Starting phenix.real_space_refine on Sat Sep 12 13:11:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lz3_30022/09_2026/6lz3_30022.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lz3_30022/09_2026/6lz3_30022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lz3_30022/09_2026/6lz3_30022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lz3_30022/09_2026/6lz3_30022.map" model { file = "/net/cci-nas-00/data/ceres_data/6lz3_30022/09_2026/6lz3_30022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lz3_30022/09_2026/6lz3_30022.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6lz3_30022/09_2026/6lz3_30022.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lz3_30022/09_2026/6lz3_30022.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 48 5.16 5 C 10228 2.51 5 N 2804 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15968 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3939 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 33, 'TRANS': 452} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.26, per 1000 atoms: 0.27 Number of scatterers: 15968 At special positions: 0 Unit cell: (82.758, 124.137, 124.137, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 8 15.00 O 2880 8.00 N 2804 7.00 C 10228 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 703.9 milliseconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 4 sheets defined 50.4% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.656A pdb=" N ARG A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 65 removed outlier: 3.774A pdb=" N ILE A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 54 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 55 " --> pdb=" O TRP A 51 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.817A pdb=" N ALA A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 121 removed outlier: 3.945A pdb=" N VAL A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 157 removed outlier: 3.683A pdb=" N ASN A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 203 removed outlier: 3.580A pdb=" N ALA A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 202 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 203 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.728A pdb=" N ASP A 212 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.563A pdb=" N ALA A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 226 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.611A pdb=" N PHE A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.602A pdb=" N LEU A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.905A pdb=" N CYS A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 297 removed outlier: 3.654A pdb=" N SER A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.664A pdb=" N PHE A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 346 removed outlier: 3.897A pdb=" N TRP A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 363 removed outlier: 3.634A pdb=" N VAL A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 378 removed outlier: 3.751A pdb=" N GLY A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 395 Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.680A pdb=" N TRP A 427 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 removed outlier: 3.564A pdb=" N ALA A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 446 through 452 Processing helix chain 'A' and resid 467 through 480 removed outlier: 3.857A pdb=" N GLY A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 480 " --> pdb=" O GLN A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.656A pdb=" N ARG B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 65 removed outlier: 3.774A pdb=" N ILE B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 54 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 55 " --> pdb=" O TRP B 51 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.817A pdb=" N ALA B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 121 removed outlier: 3.945A pdb=" N VAL B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 109 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 157 removed outlier: 3.684A pdb=" N ASN B 154 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 203 removed outlier: 3.580A pdb=" N ALA B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG B 202 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 203 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.729A pdb=" N ASP B 212 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.562A pdb=" N ALA B 224 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 226 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.612A pdb=" N PHE B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 removed outlier: 3.602A pdb=" N LEU B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.906A pdb=" N CYS B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 297 removed outlier: 3.654A pdb=" N SER B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.664A pdb=" N PHE B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 346 removed outlier: 3.897A pdb=" N TRP B 343 " --> pdb=" O MET B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 363 removed outlier: 3.634A pdb=" N VAL B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 378 removed outlier: 3.751A pdb=" N GLY B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 Processing helix chain 'B' and resid 423 through 428 removed outlier: 3.680A pdb=" N TRP B 427 " --> pdb=" O TYR B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 removed outlier: 3.564A pdb=" N ALA B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 446 through 452 Processing helix chain 'B' and resid 467 through 480 removed outlier: 3.858A pdb=" N GLY B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN B 476 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 480 " --> pdb=" O GLN B 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.655A pdb=" N ARG C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 65 removed outlier: 3.773A pdb=" N ILE C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 55 " --> pdb=" O TRP C 51 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 62 " --> pdb=" O ASN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.817A pdb=" N ALA C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 121 removed outlier: 3.945A pdb=" N VAL C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 109 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 119 " --> pdb=" O GLU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 157 removed outlier: 3.683A pdb=" N ASN C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 203 removed outlier: 3.580A pdb=" N ALA C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG C 202 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 203 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.729A pdb=" N ASP C 212 " --> pdb=" O TRP C 208 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.563A pdb=" N ALA C 224 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 226 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 removed outlier: 3.611A pdb=" N PHE C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 removed outlier: 3.603A pdb=" N LEU C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 265 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 280 removed outlier: 3.905A pdb=" N CYS C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 297 removed outlier: 3.654A pdb=" N SER C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.664A pdb=" N PHE C 322 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 346 removed outlier: 3.896A pdb=" N TRP C 343 " --> pdb=" O MET C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 363 removed outlier: 3.634A pdb=" N VAL C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 378 removed outlier: 3.751A pdb=" N GLY C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 423 through 428 removed outlier: 3.681A pdb=" N TRP C 427 " --> pdb=" O TYR C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.564A pdb=" N ALA C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 441 through 445 Processing helix chain 'C' and resid 446 through 452 Processing helix chain 'C' and resid 467 through 480 removed outlier: 3.857A pdb=" N GLY C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN C 476 " --> pdb=" O LYS C 472 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 480 " --> pdb=" O GLN C 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.656A pdb=" N ARG D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.774A pdb=" N ILE D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER D 54 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 55 " --> pdb=" O TRP D 51 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.816A pdb=" N ALA D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.945A pdb=" N VAL D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 119 " --> pdb=" O GLU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 removed outlier: 3.683A pdb=" N ASN D 154 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 removed outlier: 3.580A pdb=" N ALA D 201 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG D 202 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D 203 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 220 removed outlier: 3.728A pdb=" N ASP D 212 " --> pdb=" O TRP D 208 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.563A pdb=" N ALA D 224 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 226 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 247 removed outlier: 3.612A pdb=" N PHE D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 268 removed outlier: 3.602A pdb=" N LEU D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 280 removed outlier: 3.906A pdb=" N CYS D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 297 removed outlier: 3.655A pdb=" N SER D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 288 " --> pdb=" O SER D 284 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 296 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.664A pdb=" N PHE D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 346 removed outlier: 3.897A pdb=" N TRP D 343 " --> pdb=" O MET D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 363 removed outlier: 3.634A pdb=" N VAL D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 361 " --> pdb=" O ALA D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 378 removed outlier: 3.751A pdb=" N GLY D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 395 Processing helix chain 'D' and resid 423 through 428 removed outlier: 3.681A pdb=" N TRP D 427 " --> pdb=" O TYR D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 432 removed outlier: 3.563A pdb=" N ALA D 432 " --> pdb=" O PRO D 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 429 through 432' Processing helix chain 'D' and resid 441 through 445 Processing helix chain 'D' and resid 446 through 452 Processing helix chain 'D' and resid 467 through 480 removed outlier: 3.857A pdb=" N GLY D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLN D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 480 " --> pdb=" O GLN D 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76 removed outlier: 3.670A pdb=" N VAL A 73 " --> pdb=" O PRO A 31 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 4 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 96 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.670A pdb=" N VAL B 73 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 4 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 96 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 73 through 76 removed outlier: 3.670A pdb=" N VAL C 73 " --> pdb=" O PRO C 31 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 4 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 96 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 73 through 76 removed outlier: 3.671A pdb=" N VAL D 73 " --> pdb=" O PRO D 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D 4 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 96 " --> pdb=" O GLN D 125 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1476 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: 2.57 Time building geometry restraints manager: 2.18 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: 5109 1.34 - 1.46: 3092 1.46 - 1.57: 8182 1.57 - 1.69: 13 1.69 - 1.81: 84 Bond restraints: 16480 Sorted by residual: bond pdb=" N LEU C 310 " pdb=" CA LEU C 310 " ideal model delta sigma weight residual 1.457 1.537 -0.080 1.29e-02 6.01e+03 3.82e+01 bond pdb=" N LEU D 310 " pdb=" CA LEU D 310 " ideal model delta sigma weight residual 1.457 1.537 -0.080 1.29e-02 6.01e+03 3.81e+01 bond pdb=" N LEU A 310 " pdb=" CA LEU A 310 " ideal model delta sigma weight residual 1.457 1.537 -0.079 1.29e-02 6.01e+03 3.78e+01 bond pdb=" N LEU B 310 " pdb=" CA LEU B 310 " ideal model delta sigma weight residual 1.457 1.537 -0.079 1.29e-02 6.01e+03 3.77e+01 bond pdb=" CA HIS B 309 " pdb=" C HIS B 309 " ideal model delta sigma weight residual 1.522 1.592 -0.070 1.20e-02 6.94e+03 3.40e+01 ... (remaining 16475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 22064 3.45 - 6.89: 354 6.89 - 10.34: 66 10.34 - 13.79: 12 13.79 - 17.23: 12 Bond angle restraints: 22508 Sorted by residual: angle pdb=" C LEU A 310 " pdb=" N ARG A 311 " pdb=" CA ARG A 311 " ideal model delta sigma weight residual 121.54 135.16 -13.62 1.91e+00 2.74e-01 5.09e+01 angle pdb=" C LEU B 310 " pdb=" N ARG B 311 " pdb=" CA ARG B 311 " ideal model delta sigma weight residual 121.54 135.10 -13.56 1.91e+00 2.74e-01 5.04e+01 angle pdb=" C LEU C 310 " pdb=" N ARG C 311 " pdb=" CA ARG C 311 " ideal model delta sigma weight residual 121.54 135.09 -13.55 1.91e+00 2.74e-01 5.03e+01 angle pdb=" C LEU D 310 " pdb=" N ARG D 311 " pdb=" CA ARG D 311 " ideal model delta sigma weight residual 121.54 135.06 -13.52 1.91e+00 2.74e-01 5.01e+01 angle pdb=" N VAL A 317 " pdb=" CA VAL A 317 " pdb=" C VAL A 317 " ideal model delta sigma weight residual 111.91 106.15 5.76 8.90e-01 1.26e+00 4.19e+01 ... (remaining 22503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.03: 8752 22.03 - 44.05: 660 44.05 - 66.08: 136 66.08 - 88.10: 16 88.10 - 110.13: 12 Dihedral angle restraints: 9576 sinusoidal: 3912 harmonic: 5664 Sorted by residual: dihedral pdb=" CA THR C 395 " pdb=" C THR C 395 " pdb=" N GLY C 396 " pdb=" CA GLY C 396 " ideal model delta harmonic sigma weight residual 180.00 135.58 44.42 0 5.00e+00 4.00e-02 7.89e+01 dihedral pdb=" CA THR A 395 " pdb=" C THR A 395 " pdb=" N GLY A 396 " pdb=" CA GLY A 396 " ideal model delta harmonic sigma weight residual 180.00 135.58 44.42 0 5.00e+00 4.00e-02 7.89e+01 dihedral pdb=" CA THR D 395 " pdb=" C THR D 395 " pdb=" N GLY D 396 " pdb=" CA GLY D 396 " ideal model delta harmonic sigma weight residual 180.00 135.62 44.38 0 5.00e+00 4.00e-02 7.88e+01 ... (remaining 9573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2059 0.085 - 0.170: 246 0.170 - 0.256: 27 0.256 - 0.341: 0 0.341 - 0.426: 4 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CG LEU C 398 " pdb=" CB LEU C 398 " pdb=" CD1 LEU C 398 " pdb=" CD2 LEU C 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CG LEU B 398 " pdb=" CB LEU B 398 " pdb=" CD1 LEU B 398 " pdb=" CD2 LEU B 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CG LEU D 398 " pdb=" CB LEU D 398 " pdb=" CD1 LEU D 398 " pdb=" CD2 LEU D 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.47e+00 ... (remaining 2333 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 304 " 0.074 5.00e-02 4.00e+02 1.14e-01 2.06e+01 pdb=" N PRO A 305 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 304 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO C 305 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO C 305 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 305 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 304 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO B 305 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " -0.060 5.00e-02 4.00e+02 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1712 2.74 - 3.28: 14569 3.28 - 3.82: 25967 3.82 - 4.36: 31817 4.36 - 4.90: 53062 Nonbonded interactions: 127127 Sorted by model distance: nonbonded pdb=" O TRP C 391 " pdb=" OG1 THR C 395 " model vdw 2.201 3.040 nonbonded pdb=" O TRP B 391 " pdb=" OG1 THR B 395 " model vdw 2.201 3.040 nonbonded pdb=" O TRP D 391 " pdb=" OG1 THR D 395 " model vdw 2.201 3.040 nonbonded pdb=" O TRP A 391 " pdb=" OG1 THR A 395 " model vdw 2.202 3.040 nonbonded pdb=" O THR C 378 " pdb=" OG1 THR C 378 " model vdw 2.253 3.040 ... (remaining 127122 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.310 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.007 0.091 16484 Z= 0.363 Angle : 1.201 17.232 22508 Z= 0.653 Chirality : 0.058 0.426 2336 Planarity : 0.009 0.114 2884 Dihedral : 16.422 110.126 5920 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.68 % Favored : 90.91 % Rotamer: Outliers : 3.86 % Allowed : 8.45 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.45 (0.11), residues: 1936 helix: -4.57 (0.06), residues: 984 sheet: -3.76 (0.32), residues: 132 loop : -3.81 (0.16), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 406 TYR 0.029 0.003 TYR C 43 PHE 0.028 0.003 PHE D 313 TRP 0.052 0.003 TRP B 483 HIS 0.005 0.001 HIS C 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.36 (16480) covalent geometry : angle 1.20091 / 0.65 (22508) hydrogen bonds : bond 0.34713 / 23.27 ( 508) hydrogen bonds : angle 11.59708 / 8.08 ( 1476) Misc. bond : bond 0.01114 / 0.56 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5564 (mmt) cc_final: 0.5347 (mmt) REVERT: B 413 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6587 (tp30) REVERT: C 113 LEU cc_start: 0.8773 (tp) cc_final: 0.8564 (tp) REVERT: D 1 MET cc_start: 0.5536 (mmt) cc_final: 0.5266 (mmt) outliers start: 64 outliers final: 12 residues processed: 310 average time/residue: 0.1514 time to fit residues: 65.9160 Evaluate side-chains 175 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 475 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS A 154 ASN A 244 HIS A 246 HIS A 263 GLN B 59 HIS B 154 ASN B 244 HIS B 246 HIS B 257 HIS B 263 GLN B 365 GLN C 59 HIS C 154 ASN C 244 HIS C 246 HIS C 257 HIS C 263 GLN D 59 HIS D 154 ASN D 210 ASN D 244 HIS D 246 HIS D 263 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.160758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120611 restraints weight = 22228.465| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.48 r_work: 0.3378 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16484 Z= 0.145 Angle : 0.728 9.278 22508 Z= 0.365 Chirality : 0.044 0.150 2336 Planarity : 0.007 0.086 2884 Dihedral : 8.435 109.781 2200 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.60 % Allowed : 11.84 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.15), residues: 1936 helix: -2.98 (0.12), residues: 984 sheet: -3.44 (0.34), residues: 132 loop : -3.16 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 112 TYR 0.023 0.002 TYR C 43 PHE 0.007 0.001 PHE C 312 TRP 0.013 0.001 TRP D 443 HIS 0.004 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16480) covalent geometry : angle 0.72803 / 0.37 (22508) hydrogen bonds : bond 0.05830 / 3.88 ( 508) hydrogen bonds : angle 5.48576 / 3.82 ( 1476) Misc. bond : bond 0.00403 / 0.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.611 Fit side-chains REVERT: A 112 ARG cc_start: 0.8392 (tmm160) cc_final: 0.8148 (tmm-80) REVERT: A 113 LEU cc_start: 0.8988 (tp) cc_final: 0.8526 (mm) REVERT: B 113 LEU cc_start: 0.8747 (tp) cc_final: 0.8390 (mm) REVERT: B 474 ARG cc_start: 0.7007 (tpt90) cc_final: 0.6769 (tpt90) REVERT: C 113 LEU cc_start: 0.8939 (tp) cc_final: 0.8565 (mm) REVERT: D 1 MET cc_start: 0.5779 (mmt) cc_final: 0.5127 (mmt) REVERT: D 113 LEU cc_start: 0.8953 (tp) cc_final: 0.8673 (mm) outliers start: 43 outliers final: 25 residues processed: 203 average time/residue: 0.1344 time to fit residues: 39.9791 Evaluate side-chains 162 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 412 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 143 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 64 optimal weight: 0.0570 chunk 147 optimal weight: 10.0000 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 HIS B 99 ASN B 365 GLN C 99 ASN D 99 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.160417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120525 restraints weight = 22359.688| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.46 r_work: 0.3381 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16484 Z= 0.124 Angle : 0.615 7.338 22508 Z= 0.308 Chirality : 0.042 0.142 2336 Planarity : 0.005 0.060 2884 Dihedral : 7.215 98.113 2184 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.84 % Allowed : 13.77 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.17), residues: 1936 helix: -1.81 (0.14), residues: 1008 sheet: -3.23 (0.34), residues: 132 loop : -2.86 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.022 0.001 TYR A 43 PHE 0.012 0.001 PHE D 417 TRP 0.022 0.001 TRP A 438 HIS 0.003 0.000 HIS D 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (16480) covalent geometry : angle 0.61474 / 0.31 (22508) hydrogen bonds : bond 0.04406 / 2.88 ( 508) hydrogen bonds : angle 4.65722 / 3.24 ( 1476) Misc. bond : bond 0.00343 / 0.17 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.525 Fit side-chains REVERT: A 113 LEU cc_start: 0.9026 (tp) cc_final: 0.8497 (mm) REVERT: A 289 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7417 (tm-30) REVERT: B 113 LEU cc_start: 0.8877 (tp) cc_final: 0.8499 (mm) REVERT: B 394 ILE cc_start: 0.7729 (tp) cc_final: 0.7409 (tp) REVERT: C 89 ARG cc_start: 0.8107 (tpp-160) cc_final: 0.7869 (mmp80) REVERT: C 113 LEU cc_start: 0.8950 (tp) cc_final: 0.8634 (mm) REVERT: D 1 MET cc_start: 0.5756 (mmt) cc_final: 0.5087 (mmt) REVERT: D 86 GLN cc_start: 0.8487 (tp40) cc_final: 0.8185 (tp40) REVERT: D 113 LEU cc_start: 0.9001 (tp) cc_final: 0.8729 (mm) outliers start: 47 outliers final: 29 residues processed: 194 average time/residue: 0.1305 time to fit residues: 37.7986 Evaluate side-chains 168 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 412 PHE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 68 optimal weight: 0.0370 chunk 191 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 365 GLN C 99 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 257 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.154533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113237 restraints weight = 22261.921| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.48 r_work: 0.3272 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 16484 Z= 0.226 Angle : 0.696 8.249 22508 Z= 0.344 Chirality : 0.046 0.144 2336 Planarity : 0.005 0.059 2884 Dihedral : 6.834 82.571 2180 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.56 % Allowed : 15.28 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.18), residues: 1936 helix: -1.29 (0.15), residues: 1000 sheet: -3.26 (0.36), residues: 132 loop : -2.69 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 8 TYR 0.019 0.002 TYR D 43 PHE 0.014 0.002 PHE C 281 TRP 0.019 0.002 TRP D 6 HIS 0.006 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (16480) covalent geometry : angle 0.69643 / 0.34 (22508) hydrogen bonds : bond 0.04619 / 2.98 ( 508) hydrogen bonds : angle 4.70058 / 3.26 ( 1476) Misc. bond : bond 0.00526 / 0.26 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 135 time to evaluate : 0.606 Fit side-chains REVERT: A 113 LEU cc_start: 0.9149 (tp) cc_final: 0.8688 (mm) REVERT: A 394 ILE cc_start: 0.7994 (tp) cc_final: 0.7744 (tp) REVERT: A 409 ASN cc_start: 0.6272 (t0) cc_final: 0.5822 (t0) REVERT: B 113 LEU cc_start: 0.8930 (tp) cc_final: 0.8540 (mm) REVERT: C 89 ARG cc_start: 0.8129 (tpp-160) cc_final: 0.7835 (mmp80) REVERT: C 113 LEU cc_start: 0.8955 (tp) cc_final: 0.8629 (mm) REVERT: C 394 ILE cc_start: 0.8146 (tp) cc_final: 0.7693 (tp) REVERT: D 1 MET cc_start: 0.5853 (mmt) cc_final: 0.5022 (mmt) REVERT: D 86 GLN cc_start: 0.8551 (tp40) cc_final: 0.8288 (tp40) REVERT: D 113 LEU cc_start: 0.9099 (tp) cc_final: 0.8756 (mm) outliers start: 59 outliers final: 41 residues processed: 176 average time/residue: 0.1133 time to fit residues: 31.1123 Evaluate side-chains 176 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 412 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 365 GLN C 99 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.157932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.117302 restraints weight = 22023.626| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.48 r_work: 0.3329 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16484 Z= 0.114 Angle : 0.572 6.711 22508 Z= 0.285 Chirality : 0.041 0.128 2336 Planarity : 0.004 0.054 2884 Dihedral : 6.628 87.909 2180 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.32 % Allowed : 16.24 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.18), residues: 1936 helix: -0.92 (0.16), residues: 1036 sheet: -3.09 (0.36), residues: 132 loop : -2.56 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 8 TYR 0.019 0.001 TYR A 43 PHE 0.008 0.001 PHE D 359 TRP 0.014 0.001 TRP B 443 HIS 0.002 0.001 HIS A 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (16480) covalent geometry : angle 0.57165 / 0.29 (22508) hydrogen bonds : bond 0.03783 / 2.45 ( 508) hydrogen bonds : angle 4.28425 / 2.98 ( 1476) Misc. bond : bond 0.00378 / 0.19 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 0.717 Fit side-chains REVERT: A 113 LEU cc_start: 0.9043 (tp) cc_final: 0.8598 (mm) REVERT: A 115 GLU cc_start: 0.8893 (tp30) cc_final: 0.8643 (pt0) REVERT: A 394 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7778 (tp) REVERT: A 409 ASN cc_start: 0.6264 (t0) cc_final: 0.5968 (t0) REVERT: B 86 GLN cc_start: 0.8435 (tp40) cc_final: 0.8216 (tp40) REVERT: B 113 LEU cc_start: 0.8870 (tp) cc_final: 0.8492 (mm) REVERT: B 289 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 426 ARG cc_start: 0.8236 (tpt90) cc_final: 0.7841 (tpt90) REVERT: C 89 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7910 (mmp80) REVERT: C 113 LEU cc_start: 0.8891 (tp) cc_final: 0.8536 (mm) REVERT: C 394 ILE cc_start: 0.8066 (tp) cc_final: 0.7573 (tp) REVERT: D 1 MET cc_start: 0.5828 (mmt) cc_final: 0.4984 (mmt) REVERT: D 86 GLN cc_start: 0.8480 (tp40) cc_final: 0.8174 (tp40) REVERT: D 89 ARG cc_start: 0.8059 (tpp-160) cc_final: 0.7670 (mmp80) REVERT: D 113 LEU cc_start: 0.9004 (tp) cc_final: 0.8604 (mm) outliers start: 55 outliers final: 38 residues processed: 190 average time/residue: 0.1261 time to fit residues: 36.5759 Evaluate side-chains 179 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 412 PHE Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 449 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 92 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 160 optimal weight: 0.0670 chunk 59 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 141 optimal weight: 0.5980 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 365 GLN C 99 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.159724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119430 restraints weight = 21857.711| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.47 r_work: 0.3366 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16484 Z= 0.102 Angle : 0.548 7.194 22508 Z= 0.277 Chirality : 0.041 0.132 2336 Planarity : 0.004 0.053 2884 Dihedral : 6.445 85.587 2180 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.84 % Allowed : 16.97 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.18), residues: 1936 helix: -0.65 (0.16), residues: 1036 sheet: -2.97 (0.36), residues: 132 loop : -2.39 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 8 TYR 0.015 0.001 TYR D 415 PHE 0.011 0.001 PHE C 98 TRP 0.015 0.001 TRP B 443 HIS 0.002 0.000 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (16480) covalent geometry : angle 0.54841 / 0.28 (22508) hydrogen bonds : bond 0.03451 / 2.24 ( 508) hydrogen bonds : angle 4.08016 / 2.83 ( 1476) Misc. bond : bond 0.00319 / 0.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.708 Fit side-chains REVERT: A 113 LEU cc_start: 0.8999 (tp) cc_final: 0.8515 (mm) REVERT: A 115 GLU cc_start: 0.8880 (tp30) cc_final: 0.8659 (pt0) REVERT: A 289 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 394 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7773 (tp) REVERT: A 409 ASN cc_start: 0.6223 (t0) cc_final: 0.5972 (t0) REVERT: B 86 GLN cc_start: 0.8447 (tp40) cc_final: 0.8207 (tp40) REVERT: B 89 ARG cc_start: 0.7817 (tpp-160) cc_final: 0.7577 (mmt-90) REVERT: B 113 LEU cc_start: 0.8858 (tp) cc_final: 0.8495 (mm) REVERT: B 289 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 426 ARG cc_start: 0.8212 (tpt90) cc_final: 0.7796 (tpt90) REVERT: C 86 GLN cc_start: 0.8351 (tp40) cc_final: 0.7976 (tp40) REVERT: C 89 ARG cc_start: 0.8231 (tpp-160) cc_final: 0.7963 (mmm160) REVERT: C 113 LEU cc_start: 0.8907 (tp) cc_final: 0.8523 (mm) REVERT: C 394 ILE cc_start: 0.8146 (tp) cc_final: 0.7668 (tp) REVERT: D 86 GLN cc_start: 0.8471 (tp40) cc_final: 0.8171 (tp40) REVERT: D 89 ARG cc_start: 0.8048 (tpp-160) cc_final: 0.7664 (mmp80) REVERT: D 113 LEU cc_start: 0.8966 (tp) cc_final: 0.8528 (mm) REVERT: D 144 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8247 (mm110) REVERT: D 394 ILE cc_start: 0.8113 (tp) cc_final: 0.7632 (tp) outliers start: 47 outliers final: 35 residues processed: 193 average time/residue: 0.1271 time to fit residues: 37.3929 Evaluate side-chains 184 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 chunk 4 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.157846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117090 restraints weight = 21890.223| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.49 r_work: 0.3328 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16484 Z= 0.124 Angle : 0.564 7.019 22508 Z= 0.282 Chirality : 0.041 0.130 2336 Planarity : 0.004 0.052 2884 Dihedral : 6.264 80.821 2180 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.90 % Allowed : 17.27 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.19), residues: 1936 helix: -0.45 (0.16), residues: 1024 sheet: -2.82 (0.36), residues: 132 loop : -2.24 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 8 TYR 0.014 0.001 TYR A 43 PHE 0.008 0.001 PHE D 359 TRP 0.015 0.001 TRP B 443 HIS 0.002 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (16480) covalent geometry : angle 0.56377 / 0.28 (22508) hydrogen bonds : bond 0.03610 / 2.33 ( 508) hydrogen bonds : angle 4.08307 / 2.83 ( 1476) Misc. bond : bond 0.00387 / 0.19 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8883 (tp30) cc_final: 0.8659 (pt0) REVERT: A 394 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7842 (tp) REVERT: A 409 ASN cc_start: 0.6265 (t0) cc_final: 0.5999 (t0) REVERT: B 14 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7457 (tm-30) REVERT: B 86 GLN cc_start: 0.8451 (tp40) cc_final: 0.8216 (tp40) REVERT: B 89 ARG cc_start: 0.7810 (tpp-160) cc_final: 0.7562 (mmt-90) REVERT: B 113 LEU cc_start: 0.8843 (tp) cc_final: 0.8515 (mm) REVERT: B 394 ILE cc_start: 0.8179 (tp) cc_final: 0.7791 (tp) REVERT: C 86 GLN cc_start: 0.8381 (tp40) cc_final: 0.8015 (tp40) REVERT: C 89 ARG cc_start: 0.8221 (tpp-160) cc_final: 0.7941 (mmm160) REVERT: C 113 LEU cc_start: 0.8811 (tp) cc_final: 0.8519 (mm) REVERT: D 86 GLN cc_start: 0.8472 (tp40) cc_final: 0.8195 (tp40) REVERT: D 89 ARG cc_start: 0.7965 (tpp-160) cc_final: 0.7580 (mmp80) REVERT: D 113 LEU cc_start: 0.8960 (tp) cc_final: 0.8570 (mm) REVERT: D 394 ILE cc_start: 0.8167 (tp) cc_final: 0.7651 (tp) outliers start: 48 outliers final: 39 residues processed: 184 average time/residue: 0.1179 time to fit residues: 33.1678 Evaluate side-chains 186 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 68 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 156 optimal weight: 0.0060 chunk 22 optimal weight: 2.9990 chunk 160 optimal weight: 0.0980 chunk 180 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.115059 restraints weight = 22122.228| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.50 r_work: 0.3299 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16484 Z= 0.150 Angle : 0.591 7.073 22508 Z= 0.293 Chirality : 0.042 0.147 2336 Planarity : 0.004 0.052 2884 Dihedral : 6.277 81.294 2180 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.02 % Allowed : 17.57 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.19), residues: 1936 helix: -0.42 (0.16), residues: 1020 sheet: -2.73 (0.37), residues: 132 loop : -2.19 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 8 TYR 0.015 0.001 TYR D 43 PHE 0.009 0.001 PHE C 281 TRP 0.017 0.001 TRP B 443 HIS 0.003 0.001 HIS D 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (16480) covalent geometry : angle 0.59084 / 0.29 (22508) hydrogen bonds : bond 0.03836 / 2.46 ( 508) hydrogen bonds : angle 4.18040 / 2.90 ( 1476) Misc. bond : bond 0.00454 / 0.23 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7821 (tp) REVERT: A 409 ASN cc_start: 0.6329 (t0) cc_final: 0.6055 (t0) REVERT: B 14 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 86 GLN cc_start: 0.8454 (tp40) cc_final: 0.8211 (tp40) REVERT: B 113 LEU cc_start: 0.8793 (tp) cc_final: 0.8455 (mm) REVERT: B 394 ILE cc_start: 0.8404 (tp) cc_final: 0.8151 (tp) REVERT: C 86 GLN cc_start: 0.8424 (tp40) cc_final: 0.8135 (tp40) REVERT: C 89 ARG cc_start: 0.8114 (tpp-160) cc_final: 0.7707 (mmp80) REVERT: C 113 LEU cc_start: 0.8816 (tp) cc_final: 0.8448 (mm) REVERT: C 144 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8056 (mm110) REVERT: C 394 ILE cc_start: 0.8416 (tp) cc_final: 0.8059 (tp) REVERT: D 86 GLN cc_start: 0.8458 (tp40) cc_final: 0.8201 (tp40) REVERT: D 89 ARG cc_start: 0.7978 (tpp-160) cc_final: 0.7581 (mmp80) REVERT: D 113 LEU cc_start: 0.8977 (tp) cc_final: 0.8551 (mm) outliers start: 50 outliers final: 40 residues processed: 180 average time/residue: 0.1226 time to fit residues: 34.0241 Evaluate side-chains 180 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 110 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 173 optimal weight: 0.3980 chunk 79 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117568 restraints weight = 21987.374| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.48 r_work: 0.3339 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16484 Z= 0.110 Angle : 0.551 6.725 22508 Z= 0.275 Chirality : 0.041 0.125 2336 Planarity : 0.004 0.052 2884 Dihedral : 6.205 82.660 2180 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.08 % Allowed : 17.27 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.19), residues: 1936 helix: -0.27 (0.16), residues: 1036 sheet: -2.72 (0.37), residues: 132 loop : -2.18 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 8 TYR 0.014 0.001 TYR D 415 PHE 0.007 0.001 PHE D 359 TRP 0.020 0.001 TRP B 443 HIS 0.002 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (16480) covalent geometry : angle 0.55148 / 0.27 (22508) hydrogen bonds : bond 0.03438 / 2.21 ( 508) hydrogen bonds : angle 4.04562 / 2.82 ( 1476) Misc. bond : bond 0.00371 / 0.19 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7871 (tp) REVERT: A 409 ASN cc_start: 0.6356 (t0) cc_final: 0.6019 (t0) REVERT: A 426 ARG cc_start: 0.8193 (tpt90) cc_final: 0.7840 (tpt90) REVERT: B 14 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7552 (tm-30) REVERT: B 89 ARG cc_start: 0.7816 (tpp-160) cc_final: 0.7593 (mmt-90) REVERT: B 113 LEU cc_start: 0.8812 (tp) cc_final: 0.8457 (mm) REVERT: B 394 ILE cc_start: 0.8338 (tp) cc_final: 0.8106 (tp) REVERT: B 426 ARG cc_start: 0.8215 (tpt90) cc_final: 0.7934 (tpt90) REVERT: C 86 GLN cc_start: 0.8435 (tp40) cc_final: 0.8138 (tp40) REVERT: C 89 ARG cc_start: 0.8135 (tpp-160) cc_final: 0.7763 (mmp80) REVERT: C 113 LEU cc_start: 0.8803 (tp) cc_final: 0.8438 (mm) REVERT: C 394 ILE cc_start: 0.8410 (tp) cc_final: 0.8063 (tp) REVERT: D 89 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.7598 (mmp80) REVERT: D 113 LEU cc_start: 0.8973 (tp) cc_final: 0.8551 (mm) REVERT: D 394 ILE cc_start: 0.8344 (tp) cc_final: 0.8113 (tp) outliers start: 51 outliers final: 45 residues processed: 181 average time/residue: 0.1337 time to fit residues: 36.2870 Evaluate side-chains 187 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 156 optimal weight: 0.0570 chunk 21 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.158346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118137 restraints weight = 21942.090| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.49 r_work: 0.3342 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16484 Z= 0.108 Angle : 0.548 6.678 22508 Z= 0.272 Chirality : 0.041 0.121 2336 Planarity : 0.004 0.053 2884 Dihedral : 6.111 80.351 2180 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.96 % Allowed : 17.63 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.19), residues: 1936 helix: -0.01 (0.17), residues: 1008 sheet: -2.60 (0.37), residues: 132 loop : -2.13 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 8 TYR 0.013 0.001 TYR D 415 PHE 0.008 0.001 PHE D 359 TRP 0.023 0.001 TRP B 443 HIS 0.002 0.001 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (16480) covalent geometry : angle 0.54786 / 0.27 (22508) hydrogen bonds : bond 0.03368 / 2.17 ( 508) hydrogen bonds : angle 3.98119 / 2.77 ( 1476) Misc. bond : bond 0.00366 / 0.18 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7362 (m-80) cc_final: 0.6932 (m-10) REVERT: A 394 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7826 (tp) REVERT: A 409 ASN cc_start: 0.6352 (t0) cc_final: 0.6011 (t0) REVERT: A 426 ARG cc_start: 0.8218 (tpt90) cc_final: 0.7866 (tpt90) REVERT: B 14 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 89 ARG cc_start: 0.7836 (tpp-160) cc_final: 0.7618 (mmt-90) REVERT: B 113 LEU cc_start: 0.8788 (tp) cc_final: 0.8446 (mm) REVERT: B 180 MET cc_start: 0.5750 (ttm) cc_final: 0.5128 (tpt) REVERT: B 426 ARG cc_start: 0.8189 (tpt90) cc_final: 0.7916 (tpt90) REVERT: C 89 ARG cc_start: 0.8149 (tpp-160) cc_final: 0.7794 (mmp80) REVERT: C 113 LEU cc_start: 0.8865 (tp) cc_final: 0.8494 (mm) REVERT: C 394 ILE cc_start: 0.8430 (tp) cc_final: 0.8131 (tp) REVERT: D 89 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7600 (mmp80) REVERT: D 113 LEU cc_start: 0.9013 (tp) cc_final: 0.8557 (mm) outliers start: 49 outliers final: 43 residues processed: 175 average time/residue: 0.1334 time to fit residues: 35.0881 Evaluate side-chains 181 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 430 GLU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 181 CYS Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.117528 restraints weight = 21890.248| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.52 r_work: 0.3328 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16484 Z= 0.125 Angle : 0.558 6.692 22508 Z= 0.277 Chirality : 0.041 0.118 2336 Planarity : 0.004 0.052 2884 Dihedral : 6.076 78.947 2180 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.14 % Allowed : 17.63 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.19), residues: 1936 helix: -0.06 (0.16), residues: 1016 sheet: -2.50 (0.37), residues: 132 loop : -2.05 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 474 TYR 0.013 0.001 TYR D 415 PHE 0.008 0.001 PHE D 359 TRP 0.020 0.001 TRP B 443 HIS 0.003 0.001 HIS A 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (16480) covalent geometry : angle 0.55828 / 0.28 (22508) hydrogen bonds : bond 0.03511 / 2.26 ( 508) hydrogen bonds : angle 4.02149 / 2.80 ( 1476) Misc. bond : bond 0.00396 / 0.20 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3134.17 seconds wall clock time: 54 minutes 50.64 seconds (3290.64 seconds total)