Starting phenix.real_space_refine on Fri Sep 27 12:38:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/09_2024/6lz3_30022.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/09_2024/6lz3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/09_2024/6lz3_30022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/09_2024/6lz3_30022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/09_2024/6lz3_30022.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz3_30022/09_2024/6lz3_30022.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: C, B, D Time building chain proxies: 8.67, per 1000 atoms: 0.54 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: 3.63 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.90 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: 4.10 Time building geometry restraints manager: 4.26 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: 8776 22.03 - 44.05: 752 44.05 - 66.08: 192 66.08 - 88.10: 16 88.10 - 110.13: 12 Dihedral angle restraints: 9748 sinusoidal: 4084 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 9745 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: 0.00 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 34.110 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 16480 Z= 0.468 Angle : 1.201 17.232 22508 Z= 0.653 Chirality : 0.058 0.426 2336 Planarity : 0.009 0.114 2884 Dihedral : 17.574 110.126 6092 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.052 0.003 TRP B 483 HIS 0.005 0.001 HIS C 95 PHE 0.028 0.003 PHE D 313 TYR 0.029 0.003 TYR C 43 ARG 0.004 0.001 ARG A 406 *********************** 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 fitting. rotamer outliers: 64 poor density : 262 time to evaluate : 1.801 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: 0.6915 (OUTLIER) cc_final: 0.6586 (tp30) REVERT: C 113 LEU cc_start: 0.8772 (tp) cc_final: 0.8563 (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: 0.3403 time to fit residues: 146.4825 Evaluate side-chains 175 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 162 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 150 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 112 optimal weight: 0.0020 chunk 174 optimal weight: 5.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 244 HIS D 246 HIS D 263 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16480 Z= 0.227 Angle : 0.726 9.018 22508 Z= 0.364 Chirality : 0.044 0.158 2336 Planarity : 0.007 0.083 2884 Dihedral : 11.687 101.713 2372 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.48 % Allowed : 12.08 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.15), residues: 1936 helix: -2.99 (0.12), residues: 988 sheet: -3.42 (0.34), residues: 132 loop : -3.22 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 443 HIS 0.004 0.001 HIS C 59 PHE 0.010 0.001 PHE C 312 TYR 0.022 0.002 TYR C 43 ARG 0.012 0.001 ARG B 474 *********************** 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 219 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 1.641 Fit side-chains REVERT: A 113 LEU cc_start: 0.8840 (tp) cc_final: 0.8475 (mm) REVERT: B 474 ARG cc_start: 0.7164 (tpt90) cc_final: 0.6930 (tpt90) REVERT: C 113 LEU cc_start: 0.8804 (tp) cc_final: 0.8574 (mm) REVERT: D 1 MET cc_start: 0.5733 (mmt) cc_final: 0.5223 (mmt) REVERT: D 139 VAL cc_start: 0.8337 (t) cc_final: 0.8115 (m) outliers start: 41 outliers final: 25 residues processed: 206 average time/residue: 0.3052 time to fit residues: 90.4164 Evaluate side-chains 161 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 181 CYS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 354 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 96 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 140 optimal weight: 0.0270 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS B 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16480 Z= 0.225 Angle : 0.646 7.085 22508 Z= 0.322 Chirality : 0.043 0.131 2336 Planarity : 0.005 0.065 2884 Dihedral : 10.856 81.609 2356 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.20 % Allowed : 13.89 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.17), residues: 1936 helix: -1.86 (0.14), residues: 996 sheet: -3.21 (0.35), residues: 132 loop : -2.84 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 438 HIS 0.004 0.001 HIS B 349 PHE 0.011 0.001 PHE D 417 TYR 0.021 0.002 TYR A 43 ARG 0.004 0.000 ARG B 109 *********************** 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 208 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 155 time to evaluate : 1.605 Fit side-chains REVERT: A 113 LEU cc_start: 0.8952 (tp) cc_final: 0.8633 (mm) REVERT: A 289 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6654 (tm-30) REVERT: B 394 ILE cc_start: 0.7607 (tp) cc_final: 0.7133 (tp) REVERT: B 485 LEU cc_start: -0.3204 (OUTLIER) cc_final: -0.3412 (tp) REVERT: C 113 LEU cc_start: 0.8875 (tp) cc_final: 0.8672 (mm) REVERT: D 1 MET cc_start: 0.5682 (mmt) cc_final: 0.5180 (mmt) REVERT: D 86 GLN cc_start: 0.8388 (tp40) cc_final: 0.8098 (tp40) REVERT: D 139 VAL cc_start: 0.8338 (t) cc_final: 0.8123 (m) REVERT: D 394 ILE cc_start: 0.7714 (tp) cc_final: 0.7423 (tp) outliers start: 53 outliers final: 33 residues processed: 191 average time/residue: 0.2743 time to fit residues: 78.3229 Evaluate side-chains 170 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 412 PHE 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 252 VAL Chi-restraints excluded: chain B residue 295 SER 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 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 378 THR 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 181 CYS Chi-restraints excluded: chain D residue 252 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 19 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 365 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16480 Z= 0.246 Angle : 0.621 7.330 22508 Z= 0.308 Chirality : 0.043 0.144 2336 Planarity : 0.005 0.056 2884 Dihedral : 10.630 71.450 2353 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.08 % Allowed : 15.94 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.18), residues: 1936 helix: -1.19 (0.15), residues: 1024 sheet: -3.03 (0.36), residues: 132 loop : -2.67 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 6 HIS 0.004 0.001 HIS D 349 PHE 0.010 0.001 PHE B 312 TYR 0.019 0.002 TYR D 43 ARG 0.005 0.000 ARG D 8 *********************** 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 198 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 147 time to evaluate : 1.778 Fit side-chains REVERT: A 113 LEU cc_start: 0.8979 (tp) cc_final: 0.8663 (mm) REVERT: A 394 ILE cc_start: 0.7988 (tp) cc_final: 0.7745 (tp) REVERT: B 394 ILE cc_start: 0.8173 (tp) cc_final: 0.7774 (tp) REVERT: B 485 LEU cc_start: -0.3189 (OUTLIER) cc_final: -0.3402 (tp) REVERT: C 113 LEU cc_start: 0.8859 (tp) cc_final: 0.8579 (mm) REVERT: C 394 ILE cc_start: 0.8134 (tp) cc_final: 0.7759 (tp) REVERT: D 1 MET cc_start: 0.5805 (mmt) cc_final: 0.5172 (mmt) REVERT: D 86 GLN cc_start: 0.8405 (tp40) cc_final: 0.8120 (tp40) REVERT: D 89 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7466 (mmp80) REVERT: D 139 VAL cc_start: 0.8381 (t) cc_final: 0.8172 (m) outliers start: 51 outliers final: 35 residues processed: 180 average time/residue: 0.2535 time to fit residues: 70.2317 Evaluate side-chains 174 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 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 295 SER 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 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 99 ASN 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 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 154 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 138 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 158 optimal weight: 0.0970 chunk 128 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 0.0980 chunk 46 optimal weight: 0.0270 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN C 99 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16480 Z= 0.150 Angle : 0.553 7.208 22508 Z= 0.277 Chirality : 0.040 0.130 2336 Planarity : 0.004 0.054 2884 Dihedral : 10.170 73.740 2352 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.20 % Allowed : 16.06 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.18), residues: 1936 helix: -0.85 (0.16), residues: 1032 sheet: -2.94 (0.36), residues: 132 loop : -2.54 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 443 HIS 0.005 0.000 HIS D 100 PHE 0.013 0.001 PHE A 412 TYR 0.017 0.001 TYR A 43 ARG 0.005 0.000 ARG D 8 *********************** 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 209 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 156 time to evaluate : 1.785 Fit side-chains REVERT: A 86 GLN cc_start: 0.8416 (tp40) cc_final: 0.8156 (tp40) REVERT: A 113 LEU cc_start: 0.8893 (tp) cc_final: 0.8590 (mm) REVERT: A 289 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6542 (tm-30) REVERT: A 394 ILE cc_start: 0.8052 (tp) cc_final: 0.7765 (tp) REVERT: B 113 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8552 (mm) REVERT: B 394 ILE cc_start: 0.8181 (tp) cc_final: 0.7752 (tp) REVERT: C 86 GLN cc_start: 0.8241 (tp40) cc_final: 0.7907 (tp40) REVERT: C 113 LEU cc_start: 0.8830 (tp) cc_final: 0.8548 (mm) REVERT: C 394 ILE cc_start: 0.8196 (tp) cc_final: 0.7786 (tp) REVERT: D 1 MET cc_start: 0.5806 (mmt) cc_final: 0.5139 (mmt) REVERT: D 86 GLN cc_start: 0.8357 (tp40) cc_final: 0.8056 (tp40) REVERT: D 89 ARG cc_start: 0.7757 (tpp-160) cc_final: 0.7462 (mmp80) REVERT: D 139 VAL cc_start: 0.8334 (t) cc_final: 0.8117 (m) outliers start: 53 outliers final: 40 residues processed: 193 average time/residue: 0.2714 time to fit residues: 79.1278 Evaluate side-chains 184 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 330 THR Chi-restraints excluded: chain A residue 335 VAL 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 113 LEU 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 449 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 74 THR 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 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 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 412 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 1.9990 chunk 167 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 154 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16480 Z= 0.192 Angle : 0.561 7.042 22508 Z= 0.279 Chirality : 0.041 0.129 2336 Planarity : 0.004 0.053 2884 Dihedral : 10.060 70.931 2352 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.68 % Allowed : 16.06 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.18), residues: 1936 helix: -0.67 (0.16), residues: 1036 sheet: -2.85 (0.37), residues: 132 loop : -2.44 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 6 HIS 0.003 0.001 HIS C 349 PHE 0.010 0.001 PHE D 417 TYR 0.014 0.001 TYR D 43 ARG 0.004 0.000 ARG D 8 *********************** 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 211 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 150 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8431 (tp40) cc_final: 0.8153 (tp40) REVERT: A 113 LEU cc_start: 0.8834 (tp) cc_final: 0.8550 (mm) REVERT: A 394 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7889 (tp) REVERT: B 113 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8577 (mm) REVERT: B 394 ILE cc_start: 0.8285 (tp) cc_final: 0.7861 (tp) REVERT: C 86 GLN cc_start: 0.8273 (tp40) cc_final: 0.7954 (tp40) REVERT: C 113 LEU cc_start: 0.8846 (tp) cc_final: 0.8556 (mm) REVERT: C 394 ILE cc_start: 0.8243 (tp) cc_final: 0.7831 (tp) REVERT: D 86 GLN cc_start: 0.8314 (tp40) cc_final: 0.8048 (tp40) REVERT: D 89 ARG cc_start: 0.7687 (tpp-160) cc_final: 0.7400 (mmp80) REVERT: D 139 VAL cc_start: 0.8373 (t) cc_final: 0.8169 (m) outliers start: 61 outliers final: 42 residues processed: 195 average time/residue: 0.2644 time to fit residues: 79.0884 Evaluate side-chains 184 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 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 113 LEU 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 29 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 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 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 412 PHE 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 179 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 115 optimal weight: 0.0770 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN C 99 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16480 Z= 0.192 Angle : 0.564 7.082 22508 Z= 0.282 Chirality : 0.042 0.135 2336 Planarity : 0.004 0.052 2884 Dihedral : 9.903 70.263 2352 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.74 % Allowed : 16.49 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.19), residues: 1936 helix: -0.51 (0.16), residues: 1036 sheet: -2.72 (0.37), residues: 132 loop : -2.33 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 443 HIS 0.003 0.001 HIS D 309 PHE 0.010 0.001 PHE D 417 TYR 0.016 0.001 TYR A 43 ARG 0.005 0.000 ARG D 8 *********************** 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 206 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 144 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8784 (tp) cc_final: 0.8520 (mm) REVERT: A 394 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7921 (tp) REVERT: B 113 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8584 (mm) REVERT: C 86 GLN cc_start: 0.8267 (tp40) cc_final: 0.7952 (tp40) REVERT: C 113 LEU cc_start: 0.8858 (tp) cc_final: 0.8547 (mm) REVERT: C 394 ILE cc_start: 0.8307 (tp) cc_final: 0.7876 (tp) REVERT: D 86 GLN cc_start: 0.8317 (tp40) cc_final: 0.8059 (tp40) REVERT: D 89 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7384 (mmp80) REVERT: D 139 VAL cc_start: 0.8375 (t) cc_final: 0.8157 (m) REVERT: D 394 ILE cc_start: 0.8183 (tp) cc_final: 0.7743 (tp) outliers start: 62 outliers final: 45 residues processed: 192 average time/residue: 0.2593 time to fit residues: 75.9351 Evaluate side-chains 185 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 138 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 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 113 LEU 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 324 ILE 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 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 324 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16480 Z= 0.287 Angle : 0.622 7.730 22508 Z= 0.307 Chirality : 0.044 0.147 2336 Planarity : 0.004 0.051 2884 Dihedral : 10.283 69.557 2352 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.50 % Allowed : 17.33 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.19), residues: 1936 helix: -0.52 (0.16), residues: 1024 sheet: -2.65 (0.38), residues: 132 loop : -2.27 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 443 HIS 0.004 0.001 HIS C 349 PHE 0.012 0.001 PHE A 281 TYR 0.013 0.002 TYR B 293 ARG 0.005 0.000 ARG D 8 *********************** 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 197 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 139 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8800 (tp) cc_final: 0.8500 (mm) REVERT: B 394 ILE cc_start: 0.8193 (tp) cc_final: 0.7811 (tp) REVERT: C 86 GLN cc_start: 0.8268 (tp40) cc_final: 0.8028 (tp40) REVERT: C 113 LEU cc_start: 0.8839 (tp) cc_final: 0.8537 (mm) REVERT: C 394 ILE cc_start: 0.8456 (tp) cc_final: 0.8160 (tp) REVERT: D 86 GLN cc_start: 0.8386 (tp40) cc_final: 0.8153 (tp40) REVERT: D 89 ARG cc_start: 0.7699 (tpp-160) cc_final: 0.7384 (mmp80) REVERT: D 139 VAL cc_start: 0.8427 (t) cc_final: 0.8190 (m) outliers start: 58 outliers final: 46 residues processed: 182 average time/residue: 0.2621 time to fit residues: 72.5984 Evaluate side-chains 181 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 135 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 330 THR Chi-restraints excluded: chain A residue 335 VAL 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 113 LEU 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 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 187 ILE 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 430 GLU Chi-restraints excluded: chain C residue 431 LEU 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 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 335 VAL Chi-restraints excluded: chain D residue 384 LEU 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 177 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 172 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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** D 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 16480 Z= 0.446 Angle : 0.735 8.157 22508 Z= 0.360 Chirality : 0.048 0.158 2336 Planarity : 0.005 0.051 2884 Dihedral : 11.115 74.406 2352 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 3.50 % Allowed : 17.51 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.18), residues: 1936 helix: -0.72 (0.16), residues: 1008 sheet: -2.57 (0.40), residues: 132 loop : -2.35 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 443 HIS 0.007 0.002 HIS A 349 PHE 0.020 0.002 PHE D 417 TYR 0.028 0.002 TYR A 43 ARG 0.007 0.001 ARG D 8 *********************** 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 187 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 129 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 113 LEU cc_start: 0.8847 (tp) cc_final: 0.8496 (mm) REVERT: A 479 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4861 (tp) REVERT: B 113 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8696 (mm) REVERT: C 113 LEU cc_start: 0.8895 (tp) cc_final: 0.8552 (mm) REVERT: D 479 LEU cc_start: 0.4690 (OUTLIER) cc_final: 0.4438 (tp) outliers start: 58 outliers final: 49 residues processed: 173 average time/residue: 0.2694 time to fit residues: 70.9136 Evaluate side-chains 177 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 125 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 330 THR 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 A residue 431 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 LEU 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 113 LEU Chi-restraints excluded: chain B residue 178 LEU 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 178 LEU Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 187 ILE 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 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 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 335 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 479 LEU 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 182 optimal weight: 0.9990 chunk 111 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 176 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16480 Z= 0.185 Angle : 0.585 7.440 22508 Z= 0.293 Chirality : 0.042 0.133 2336 Planarity : 0.004 0.052 2884 Dihedral : 10.268 75.937 2352 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.90 % Allowed : 18.42 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.19), residues: 1936 helix: -0.34 (0.16), residues: 1004 sheet: -2.59 (0.38), residues: 132 loop : -2.18 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 443 HIS 0.002 0.001 HIS D 309 PHE 0.013 0.001 PHE D 417 TYR 0.012 0.001 TYR B 44 ARG 0.005 0.000 ARG D 8 ********************** 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 184 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.7693 (tpp-160) cc_final: 0.7386 (mmp80) REVERT: A 113 LEU cc_start: 0.8697 (tp) cc_final: 0.8443 (mm) REVERT: A 479 LEU cc_start: 0.4935 (OUTLIER) cc_final: 0.4688 (tp) REVERT: B 113 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8556 (mm) REVERT: B 144 GLN cc_start: 0.7324 (mm110) cc_final: 0.7100 (mm110) REVERT: C 113 LEU cc_start: 0.8859 (tp) cc_final: 0.8552 (mm) REVERT: C 144 GLN cc_start: 0.7334 (mm110) cc_final: 0.7113 (mm110) REVERT: C 479 LEU cc_start: 0.4575 (OUTLIER) cc_final: 0.4317 (tp) REVERT: D 89 ARG cc_start: 0.7696 (tpp-160) cc_final: 0.7456 (mmm160) outliers start: 48 outliers final: 42 residues processed: 170 average time/residue: 0.2745 time to fit residues: 70.8310 Evaluate side-chains 176 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 131 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 123 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 431 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 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 99 ASN Chi-restraints excluded: chain B residue 113 LEU 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 205 THR 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 479 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 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 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 162 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 42 optimal weight: 0.0970 chunk 152 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 365 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.155876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115948 restraints weight = 22174.144| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.49 r_work: 0.3313 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 16480 Z= 0.248 Angle : 0.781 59.060 22508 Z= 0.436 Chirality : 0.047 0.903 2336 Planarity : 0.004 0.055 2884 Dihedral : 10.288 75.740 2352 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.02 % Allowed : 18.60 % Favored : 78.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.19), residues: 1936 helix: -0.34 (0.16), residues: 1004 sheet: -2.54 (0.38), residues: 132 loop : -2.19 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 443 HIS 0.004 0.001 HIS B 100 PHE 0.013 0.001 PHE D 417 TYR 0.012 0.001 TYR B 44 ARG 0.004 0.000 ARG D 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3015.46 seconds wall clock time: 54 minutes 36.88 seconds (3276.88 seconds total)