Starting phenix.real_space_refine on Thu May 22 19:24:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efh_28082/05_2025/8efh_28082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efh_28082/05_2025/8efh_28082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8efh_28082/05_2025/8efh_28082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efh_28082/05_2025/8efh_28082.map" model { file = "/net/cci-nas-00/data/ceres_data/8efh_28082/05_2025/8efh_28082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efh_28082/05_2025/8efh_28082.cif" } resolution = 3.3 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 138 5.16 5 C 14639 2.51 5 N 3941 2.21 5 O 4492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23228 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5918 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 28, 'TRANS': 705} Chain breaks: 3 Chain: "F" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "B" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "E" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "O" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "P" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.79, per 1000 atoms: 0.64 Number of scatterers: 23228 At special positions: 0 Unit cell: (162.778, 100.254, 249.018, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 12 15.00 Mg 6 11.99 O 4492 8.00 N 3941 7.00 C 14639 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: 5.54 Conformation dependent library (CDL) restraints added in 2.8 seconds 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5462 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 32 sheets defined 55.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.903A pdb=" N ARG A 17 " --> pdb=" O PRO A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.683A pdb=" N VAL A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 removed outlier: 3.682A pdb=" N TYR A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.969A pdb=" N ILE A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 217 through 231 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.979A pdb=" N VAL A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.078A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.700A pdb=" N LEU A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.842A pdb=" N GLN A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.695A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 359 Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 472 through 505 Processing helix chain 'A' and resid 517 through 525 removed outlier: 4.066A pdb=" N ILE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.641A pdb=" N MET A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 592 through 598 Processing helix chain 'A' and resid 603 through 610 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 646 through 663 Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 697 through 708 removed outlier: 4.193A pdb=" N GLY A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 723 through 726 removed outlier: 3.763A pdb=" N ASN A 726 " --> pdb=" O ARG A 723 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 723 through 726' Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 768 through 781 removed outlier: 3.603A pdb=" N GLU A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.935A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.980A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 233 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 285 removed outlier: 3.789A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.964A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 352 through 356 removed outlier: 4.048A pdb=" N TRP F 356 " --> pdb=" O GLN F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 367 through 372 removed outlier: 3.852A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS F 371 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.666A pdb=" N SER B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 61' Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 4.084A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.734A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.552A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.557A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.590A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.986A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.801A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 257' Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.589A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.919A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.787A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.736A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.669A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 61' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.532A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.815A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.931A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.581A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 4.075A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.931A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.760A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.787A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.529A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.019A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.909A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 55 through 61' Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.888A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.639A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.700A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.567A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.814A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.952A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.614A pdb=" N GLU D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.585A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.845A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.169A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.741A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.567A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.846A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 62 removed outlier: 3.887A pdb=" N ARG E 62 " --> pdb=" O GLN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.735A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.693A pdb=" N GLY E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.575A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.672A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 217 removed outlier: 3.991A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 removed outlier: 3.760A pdb=" N GLU E 226 " --> pdb=" O ASP E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.709A pdb=" N ARG E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 257' Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.510A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 285 removed outlier: 4.119A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.004A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 removed outlier: 3.534A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 355 removed outlier: 3.980A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 removed outlier: 4.140A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 210 removed outlier: 4.184A pdb=" N GLN O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN O 210 " --> pdb=" O SER O 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 208 removed outlier: 3.623A pdb=" N ARG P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 7.870A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG A 54 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 4.108A pdb=" N PHE A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS A 122 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN A 172 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 178 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR A 455 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 252 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 246 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY A 245 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR A 265 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A 247 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A 263 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG A 249 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA A 261 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS A 251 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 233 removed outlier: 3.517A pdb=" N SER A 241 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564 removed outlier: 4.193A pdb=" N PHE A 577 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.829A pdb=" N ILE A 713 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 763 " --> pdb=" O ILE A 713 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 29 through 31 removed outlier: 3.828A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.631A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 176 through 178 removed outlier: 3.541A pdb=" N SER F 155 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AB3, first strand: chain 'F' and resid 238 through 242 removed outlier: 5.293A pdb=" N LEU F 242 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.969A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.818A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AB8, first strand: chain 'B' and resid 238 through 242 removed outlier: 4.713A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 29 through 31 removed outlier: 7.249A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.898A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 165 through 166 Processing sheet with id=AC4, first strand: chain 'C' and resid 238 through 242 removed outlier: 6.829A pdb=" N LYS C 238 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR C 249 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR C 240 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL C 247 " --> pdb=" O TYR C 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.642A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.585A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AC9, first strand: chain 'D' and resid 238 through 240 Processing sheet with id=AD1, first strand: chain 'E' and resid 29 through 31 removed outlier: 4.051A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.616A pdb=" N VAL E 35 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD4, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.586A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 238 through 240 1267 hydrogen bonds defined for protein. 3453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.32 Time building geometry restraints manager: 6.51 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: 7644 1.34 - 1.46: 4886 1.46 - 1.58: 10890 1.58 - 1.70: 18 1.70 - 1.82: 241 Bond restraints: 23679 Sorted by residual: bond pdb=" CD GLU P 131 " pdb=" OE1 GLU P 131 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.72e+00 bond pdb=" CG GLU P 131 " pdb=" CD GLU P 131 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.51e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 23674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 31500 1.73 - 3.45: 392 3.45 - 5.18: 91 5.18 - 6.90: 29 6.90 - 8.63: 5 Bond angle restraints: 32017 Sorted by residual: angle pdb=" N GLU P 131 " pdb=" CA GLU P 131 " pdb=" CB GLU P 131 " ideal model delta sigma weight residual 110.39 117.07 -6.68 1.66e+00 3.63e-01 1.62e+01 angle pdb=" C ILE P 130 " pdb=" N GLU P 131 " pdb=" CA GLU P 131 " ideal model delta sigma weight residual 120.72 114.13 6.59 1.67e+00 3.59e-01 1.56e+01 angle pdb=" CB ARG P 133 " pdb=" CG ARG P 133 " pdb=" CD ARG P 133 " ideal model delta sigma weight residual 111.30 118.96 -7.66 2.30e+00 1.89e-01 1.11e+01 angle pdb=" C GLU O 138 " pdb=" N GLU O 139 " pdb=" CA GLU O 139 " ideal model delta sigma weight residual 120.72 115.22 5.50 1.67e+00 3.59e-01 1.08e+01 angle pdb=" CA GLU P 131 " pdb=" CB GLU P 131 " pdb=" CG GLU P 131 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 ... (remaining 32012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 14100 35.11 - 70.22: 269 70.22 - 105.32: 21 105.32 - 140.43: 6 140.43 - 175.54: 11 Dihedral angle restraints: 14407 sinusoidal: 5921 harmonic: 8486 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 115.54 -175.54 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP A2002 " pdb=" O5' ADP A2002 " pdb=" PA ADP A2002 " pdb=" O2A ADP A2002 " ideal model delta sinusoidal sigma weight residual -60.00 109.41 -169.41 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 99.62 -159.61 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 14404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2394 0.035 - 0.070: 779 0.070 - 0.104: 272 0.104 - 0.139: 90 0.139 - 0.174: 6 Chirality restraints: 3541 Sorted by residual: chirality pdb=" CB ILE A 580 " pdb=" CA ILE A 580 " pdb=" CG1 ILE A 580 " pdb=" CG2 ILE A 580 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CB ILE P 130 " pdb=" CA ILE P 130 " pdb=" CG1 ILE P 130 " pdb=" CG2 ILE P 130 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CA GLU P 131 " pdb=" N GLU P 131 " pdb=" C GLU P 131 " pdb=" CB GLU P 131 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 3538 not shown) Planarity restraints: 4122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 366 " -0.041 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO C 367 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET P 127 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C MET P 127 " 0.039 2.00e-02 2.50e+03 pdb=" O MET P 127 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS P 128 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 111 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO D 112 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " -0.028 5.00e-02 4.00e+02 ... (remaining 4119 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 192 2.63 - 3.20: 20473 3.20 - 3.76: 35493 3.76 - 4.33: 47786 4.33 - 4.90: 80851 Nonbonded interactions: 184795 Sorted by model distance: nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.060 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.067 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.111 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.117 2.170 nonbonded pdb=" O3B ADP F 401 " pdb="MG MG F 402 " model vdw 2.121 2.170 ... (remaining 184790 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.370 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 52.170 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23679 Z= 0.113 Angle : 0.544 8.626 32017 Z= 0.276 Chirality : 0.041 0.174 3541 Planarity : 0.004 0.063 4122 Dihedral : 15.521 175.539 8945 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % 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: 1.18 (0.16), residues: 2899 helix: 1.88 (0.15), residues: 1362 sheet: 0.12 (0.26), residues: 435 loop : -0.27 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 79 HIS 0.003 0.001 HIS C 73 PHE 0.029 0.001 PHE A 359 TYR 0.028 0.001 TYR P 162 ARG 0.008 0.000 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.18156 ( 1265) hydrogen bonds : angle 5.78549 ( 3453) covalent geometry : bond 0.00235 (23679) covalent geometry : angle 0.54377 (32017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8424 (ppp) cc_final: 0.8194 (ppp) REVERT: C 143 TYR cc_start: 0.8462 (m-80) cc_final: 0.8194 (m-80) REVERT: D 47 MET cc_start: 0.6811 (tpt) cc_final: 0.5912 (ptp) REVERT: O 130 ILE cc_start: 0.8223 (tp) cc_final: 0.7965 (tt) REVERT: P 89 ASN cc_start: 0.7904 (m-40) cc_final: 0.7582 (m-40) REVERT: P 93 GLN cc_start: 0.7888 (mp-120) cc_final: 0.7647 (mp10) REVERT: P 175 ASP cc_start: 0.8314 (m-30) cc_final: 0.7990 (m-30) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.3401 time to fit residues: 119.7176 Evaluate side-chains 188 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** 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 = 0.3813 r_free = 0.3813 target = 0.124144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.083219 restraints weight = 41418.274| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.26 r_work: 0.3044 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23679 Z= 0.151 Angle : 0.579 7.330 32017 Z= 0.292 Chirality : 0.043 0.158 3541 Planarity : 0.004 0.052 4122 Dihedral : 11.492 175.441 3238 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.48 % Allowed : 6.94 % Favored : 92.58 % 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: 0.94 (0.16), residues: 2899 helix: 1.72 (0.14), residues: 1397 sheet: -0.01 (0.25), residues: 428 loop : -0.52 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 130 HIS 0.006 0.001 HIS D 73 PHE 0.020 0.001 PHE A 46 TYR 0.023 0.001 TYR P 162 ARG 0.008 0.000 ARG P 133 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 1265) hydrogen bonds : angle 4.52576 ( 3453) covalent geometry : bond 0.00352 (23679) covalent geometry : angle 0.57851 (32017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8485 (ppp) cc_final: 0.8229 (ppp) REVERT: A 554 ASP cc_start: 0.7663 (m-30) cc_final: 0.7452 (m-30) REVERT: A 599 ASP cc_start: 0.8344 (t0) cc_final: 0.7994 (t70) REVERT: F 176 MET cc_start: 0.8486 (mtt) cc_final: 0.8204 (mtt) REVERT: D 47 MET cc_start: 0.7556 (tpt) cc_final: 0.6114 (ptp) REVERT: E 223 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6632 (m-80) REVERT: E 227 MET cc_start: 0.7706 (mmm) cc_final: 0.7167 (mmm) REVERT: O 127 MET cc_start: 0.7562 (ttm) cc_final: 0.6933 (tpt) REVERT: P 111 GLN cc_start: 0.7479 (pp30) cc_final: 0.7213 (pp30) outliers start: 12 outliers final: 9 residues processed: 215 average time/residue: 0.3567 time to fit residues: 119.4681 Evaluate side-chains 197 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain P residue 131 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 250 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 198 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 30.0000 chunk 126 optimal weight: 0.4980 chunk 184 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.124802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.083546 restraints weight = 41276.679| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.11 r_work: 0.3055 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23679 Z= 0.115 Angle : 0.536 7.644 32017 Z= 0.268 Chirality : 0.042 0.173 3541 Planarity : 0.004 0.045 4122 Dihedral : 11.015 178.453 3238 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.88 % Allowed : 8.55 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.16), residues: 2899 helix: 1.93 (0.14), residues: 1369 sheet: 0.05 (0.25), residues: 428 loop : -0.43 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 130 HIS 0.004 0.001 HIS C 73 PHE 0.014 0.001 PHE A 46 TYR 0.022 0.001 TYR P 162 ARG 0.003 0.000 ARG P 133 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 1265) hydrogen bonds : angle 4.23400 ( 3453) covalent geometry : bond 0.00257 (23679) covalent geometry : angle 0.53584 (32017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.7139 (m-80) cc_final: 0.6846 (m-80) REVERT: A 554 ASP cc_start: 0.7599 (m-30) cc_final: 0.7321 (m-30) REVERT: A 599 ASP cc_start: 0.8346 (t0) cc_final: 0.8038 (t70) REVERT: F 107 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: F 176 MET cc_start: 0.8390 (mtt) cc_final: 0.8058 (mtt) REVERT: D 47 MET cc_start: 0.7542 (tpt) cc_final: 0.6172 (ptm) REVERT: E 223 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6681 (m-80) REVERT: E 227 MET cc_start: 0.7697 (mmm) cc_final: 0.7173 (mmm) REVERT: O 101 ARG cc_start: 0.8258 (tmm160) cc_final: 0.8056 (mmp80) REVERT: O 127 MET cc_start: 0.7586 (ttm) cc_final: 0.6833 (tpt) REVERT: O 144 GLN cc_start: 0.4627 (tm-30) cc_final: 0.4402 (tm-30) REVERT: P 127 MET cc_start: 0.6989 (mtp) cc_final: 0.6484 (mmm) REVERT: P 141 MET cc_start: 0.8289 (ptm) cc_final: 0.8025 (ptp) REVERT: P 162 TYR cc_start: 0.8081 (t80) cc_final: 0.7725 (t80) outliers start: 22 outliers final: 12 residues processed: 222 average time/residue: 0.3446 time to fit residues: 118.8954 Evaluate side-chains 205 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 131 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 169 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN C 73 HIS O 144 GLN ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** 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 = 0.3791 r_free = 0.3791 target = 0.122622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081416 restraints weight = 41718.333| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.32 r_work: 0.2996 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23679 Z= 0.163 Angle : 0.577 8.583 32017 Z= 0.289 Chirality : 0.044 0.181 3541 Planarity : 0.004 0.048 4122 Dihedral : 10.362 166.673 3238 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.40 % Allowed : 9.71 % Favored : 88.88 % 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 (0.16), residues: 2899 helix: 1.78 (0.14), residues: 1403 sheet: 0.00 (0.24), residues: 428 loop : -0.61 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 130 HIS 0.006 0.001 HIS D 73 PHE 0.016 0.001 PHE F 255 TYR 0.019 0.001 TYR P 162 ARG 0.009 0.000 ARG P 133 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 1265) hydrogen bonds : angle 4.20682 ( 3453) covalent geometry : bond 0.00390 (23679) covalent geometry : angle 0.57727 (32017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8359 (ppp) cc_final: 0.7550 (ppp) REVERT: A 275 PHE cc_start: 0.7198 (m-80) cc_final: 0.6898 (m-80) REVERT: A 554 ASP cc_start: 0.7706 (m-30) cc_final: 0.7447 (m-30) REVERT: A 599 ASP cc_start: 0.8368 (t0) cc_final: 0.8055 (t70) REVERT: F 107 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: D 47 MET cc_start: 0.7660 (tpt) cc_final: 0.6015 (ptp) REVERT: E 223 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: O 101 ARG cc_start: 0.8247 (tmm160) cc_final: 0.8046 (mmp80) REVERT: O 127 MET cc_start: 0.7548 (ttm) cc_final: 0.6873 (tpt) REVERT: O 144 GLN cc_start: 0.4875 (tm130) cc_final: 0.4671 (tm-30) REVERT: P 89 ASN cc_start: 0.8311 (m-40) cc_final: 0.7849 (t0) REVERT: P 93 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8069 (mm-40) outliers start: 35 outliers final: 19 residues processed: 221 average time/residue: 0.3530 time to fit residues: 122.5497 Evaluate side-chains 206 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 216 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 246 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 276 GLN P 93 GLN ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.121159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.079908 restraints weight = 41408.314| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.22 r_work: 0.2972 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23679 Z= 0.190 Angle : 0.594 9.132 32017 Z= 0.299 Chirality : 0.045 0.190 3541 Planarity : 0.004 0.041 4122 Dihedral : 10.113 157.829 3238 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.81 % Allowed : 10.47 % Favored : 87.72 % 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: 0.77 (0.16), residues: 2899 helix: 1.67 (0.14), residues: 1397 sheet: -0.05 (0.25), residues: 428 loop : -0.77 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 130 HIS 0.006 0.001 HIS D 73 PHE 0.017 0.001 PHE F 255 TYR 0.027 0.001 TYR P 162 ARG 0.007 0.000 ARG P 125 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 1265) hydrogen bonds : angle 4.22117 ( 3453) covalent geometry : bond 0.00462 (23679) covalent geometry : angle 0.59398 (32017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7521 (ppp) REVERT: A 275 PHE cc_start: 0.7194 (m-80) cc_final: 0.6863 (m-80) REVERT: A 388 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7959 (mpp) REVERT: A 554 ASP cc_start: 0.7730 (m-30) cc_final: 0.7453 (m-30) REVERT: A 599 ASP cc_start: 0.8443 (t0) cc_final: 0.8111 (t70) REVERT: F 107 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: D 47 MET cc_start: 0.7755 (tpt) cc_final: 0.6053 (ptp) REVERT: E 72 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8181 (mm-30) REVERT: O 127 MET cc_start: 0.7575 (ttm) cc_final: 0.6906 (tpt) REVERT: P 89 ASN cc_start: 0.8334 (m-40) cc_final: 0.8104 (m-40) REVERT: P 127 MET cc_start: 0.6740 (ptm) cc_final: 0.5703 (tpp) REVERT: P 162 TYR cc_start: 0.8056 (t80) cc_final: 0.7744 (t80) outliers start: 45 outliers final: 27 residues processed: 226 average time/residue: 0.3656 time to fit residues: 129.1294 Evaluate side-chains 213 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 100 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 233 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 216 optimal weight: 0.4980 chunk 193 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** O 144 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.123502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.082186 restraints weight = 41141.166| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.23 r_work: 0.3021 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23679 Z= 0.108 Angle : 0.542 10.006 32017 Z= 0.270 Chirality : 0.042 0.203 3541 Planarity : 0.004 0.042 4122 Dihedral : 9.714 153.649 3238 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.36 % Allowed : 11.12 % Favored : 87.52 % 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 (0.16), residues: 2899 helix: 1.78 (0.14), residues: 1397 sheet: 0.04 (0.24), residues: 438 loop : -0.59 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 130 HIS 0.003 0.001 HIS P 153 PHE 0.012 0.001 PHE A 621 TYR 0.037 0.001 TYR P 60 ARG 0.006 0.000 ARG P 125 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 1265) hydrogen bonds : angle 4.08158 ( 3453) covalent geometry : bond 0.00237 (23679) covalent geometry : angle 0.54235 (32017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7441 (ppp) REVERT: A 275 PHE cc_start: 0.7212 (m-80) cc_final: 0.6943 (m-80) REVERT: A 388 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7744 (mpp) REVERT: A 554 ASP cc_start: 0.7669 (m-30) cc_final: 0.7365 (m-30) REVERT: A 599 ASP cc_start: 0.8401 (t0) cc_final: 0.8089 (t70) REVERT: F 107 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: B 176 MET cc_start: 0.8209 (mtt) cc_final: 0.7922 (mtt) REVERT: D 47 MET cc_start: 0.7728 (tpt) cc_final: 0.6091 (ptp) REVERT: E 72 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8071 (mm-30) REVERT: O 127 MET cc_start: 0.7573 (ttm) cc_final: 0.6904 (tpt) REVERT: P 89 ASN cc_start: 0.8330 (m-40) cc_final: 0.8103 (m-40) REVERT: P 127 MET cc_start: 0.6728 (ptm) cc_final: 0.5707 (tpt) REVERT: P 162 TYR cc_start: 0.8046 (t80) cc_final: 0.7606 (t80) outliers start: 34 outliers final: 24 residues processed: 218 average time/residue: 0.3629 time to fit residues: 122.9259 Evaluate side-chains 216 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 69 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 282 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 114 optimal weight: 0.0970 chunk 217 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 chunk 48 optimal weight: 20.0000 chunk 218 optimal weight: 0.7980 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 222 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** 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 = 0.3811 r_free = 0.3811 target = 0.124053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.082856 restraints weight = 41392.500| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.20 r_work: 0.3029 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23679 Z= 0.106 Angle : 0.536 10.920 32017 Z= 0.265 Chirality : 0.042 0.212 3541 Planarity : 0.004 0.041 4122 Dihedral : 9.311 154.847 3238 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.44 % Allowed : 11.88 % Favored : 86.68 % 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: 1.06 (0.16), residues: 2899 helix: 1.83 (0.14), residues: 1396 sheet: 0.08 (0.25), residues: 438 loop : -0.50 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 130 HIS 0.004 0.001 HIS P 153 PHE 0.015 0.001 PHE A 621 TYR 0.034 0.001 TYR P 60 ARG 0.008 0.000 ARG P 125 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 1265) hydrogen bonds : angle 3.99782 ( 3453) covalent geometry : bond 0.00234 (23679) covalent geometry : angle 0.53585 (32017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7526 (ppp) REVERT: A 275 PHE cc_start: 0.7154 (m-80) cc_final: 0.6921 (m-80) REVERT: A 388 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7664 (mpp) REVERT: A 554 ASP cc_start: 0.7646 (m-30) cc_final: 0.7336 (m-30) REVERT: A 599 ASP cc_start: 0.8395 (t0) cc_final: 0.8105 (t70) REVERT: F 107 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: B 325 MET cc_start: 0.8844 (tpt) cc_final: 0.8626 (tpt) REVERT: D 47 MET cc_start: 0.7680 (tpt) cc_final: 0.6159 (ptp) REVERT: O 127 MET cc_start: 0.7580 (ttm) cc_final: 0.6922 (tpt) REVERT: O 182 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8397 (pmt-80) REVERT: P 89 ASN cc_start: 0.8297 (m-40) cc_final: 0.8063 (m-40) REVERT: P 127 MET cc_start: 0.6549 (ptm) cc_final: 0.5616 (tpt) REVERT: P 162 TYR cc_start: 0.8125 (t80) cc_final: 0.7605 (t80) outliers start: 36 outliers final: 27 residues processed: 219 average time/residue: 0.3622 time to fit residues: 122.2815 Evaluate side-chains 215 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 154 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 265 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** 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 = 0.3801 r_free = 0.3801 target = 0.123272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.081970 restraints weight = 41216.129| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.15 r_work: 0.3015 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23679 Z= 0.128 Angle : 0.556 11.194 32017 Z= 0.276 Chirality : 0.042 0.188 3541 Planarity : 0.004 0.041 4122 Dihedral : 9.196 161.564 3238 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.48 % Allowed : 12.20 % Favored : 86.32 % 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 (0.16), residues: 2899 helix: 1.72 (0.14), residues: 1425 sheet: 0.08 (0.25), residues: 438 loop : -0.60 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 130 HIS 0.004 0.001 HIS D 73 PHE 0.015 0.001 PHE A 621 TYR 0.034 0.001 TYR P 60 ARG 0.013 0.000 ARG P 133 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 1265) hydrogen bonds : angle 4.01667 ( 3453) covalent geometry : bond 0.00297 (23679) covalent geometry : angle 0.55567 (32017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7429 (ppp) REVERT: A 275 PHE cc_start: 0.7177 (m-80) cc_final: 0.6932 (m-80) REVERT: A 388 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7666 (mpp) REVERT: A 554 ASP cc_start: 0.7661 (m-30) cc_final: 0.7356 (m-30) REVERT: A 599 ASP cc_start: 0.8402 (t0) cc_final: 0.8116 (t70) REVERT: F 107 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: D 47 MET cc_start: 0.7687 (tpt) cc_final: 0.6184 (ptp) REVERT: E 72 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8087 (mm-30) REVERT: O 127 MET cc_start: 0.7578 (ttm) cc_final: 0.6932 (tpt) REVERT: O 182 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8411 (pmt-80) REVERT: P 89 ASN cc_start: 0.8297 (m-40) cc_final: 0.8083 (m-40) REVERT: P 127 MET cc_start: 0.6553 (ptm) cc_final: 0.5630 (tpt) REVERT: P 162 TYR cc_start: 0.8125 (t80) cc_final: 0.7569 (t80) outliers start: 37 outliers final: 30 residues processed: 216 average time/residue: 0.3651 time to fit residues: 121.4066 Evaluate side-chains 218 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 103 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 256 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 205 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.123349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.081566 restraints weight = 41330.178| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.14 r_work: 0.3014 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23679 Z= 0.124 Angle : 0.559 11.929 32017 Z= 0.277 Chirality : 0.042 0.181 3541 Planarity : 0.004 0.057 4122 Dihedral : 9.107 178.811 3238 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.52 % Allowed : 12.04 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.98 (0.16), residues: 2899 helix: 1.74 (0.14), residues: 1421 sheet: 0.09 (0.25), residues: 438 loop : -0.58 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 130 HIS 0.004 0.001 HIS D 73 PHE 0.015 0.001 PHE A 621 TYR 0.033 0.001 TYR P 60 ARG 0.010 0.000 ARG P 133 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1265) hydrogen bonds : angle 4.01640 ( 3453) covalent geometry : bond 0.00288 (23679) covalent geometry : angle 0.55858 (32017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7417 (ppp) REVERT: A 275 PHE cc_start: 0.7160 (m-80) cc_final: 0.6923 (m-80) REVERT: A 388 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7558 (mpp) REVERT: A 502 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8415 (mtmm) REVERT: A 554 ASP cc_start: 0.7675 (m-30) cc_final: 0.7379 (m-30) REVERT: A 599 ASP cc_start: 0.8387 (t0) cc_final: 0.8111 (t70) REVERT: F 107 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: D 47 MET cc_start: 0.7690 (tpt) cc_final: 0.6193 (ptp) REVERT: E 72 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8087 (mm-30) REVERT: E 313 MET cc_start: 0.8492 (ttm) cc_final: 0.8167 (mmm) REVERT: O 127 MET cc_start: 0.7588 (ttm) cc_final: 0.6948 (tpt) REVERT: O 182 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8426 (ttp80) REVERT: P 89 ASN cc_start: 0.8282 (m-40) cc_final: 0.8057 (m-40) REVERT: P 127 MET cc_start: 0.6569 (ptm) cc_final: 0.5639 (tpt) outliers start: 38 outliers final: 32 residues processed: 215 average time/residue: 0.3659 time to fit residues: 121.7147 Evaluate side-chains 220 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 159 optimal weight: 0.0570 chunk 33 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 0.0070 chunk 70 optimal weight: 30.0000 chunk 146 optimal weight: 0.2980 chunk 181 optimal weight: 0.6980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** 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 = 0.3831 r_free = 0.3831 target = 0.125402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.083629 restraints weight = 41340.364| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.13 r_work: 0.3046 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23679 Z= 0.096 Angle : 0.541 12.103 32017 Z= 0.266 Chirality : 0.041 0.179 3541 Planarity : 0.004 0.069 4122 Dihedral : 8.601 153.843 3238 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.32 % Allowed : 12.32 % Favored : 86.36 % 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: 1.09 (0.16), residues: 2899 helix: 1.79 (0.14), residues: 1426 sheet: 0.17 (0.25), residues: 428 loop : -0.48 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 130 HIS 0.004 0.001 HIS P 153 PHE 0.015 0.001 PHE A 621 TYR 0.034 0.001 TYR P 60 ARG 0.013 0.000 ARG P 133 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 1265) hydrogen bonds : angle 3.95427 ( 3453) covalent geometry : bond 0.00198 (23679) covalent geometry : angle 0.54109 (32017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7399 (ppp) REVERT: A 388 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7406 (mpp) REVERT: A 554 ASP cc_start: 0.7685 (m-30) cc_final: 0.7357 (m-30) REVERT: A 599 ASP cc_start: 0.8386 (t0) cc_final: 0.8120 (t70) REVERT: F 107 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: C 325 MET cc_start: 0.8749 (mmp) cc_final: 0.8460 (mmt) REVERT: D 47 MET cc_start: 0.7605 (tpt) cc_final: 0.6236 (ptp) REVERT: E 313 MET cc_start: 0.8459 (ttm) cc_final: 0.8224 (mmm) REVERT: O 127 MET cc_start: 0.7559 (ttm) cc_final: 0.6900 (tpt) REVERT: O 182 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8463 (pmt-80) REVERT: P 89 ASN cc_start: 0.8310 (m-40) cc_final: 0.8082 (m-40) REVERT: P 127 MET cc_start: 0.6579 (ptm) cc_final: 0.5665 (tpt) outliers start: 33 outliers final: 25 residues processed: 218 average time/residue: 0.3545 time to fit residues: 120.1797 Evaluate side-chains 215 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 52 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 chunk 206 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 207 optimal weight: 0.1980 chunk 263 optimal weight: 6.9990 chunk 64 optimal weight: 0.0070 chunk 183 optimal weight: 1.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.124678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082882 restraints weight = 41107.226| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.08 r_work: 0.3040 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23679 Z= 0.110 Angle : 0.553 12.538 32017 Z= 0.272 Chirality : 0.042 0.174 3541 Planarity : 0.004 0.042 4122 Dihedral : 8.410 150.704 3238 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.28 % Allowed : 12.24 % Favored : 86.48 % 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: 1.13 (0.16), residues: 2899 helix: 1.84 (0.14), residues: 1421 sheet: 0.14 (0.25), residues: 438 loop : -0.45 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 130 HIS 0.004 0.001 HIS P 153 PHE 0.014 0.001 PHE A 621 TYR 0.035 0.001 TYR P 162 ARG 0.017 0.000 ARG P 133 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 1265) hydrogen bonds : angle 3.94421 ( 3453) covalent geometry : bond 0.00246 (23679) covalent geometry : angle 0.55299 (32017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13381.35 seconds wall clock time: 232 minutes 24.28 seconds (13944.28 seconds total)