Starting phenix.real_space_refine on Sun Aug 24 10:03:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8i_29856/08_2025/8g8i_29856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8i_29856/08_2025/8g8i_29856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8i_29856/08_2025/8g8i_29856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8i_29856/08_2025/8g8i_29856.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8i_29856/08_2025/8g8i_29856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8i_29856/08_2025/8g8i_29856.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 12820 2.51 5 N 2970 2.21 5 O 3515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 286 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19335 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3867 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "B" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3867 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "C" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3867 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "D" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3867 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "E" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3867 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Time building chain proxies: 3.92, per 1000 atoms: 0.20 Number of scatterers: 19335 At special positions: 0 Unit cell: (83.19, 84.075, 238.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 3515 8.00 N 2970 7.00 C 12820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 700.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 0 sheets defined 96.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.960A pdb=" N VAL A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 62 through 75 removed outlier: 4.042A pdb=" N ILE A 75 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.599A pdb=" N VAL A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.729A pdb=" N ASN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.572A pdb=" N ILE A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.659A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 160 removed outlier: 3.568A pdb=" N LEU A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 173 Processing helix chain 'A' and resid 175 through 194 Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 209 through 222 removed outlier: 4.189A pdb=" N GLU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 243 removed outlier: 3.808A pdb=" N GLY A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.547A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 271 removed outlier: 4.295A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.757A pdb=" N ASN A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.950A pdb=" N ILE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.650A pdb=" N GLY A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.636A pdb=" N LEU A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.628A pdb=" N VAL A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP A 388 " --> pdb=" O TRP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 404 removed outlier: 3.617A pdb=" N ILE A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 420 through 439 Processing helix chain 'A' and resid 441 through 453 removed outlier: 3.653A pdb=" N ILE A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.506A pdb=" N GLU A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.843A pdb=" N VAL B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 62 removed outlier: 3.645A pdb=" N ASN B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 75 Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.557A pdb=" N VAL B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 111 removed outlier: 3.516A pdb=" N ASN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.585A pdb=" N ILE B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 145 removed outlier: 3.573A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 160 Processing helix chain 'B' and resid 160 through 173 Processing helix chain 'B' and resid 175 through 194 Processing helix chain 'B' and resid 196 through 209 removed outlier: 3.937A pdb=" N ASN B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.686A pdb=" N GLY B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 258 Processing helix chain 'B' and resid 258 through 271 removed outlier: 4.136A pdb=" N ILE B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 292 removed outlier: 3.530A pdb=" N VAL B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 307 removed outlier: 3.882A pdb=" N ASN B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.901A pdb=" N ILE B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 removed outlier: 3.725A pdb=" N VAL B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.508A pdb=" N SER B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 369 Processing helix chain 'B' and resid 371 through 390 removed outlier: 3.568A pdb=" N GLY B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 405 removed outlier: 3.550A pdb=" N ILE B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 418 Processing helix chain 'B' and resid 420 through 439 Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.503A pdb=" N ASP B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.537A pdb=" N VAL C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 62 removed outlier: 3.545A pdb=" N ASN C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 75 removed outlier: 3.754A pdb=" N ILE C 75 " --> pdb=" O LYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 96 removed outlier: 3.595A pdb=" N VAL C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 111 through 124 removed outlier: 3.528A pdb=" N ILE C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 145 removed outlier: 3.636A pdb=" N VAL C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 160 removed outlier: 3.544A pdb=" N LEU C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 173 Processing helix chain 'C' and resid 175 through 194 removed outlier: 4.019A pdb=" N GLU C 192 " --> pdb=" O TYR C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 224 through 243 removed outlier: 3.922A pdb=" N GLY C 243 " --> pdb=" O VAL C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.510A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 271 removed outlier: 3.858A pdb=" N ILE C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 291 Processing helix chain 'C' and resid 294 through 307 removed outlier: 3.594A pdb=" N ASN C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.776A pdb=" N ILE C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 341 removed outlier: 3.783A pdb=" N VAL C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 356 removed outlier: 3.713A pdb=" N LEU C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.545A pdb=" N ILE C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 390 removed outlier: 3.644A pdb=" N VAL C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP C 388 " --> pdb=" O TRP C 384 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 405 removed outlier: 3.627A pdb=" N ILE C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 418 Processing helix chain 'C' and resid 420 through 439 Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 454 through 465 removed outlier: 3.550A pdb=" N VAL C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 removed outlier: 3.813A pdb=" N ASN D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.526A pdb=" N VAL D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 62 through 75 removed outlier: 3.717A pdb=" N ILE D 75 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 95 Processing helix chain 'D' and resid 98 through 111 removed outlier: 3.522A pdb=" N ASN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 124 removed outlier: 3.707A pdb=" N ILE D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 145 removed outlier: 4.065A pdb=" N VAL D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 160 removed outlier: 3.575A pdb=" N LEU D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 173 Processing helix chain 'D' and resid 175 through 194 removed outlier: 3.899A pdb=" N GLU D 192 " --> pdb=" O TYR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 209 through 222 removed outlier: 3.969A pdb=" N GLU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.500A pdb=" N VAL D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 removed outlier: 3.570A pdb=" N LEU D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 271 removed outlier: 3.679A pdb=" N ILE D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 292 removed outlier: 3.600A pdb=" N VAL D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 306 Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.533A pdb=" N ILE D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 340 Processing helix chain 'D' and resid 343 through 354 Processing helix chain 'D' and resid 356 through 369 Processing helix chain 'D' and resid 371 through 390 removed outlier: 3.687A pdb=" N LYS D 383 " --> pdb=" O PHE D 379 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP D 388 " --> pdb=" O TRP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 404 removed outlier: 3.638A pdb=" N SER D 404 " --> pdb=" O ARG D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 418 Processing helix chain 'D' and resid 420 through 439 removed outlier: 3.506A pdb=" N GLY D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 454 removed outlier: 4.213A pdb=" N ASP D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 465 Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.810A pdb=" N ASN E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 26 Processing helix chain 'E' and resid 28 through 47 removed outlier: 3.693A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 62 removed outlier: 3.633A pdb=" N ASN E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 75 removed outlier: 4.073A pdb=" N ILE E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 94 removed outlier: 3.505A pdb=" N VAL E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 109 Processing helix chain 'E' and resid 111 through 124 removed outlier: 4.099A pdb=" N ILE E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 145 removed outlier: 3.827A pdb=" N VAL E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 160 removed outlier: 3.584A pdb=" N ASN E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 173 Processing helix chain 'E' and resid 175 through 194 removed outlier: 3.554A pdb=" N GLU E 192 " --> pdb=" O TYR E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 removed outlier: 3.612A pdb=" N SER E 208 " --> pdb=" O LYS E 204 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 222 removed outlier: 3.509A pdb=" N GLU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 243 Processing helix chain 'E' and resid 245 through 258 Processing helix chain 'E' and resid 258 through 271 removed outlier: 3.600A pdb=" N ILE E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 292 removed outlier: 3.668A pdb=" N VAL E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 305 Processing helix chain 'E' and resid 307 through 320 Processing helix chain 'E' and resid 322 through 341 removed outlier: 3.677A pdb=" N GLY E 341 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 356 removed outlier: 3.712A pdb=" N ASN E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 369 Processing helix chain 'E' and resid 371 through 389 Processing helix chain 'E' and resid 392 through 404 Processing helix chain 'E' and resid 405 through 419 removed outlier: 3.532A pdb=" N GLY E 419 " --> pdb=" O TRP E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 438 Processing helix chain 'E' and resid 441 through 453 Processing helix chain 'E' and resid 454 through 465 1554 hydrogen bonds defined for protein. 4662 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: 3.20 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6075 1.34 - 1.46: 3804 1.46 - 1.58: 9771 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 19710 Sorted by residual: bond pdb=" CA ASN C 223 " pdb=" C ASN C 223 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.06e+00 bond pdb=" C GLY C 438 " pdb=" N GLY C 439 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.53e-01 bond pdb=" CA ASN B 196 " pdb=" CB ASN B 196 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.35e-02 5.49e+03 7.41e-01 bond pdb=" CG1 ILE A 53 " pdb=" CD1 ILE A 53 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.34e-01 bond pdb=" N ASN B 294 " pdb=" CA ASN B 294 " ideal model delta sigma weight residual 1.463 1.455 0.007 8.80e-03 1.29e+04 7.01e-01 ... (remaining 19705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 26018 1.48 - 2.96: 506 2.96 - 4.44: 79 4.44 - 5.92: 11 5.92 - 7.40: 6 Bond angle restraints: 26620 Sorted by residual: angle pdb=" N ARG E 371 " pdb=" CA ARG E 371 " pdb=" C ARG E 371 " ideal model delta sigma weight residual 112.97 109.88 3.09 1.06e+00 8.90e-01 8.52e+00 angle pdb=" N ILE E 271 " pdb=" CA ILE E 271 " pdb=" C ILE E 271 " ideal model delta sigma weight residual 112.98 109.38 3.60 1.25e+00 6.40e-01 8.27e+00 angle pdb=" N LYS B 175 " pdb=" CA LYS B 175 " pdb=" C LYS B 175 " ideal model delta sigma weight residual 112.97 110.23 2.74 1.06e+00 8.90e-01 6.67e+00 angle pdb=" N ILE B 26 " pdb=" CA ILE B 26 " pdb=" C ILE B 26 " ideal model delta sigma weight residual 112.98 109.93 3.05 1.25e+00 6.40e-01 5.97e+00 angle pdb=" N ARG D 126 " pdb=" CA ARG D 126 " pdb=" C ARG D 126 " ideal model delta sigma weight residual 110.44 107.71 2.73 1.20e+00 6.94e-01 5.17e+00 ... (remaining 26615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10599 17.97 - 35.94: 1013 35.94 - 53.91: 162 53.91 - 71.89: 84 71.89 - 89.86: 52 Dihedral angle restraints: 11910 sinusoidal: 5120 harmonic: 6790 Sorted by residual: dihedral pdb=" CA ASN A 147 " pdb=" C ASN A 147 " pdb=" N PRO A 148 " pdb=" CA PRO A 148 " ideal model delta harmonic sigma weight residual -180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU C 452 " pdb=" C LEU C 452 " pdb=" N LEU C 453 " pdb=" CA LEU C 453 " ideal model delta harmonic sigma weight residual 180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA GLU A 270 " pdb=" C GLU A 270 " pdb=" N ILE A 271 " pdb=" CA ILE A 271 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 11907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1568 0.027 - 0.053: 981 0.053 - 0.080: 397 0.080 - 0.106: 80 0.106 - 0.133: 34 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA PRO A 148 " pdb=" N PRO A 148 " pdb=" C PRO A 148 " pdb=" CB PRO A 148 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CB ILE A 75 " pdb=" CA ILE A 75 " pdb=" CG1 ILE A 75 " pdb=" CG2 ILE A 75 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CG LEU D 349 " pdb=" CB LEU D 349 " pdb=" CD1 LEU D 349 " pdb=" CD2 LEU D 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 3057 not shown) Planarity restraints: 3315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 258 " 0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO C 259 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 259 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 259 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 160 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO A 161 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 454 " 0.033 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO B 455 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 455 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 455 " 0.029 5.00e-02 4.00e+02 ... (remaining 3312 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3786 2.78 - 3.31: 19764 3.31 - 3.84: 31482 3.84 - 4.37: 33985 4.37 - 4.90: 59548 Nonbonded interactions: 148565 Sorted by model distance: nonbonded pdb=" O GLU A 351 " pdb=" OG SER A 355 " model vdw 2.245 3.040 nonbonded pdb=" O LYS A 302 " pdb=" OG SER A 306 " model vdw 2.261 3.040 nonbonded pdb=" O LYS D 204 " pdb=" OG SER D 208 " model vdw 2.264 3.040 nonbonded pdb=" O SER A 61 " pdb=" OG SER A 61 " model vdw 2.278 3.040 nonbonded pdb=" O SER E 110 " pdb=" OG SER E 110 " model vdw 2.308 3.040 ... (remaining 148560 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.920 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.004 0.033 19710 Z= 0.154 Angle : 0.551 7.405 26620 Z= 0.308 Chirality : 0.039 0.133 3060 Planarity : 0.004 0.057 3315 Dihedral : 16.256 89.857 7470 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.15), residues: 2315 helix: 0.22 (0.10), residues: 2105 sheet: None (None), residues: 0 loop : -3.55 (0.34), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 126 TYR 0.010 0.001 TYR B 237 PHE 0.014 0.002 PHE A 379 TRP 0.021 0.002 TRP A 415 HIS 0.004 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00355 (19710) covalent geometry : angle 0.55105 (26620) hydrogen bonds : bond 0.15133 ( 1554) hydrogen bonds : angle 4.99941 ( 4662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 125 ASN cc_start: 0.7336 (m-40) cc_final: 0.7110 (m-40) REVERT: A 156 LEU cc_start: 0.8386 (tp) cc_final: 0.8137 (tp) REVERT: B 3 TYR cc_start: 0.6960 (t80) cc_final: 0.6655 (t80) REVERT: B 162 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 16 ILE cc_start: 0.8639 (mm) cc_final: 0.8365 (mm) REVERT: C 187 LEU cc_start: 0.8290 (tp) cc_final: 0.7931 (tt) REVERT: D 257 SER cc_start: 0.7783 (p) cc_final: 0.7335 (t) REVERT: E 89 LYS cc_start: 0.7495 (tmtt) cc_final: 0.7267 (tmtt) REVERT: E 217 LEU cc_start: 0.8387 (mt) cc_final: 0.8087 (mt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1524 time to fit residues: 87.3786 Evaluate side-chains 190 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 0.8980 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 13 ASN A 147 ASN B 125 ASN B 272 ASN C 49 ASN C 209 ASN D 13 ASN D 62 ASN D 146 ASN D 391 ASN E 49 ASN E 245 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.159141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153469 restraints weight = 22326.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153149 restraints weight = 30281.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152991 restraints weight = 25045.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152606 restraints weight = 27191.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152932 restraints weight = 22259.333| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19710 Z= 0.115 Angle : 0.509 9.988 26620 Z= 0.253 Chirality : 0.038 0.181 3060 Planarity : 0.003 0.038 3315 Dihedral : 3.788 19.036 2400 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.29 % Allowed : 8.46 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.17), residues: 2315 helix: 1.72 (0.10), residues: 2170 sheet: None (None), residues: 0 loop : -3.10 (0.41), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 143 TYR 0.015 0.001 TYR C 188 PHE 0.012 0.001 PHE D 458 TRP 0.014 0.001 TRP C 219 HIS 0.002 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00261 (19710) covalent geometry : angle 0.50933 (26620) hydrogen bonds : bond 0.03481 ( 1554) hydrogen bonds : angle 3.20279 ( 4662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 TYR cc_start: 0.6777 (t80) cc_final: 0.6541 (t80) REVERT: B 69 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6885 (mp) REVERT: B 162 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6980 (mm-30) REVERT: C 16 ILE cc_start: 0.8842 (mm) cc_final: 0.8397 (mm) REVERT: C 187 LEU cc_start: 0.8429 (tp) cc_final: 0.8148 (tt) REVERT: C 355 SER cc_start: 0.8625 (p) cc_final: 0.8418 (m) REVERT: C 452 LEU cc_start: 0.8485 (tp) cc_final: 0.8146 (tt) REVERT: D 12 GLU cc_start: 0.7240 (tp30) cc_final: 0.6947 (tp30) REVERT: D 37 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6387 (tt0) REVERT: D 67 GLU cc_start: 0.7428 (tp30) cc_final: 0.7197 (tp30) REVERT: D 114 ILE cc_start: 0.9085 (mm) cc_final: 0.8845 (mt) REVERT: D 125 ASN cc_start: 0.7733 (m-40) cc_final: 0.6276 (t0) REVERT: D 146 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.7107 (p0) REVERT: D 257 SER cc_start: 0.7697 (p) cc_final: 0.7262 (t) REVERT: E 89 LYS cc_start: 0.7678 (tmtt) cc_final: 0.7464 (tmtt) REVERT: E 200 LEU cc_start: 0.8451 (tt) cc_final: 0.7746 (mm) REVERT: E 290 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7984 (tt0) outliers start: 28 outliers final: 13 residues processed: 266 average time/residue: 0.1419 time to fit residues: 59.3174 Evaluate side-chains 191 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 463 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 194 optimal weight: 0.3980 chunk 140 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN D 392 ASN E 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144975 restraints weight = 23065.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144418 restraints weight = 31412.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144486 restraints weight = 27273.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144370 restraints weight = 24796.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144523 restraints weight = 21121.352| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19710 Z= 0.170 Angle : 0.568 8.678 26620 Z= 0.280 Chirality : 0.040 0.178 3060 Planarity : 0.003 0.035 3315 Dihedral : 3.818 21.159 2400 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.61 % Allowed : 12.18 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.17), residues: 2315 helix: 2.02 (0.11), residues: 2170 sheet: None (None), residues: 0 loop : -2.85 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.010 0.001 TYR A 249 PHE 0.018 0.002 PHE B 66 TRP 0.018 0.001 TRP D 384 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00419 (19710) covalent geometry : angle 0.56818 (26620) hydrogen bonds : bond 0.04032 ( 1554) hydrogen bonds : angle 3.31620 ( 4662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: B 69 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6819 (mp) REVERT: B 162 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6978 (mm-30) REVERT: B 272 ASN cc_start: 0.6695 (m-40) cc_final: 0.6453 (t0) REVERT: C 16 ILE cc_start: 0.9014 (mm) cc_final: 0.8500 (mm) REVERT: C 355 SER cc_start: 0.8702 (p) cc_final: 0.8444 (m) REVERT: D 125 ASN cc_start: 0.7842 (m-40) cc_final: 0.6395 (t0) REVERT: D 143 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7655 (ttm170) REVERT: D 146 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.7112 (p0) REVERT: E 89 LYS cc_start: 0.7650 (tmtt) cc_final: 0.7320 (tmtt) REVERT: E 123 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6855 (tm-30) REVERT: E 200 LEU cc_start: 0.8475 (tt) cc_final: 0.7937 (mm) outliers start: 35 outliers final: 22 residues processed: 223 average time/residue: 0.1451 time to fit residues: 50.6396 Evaluate side-chains 178 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN D 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.153846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147214 restraints weight = 22737.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146541 restraints weight = 33472.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146808 restraints weight = 29578.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147220 restraints weight = 25454.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147239 restraints weight = 21046.871| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19710 Z= 0.118 Angle : 0.477 9.630 26620 Z= 0.234 Chirality : 0.037 0.149 3060 Planarity : 0.003 0.033 3315 Dihedral : 3.572 19.063 2400 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.75 % Allowed : 13.66 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.11 (0.17), residues: 2315 helix: 2.35 (0.10), residues: 2175 sheet: None (None), residues: 0 loop : -3.10 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 143 TYR 0.017 0.001 TYR E 3 PHE 0.009 0.001 PHE D 213 TRP 0.012 0.001 TRP D 384 HIS 0.002 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00285 (19710) covalent geometry : angle 0.47665 (26620) hydrogen bonds : bond 0.03133 ( 1554) hydrogen bonds : angle 2.90802 ( 4662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6732 (mp) REVERT: B 344 MET cc_start: 0.6828 (tpp) cc_final: 0.6585 (tpt) REVERT: C 16 ILE cc_start: 0.8967 (mm) cc_final: 0.8427 (mm) REVERT: C 208 SER cc_start: 0.8505 (p) cc_final: 0.8142 (m) REVERT: C 355 SER cc_start: 0.8683 (p) cc_final: 0.8472 (m) REVERT: D 37 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6448 (tt0) REVERT: D 143 ARG cc_start: 0.7999 (tpp80) cc_final: 0.7721 (ttm170) REVERT: D 146 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7177 (p0) REVERT: E 89 LYS cc_start: 0.7622 (tmtt) cc_final: 0.7302 (tmtt) REVERT: E 123 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6947 (tm-30) REVERT: E 200 LEU cc_start: 0.8505 (tt) cc_final: 0.7911 (mm) REVERT: E 290 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8126 (tt0) REVERT: E 344 MET cc_start: 0.5276 (tpp) cc_final: 0.4909 (tpp) outliers start: 38 outliers final: 23 residues processed: 206 average time/residue: 0.1412 time to fit residues: 46.2341 Evaluate side-chains 179 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 14 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 chunk 39 optimal weight: 0.0570 chunk 134 optimal weight: 0.0470 chunk 180 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN D 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151915 restraints weight = 22160.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151315 restraints weight = 33074.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151787 restraints weight = 29324.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151821 restraints weight = 22155.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152060 restraints weight = 19467.871| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19710 Z= 0.087 Angle : 0.434 8.661 26620 Z= 0.212 Chirality : 0.036 0.136 3060 Planarity : 0.002 0.032 3315 Dihedral : 3.287 16.038 2400 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.38 % Allowed : 14.76 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.70 (0.17), residues: 2315 helix: 2.73 (0.10), residues: 2165 sheet: None (None), residues: 0 loop : -2.61 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 143 TYR 0.010 0.001 TYR E 3 PHE 0.009 0.001 PHE A 25 TRP 0.008 0.001 TRP D 219 HIS 0.001 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00190 (19710) covalent geometry : angle 0.43354 (26620) hydrogen bonds : bond 0.02493 ( 1554) hydrogen bonds : angle 2.54841 ( 4662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: B 69 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6431 (mp) REVERT: B 316 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6271 (tm-30) REVERT: B 352 LEU cc_start: 0.8161 (tp) cc_final: 0.7847 (tt) REVERT: B 393 MET cc_start: 0.7090 (mmm) cc_final: 0.6698 (mmt) REVERT: C 16 ILE cc_start: 0.8975 (mm) cc_final: 0.8407 (mm) REVERT: C 72 TRP cc_start: 0.7523 (OUTLIER) cc_final: 0.6722 (m-90) REVERT: C 102 LEU cc_start: 0.7847 (mp) cc_final: 0.7436 (tt) REVERT: C 143 ARG cc_start: 0.7310 (tpt-90) cc_final: 0.7082 (ttm170) REVERT: D 37 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6570 (tt0) REVERT: D 125 ASN cc_start: 0.7871 (m-40) cc_final: 0.6301 (t0) REVERT: E 89 LYS cc_start: 0.7568 (tmtt) cc_final: 0.7284 (tmtt) REVERT: E 123 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6951 (tm-30) REVERT: E 143 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7308 (ttt90) REVERT: E 200 LEU cc_start: 0.8508 (tt) cc_final: 0.7644 (mm) REVERT: E 290 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7987 (tt0) outliers start: 30 outliers final: 19 residues processed: 211 average time/residue: 0.1387 time to fit residues: 46.4823 Evaluate side-chains 177 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 72 TRP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 120 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.156727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149909 restraints weight = 22181.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.149197 restraints weight = 29699.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149456 restraints weight = 28571.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149715 restraints weight = 24282.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149753 restraints weight = 20966.448| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19710 Z= 0.096 Angle : 0.456 10.945 26620 Z= 0.219 Chirality : 0.036 0.136 3060 Planarity : 0.002 0.029 3315 Dihedral : 3.184 15.371 2400 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.98 % Allowed : 14.99 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.84 (0.17), residues: 2315 helix: 2.84 (0.10), residues: 2170 sheet: None (None), residues: 0 loop : -3.01 (0.45), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 143 TYR 0.008 0.001 TYR A 249 PHE 0.019 0.001 PHE E 458 TRP 0.009 0.001 TRP D 219 HIS 0.002 0.000 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00225 (19710) covalent geometry : angle 0.45551 (26620) hydrogen bonds : bond 0.02621 ( 1554) hydrogen bonds : angle 2.57461 ( 4662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: B 69 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6490 (mp) REVERT: B 393 MET cc_start: 0.7136 (mmm) cc_final: 0.6751 (mmt) REVERT: C 16 ILE cc_start: 0.8988 (mm) cc_final: 0.8408 (mm) REVERT: C 72 TRP cc_start: 0.7597 (OUTLIER) cc_final: 0.6737 (m-90) REVERT: C 208 SER cc_start: 0.8510 (p) cc_final: 0.8148 (m) REVERT: D 37 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6521 (tt0) REVERT: D 125 ASN cc_start: 0.7806 (m-40) cc_final: 0.6261 (t0) REVERT: D 143 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7704 (ttm170) REVERT: E 89 LYS cc_start: 0.7623 (tmtt) cc_final: 0.7335 (tmtt) REVERT: E 123 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6878 (tm-30) REVERT: E 143 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7454 (ttt90) REVERT: E 200 LEU cc_start: 0.8518 (tt) cc_final: 0.7950 (mm) REVERT: E 290 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8000 (tt0) outliers start: 43 outliers final: 28 residues processed: 202 average time/residue: 0.1365 time to fit residues: 43.8085 Evaluate side-chains 183 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 72 TRP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 93 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN D 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149483 restraints weight = 22505.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149219 restraints weight = 31010.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149561 restraints weight = 27024.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149234 restraints weight = 21780.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149307 restraints weight = 22506.653| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19710 Z= 0.105 Angle : 0.474 10.695 26620 Z= 0.226 Chirality : 0.036 0.139 3060 Planarity : 0.002 0.027 3315 Dihedral : 3.177 15.150 2400 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.93 % Allowed : 15.49 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.91 (0.17), residues: 2315 helix: 2.89 (0.10), residues: 2170 sheet: None (None), residues: 0 loop : -3.00 (0.45), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 143 TYR 0.008 0.001 TYR A 249 PHE 0.020 0.001 PHE A 25 TRP 0.009 0.001 TRP D 219 HIS 0.002 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00250 (19710) covalent geometry : angle 0.47400 (26620) hydrogen bonds : bond 0.02710 ( 1554) hydrogen bonds : angle 2.59379 ( 4662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.797 Fit side-chains REVERT: B 69 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6624 (mp) REVERT: B 393 MET cc_start: 0.7237 (mmm) cc_final: 0.6878 (mmt) REVERT: C 16 ILE cc_start: 0.9001 (mm) cc_final: 0.8385 (mm) REVERT: C 72 TRP cc_start: 0.7560 (OUTLIER) cc_final: 0.6633 (m-90) REVERT: C 208 SER cc_start: 0.8532 (p) cc_final: 0.8231 (m) REVERT: C 305 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8722 (mt) REVERT: D 37 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6560 (tt0) REVERT: D 125 ASN cc_start: 0.7809 (m-40) cc_final: 0.6246 (t0) REVERT: D 143 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7692 (ttm170) REVERT: E 89 LYS cc_start: 0.7717 (tmtt) cc_final: 0.7407 (tmtt) REVERT: E 123 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6931 (tm-30) REVERT: E 149 LYS cc_start: 0.7119 (mttt) cc_final: 0.6914 (mttp) REVERT: E 200 LEU cc_start: 0.8560 (tt) cc_final: 0.7951 (mm) REVERT: E 290 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7976 (tt0) outliers start: 42 outliers final: 33 residues processed: 194 average time/residue: 0.1283 time to fit residues: 39.9715 Evaluate side-chains 188 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 72 TRP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 88 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN C 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147293 restraints weight = 22531.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145894 restraints weight = 31109.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145152 restraints weight = 25759.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145361 restraints weight = 25504.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145632 restraints weight = 21415.456| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19710 Z= 0.127 Angle : 0.509 10.601 26620 Z= 0.242 Chirality : 0.037 0.153 3060 Planarity : 0.002 0.026 3315 Dihedral : 3.281 17.009 2400 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.21 % Allowed : 15.68 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.89 (0.17), residues: 2315 helix: 2.85 (0.10), residues: 2165 sheet: None (None), residues: 0 loop : -2.48 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 143 TYR 0.009 0.001 TYR C 188 PHE 0.011 0.001 PHE C 280 TRP 0.012 0.001 TRP D 219 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00312 (19710) covalent geometry : angle 0.50936 (26620) hydrogen bonds : bond 0.03075 ( 1554) hydrogen bonds : angle 2.75479 ( 4662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: B 69 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6690 (mp) REVERT: B 393 MET cc_start: 0.7351 (mmm) cc_final: 0.7005 (mmt) REVERT: C 16 ILE cc_start: 0.8976 (mm) cc_final: 0.8383 (mm) REVERT: C 72 TRP cc_start: 0.7608 (OUTLIER) cc_final: 0.6536 (m-90) REVERT: C 208 SER cc_start: 0.8534 (p) cc_final: 0.8272 (m) REVERT: D 125 ASN cc_start: 0.7903 (m-40) cc_final: 0.6277 (t0) REVERT: D 143 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7726 (ttm170) REVERT: D 217 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8303 (mm) REVERT: D 303 LEU cc_start: 0.8297 (tt) cc_final: 0.8091 (tp) REVERT: E 89 LYS cc_start: 0.7740 (tmtt) cc_final: 0.7368 (tmtt) REVERT: E 123 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6997 (tm-30) REVERT: E 143 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7585 (ttt90) REVERT: E 149 LYS cc_start: 0.7191 (mttt) cc_final: 0.6963 (mttp) REVERT: E 290 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8026 (tt0) REVERT: E 344 MET cc_start: 0.4897 (tpp) cc_final: 0.4683 (tpt) outliers start: 48 outliers final: 34 residues processed: 193 average time/residue: 0.1308 time to fit residues: 40.6307 Evaluate side-chains 183 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 72 TRP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 165 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 97 optimal weight: 0.0050 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.156729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150768 restraints weight = 22068.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149501 restraints weight = 28788.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.148664 restraints weight = 26962.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148729 restraints weight = 25262.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148926 restraints weight = 21880.781| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 19710 Z= 0.094 Angle : 0.477 10.684 26620 Z= 0.226 Chirality : 0.036 0.153 3060 Planarity : 0.002 0.027 3315 Dihedral : 3.115 16.128 2400 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.75 % Allowed : 16.51 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.08 (0.17), residues: 2315 helix: 3.00 (0.10), residues: 2160 sheet: None (None), residues: 0 loop : -2.59 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 143 TYR 0.010 0.001 TYR D 249 PHE 0.011 0.001 PHE D 213 TRP 0.010 0.001 TRP D 219 HIS 0.001 0.000 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00222 (19710) covalent geometry : angle 0.47722 (26620) hydrogen bonds : bond 0.02518 ( 1554) hydrogen bonds : angle 2.49520 ( 4662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.6936 (tp30) cc_final: 0.6691 (tp30) REVERT: A 53 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8292 (mt) REVERT: A 125 ASN cc_start: 0.6947 (m110) cc_final: 0.5648 (t0) REVERT: B 69 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6695 (mp) REVERT: B 352 LEU cc_start: 0.8113 (tp) cc_final: 0.7653 (tt) REVERT: B 393 MET cc_start: 0.7278 (mmm) cc_final: 0.6940 (mmt) REVERT: C 16 ILE cc_start: 0.8926 (mm) cc_final: 0.8292 (mm) REVERT: C 50 MET cc_start: 0.6861 (mmm) cc_final: 0.4832 (ttt) REVERT: C 72 TRP cc_start: 0.7563 (OUTLIER) cc_final: 0.6563 (m-90) REVERT: C 208 SER cc_start: 0.8542 (p) cc_final: 0.8247 (m) REVERT: C 464 GLU cc_start: 0.6143 (tp30) cc_final: 0.5904 (mt-10) REVERT: D 37 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6477 (tt0) REVERT: D 143 ARG cc_start: 0.8016 (tpp80) cc_final: 0.7679 (ttm170) REVERT: E 89 LYS cc_start: 0.7649 (tmtt) cc_final: 0.7340 (tmtt) REVERT: E 123 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6929 (tm-30) REVERT: E 143 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7583 (ttt90) REVERT: E 290 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7962 (tt0) outliers start: 38 outliers final: 30 residues processed: 199 average time/residue: 0.1350 time to fit residues: 43.3273 Evaluate side-chains 182 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 72 TRP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 217 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150111 restraints weight = 22259.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149292 restraints weight = 31895.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149195 restraints weight = 27741.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149185 restraints weight = 25623.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149351 restraints weight = 21322.317| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 19710 Z= 0.104 Angle : 0.493 10.828 26620 Z= 0.236 Chirality : 0.036 0.159 3060 Planarity : 0.002 0.026 3315 Dihedral : 3.113 15.964 2400 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 17.06 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.13 (0.17), residues: 2315 helix: 3.03 (0.10), residues: 2160 sheet: None (None), residues: 0 loop : -2.57 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 143 TYR 0.010 0.001 TYR D 249 PHE 0.013 0.001 PHE D 213 TRP 0.010 0.001 TRP D 219 HIS 0.002 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00249 (19710) covalent geometry : angle 0.49250 (26620) hydrogen bonds : bond 0.02620 ( 1554) hydrogen bonds : angle 2.53045 ( 4662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.6911 (tp30) cc_final: 0.6703 (tp30) REVERT: A 53 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8381 (mt) REVERT: A 125 ASN cc_start: 0.6914 (m110) cc_final: 0.5679 (t0) REVERT: B 69 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6576 (mp) REVERT: B 393 MET cc_start: 0.7305 (mmm) cc_final: 0.6948 (mmt) REVERT: C 16 ILE cc_start: 0.8939 (mm) cc_final: 0.8281 (mm) REVERT: C 72 TRP cc_start: 0.7593 (OUTLIER) cc_final: 0.6566 (m-90) REVERT: C 208 SER cc_start: 0.8488 (p) cc_final: 0.8216 (m) REVERT: C 461 LEU cc_start: 0.8804 (tp) cc_final: 0.8534 (tp) REVERT: C 464 GLU cc_start: 0.6166 (tp30) cc_final: 0.5965 (mt-10) REVERT: D 37 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6475 (tt0) REVERT: D 143 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7698 (ttm170) REVERT: D 217 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8245 (mm) REVERT: E 89 LYS cc_start: 0.7666 (tmtt) cc_final: 0.7340 (tmtt) REVERT: E 123 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6901 (tm-30) REVERT: E 143 ARG cc_start: 0.8130 (tpp80) cc_final: 0.7580 (ttt90) REVERT: E 290 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7951 (tt0) outliers start: 37 outliers final: 30 residues processed: 187 average time/residue: 0.1291 time to fit residues: 38.9839 Evaluate side-chains 188 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 72 TRP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 431 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 0.0670 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 ASN C 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151553 restraints weight = 22218.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.151268 restraints weight = 28258.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.151172 restraints weight = 26564.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150952 restraints weight = 25503.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151159 restraints weight = 22101.217| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19710 Z= 0.097 Angle : 0.489 10.743 26620 Z= 0.232 Chirality : 0.036 0.170 3060 Planarity : 0.002 0.027 3315 Dihedral : 3.074 15.598 2400 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.75 % Allowed : 17.10 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.20 (0.17), residues: 2315 helix: 3.07 (0.10), residues: 2160 sheet: None (None), residues: 0 loop : -2.56 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.010 0.001 TYR D 249 PHE 0.018 0.001 PHE B 66 TRP 0.009 0.001 TRP D 219 HIS 0.002 0.000 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00229 (19710) covalent geometry : angle 0.48898 (26620) hydrogen bonds : bond 0.02515 ( 1554) hydrogen bonds : angle 2.47437 ( 4662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.32 seconds wall clock time: 43 minutes 32.14 seconds (2612.14 seconds total)