Starting phenix.real_space_refine on Mon Jun 16 18:56:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8i_29856/06_2025/8g8i_29856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8i_29856/06_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_29856/06_2025/8g8i_29856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8i_29856/06_2025/8g8i_29856.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8i_29856/06_2025/8g8i_29856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8i_29856/06_2025/8g8i_29856.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.90, per 1000 atoms: 0.62 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: 5.03 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.04 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: 6.14 Time building geometry restraints manager: 5.80 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: 0.04 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: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 43.920 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.760 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (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 TRP 0.021 0.002 TRP A 415 HIS 0.004 0.001 HIS A 397 PHE 0.014 0.002 PHE A 379 TYR 0.010 0.001 TYR B 237 ARG 0.003 0.000 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.15133 ( 1554) hydrogen bonds : angle 4.99941 ( 4662) covalent geometry : bond 0.00355 (19710) covalent geometry : angle 0.55105 (26620) *********************** 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 : 2.110 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: 0.3215 time to fit residues: 183.1279 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 : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 147 ASN B 125 ASN B 272 ASN C 49 ASN C 209 ASN D 13 ASN D 146 ASN D 209 ASN D 391 ASN E 49 ASN E 321 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145909 restraints weight = 22845.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145502 restraints weight = 36431.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145853 restraints weight = 31427.632| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19710 Z= 0.172 Angle : 0.590 9.983 26620 Z= 0.293 Chirality : 0.040 0.178 3060 Planarity : 0.004 0.039 3315 Dihedral : 4.027 22.257 2400 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.56 % Allowed : 9.66 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.17), residues: 2315 helix: 1.51 (0.10), residues: 2165 sheet: None (None), residues: 0 loop : -3.34 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 219 HIS 0.003 0.001 HIS A 368 PHE 0.013 0.001 PHE D 213 TYR 0.017 0.001 TYR C 188 ARG 0.004 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 1554) hydrogen bonds : angle 3.50782 ( 4662) covalent geometry : bond 0.00424 (19710) covalent geometry : angle 0.59007 (26620) *********************** 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 261 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 2.197 Fit side-chains REVERT: B 3 TYR cc_start: 0.6762 (t80) cc_final: 0.6526 (t80) REVERT: B 69 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6894 (mp) REVERT: B 162 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6991 (mm-30) REVERT: C 16 ILE cc_start: 0.8922 (mm) cc_final: 0.8470 (mm) REVERT: C 355 SER cc_start: 0.8653 (p) cc_final: 0.8416 (m) REVERT: C 452 LEU cc_start: 0.8528 (tp) cc_final: 0.8221 (tt) REVERT: C 459 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8290 (tt0) REVERT: D 12 GLU cc_start: 0.7233 (tp30) cc_final: 0.6981 (tp30) REVERT: D 114 ILE cc_start: 0.9070 (mm) cc_final: 0.8860 (mt) REVERT: D 125 ASN cc_start: 0.7797 (m-40) cc_final: 0.6376 (t0) REVERT: D 146 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7101 (p0) REVERT: D 257 SER cc_start: 0.7683 (p) cc_final: 0.7290 (t) REVERT: E 89 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7425 (tmtt) REVERT: E 200 LEU cc_start: 0.8493 (tt) cc_final: 0.7921 (mm) REVERT: E 290 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8023 (tt0) outliers start: 34 outliers final: 19 residues processed: 252 average time/residue: 0.2961 time to fit residues: 117.6018 Evaluate side-chains 186 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 2.131 ------------------------------------------------------------------------------- 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 C residue 70 LEU Chi-restraints excluded: chain C residue 382 ILE 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 374 VAL 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 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 165 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 176 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN B 272 ASN D 294 ASN D 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144491 restraints weight = 22616.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143808 restraints weight = 30014.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.144067 restraints weight = 27910.534| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19710 Z= 0.146 Angle : 0.519 8.567 26620 Z= 0.257 Chirality : 0.038 0.137 3060 Planarity : 0.003 0.036 3315 Dihedral : 3.790 20.913 2400 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.56 % Allowed : 13.15 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.17), residues: 2315 helix: 2.00 (0.11), residues: 2170 sheet: None (None), residues: 0 loop : -3.10 (0.41), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 384 HIS 0.003 0.001 HIS B 368 PHE 0.014 0.001 PHE E 458 TYR 0.012 0.001 TYR A 249 ARG 0.004 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 1554) hydrogen bonds : angle 3.18380 ( 4662) covalent geometry : bond 0.00357 (19710) covalent geometry : angle 0.51916 (26620) *********************** 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 229 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 2.203 Fit side-chains REVERT: B 69 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6838 (mp) REVERT: B 162 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6989 (mm-30) REVERT: C 16 ILE cc_start: 0.8963 (mm) cc_final: 0.8433 (mm) REVERT: C 208 SER cc_start: 0.8530 (p) cc_final: 0.8162 (m) REVERT: C 355 SER cc_start: 0.8747 (p) cc_final: 0.8523 (m) REVERT: D 37 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6410 (tt0) REVERT: D 114 ILE cc_start: 0.9065 (mm) cc_final: 0.8861 (mt) REVERT: D 125 ASN cc_start: 0.7967 (m-40) cc_final: 0.6472 (t0) REVERT: D 143 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7636 (ttm170) REVERT: D 146 ASN cc_start: 0.7390 (OUTLIER) cc_final: 0.7035 (p0) REVERT: E 89 LYS cc_start: 0.7668 (tmtt) cc_final: 0.7373 (tmtt) REVERT: E 123 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6675 (tm-30) REVERT: E 200 LEU cc_start: 0.8519 (tt) cc_final: 0.7857 (mm) outliers start: 34 outliers final: 21 residues processed: 221 average time/residue: 0.2871 time to fit residues: 100.6051 Evaluate side-chains 182 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 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 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 D residue 146 ASN Chi-restraints excluded: chain D residue 207 LEU 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 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 210 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN B 272 ASN D 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148397 restraints weight = 22648.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146871 restraints weight = 30349.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145609 restraints weight = 30446.517| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19710 Z= 0.107 Angle : 0.462 9.471 26620 Z= 0.226 Chirality : 0.037 0.175 3060 Planarity : 0.003 0.033 3315 Dihedral : 3.500 18.165 2400 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.61 % Allowed : 14.11 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.17), residues: 2315 helix: 2.39 (0.10), residues: 2175 sheet: None (None), residues: 0 loop : -3.18 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 219 HIS 0.003 0.001 HIS A 368 PHE 0.008 0.001 PHE B 164 TYR 0.017 0.001 TYR E 3 ARG 0.003 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 1554) hydrogen bonds : angle 2.81216 ( 4662) covalent geometry : bond 0.00253 (19710) covalent geometry : angle 0.46241 (26620) *********************** 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 212 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 2.174 Fit side-chains REVERT: B 69 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6821 (mp) REVERT: B 352 LEU cc_start: 0.8145 (tp) cc_final: 0.7810 (tt) REVERT: C 16 ILE cc_start: 0.8977 (mm) cc_final: 0.8441 (mm) REVERT: C 208 SER cc_start: 0.8600 (p) cc_final: 0.8211 (m) REVERT: D 37 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6471 (tt0) REVERT: D 143 ARG cc_start: 0.7941 (tpp80) cc_final: 0.7672 (ttm170) REVERT: D 146 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.7162 (p0) REVERT: E 89 LYS cc_start: 0.7683 (tmtt) cc_final: 0.7374 (tmtt) REVERT: E 123 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6599 (tm-30) REVERT: E 143 ARG cc_start: 0.7408 (tpt-90) cc_final: 0.7094 (ttt90) REVERT: E 200 LEU cc_start: 0.8485 (tt) cc_final: 0.7605 (mm) REVERT: E 344 MET cc_start: 0.5281 (tpp) cc_final: 0.5052 (tpp) outliers start: 35 outliers final: 23 residues processed: 203 average time/residue: 0.3018 time to fit residues: 96.6667 Evaluate side-chains 175 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 431 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 386 VAL 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 382 ILE 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 354 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 79 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN B 272 ASN D 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147105 restraints weight = 22643.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146724 restraints weight = 31439.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146525 restraints weight = 28230.056| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19710 Z= 0.115 Angle : 0.471 10.808 26620 Z= 0.229 Chirality : 0.037 0.148 3060 Planarity : 0.002 0.031 3315 Dihedral : 3.428 17.587 2400 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.98 % Allowed : 14.76 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.17), residues: 2315 helix: 2.59 (0.10), residues: 2165 sheet: None (None), residues: 0 loop : -2.80 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 219 HIS 0.002 0.001 HIS A 368 PHE 0.009 0.001 PHE A 25 TYR 0.013 0.001 TYR E 3 ARG 0.004 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 1554) hydrogen bonds : angle 2.79746 ( 4662) covalent geometry : bond 0.00277 (19710) covalent geometry : angle 0.47113 (26620) *********************** 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 207 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 2.152 Fit side-chains revert: symmetry clash REVERT: B 69 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6655 (mp) REVERT: C 16 ILE cc_start: 0.9004 (mm) cc_final: 0.8437 (mm) REVERT: C 208 SER cc_start: 0.8501 (p) cc_final: 0.8192 (m) REVERT: D 125 ASN cc_start: 0.7936 (m-40) cc_final: 0.6420 (t0) REVERT: D 146 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.7044 (p0) REVERT: E 89 LYS cc_start: 0.7695 (tmtt) cc_final: 0.7366 (tmtt) REVERT: E 123 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6605 (tm-30) REVERT: E 200 LEU cc_start: 0.8537 (tt) cc_final: 0.7956 (mm) outliers start: 43 outliers final: 29 residues processed: 197 average time/residue: 0.3003 time to fit residues: 95.2313 Evaluate side-chains 180 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 2.462 ------------------------------------------------------------------------------- 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 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 382 ILE Chi-restraints excluded: chain B residue 386 VAL 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 382 ILE Chi-restraints excluded: chain C residue 393 MET 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 332 VAL Chi-restraints excluded: chain D residue 354 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 143 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 223 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.154625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148978 restraints weight = 22637.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147366 restraints weight = 30049.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.146132 restraints weight = 31316.625| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3405 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= 0.097 Angle : 0.451 10.559 26620 Z= 0.218 Chirality : 0.036 0.141 3060 Planarity : 0.002 0.029 3315 Dihedral : 3.297 16.033 2400 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.84 % Allowed : 15.54 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.17), residues: 2315 helix: 2.78 (0.10), residues: 2165 sheet: None (None), residues: 0 loop : -2.66 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 219 HIS 0.002 0.000 HIS A 368 PHE 0.019 0.001 PHE E 458 TYR 0.010 0.001 TYR E 3 ARG 0.005 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.02708 ( 1554) hydrogen bonds : angle 2.62603 ( 4662) covalent geometry : bond 0.00227 (19710) covalent geometry : angle 0.45060 (26620) *********************** 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 211 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 2.468 Fit side-chains REVERT: B 69 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6835 (mp) REVERT: B 352 LEU cc_start: 0.8163 (tp) cc_final: 0.7822 (tt) REVERT: B 393 MET cc_start: 0.7031 (mmm) cc_final: 0.6726 (mmt) REVERT: C 16 ILE cc_start: 0.8968 (mm) cc_final: 0.8396 (mm) REVERT: C 208 SER cc_start: 0.8590 (p) cc_final: 0.8275 (m) REVERT: C 461 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8539 (tp) REVERT: D 37 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6485 (tt0) REVERT: D 125 ASN cc_start: 0.7894 (m-40) cc_final: 0.6375 (t0) REVERT: D 143 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7764 (ttm170) REVERT: E 89 LYS cc_start: 0.7705 (tmtt) cc_final: 0.7405 (tmtt) REVERT: E 123 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6586 (tm-30) REVERT: E 200 LEU cc_start: 0.8533 (tt) cc_final: 0.7909 (mm) outliers start: 40 outliers final: 29 residues processed: 199 average time/residue: 0.3543 time to fit residues: 114.0046 Evaluate side-chains 182 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 2.442 ------------------------------------------------------------------------------- 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 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 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 72 TRP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 354 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 186 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 115 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 93 optimal weight: 0.0040 chunk 210 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 E 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.155515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.148573 restraints weight = 22272.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147726 restraints weight = 31022.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.148107 restraints weight = 28758.451| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19710 Z= 0.096 Angle : 0.459 10.782 26620 Z= 0.222 Chirality : 0.036 0.142 3060 Planarity : 0.002 0.027 3315 Dihedral : 3.199 15.188 2400 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.07 % Allowed : 16.14 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.17), residues: 2315 helix: 2.90 (0.10), residues: 2165 sheet: None (None), residues: 0 loop : -2.53 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 219 HIS 0.001 0.000 HIS A 368 PHE 0.015 0.001 PHE A 25 TYR 0.017 0.001 TYR C 188 ARG 0.004 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.02600 ( 1554) hydrogen bonds : angle 2.55230 ( 4662) covalent geometry : bond 0.00223 (19710) covalent geometry : angle 0.45870 (26620) *********************** 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 214 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 3.222 Fit side-chains REVERT: B 8 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7567 (tm-30) REVERT: B 69 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6840 (mp) REVERT: B 393 MET cc_start: 0.7045 (mmm) cc_final: 0.6759 (mmt) REVERT: C 16 ILE cc_start: 0.8980 (mm) cc_final: 0.8377 (mm) REVERT: C 208 SER cc_start: 0.8561 (p) cc_final: 0.8253 (m) REVERT: C 461 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8466 (tp) REVERT: D 37 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6498 (tt0) REVERT: D 143 ARG cc_start: 0.8045 (tpp80) cc_final: 0.7636 (ttm170) REVERT: E 89 LYS cc_start: 0.7650 (tmtt) cc_final: 0.7343 (tmtt) REVERT: E 123 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6531 (tm-30) REVERT: E 143 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7567 (ttt90) REVERT: E 200 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.7940 (mm) outliers start: 45 outliers final: 34 residues processed: 199 average time/residue: 0.3466 time to fit residues: 110.5102 Evaluate side-chains 199 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 2.725 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 381 VAL 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 200 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 LEU 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 C residue 461 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 354 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 186 LEU Chi-restraints excluded: chain E residue 200 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 9 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 ASN C 391 ASN D 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145219 restraints weight = 22696.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145249 restraints weight = 27856.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145287 restraints weight = 25734.204| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19710 Z= 0.154 Angle : 0.537 10.744 26620 Z= 0.260 Chirality : 0.038 0.140 3060 Planarity : 0.003 0.026 3315 Dihedral : 3.421 18.276 2400 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.21 % Allowed : 16.74 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.17), residues: 2315 helix: 2.79 (0.10), residues: 2160 sheet: None (None), residues: 0 loop : -2.68 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 219 HIS 0.003 0.001 HIS A 368 PHE 0.012 0.001 PHE C 280 TYR 0.009 0.001 TYR E 3 ARG 0.005 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 1554) hydrogen bonds : angle 2.90287 ( 4662) covalent geometry : bond 0.00384 (19710) covalent geometry : angle 0.53727 (26620) *********************** 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 204 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 2.432 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.6855 (tp30) cc_final: 0.6636 (tp30) REVERT: A 125 ASN cc_start: 0.7225 (m-40) cc_final: 0.5929 (t0) REVERT: B 8 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 69 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6820 (mp) REVERT: B 393 MET cc_start: 0.7109 (mmm) cc_final: 0.6787 (mmt) REVERT: C 16 ILE cc_start: 0.9011 (mm) cc_final: 0.8408 (mm) REVERT: C 208 SER cc_start: 0.8525 (p) cc_final: 0.8297 (m) REVERT: C 461 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8645 (tp) REVERT: D 37 GLU cc_start: 0.7477 (tm-30) cc_final: 0.6585 (tt0) REVERT: D 125 ASN cc_start: 0.7979 (m-40) cc_final: 0.6498 (t0) REVERT: D 143 ARG cc_start: 0.8037 (tpp80) cc_final: 0.7678 (ttm170) REVERT: E 89 LYS cc_start: 0.7730 (tmtt) cc_final: 0.7364 (tmtt) REVERT: E 123 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6693 (tm-30) REVERT: E 143 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7583 (ttt90) REVERT: E 149 LYS cc_start: 0.7163 (mttt) cc_final: 0.6917 (mttp) outliers start: 48 outliers final: 41 residues processed: 194 average time/residue: 0.3247 time to fit residues: 99.8911 Evaluate side-chains 188 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 2.405 ------------------------------------------------------------------------------- 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 185 VAL 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 381 VAL 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 136 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 VAL 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 C residue 461 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 332 VAL 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 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 179 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 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 = 0.3785 r_free = 0.3785 target = 0.155299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.149334 restraints weight = 22323.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.147326 restraints weight = 29381.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.146561 restraints weight = 32279.512| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 19710 Z= 0.097 Angle : 0.480 10.928 26620 Z= 0.231 Chirality : 0.036 0.146 3060 Planarity : 0.002 0.028 3315 Dihedral : 3.219 16.860 2400 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.98 % Allowed : 17.24 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.17), residues: 2315 helix: 2.97 (0.10), residues: 2160 sheet: None (None), residues: 0 loop : -2.69 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 219 HIS 0.002 0.000 HIS B 368 PHE 0.013 0.001 PHE D 427 TYR 0.012 0.001 TYR D 249 ARG 0.004 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.02628 ( 1554) hydrogen bonds : angle 2.57208 ( 4662) covalent geometry : bond 0.00226 (19710) covalent geometry : angle 0.48046 (26620) *********************** 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 208 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 2.939 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.6955 (tp30) cc_final: 0.6737 (tp30) REVERT: A 125 ASN cc_start: 0.7108 (m-40) cc_final: 0.5754 (t0) REVERT: B 12 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6667 (mt-10) REVERT: B 69 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6884 (mp) REVERT: B 352 LEU cc_start: 0.8149 (tp) cc_final: 0.7761 (tt) REVERT: B 393 MET cc_start: 0.7107 (mmm) cc_final: 0.6819 (mmt) REVERT: C 16 ILE cc_start: 0.8947 (mm) cc_final: 0.8329 (mm) REVERT: C 208 SER cc_start: 0.8552 (p) cc_final: 0.8286 (m) REVERT: C 461 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8364 (tp) REVERT: D 37 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6528 (tt0) REVERT: E 89 LYS cc_start: 0.7721 (tmtt) cc_final: 0.7401 (tmtt) REVERT: E 123 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6605 (tm-30) REVERT: E 143 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7596 (ttt90) outliers start: 43 outliers final: 35 residues processed: 198 average time/residue: 0.3236 time to fit residues: 103.1046 Evaluate side-chains 184 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 2.212 ------------------------------------------------------------------------------- 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 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 381 VAL 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 72 TRP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 332 VAL 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 186 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 210 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 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 = 0.3783 r_free = 0.3783 target = 0.155102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149175 restraints weight = 22380.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 81)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.147921 restraints weight = 28551.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146575 restraints weight = 30577.026| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 19710 Z= 0.104 Angle : 0.499 11.346 26620 Z= 0.238 Chirality : 0.036 0.153 3060 Planarity : 0.002 0.029 3315 Dihedral : 3.170 16.273 2400 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.93 % Allowed : 17.84 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.17), residues: 2315 helix: 3.00 (0.10), residues: 2160 sheet: None (None), residues: 0 loop : -2.71 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 219 HIS 0.002 0.001 HIS B 368 PHE 0.013 0.001 PHE D 213 TYR 0.012 0.001 TYR D 249 ARG 0.005 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.02684 ( 1554) hydrogen bonds : angle 2.56537 ( 4662) covalent geometry : bond 0.00246 (19710) covalent geometry : angle 0.49888 (26620) ********************** 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 203 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 2.249 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.6950 (tp30) cc_final: 0.6749 (tp30) REVERT: A 125 ASN cc_start: 0.7029 (m-40) cc_final: 0.5691 (t0) REVERT: B 69 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6842 (mp) REVERT: B 393 MET cc_start: 0.7111 (mmm) cc_final: 0.6836 (mmt) REVERT: C 16 ILE cc_start: 0.8946 (mm) cc_final: 0.8317 (mm) REVERT: C 50 MET cc_start: 0.6925 (mmm) cc_final: 0.4859 (ttt) REVERT: C 208 SER cc_start: 0.8545 (p) cc_final: 0.8291 (m) REVERT: D 37 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6498 (tt0) REVERT: D 143 ARG cc_start: 0.7815 (tpt-90) cc_final: 0.7290 (ttm170) REVERT: E 89 LYS cc_start: 0.7641 (tmtt) cc_final: 0.7337 (tmtt) REVERT: E 123 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6572 (tm-30) REVERT: E 143 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7630 (ttt90) outliers start: 42 outliers final: 36 residues processed: 195 average time/residue: 0.2775 time to fit residues: 87.5286 Evaluate side-chains 189 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 2.286 ------------------------------------------------------------------------------- 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 195 ASP Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 381 VAL 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 136 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 234 VAL 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 435 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 332 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 348 ASP Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 169 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 D 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149741 restraints weight = 22423.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148126 restraints weight = 31607.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147306 restraints weight = 30217.967| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 19710 Z= 0.100 Angle : 0.495 10.942 26620 Z= 0.234 Chirality : 0.036 0.175 3060 Planarity : 0.002 0.030 3315 Dihedral : 3.126 15.746 2400 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.79 % Allowed : 17.84 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.17), residues: 2315 helix: 3.05 (0.10), residues: 2160 sheet: None (None), residues: 0 loop : -2.64 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 219 HIS 0.002 0.000 HIS B 368 PHE 0.017 0.001 PHE D 213 TYR 0.012 0.001 TYR D 249 ARG 0.005 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.02604 ( 1554) hydrogen bonds : angle 2.53059 ( 4662) covalent geometry : bond 0.00238 (19710) covalent geometry : angle 0.49524 (26620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5367.26 seconds wall clock time: 96 minutes 34.89 seconds (5794.89 seconds total)