Starting phenix.real_space_refine on Sat Aug 23 23:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8op1_17035/08_2025/8op1_17035.cif Found real_map, /net/cci-nas-00/data/ceres_data/8op1_17035/08_2025/8op1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8op1_17035/08_2025/8op1_17035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8op1_17035/08_2025/8op1_17035.map" model { file = "/net/cci-nas-00/data/ceres_data/8op1_17035/08_2025/8op1_17035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8op1_17035/08_2025/8op1_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-2.0-5787/lib/python3.9/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: 3.15, per 1000 atoms: 0.20 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: 1.02 Conformation dependent library (CDL) restraints added in 637.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.51 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: 1.85 Time building geometry restraints manager: 1.44 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: 8507 17.60 - 35.19: 855 35.19 - 52.79: 156 52.79 - 70.39: 29 70.39 - 87.98: 53 Dihedral angle restraints: 9600 sinusoidal: 4165 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 9597 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: 4.770 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.170 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 15.507 87.981 6130 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 aren 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 covalent geometry : bond 0.00615 (15720) covalent geometry : angle 0.74652 (21315) hydrogen bonds : bond 0.13089 ( 851) hydrogen bonds : angle 6.06503 ( 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 : 0.383 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: 0.0893 time to fit residues: 25.6977 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 : 0.510 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4324 r_free = 0.4324 target = 0.192141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154619 restraints weight = 22855.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156790 restraints weight = 19085.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.157601 restraints weight = 14158.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.157878 restraints weight = 10813.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158029 restraints weight = 10083.433| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1341 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= 0.130 Angle : 0.544 6.963 21315 Z= 0.288 Chirality : 0.041 0.200 2450 Planarity : 0.004 0.041 2620 Dihedral : 11.204 73.652 2590 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.76 % Allowed : 8.83 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.19), residues: 1880 helix: 0.81 (0.15), residues: 1157 sheet: 2.02 (0.62), residues: 68 loop : -0.97 (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 0.016 0.001 PHE E 219 TRP 0.002 0.001 TRP E 260 HIS 0.006 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00284 (15720) covalent geometry : angle 0.54384 (21315) hydrogen bonds : bond 0.03994 ( 851) hydrogen bonds : angle 4.34068 ( 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 190 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.392 Fit side-chains REVERT: A 50 MET cc_start: 0.8349 (mpp) cc_final: 0.8120 (mpp) REVERT: B 50 MET cc_start: 0.6920 (mpp) cc_final: 0.6434 (mpp) REVERT: B 175 ASP cc_start: 0.7118 (m-30) cc_final: 0.6568 (t0) REVERT: C 71 MET cc_start: 0.6364 (ptm) cc_final: 0.6131 (ptm) REVERT: C 80 ILE cc_start: 0.6829 (mm) cc_final: 0.6536 (tp) REVERT: C 257 MET cc_start: 0.8409 (mmm) cc_final: 0.8048 (mmt) REVERT: D 138 MET cc_start: 0.7757 (mtp) cc_final: 0.6381 (tmm) outliers start: 12 outliers final: 9 residues processed: 185 average time/residue: 0.0984 time to fit residues: 28.1848 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 : 0.550 ------------------------------------------------------------------------------- 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: 0.7980 chunk 179 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 184 optimal weight: 0.1980 chunk 167 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 89 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.186232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.154395 restraints weight = 22225.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153554 restraints weight = 21827.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.155217 restraints weight = 18050.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155740 restraints weight = 12781.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156123 restraints weight = 11469.875| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15720 Z= 0.126 Angle : 0.518 7.769 21315 Z= 0.271 Chirality : 0.040 0.181 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.127 73.617 2590 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.52 % Allowed : 11.49 % Favored : 86.98 % 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 aren not related in a simple way. whole: 0.61 (0.19), residues: 1880 helix: 1.05 (0.15), residues: 1160 sheet: 2.00 (0.63), residues: 68 loop : -0.87 (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 A 210 PHE 0.011 0.001 PHE D 226 TRP 0.002 0.000 TRP D 260 HIS 0.018 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00278 (15720) covalent geometry : angle 0.51768 (21315) hydrogen bonds : bond 0.03734 ( 851) hydrogen bonds : angle 4.10303 ( 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 197 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: B 50 MET cc_start: 0.6741 (mpp) cc_final: 0.6347 (mtt) REVERT: B 88 TYR cc_start: 0.8023 (m-80) cc_final: 0.7337 (m-80) REVERT: B 256 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7915 (m) REVERT: C 80 ILE cc_start: 0.6875 (mm) cc_final: 0.6553 (tp) REVERT: C 126 ASN cc_start: 0.8030 (m-40) cc_final: 0.7760 (t0) REVERT: C 257 MET cc_start: 0.8392 (mmm) cc_final: 0.8098 (mmt) REVERT: D 138 MET cc_start: 0.7747 (mtp) cc_final: 0.6515 (tmm) REVERT: E 12 LEU cc_start: 0.8518 (tt) cc_final: 0.8128 (tp) outliers start: 24 outliers final: 17 residues processed: 190 average time/residue: 0.1127 time to fit residues: 33.6623 Evaluate side-chains 175 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL 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 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 0.0000 chunk 171 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 31 optimal weight: 0.0040 chunk 59 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN C 89 HIS C 151 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 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 = 0.187339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154845 restraints weight = 22124.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.153888 restraints weight = 21334.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155412 restraints weight = 17468.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.156179 restraints weight = 13123.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.156199 restraints weight = 12135.023| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15720 Z= 0.113 Angle : 0.495 8.269 21315 Z= 0.259 Chirality : 0.039 0.166 2450 Planarity : 0.003 0.031 2620 Dihedral : 11.115 73.605 2590 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.10 % Allowed : 12.57 % Favored : 85.33 % 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 aren not related in a simple way. whole: 0.86 (0.20), residues: 1880 helix: 1.22 (0.15), residues: 1162 sheet: 2.00 (0.62), residues: 68 loop : -0.71 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 73 TYR 0.026 0.001 TYR B 353 PHE 0.010 0.001 PHE D 226 TRP 0.002 0.000 TRP C 260 HIS 0.011 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00248 (15720) covalent geometry : angle 0.49458 (21315) hydrogen bonds : bond 0.03490 ( 851) hydrogen bonds : angle 3.99057 ( 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 208 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.638 Fit side-chains REVERT: A 50 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7833 (mpt) REVERT: B 50 MET cc_start: 0.6644 (mpp) cc_final: 0.6299 (mtt) REVERT: B 175 ASP cc_start: 0.6869 (m-30) cc_final: 0.6597 (t0) REVERT: B 256 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7811 (m) REVERT: C 67 MET cc_start: 0.8533 (mmm) cc_final: 0.7776 (mmt) REVERT: C 80 ILE cc_start: 0.7026 (mm) cc_final: 0.6671 (tp) REVERT: C 126 ASN cc_start: 0.8133 (m-40) cc_final: 0.7887 (t0) REVERT: C 201 LEU cc_start: 0.6738 (mp) cc_final: 0.6522 (tp) REVERT: D 27 ARG cc_start: 0.2988 (OUTLIER) cc_final: 0.1849 (mmp-170) REVERT: D 138 MET cc_start: 0.7782 (mtp) cc_final: 0.6520 (tmm) REVERT: E 12 LEU cc_start: 0.8460 (tt) cc_final: 0.8111 (tp) outliers start: 33 outliers final: 21 residues processed: 193 average time/residue: 0.1201 time to fit residues: 36.1701 Evaluate side-chains 186 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 66 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN B 43 HIS C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.187633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.148879 restraints weight = 22994.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149147 restraints weight = 19582.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.150615 restraints weight = 15136.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150777 restraints weight = 11669.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151179 restraints weight = 10916.260| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15720 Z= 0.231 Angle : 0.600 9.153 21315 Z= 0.313 Chirality : 0.043 0.151 2450 Planarity : 0.004 0.035 2620 Dihedral : 11.074 73.658 2590 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.54 % Allowed : 13.02 % Favored : 84.44 % 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 aren not related in a simple way. whole: 0.50 (0.19), residues: 1880 helix: 0.89 (0.15), residues: 1161 sheet: 1.91 (0.61), residues: 68 loop : -0.76 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 73 TYR 0.019 0.002 TYR D 23 PHE 0.012 0.002 PHE B 223 TRP 0.004 0.001 TRP A 260 HIS 0.007 0.002 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00541 (15720) covalent geometry : angle 0.60036 (21315) hydrogen bonds : bond 0.04314 ( 851) hydrogen bonds : angle 4.31719 ( 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: 40 poor density : 164 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7921 (mpt) REVERT: B 50 MET cc_start: 0.6700 (mpp) cc_final: 0.6408 (mtt) REVERT: B 158 MET cc_start: 0.7902 (mmt) cc_final: 0.7672 (mmt) REVERT: B 256 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8223 (m) REVERT: C 80 ILE cc_start: 0.7026 (mm) cc_final: 0.6578 (tp) REVERT: C 126 ASN cc_start: 0.8284 (m-40) cc_final: 0.8016 (t0) REVERT: D 27 ARG cc_start: 0.3345 (OUTLIER) cc_final: 0.1904 (mmp-170) REVERT: D 138 MET cc_start: 0.7792 (mtp) cc_final: 0.6836 (tmm) outliers start: 40 outliers final: 29 residues processed: 188 average time/residue: 0.1207 time to fit residues: 35.1408 Evaluate side-chains 189 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 71 MET Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 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 89 HIS 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 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE 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: 0.9990 chunk 175 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 132 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** 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 = 0.192071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.153929 restraints weight = 22892.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.154688 restraints weight = 19290.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155658 restraints weight = 15613.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156387 restraints weight = 11360.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.156368 restraints weight = 10512.685| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2112 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= 0.132 Angle : 0.532 11.073 21315 Z= 0.272 Chirality : 0.040 0.179 2450 Planarity : 0.003 0.034 2620 Dihedral : 11.080 73.634 2590 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.60 % Allowed : 14.10 % Favored : 83.30 % 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 aren not related in a simple way. whole: 0.77 (0.19), residues: 1880 helix: 1.12 (0.15), residues: 1161 sheet: 1.84 (0.61), residues: 68 loop : -0.66 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.014 0.001 TYR B 353 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 covalent geometry : bond 0.00300 (15720) covalent geometry : angle 0.53170 (21315) hydrogen bonds : bond 0.03619 ( 851) hydrogen bonds : angle 4.04959 ( 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 203 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.607 Fit side-chains REVERT: A 73 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8257 (ttt90) REVERT: A 83 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7131 (mm) REVERT: B 50 MET cc_start: 0.6678 (mpp) cc_final: 0.6406 (mtt) REVERT: B 175 ASP cc_start: 0.7058 (m-30) cc_final: 0.6562 (t70) REVERT: B 248 MET cc_start: 0.7090 (mmm) cc_final: 0.6850 (mtp) REVERT: B 256 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7848 (m) REVERT: C 80 ILE cc_start: 0.6831 (mm) cc_final: 0.6380 (tp) REVERT: C 126 ASN cc_start: 0.8295 (m-40) cc_final: 0.8051 (t0) REVERT: C 271 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7521 (mtm) REVERT: D 138 MET cc_start: 0.7617 (mtp) cc_final: 0.6627 (tmm) REVERT: E 12 LEU cc_start: 0.8494 (tt) cc_final: 0.7894 (mp) REVERT: E 198 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7813 (mtmt) REVERT: E 304 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7238 (mt) outliers start: 41 outliers final: 29 residues processed: 187 average time/residue: 0.1203 time to fit residues: 34.9713 Evaluate side-chains 191 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 PHE 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 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 182 VAL 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 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 89 HIS 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 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: 0.4980 chunk 184 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 HIS C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 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 = 0.4294 r_free = 0.4294 target = 0.187835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.151464 restraints weight = 22489.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.152750 restraints weight = 19128.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.153941 restraints weight = 14792.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154264 restraints weight = 10823.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.154585 restraints weight = 10715.646| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2165 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= 0.149 Angle : 0.541 9.800 21315 Z= 0.277 Chirality : 0.040 0.181 2450 Planarity : 0.003 0.033 2620 Dihedral : 11.045 73.635 2590 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.79 % Allowed : 14.67 % Favored : 82.54 % 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 aren not related in a simple way. whole: 0.79 (0.19), residues: 1880 helix: 1.12 (0.15), residues: 1160 sheet: 1.85 (0.62), residues: 68 loop : -0.64 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 27 TYR 0.029 0.001 TYR C 353 PHE 0.010 0.001 PHE D 226 TRP 0.003 0.001 TRP A 260 HIS 0.008 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00342 (15720) covalent geometry : angle 0.54146 (21315) hydrogen bonds : bond 0.03733 ( 851) hydrogen bonds : angle 4.07406 ( 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 206 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.623 Fit side-chains REVERT: A 73 ARG cc_start: 0.8586 (ttm170) cc_final: 0.8266 (ttt90) REVERT: A 83 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7205 (mm) REVERT: B 50 MET cc_start: 0.6661 (mpp) cc_final: 0.6399 (mtt) REVERT: B 248 MET cc_start: 0.7090 (mmm) cc_final: 0.6832 (mtp) REVERT: B 256 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7976 (m) REVERT: C 80 ILE cc_start: 0.6892 (mm) cc_final: 0.6424 (tp) REVERT: C 194 MET cc_start: 0.7826 (tpt) cc_final: 0.7621 (mtp) REVERT: C 271 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7352 (mtm) REVERT: D 138 MET cc_start: 0.7749 (mtp) cc_final: 0.6713 (tmm) REVERT: E 12 LEU cc_start: 0.8521 (tt) cc_final: 0.7965 (mp) REVERT: E 198 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7806 (mtmt) REVERT: E 304 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7448 (mt) outliers start: 44 outliers final: 30 residues processed: 193 average time/residue: 0.1160 time to fit residues: 35.0062 Evaluate side-chains 190 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 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 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 167 VAL 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 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 Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 13 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 114 optimal weight: 0.1980 chunk 169 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 134 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 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 = 0.4317 r_free = 0.4317 target = 0.190351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.154002 restraints weight = 22725.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.154920 restraints weight = 18688.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156156 restraints weight = 14633.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.156659 restraints weight = 10958.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.156940 restraints weight = 10649.960| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15720 Z= 0.118 Angle : 0.526 10.998 21315 Z= 0.267 Chirality : 0.039 0.180 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.053 73.636 2590 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.54 % Allowed : 15.56 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.20), residues: 1880 helix: 1.24 (0.15), residues: 1172 sheet: 1.67 (0.62), residues: 70 loop : -0.65 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.025 0.001 TYR C 353 PHE 0.010 0.001 PHE D 226 TRP 0.002 0.000 TRP A 260 HIS 0.011 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00265 (15720) covalent geometry : angle 0.52595 (21315) hydrogen bonds : bond 0.03495 ( 851) hydrogen bonds : angle 3.97818 ( 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 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.579 Fit side-chains REVERT: A 73 ARG cc_start: 0.8526 (ttm170) cc_final: 0.8067 (ttm110) REVERT: A 83 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7137 (mm) REVERT: B 50 MET cc_start: 0.6652 (mpp) cc_final: 0.6404 (mtt) REVERT: B 175 ASP cc_start: 0.6930 (m-30) cc_final: 0.6480 (t70) REVERT: B 248 MET cc_start: 0.7036 (mmm) cc_final: 0.6798 (mtp) REVERT: B 256 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7784 (m) REVERT: C 26 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6983 (mt0) REVERT: C 80 ILE cc_start: 0.6919 (mm) cc_final: 0.6524 (tp) REVERT: C 194 MET cc_start: 0.7866 (tpt) cc_final: 0.7654 (mtp) REVERT: C 201 LEU cc_start: 0.6731 (mm) cc_final: 0.6205 (tp) REVERT: C 271 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7347 (mtm) REVERT: D 50 MET cc_start: 0.7161 (mtp) cc_final: 0.6869 (ptm) REVERT: D 138 MET cc_start: 0.7746 (mtp) cc_final: 0.6845 (tmm) REVERT: E 12 LEU cc_start: 0.8464 (tt) cc_final: 0.7899 (mp) REVERT: E 198 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7762 (mtmt) REVERT: E 304 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7361 (mt) outliers start: 40 outliers final: 30 residues processed: 187 average time/residue: 0.1114 time to fit residues: 32.8517 Evaluate side-chains 191 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain C residue 151 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 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 158 MET Chi-restraints excluded: chain D residue 167 VAL 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 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: 2.9990 chunk 168 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN C 26 GLN C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.191673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153386 restraints weight = 22773.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155098 restraints weight = 18993.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.155880 restraints weight = 14234.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156390 restraints weight = 11040.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.156395 restraints weight = 10348.543| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15720 Z= 0.140 Angle : 0.564 18.794 21315 Z= 0.281 Chirality : 0.040 0.178 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.026 73.628 2590 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.54 % Allowed : 16.25 % Favored : 81.21 % 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 aren not related in a simple way. whole: 0.88 (0.20), residues: 1880 helix: 1.22 (0.15), residues: 1172 sheet: 1.68 (0.62), residues: 70 loop : -0.65 (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 353 PHE 0.011 0.001 PHE D 226 TRP 0.002 0.001 TRP A 260 HIS 0.009 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00321 (15720) covalent geometry : angle 0.56370 (21315) hydrogen bonds : bond 0.03597 ( 851) hydrogen bonds : angle 4.01822 ( 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 200 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.512 Fit side-chains REVERT: A 73 ARG cc_start: 0.8477 (ttm170) cc_final: 0.8199 (ttt90) REVERT: A 83 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7195 (mm) REVERT: B 50 MET cc_start: 0.6640 (mpp) cc_final: 0.6405 (mtt) REVERT: B 248 MET cc_start: 0.7067 (mmm) cc_final: 0.6794 (mtp) REVERT: B 256 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7924 (m) REVERT: C 80 ILE cc_start: 0.6815 (mm) cc_final: 0.6377 (tp) REVERT: C 194 MET cc_start: 0.7886 (tpt) cc_final: 0.7662 (mtp) REVERT: C 201 LEU cc_start: 0.6952 (mm) cc_final: 0.6358 (tp) REVERT: C 271 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7243 (mtm) REVERT: D 50 MET cc_start: 0.7188 (mtp) cc_final: 0.6889 (ptm) REVERT: D 138 MET cc_start: 0.7606 (mtp) cc_final: 0.6818 (tmm) REVERT: E 12 LEU cc_start: 0.8479 (tt) cc_final: 0.7973 (mp) REVERT: E 304 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7250 (mt) outliers start: 40 outliers final: 30 residues processed: 185 average time/residue: 0.1108 time to fit residues: 32.1348 Evaluate side-chains 189 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 35 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 151 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 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 167 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 14 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 176 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.197664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.168651 restraints weight = 21960.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.168647 restraints weight = 25393.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.170366 restraints weight = 21311.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.170550 restraints weight = 14436.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.171200 restraints weight = 13931.851| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15720 Z= 0.132 Angle : 0.563 14.339 21315 Z= 0.282 Chirality : 0.040 0.158 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.027 73.621 2590 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.41 % Allowed : 16.44 % Favored : 81.14 % 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 aren not related in a simple way. whole: 0.93 (0.20), residues: 1880 helix: 1.25 (0.15), residues: 1172 sheet: 1.66 (0.62), residues: 70 loop : -0.62 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 184 TYR 0.017 0.001 TYR C 353 PHE 0.015 0.001 PHE B 61 TRP 0.002 0.001 TRP C 260 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00301 (15720) covalent geometry : angle 0.56348 (21315) hydrogen bonds : bond 0.03531 ( 851) hydrogen bonds : angle 4.01222 ( 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 196 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.604 Fit side-chains REVERT: A 73 ARG cc_start: 0.8552 (ttm170) cc_final: 0.8291 (ttt90) REVERT: A 83 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7248 (mm) REVERT: A 138 MET cc_start: 0.7061 (mtt) cc_final: 0.6705 (ptt) REVERT: B 50 MET cc_start: 0.6653 (mpp) cc_final: 0.6421 (mtt) REVERT: B 248 MET cc_start: 0.7036 (mmm) cc_final: 0.6835 (mtp) REVERT: B 256 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7903 (m) REVERT: C 80 ILE cc_start: 0.7084 (mm) cc_final: 0.6689 (tp) REVERT: C 194 MET cc_start: 0.7756 (tpt) cc_final: 0.7551 (mtp) REVERT: C 271 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7121 (mtm) REVERT: D 138 MET cc_start: 0.7562 (mtp) cc_final: 0.6832 (tmm) REVERT: E 12 LEU cc_start: 0.8350 (tt) cc_final: 0.7802 (mp) REVERT: E 304 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7287 (mt) outliers start: 38 outliers final: 33 residues processed: 184 average time/residue: 0.1067 time to fit residues: 31.1113 Evaluate side-chains 191 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 35 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 151 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 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 167 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 0.0770 chunk 150 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 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 = 0.4449 r_free = 0.4449 target = 0.198489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.169759 restraints weight = 21659.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.169200 restraints weight = 25517.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.171557 restraints weight = 20509.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.171360 restraints weight = 13714.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.171701 restraints weight = 12845.588| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15720 Z= 0.123 Angle : 0.545 11.901 21315 Z= 0.274 Chirality : 0.039 0.155 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.026 73.627 2590 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.54 % Allowed : 16.57 % Favored : 80.89 % 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 aren not related in a simple way. whole: 0.96 (0.20), residues: 1880 helix: 1.30 (0.15), residues: 1172 sheet: 1.54 (0.70), residues: 60 loop : -0.61 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 184 TYR 0.017 0.001 TYR C 353 PHE 0.010 0.001 PHE D 226 TRP 0.002 0.000 TRP C 260 HIS 0.005 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00281 (15720) covalent geometry : angle 0.54484 (21315) hydrogen bonds : bond 0.03495 ( 851) hydrogen bonds : angle 3.97475 ( 2460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2372.02 seconds wall clock time: 42 minutes 4.74 seconds (2524.74 seconds total)