Starting phenix.real_space_refine on Fri Jun 13 21:09:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8op1_17035/06_2025/8op1_17035.cif Found real_map, /net/cci-nas-00/data/ceres_data/8op1_17035/06_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_17035/06_2025/8op1_17035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8op1_17035/06_2025/8op1_17035.map" model { file = "/net/cci-nas-00/data/ceres_data/8op1_17035/06_2025/8op1_17035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8op1_17035/06_2025/8op1_17035.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.68, per 1000 atoms: 0.69 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: 3.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 4.82 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: 4.56 Time building geometry restraints manager: 4.49 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: 0.00 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: 7.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 39.710 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.610 ------------------------------------------------------------------------------- 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 : 12.80 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (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 TRP 0.004 0.001 TRP E 260 HIS 0.010 0.002 HIS E 216 PHE 0.014 0.002 PHE A 226 TYR 0.031 0.002 TYR D 301 ARG 0.008 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.13089 ( 851) hydrogen bonds : angle 6.06503 ( 2460) covalent geometry : bond 0.00615 (15720) covalent geometry : angle 0.74652 (21315) *********************** 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 : 1.553 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: 0.2541 time to fit residues: 72.9010 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 : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 168 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** E 43 HIS ** 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 = 0.4313 r_free = 0.4313 target = 0.191092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.152983 restraints weight = 22875.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.154090 restraints weight = 19242.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155104 restraints weight = 15544.216| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15720 Z= 0.141 Angle : 0.555 6.911 21315 Z= 0.294 Chirality : 0.041 0.195 2450 Planarity : 0.004 0.042 2620 Dihedral : 11.207 73.682 2590 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.76 % Allowed : 8.63 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1880 helix: 0.75 (0.15), residues: 1156 sheet: 2.03 (0.62), residues: 68 loop : -1.01 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 260 HIS 0.007 0.001 HIS D 216 PHE 0.015 0.001 PHE E 219 TYR 0.016 0.001 TYR A 210 ARG 0.005 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 851) hydrogen bonds : angle 4.40610 ( 2460) covalent geometry : bond 0.00316 (15720) covalent geometry : angle 0.55510 (21315) *********************** 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 183 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 1.528 Fit side-chains REVERT: A 50 MET cc_start: 0.8360 (mpp) cc_final: 0.8136 (mpp) REVERT: B 50 MET cc_start: 0.6932 (mpp) cc_final: 0.6441 (mpp) REVERT: C 80 ILE cc_start: 0.6813 (mm) cc_final: 0.6519 (tp) REVERT: C 257 MET cc_start: 0.8397 (mmm) cc_final: 0.8046 (mmt) REVERT: D 138 MET cc_start: 0.7760 (mtp) cc_final: 0.6390 (tmm) outliers start: 12 outliers final: 9 residues processed: 178 average time/residue: 0.2525 time to fit residues: 69.3205 Evaluate side-chains 159 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 147 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 156 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 43 HIS ** 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 = 0.4297 r_free = 0.4297 target = 0.189728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.151530 restraints weight = 22761.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.152424 restraints weight = 20063.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.153562 restraints weight = 15367.704| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15720 Z= 0.166 Angle : 0.552 7.896 21315 Z= 0.289 Chirality : 0.042 0.184 2450 Planarity : 0.003 0.035 2620 Dihedral : 11.120 73.672 2590 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.71 % Allowed : 11.62 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1880 helix: 0.87 (0.15), residues: 1160 sheet: 1.98 (0.63), residues: 68 loop : -0.95 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 260 HIS 0.013 0.002 HIS C 151 PHE 0.013 0.001 PHE D 226 TYR 0.014 0.002 TYR D 23 ARG 0.005 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 851) hydrogen bonds : angle 4.24544 ( 2460) covalent geometry : bond 0.00381 (15720) covalent geometry : angle 0.55180 (21315) *********************** 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 195 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.567 Fit side-chains REVERT: B 50 MET cc_start: 0.6701 (mpp) cc_final: 0.6461 (mtt) REVERT: B 256 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.8012 (m) REVERT: C 80 ILE cc_start: 0.6927 (mm) cc_final: 0.6534 (tp) REVERT: C 126 ASN cc_start: 0.8147 (m-40) cc_final: 0.7802 (t0) REVERT: C 257 MET cc_start: 0.8505 (mmm) cc_final: 0.8191 (mmt) REVERT: D 138 MET cc_start: 0.7767 (mtp) cc_final: 0.6444 (tmm) REVERT: D 142 MET cc_start: 0.5788 (ppp) cc_final: 0.5584 (ppp) outliers start: 27 outliers final: 17 residues processed: 188 average time/residue: 0.2378 time to fit residues: 69.6198 Evaluate side-chains 168 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 270 ILE 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 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 D residue 357 LEU 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 17 optimal weight: 0.0980 chunk 84 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 150 optimal weight: 0.4980 chunk 143 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN B 126 ASN C 45 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 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4298 r_free = 0.4298 target = 0.188724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151652 restraints weight = 22395.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.153318 restraints weight = 18272.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.154524 restraints weight = 13313.003| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15720 Z= 0.127 Angle : 0.513 8.347 21315 Z= 0.269 Chirality : 0.040 0.166 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.106 73.612 2590 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.16 % Allowed : 12.76 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 1880 helix: 1.07 (0.15), residues: 1163 sheet: 1.93 (0.62), residues: 68 loop : -0.78 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 260 HIS 0.012 0.001 HIS C 89 PHE 0.011 0.001 PHE D 226 TYR 0.012 0.001 TYR D 23 ARG 0.005 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 851) hydrogen bonds : angle 4.07614 ( 2460) covalent geometry : bond 0.00285 (15720) covalent geometry : angle 0.51257 (21315) *********************** 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 198 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.957 Fit side-chains REVERT: B 50 MET cc_start: 0.6679 (mpp) cc_final: 0.6367 (mtt) REVERT: B 67 MET cc_start: 0.8007 (mmm) cc_final: 0.7718 (mmm) REVERT: B 248 MET cc_start: 0.7175 (mmm) cc_final: 0.6697 (mtm) REVERT: B 256 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7911 (m) REVERT: C 26 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7212 (mt0) REVERT: C 67 MET cc_start: 0.8535 (mmm) cc_final: 0.7711 (mmt) REVERT: C 80 ILE cc_start: 0.6861 (mm) cc_final: 0.6519 (tp) REVERT: C 126 ASN cc_start: 0.8236 (m-40) cc_final: 0.7944 (t0) REVERT: D 27 ARG cc_start: 0.3052 (OUTLIER) cc_final: 0.1863 (mmp-170) REVERT: D 138 MET cc_start: 0.7784 (mtp) cc_final: 0.6385 (tmm) REVERT: E 12 LEU cc_start: 0.8615 (tt) cc_final: 0.8249 (tp) outliers start: 34 outliers final: 23 residues processed: 182 average time/residue: 0.2403 time to fit residues: 68.6895 Evaluate side-chains 183 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL 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 256 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU 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 D residue 357 LEU 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 104 optimal weight: 1.9990 chunk 128 optimal weight: 0.0870 chunk 93 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 118 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 0.0070 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN 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 43 HIS ** 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 = 0.4322 r_free = 0.4322 target = 0.191244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.154658 restraints weight = 22628.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.156079 restraints weight = 18525.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.157322 restraints weight = 13883.469| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15720 Z= 0.103 Angle : 0.487 8.902 21315 Z= 0.255 Chirality : 0.039 0.159 2450 Planarity : 0.003 0.033 2620 Dihedral : 11.110 73.600 2590 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.48 % Allowed : 13.14 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1880 helix: 1.28 (0.15), residues: 1159 sheet: 1.91 (0.62), residues: 68 loop : -0.64 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 260 HIS 0.013 0.001 HIS C 89 PHE 0.010 0.001 PHE D 226 TYR 0.010 0.001 TYR C 353 ARG 0.004 0.000 ARG C 184 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 851) hydrogen bonds : angle 3.93355 ( 2460) covalent geometry : bond 0.00221 (15720) covalent geometry : angle 0.48721 (21315) *********************** 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 213 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7901 (mpt) REVERT: B 50 MET cc_start: 0.6656 (mpp) cc_final: 0.6360 (mtt) REVERT: B 175 ASP cc_start: 0.7086 (m-30) cc_final: 0.6706 (t0) REVERT: B 248 MET cc_start: 0.7062 (mmm) cc_final: 0.6781 (mtp) REVERT: B 256 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7778 (m) REVERT: C 26 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7144 (mt0) REVERT: C 80 ILE cc_start: 0.6961 (mm) cc_final: 0.6602 (tp) REVERT: C 126 ASN cc_start: 0.8244 (m-40) cc_final: 0.8027 (t0) REVERT: D 27 ARG cc_start: 0.2962 (OUTLIER) cc_final: 0.1744 (mmp-170) REVERT: D 91 LYS cc_start: 0.7406 (ttmm) cc_final: 0.6985 (ptmm) REVERT: D 138 MET cc_start: 0.7784 (mtp) cc_final: 0.6634 (tmm) outliers start: 39 outliers final: 26 residues processed: 200 average time/residue: 0.2701 time to fit residues: 84.1396 Evaluate side-chains 182 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 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 D residue 12 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 301 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 48 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 169 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 43 HIS ** 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 = 0.4318 r_free = 0.4318 target = 0.192013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.153723 restraints weight = 22886.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.154174 restraints weight = 19451.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155425 restraints weight = 16420.611| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15720 Z= 0.143 Angle : 0.535 11.077 21315 Z= 0.273 Chirality : 0.040 0.150 2450 Planarity : 0.003 0.033 2620 Dihedral : 11.048 73.606 2590 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.79 % Allowed : 13.65 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1880 helix: 1.21 (0.15), residues: 1163 sheet: 1.89 (0.62), residues: 68 loop : -0.61 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 260 HIS 0.011 0.001 HIS C 89 PHE 0.011 0.001 PHE D 226 TYR 0.017 0.001 TYR B 353 ARG 0.004 0.000 ARG C 184 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 851) hydrogen bonds : angle 4.00816 ( 2460) covalent geometry : bond 0.00327 (15720) covalent geometry : angle 0.53475 (21315) *********************** 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 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8571 (ttm170) cc_final: 0.8289 (ttt90) REVERT: A 83 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7180 (mm) REVERT: B 50 MET cc_start: 0.6659 (mpp) cc_final: 0.6406 (mtt) REVERT: B 175 ASP cc_start: 0.7233 (m-30) cc_final: 0.6746 (t0) REVERT: B 256 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7961 (m) REVERT: C 26 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7148 (mt0) REVERT: C 80 ILE cc_start: 0.6819 (mm) cc_final: 0.6379 (tp) REVERT: C 126 ASN cc_start: 0.8307 (m-40) cc_final: 0.8073 (t0) REVERT: C 271 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7691 (mtm) REVERT: D 27 ARG cc_start: 0.3290 (OUTLIER) cc_final: 0.1946 (mmp-170) REVERT: D 50 MET cc_start: 0.7131 (mtp) cc_final: 0.6824 (ptm) REVERT: D 138 MET cc_start: 0.7775 (mtp) cc_final: 0.6802 (tmm) REVERT: E 304 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7307 (mt) outliers start: 44 outliers final: 27 residues processed: 187 average time/residue: 0.2425 time to fit residues: 70.0289 Evaluate side-chains 186 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 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 151 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU 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 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 167 VAL Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 chunk 17 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 216 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 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.194492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.157526 restraints weight = 22981.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.158497 restraints weight = 20655.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.159408 restraints weight = 16559.097| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15720 Z= 0.108 Angle : 0.518 12.461 21315 Z= 0.260 Chirality : 0.039 0.177 2450 Planarity : 0.003 0.031 2620 Dihedral : 11.078 73.614 2590 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.22 % Allowed : 14.60 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1880 helix: 1.37 (0.15), residues: 1172 sheet: 2.00 (0.63), residues: 68 loop : -0.63 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 260 HIS 0.010 0.001 HIS C 89 PHE 0.009 0.001 PHE D 226 TYR 0.015 0.001 TYR B 353 ARG 0.004 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 851) hydrogen bonds : angle 3.87082 ( 2460) covalent geometry : bond 0.00236 (15720) covalent geometry : angle 0.51778 (21315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.570 Fit side-chains REVERT: A 83 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7068 (mm) REVERT: B 12 LEU cc_start: 0.8698 (tt) cc_final: 0.8439 (mt) REVERT: B 50 MET cc_start: 0.6624 (mpp) cc_final: 0.6384 (mtt) REVERT: B 175 ASP cc_start: 0.7117 (m-30) cc_final: 0.6646 (t0) REVERT: B 248 MET cc_start: 0.7124 (mmm) cc_final: 0.6914 (mtm) REVERT: B 256 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7760 (m) REVERT: C 26 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7111 (mt0) REVERT: C 80 ILE cc_start: 0.6898 (mm) cc_final: 0.6527 (tp) REVERT: C 257 MET cc_start: 0.8391 (mmm) cc_final: 0.7897 (mmt) REVERT: D 27 ARG cc_start: 0.3250 (OUTLIER) cc_final: 0.1901 (mmp-170) REVERT: D 50 MET cc_start: 0.7100 (mtp) cc_final: 0.6889 (ptm) REVERT: D 91 LYS cc_start: 0.7232 (ttmm) cc_final: 0.6978 (ptmm) REVERT: D 138 MET cc_start: 0.7627 (mtp) cc_final: 0.6657 (tmm) REVERT: E 12 LEU cc_start: 0.8434 (tt) cc_final: 0.7966 (mp) outliers start: 35 outliers final: 26 residues processed: 189 average time/residue: 0.2366 time to fit residues: 69.8093 Evaluate side-chains 185 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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** E 249 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.196416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.167448 restraints weight = 21829.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.166206 restraints weight = 26032.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.167766 restraints weight = 22045.526| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2344 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= 0.149 Angle : 0.537 11.025 21315 Z= 0.274 Chirality : 0.040 0.185 2450 Planarity : 0.003 0.032 2620 Dihedral : 11.020 73.608 2590 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.54 % Allowed : 15.05 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1880 helix: 1.28 (0.15), residues: 1169 sheet: 1.81 (0.63), residues: 70 loop : -0.63 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 260 HIS 0.011 0.001 HIS C 89 PHE 0.012 0.001 PHE B 61 TYR 0.030 0.001 TYR C 353 ARG 0.004 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 851) hydrogen bonds : angle 3.97969 ( 2460) covalent geometry : bond 0.00342 (15720) covalent geometry : angle 0.53709 (21315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 1.732 Fit side-chains REVERT: A 83 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7292 (mm) REVERT: B 50 MET cc_start: 0.6647 (mpp) cc_final: 0.6426 (mtt) REVERT: C 26 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.7081 (mt0) REVERT: C 80 ILE cc_start: 0.7000 (mm) cc_final: 0.6558 (tp) REVERT: C 271 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7481 (mtm) REVERT: D 138 MET cc_start: 0.7687 (mtp) cc_final: 0.6713 (tmm) REVERT: E 304 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7129 (mt) outliers start: 40 outliers final: 27 residues processed: 183 average time/residue: 0.2372 time to fit residues: 67.6332 Evaluate side-chains 182 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 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 C residue 26 GLN 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 D residue 12 LEU 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 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR 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 64 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** D 360 ASN ** 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 = 0.4437 r_free = 0.4437 target = 0.197218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.167970 restraints weight = 21788.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.167164 restraints weight = 26108.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.169245 restraints weight = 20128.694| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15720 Z= 0.134 Angle : 0.535 11.400 21315 Z= 0.271 Chirality : 0.040 0.177 2450 Planarity : 0.003 0.052 2620 Dihedral : 11.011 73.629 2590 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.29 % Allowed : 15.68 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1880 helix: 1.27 (0.15), residues: 1169 sheet: 1.82 (0.63), residues: 70 loop : -0.60 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 260 HIS 0.009 0.001 HIS C 89 PHE 0.013 0.001 PHE B 61 TYR 0.028 0.001 TYR C 353 ARG 0.005 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 851) hydrogen bonds : angle 3.95132 ( 2460) covalent geometry : bond 0.00304 (15720) covalent geometry : angle 0.53535 (21315) *********************** 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 191 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 1.618 Fit side-chains REVERT: A 83 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7237 (mm) REVERT: B 50 MET cc_start: 0.6638 (mpp) cc_final: 0.6431 (mtt) REVERT: B 175 ASP cc_start: 0.6839 (m-30) cc_final: 0.6440 (t70) REVERT: C 26 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.7046 (mt0) REVERT: C 80 ILE cc_start: 0.7041 (mm) cc_final: 0.6668 (tp) REVERT: C 201 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6432 (pt) REVERT: C 271 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7475 (mtm) REVERT: D 138 MET cc_start: 0.7714 (mtp) cc_final: 0.6935 (tmm) REVERT: E 304 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7145 (mt) outliers start: 36 outliers final: 29 residues processed: 178 average time/residue: 0.2284 time to fit residues: 64.9970 Evaluate side-chains 186 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 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 201 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR 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 160 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 112 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 172 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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** ** 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 = 0.4446 r_free = 0.4446 target = 0.198206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.168638 restraints weight = 21860.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.167979 restraints weight = 26827.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.170383 restraints weight = 20270.358| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2543 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= 0.123 Angle : 0.560 18.991 21315 Z= 0.276 Chirality : 0.039 0.158 2450 Planarity : 0.003 0.037 2620 Dihedral : 11.011 73.625 2590 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.22 % Allowed : 15.81 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1880 helix: 1.32 (0.15), residues: 1169 sheet: 1.79 (0.63), residues: 70 loop : -0.57 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 260 HIS 0.010 0.001 HIS C 89 PHE 0.010 0.001 PHE D 226 TYR 0.021 0.001 TYR C 353 ARG 0.005 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 851) hydrogen bonds : angle 3.90634 ( 2460) covalent geometry : bond 0.00277 (15720) covalent geometry : angle 0.56018 (21315) ********************** 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: 35 poor density : 161 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7222 (mm) REVERT: B 50 MET cc_start: 0.6625 (mpp) cc_final: 0.6424 (mtt) REVERT: B 175 ASP cc_start: 0.6811 (m-30) cc_final: 0.6480 (t0) REVERT: C 26 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.7115 (mt0) REVERT: C 67 MET cc_start: 0.8500 (mmm) cc_final: 0.7855 (mmt) REVERT: C 80 ILE cc_start: 0.7096 (mm) cc_final: 0.6729 (tp) REVERT: C 201 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6408 (pt) REVERT: C 271 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7394 (mtm) REVERT: D 138 MET cc_start: 0.7555 (mtp) cc_final: 0.6916 (tmm) outliers start: 35 outliers final: 29 residues processed: 184 average time/residue: 0.2319 time to fit residues: 66.7847 Evaluate side-chains 186 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 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 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 201 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU 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 189 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 155 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 45 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** ** 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 = 0.4447 r_free = 0.4447 target = 0.198361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.168881 restraints weight = 21856.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.168238 restraints weight = 26916.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.169920 restraints weight = 21340.338| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15720 Z= 0.122 Angle : 0.555 11.815 21315 Z= 0.277 Chirality : 0.039 0.156 2450 Planarity : 0.003 0.043 2620 Dihedral : 11.010 73.627 2590 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.29 % Allowed : 16.13 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1880 helix: 1.33 (0.15), residues: 1172 sheet: 1.60 (0.70), residues: 60 loop : -0.53 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 260 HIS 0.004 0.001 HIS C 89 PHE 0.015 0.001 PHE B 61 TYR 0.019 0.001 TYR C 353 ARG 0.005 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 851) hydrogen bonds : angle 3.91449 ( 2460) covalent geometry : bond 0.00275 (15720) covalent geometry : angle 0.55547 (21315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4608.69 seconds wall clock time: 82 minutes 39.14 seconds (4959.14 seconds total)