residues: 68 loop : -0.67 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 73 TYR 0.018 0.001 TYR B 353 PHE 0.011 0.001 PHE D 226 TRP 0.002 0.000 TRP D 260 HIS 0.010 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15720) covalent geometry : angle 0.51933 / 0.27 (21315) hydrogen bonds : bond 0.03704 / 2.54 ( 851) hydrogen bonds : angle 4.06915 / 2.86 ( 2460) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7884 (mpt) REVERT: B 50 MET cc_start: 0.6691 (mpp) cc_final: 0.6382 (mtt) REVERT: B 88 TYR cc_start: 0.7991 (m-80) cc_final: 0.7402 (m-80) REVERT: B 256 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.8013 (m) REVERT: C 80 ILE cc_start: 0.6879 (mm) cc_final: 0.6461 (tp) REVERT: C 126 ASN cc_start: 0.8222 (m-40) cc_final: 0.7983 (t0) REVERT: C 201 LEU cc_start: 0.6757 (mp) cc_final: 0.6514 (tp) REVERT: C 271 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7606 (mtm) REVERT: D 27 ARG cc_start: 0.3293 (OUTLIER) cc_final: 0.1939 (mmp-170) REVERT: D 138 MET cc_start: 0.7813 (mtp) cc_final: 0.6634 (tmm) REVERT: E 12 LEU cc_start: 0.8569 (tt) cc_final: 0.8248 (tp) outliers start: 37 outliers final: 26 residues processed: 191 average time/residue: 0.1019 time to fit residues: 30.2790 Evaluate side-chains 186 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 67 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 181 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.191061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.152793 restraints weight = 22847.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.153942 restraints weight = 19872.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155112 restraints weight = 15970.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.155517 restraints weight = 11366.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155709 restraints weight = 10538.459| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15720 Z= 0.148 Angle : 0.526 10.171 21315 Z= 0.272 Chirality : 0.040 0.150 2450 Planarity : 0.003 0.033 2620 Dihedral : 5.646 58.746 2450 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.67 % Allowed : 13.65 % Favored : 83.68 % 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: 1880 helix: 1.13 (0.15), residues: 1161 sheet: 1.87 (0.61), residues: 68 loop : -0.63 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 73 TYR 0.017 0.001 TYR C 337 PHE 0.010 0.001 PHE D 226 TRP 0.003 0.001 TRP D 260 HIS 0.010 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (15720) covalent geometry : angle 0.52629 / 0.27 (21315) hydrogen bonds : bond 0.03710 / 2.55 ( 851) hydrogen bonds : angle 4.07242 / 2.87 ( 2460) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.386 Fit side-chains REVERT: A 73 ARG cc_start: 0.8591 (ttm170) cc_final: 0.8266 (ttt90) REVERT: A 83 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7205 (mm) REVERT: B 50 MET cc_start: 0.6677 (mpp) cc_final: 0.6400 (mtt) REVERT: B 248 MET cc_start: 0.7191 (mmm) cc_final: 0.6912 (mtp) REVERT: B 256 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.8021 (m) REVERT: C 26 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6953 (mt0) REVERT: C 80 ILE cc_start: 0.6834 (mm) cc_final: 0.6379 (tp) REVERT: C 126 ASN cc_start: 0.8305 (m-40) cc_final: 0.8055 (t0) REVERT: C 201 LEU cc_start: 0.6769 (mp) cc_final: 0.6559 (tp) REVERT: C 257 MET cc_start: 0.8349 (mmm) cc_final: 0.7954 (mmt) REVERT: C 271 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7452 (mtm) REVERT: D 27 ARG cc_start: 0.3214 (OUTLIER) cc_final: 0.1794 (mmp-170) REVERT: D 138 MET cc_start: 0.7787 (mtp) cc_final: 0.6819 (tmm) REVERT: D 357 LEU cc_start: 0.8380 (tp) cc_final: 0.8153 (pp) REVERT: E 304 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7232 (mt) outliers start: 42 outliers final: 27 residues processed: 187 average time/residue: 0.0979 time to fit residues: 28.4883 Evaluate side-chains 190 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 179 optimal weight: 0.8980 chunk 184 optimal weight: 0.0970 chunk 168 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 HIS C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** 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 = 0.4322 r_free = 0.4322 target = 0.192339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.154332 restraints weight = 22831.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155660 restraints weight = 19660.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156685 restraints weight = 15185.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157088 restraints weight = 10902.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157088 restraints weight = 10344.933| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15720 Z= 0.124 Angle : 0.523 12.336 21315 Z= 0.266 Chirality : 0.039 0.183 2450 Planarity : 0.003 0.033 2620 Dihedral : 5.573 59.706 2450 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.54 % Allowed : 14.29 % Favored : 83.17 % 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: 0.91 (0.20), residues: 1880 helix: 1.23 (0.15), residues: 1173 sheet: 1.96 (0.62), residues: 68 loop : -0.64 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.020 0.001 TYR C 337 PHE 0.010 0.001 PHE D 226 TRP 0.002 0.000 TRP A 260 HIS 0.012 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15720) covalent geometry : angle 0.52264 / 0.27 (21315) hydrogen bonds : bond 0.03534 / 2.43 ( 851) hydrogen bonds : angle 3.97354 / 2.79 ( 2460) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.659 Fit side-chains REVERT: A 73 ARG cc_start: 0.8546 (ttm170) cc_final: 0.8271 (ttt90) REVERT: A 83 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7145 (mm) REVERT: B 50 MET cc_start: 0.6648 (mpp) cc_final: 0.6392 (mtt) REVERT: B 67 MET cc_start: 0.7686 (mmm) cc_final: 0.7313 (tpt) REVERT: B 175 ASP cc_start: 0.7000 (m-30) cc_final: 0.6595 (t0) REVERT: B 248 MET cc_start: 0.7147 (mmm) cc_final: 0.6857 (mtp) REVERT: B 256 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7918 (m) REVERT: C 26 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6901 (mt0) REVERT: C 80 ILE cc_start: 0.6887 (mm) cc_final: 0.6490 (tp) REVERT: C 126 ASN cc_start: 0.8279 (m-40) cc_final: 0.8058 (t0) REVERT: C 194 MET cc_start: 0.7871 (tpt) cc_final: 0.7646 (mtp) REVERT: C 257 MET cc_start: 0.8418 (mmm) cc_final: 0.8027 (mmt) REVERT: C 271 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7413 (mtm) REVERT: D 27 ARG cc_start: 0.3419 (OUTLIER) cc_final: 0.3050 (mtt-85) REVERT: D 50 MET cc_start: 0.7163 (mtp) cc_final: 0.6863 (ptm) REVERT: D 138 MET cc_start: 0.7614 (mtp) cc_final: 0.6820 (tmm) REVERT: E 12 LEU cc_start: 0.8483 (tt) cc_final: 0.7961 (mp) REVERT: E 198 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7763 (mtmt) REVERT: E 304 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7178 (mt) outliers start: 40 outliers final: 26 residues processed: 187 average time/residue: 0.0991 time to fit residues: 28.9794 Evaluate side-chains 186 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 304 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 13 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 169 optimal weight: 0.0040 chunk 88 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.192514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154330 restraints weight = 22977.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155469 restraints weight = 19682.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156727 restraints weight = 14921.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157056 restraints weight = 11045.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157337 restraints weight = 10628.103| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15720 Z= 0.124 Angle : 0.534 16.653 21315 Z= 0.269 Chirality : 0.039 0.183 2450 Planarity : 0.003 0.032 2620 Dihedral : 5.500 58.856 2450 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.41 % Allowed : 14.79 % Favored : 82.79 % 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: 0.97 (0.20), residues: 1880 helix: 1.28 (0.15), residues: 1172 sheet: 1.78 (0.63), residues: 70 loop : -0.61 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 73 TYR 0.019 0.001 TYR C 337 PHE 0.010 0.001 PHE D 226 TRP 0.002 0.000 TRP A 260 HIS 0.010 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15720) covalent geometry : angle 0.53440 / 0.27 (21315) hydrogen bonds : bond 0.03524 / 2.42 ( 851) hydrogen bonds : angle 3.95142 / 2.78 ( 2460) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.619 Fit side-chains REVERT: A 73 ARG cc_start: 0.8509 (ttm170) cc_final: 0.8223 (ttt90) REVERT: A 83 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7128 (mm) REVERT: B 50 MET cc_start: 0.6631 (mpp) cc_final: 0.6378 (mtt) REVERT: B 175 ASP cc_start: 0.6852 (m-30) cc_final: 0.6510 (t0) REVERT: B 248 MET cc_start: 0.7079 (mmm) cc_final: 0.6813 (mtp) REVERT: B 256 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7922 (m) REVERT: C 26 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.7032 (mt0) REVERT: C 80 ILE cc_start: 0.6937 (mm) cc_final: 0.6549 (tp) REVERT: C 126 ASN cc_start: 0.8320 (m-40) cc_final: 0.8076 (t0) REVERT: C 194 MET cc_start: 0.7849 (tpt) cc_final: 0.7647 (mtp) REVERT: C 257 MET cc_start: 0.8392 (mmm) cc_final: 0.8006 (mmt) REVERT: C 271 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7407 (mtm) REVERT: C 272 LEU cc_start: 0.8006 (mt) cc_final: 0.7764 (tp) REVERT: D 27 ARG cc_start: 0.3524 (OUTLIER) cc_final: 0.3119 (mtt-85) REVERT: D 50 MET cc_start: 0.7176 (mtp) cc_final: 0.6869 (ptm) REVERT: D 138 MET cc_start: 0.7626 (mtp) cc_final: 0.6682 (tmm) REVERT: E 12 LEU cc_start: 0.8462 (tt) cc_final: 0.7929 (mp) REVERT: E 198 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7756 (mtmt) REVERT: E 304 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7221 (mt) outliers start: 38 outliers final: 29 residues processed: 184 average time/residue: 0.0986 time to fit residues: 28.4807 Evaluate side-chains 188 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 304 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 20 optimal weight: 1.9990 chunk 125 optimal weight: 0.0020 chunk 168 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** 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 = 0.4451 r_free = 0.4451 target = 0.198926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.170125 restraints weight = 21882.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.170240 restraints weight = 23826.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.171734 restraints weight = 19044.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.172136 restraints weight = 13662.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.172452 restraints weight = 12222.785| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15720 Z= 0.108 Angle : 0.522 11.285 21315 Z= 0.264 Chirality : 0.039 0.175 2450 Planarity : 0.003 0.031 2620 Dihedral : 5.397 58.606 2450 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.10 % Allowed : 15.68 % Favored : 82.22 % 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: 1.06 (0.20), residues: 1880 helix: 1.35 (0.15), residues: 1172 sheet: 1.79 (0.62), residues: 70 loop : -0.57 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 184 TYR 0.019 0.001 TYR C 337 PHE 0.010 0.001 PHE D 226 TRP 0.001 0.000 TRP C 260 HIS 0.010 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15720) covalent geometry : angle 0.52191 / 0.26 (21315) hydrogen bonds : bond 0.03404 / 2.33 ( 851) hydrogen bonds : angle 3.90277 / 2.74 ( 2460) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.605 Fit side-chains REVERT: A 83 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7201 (mm) REVERT: B 50 MET cc_start: 0.6633 (mpp) cc_final: 0.6393 (mtt) REVERT: B 175 ASP cc_start: 0.6861 (m-30) cc_final: 0.6595 (t0) REVERT: B 248 MET cc_start: 0.6923 (mmm) cc_final: 0.6715 (mtp) REVERT: B 256 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7791 (m) REVERT: C 26 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6924 (mt0) REVERT: C 80 ILE cc_start: 0.7001 (mm) cc_final: 0.6667 (tp) REVERT: C 257 MET cc_start: 0.8343 (mmm) cc_final: 0.7979 (mmt) REVERT: C 271 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7389 (mtm) REVERT: C 272 LEU cc_start: 0.8006 (mt) cc_final: 0.7787 (tp) REVERT: D 138 MET cc_start: 0.7188 (mtp) cc_final: 0.6794 (tmm) REVERT: E 12 LEU cc_start: 0.8282 (tt) cc_final: 0.7878 (mp) outliers start: 33 outliers final: 27 residues processed: 185 average time/residue: 0.1068 time to fit residues: 31.1606 Evaluate side-chains 188 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 14 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 134 optimal weight: 0.0570 chunk 179 optimal weight: 0.0070 chunk 130 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN E 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.199761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.170909 restraints weight = 22023.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.170977 restraints weight = 23749.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.172872 restraints weight = 19203.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.172941 restraints weight = 12949.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.173052 restraints weight = 12670.863| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15720 Z= 0.108 Angle : 0.550 17.820 21315 Z= 0.272 Chirality : 0.039 0.171 2450 Planarity : 0.003 0.031 2620 Dihedral : 5.334 59.527 2450 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.22 % Allowed : 15.68 % Favored : 82.10 % 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: 1.09 (0.20), residues: 1880 helix: 1.39 (0.15), residues: 1173 sheet: 1.63 (0.70), residues: 60 loop : -0.55 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 184 TYR 0.020 0.001 TYR C 337 PHE 0.010 0.001 PHE D 226 TRP 0.002 0.000 TRP C 260 HIS 0.008 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15720) covalent geometry : angle 0.55007 / 0.27 (21315) hydrogen bonds : bond 0.03338 / 2.29 ( 851) hydrogen bonds : angle 3.88157 / 2.72 ( 2460) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.461 Fit side-chains REVERT: A 67 MET cc_start: 0.7791 (mmm) cc_final: 0.7589 (mmm) REVERT: A 83 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7169 (mm) REVERT: B 50 MET cc_start: 0.6649 (mpp) cc_final: 0.6406 (mtt) REVERT: B 175 ASP cc_start: 0.6913 (m-30) cc_final: 0.6609 (t0) REVERT: B 256 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7774 (m) REVERT: C 26 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6944 (mt0) REVERT: C 80 ILE cc_start: 0.7045 (mm) cc_final: 0.6735 (tp) REVERT: C 257 MET cc_start: 0.8349 (mmm) cc_final: 0.7988 (mmt) REVERT: C 271 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7309 (mtm) REVERT: E 12 LEU cc_start: 0.8277 (tt) cc_final: 0.7896 (mp) outliers start: 35 outliers final: 27 residues processed: 189 average time/residue: 0.1005 time to fit residues: 30.6338 Evaluate side-chains 188 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 86 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 126 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 26 GLN C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN E 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.197167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.167492 restraints weight = 21673.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.167013 restraints weight = 25731.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.168683 restraints weight = 21900.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.169398 restraints weight = 14988.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.169638 restraints weight = 14034.133| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15720 Z= 0.145 Angle : 0.563 11.621 21315 Z= 0.283 Chirality : 0.040 0.156 2450 Planarity : 0.003 0.032 2620 Dihedral : 5.444 57.410 2450 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.29 % Allowed : 16.06 % Favored : 81.65 % 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: 0.95 (0.20), residues: 1880 helix: 1.29 (0.15), residues: 1169 sheet: 1.61 (0.70), residues: 60 loop : -0.60 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 184 TYR 0.024 0.001 TYR E 69 PHE 0.018 0.001 PHE B 61 TRP 0.002 0.001 TRP D 260 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (15720) covalent geometry : angle 0.56280 / 0.28 (21315) hydrogen bonds : bond 0.03651 / 2.48 ( 851) hydrogen bonds : angle 3.99436 / 2.80 ( 2460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2217.54 seconds wall clock time: 39 minutes 20.29 seconds (2360.29 seconds total)