Starting phenix.real_space_refine on Fri Jun 13 03:29:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9emn_19821/06_2025/9emn_19821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9emn_19821/06_2025/9emn_19821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9emn_19821/06_2025/9emn_19821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9emn_19821/06_2025/9emn_19821.map" model { file = "/net/cci-nas-00/data/ceres_data/9emn_19821/06_2025/9emn_19821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9emn_19821/06_2025/9emn_19821.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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 76 5.16 5 C 9332 2.51 5 N 2605 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14680 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3668 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 426} Chain breaks: 4 Chain: "B" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3676 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 427} Chain breaks: 4 Chain: "C" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3668 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 426} Chain breaks: 4 Chain: "D" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3668 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 426} Chain breaks: 4 Time building chain proxies: 9.25, per 1000 atoms: 0.63 Number of scatterers: 14680 At special positions: 0 Unit cell: (109.032, 110.88, 147.84, 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 76 16.00 O 2667 8.00 N 2605 7.00 C 9332 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: 3.28 Conformation dependent library (CDL) restraints added in 2.0 seconds 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3418 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 17 sheets defined 33.3% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 31 through 37 removed outlier: 3.872A pdb=" N GLN A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 47 removed outlier: 3.573A pdb=" N ARG A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.697A pdb=" N MET A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.587A pdb=" N LEU A 112 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.518A pdb=" N LYS A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.519A pdb=" N VAL A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 259 through 267 removed outlier: 3.813A pdb=" N CYS A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 removed outlier: 3.542A pdb=" N ILE A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.673A pdb=" N LEU A 443 " --> pdb=" O HIS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 466 removed outlier: 3.522A pdb=" N VAL A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 495 through 501 removed outlier: 4.367A pdb=" N ILE A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 68 through 79 removed outlier: 3.592A pdb=" N GLY B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 79 " --> pdb=" O ARG B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 4.193A pdb=" N LYS B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 141 through 152 removed outlier: 3.684A pdb=" N GLN B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.502A pdb=" N SER B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.830A pdb=" N GLN B 191 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 192 " --> pdb=" O GLU B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 188 through 192' Processing helix chain 'B' and resid 201 through 213 removed outlier: 3.755A pdb=" N GLN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 249 through 254 removed outlier: 4.140A pdb=" N ARG B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 254' Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.512A pdb=" N LEU B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 268 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 289 removed outlier: 3.520A pdb=" N ILE B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.508A pdb=" N GLU B 323 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU B 324 " --> pdb=" O TYR B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 324' Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.849A pdb=" N HIS B 439 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 466 removed outlier: 3.722A pdb=" N VAL B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 495 through 501 removed outlier: 4.162A pdb=" N ILE B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 48 removed outlier: 3.528A pdb=" N GLU C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 79 removed outlier: 3.693A pdb=" N GLN C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET C 74 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 79 " --> pdb=" O ARG C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.667A pdb=" N ALA C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 187 removed outlier: 4.010A pdb=" N LEU C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.531A pdb=" N GLU C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 266 removed outlier: 3.867A pdb=" N GLN C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 289 removed outlier: 3.563A pdb=" N ILE C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN C 282 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 288 " --> pdb=" O LYS C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 3.803A pdb=" N GLU C 324 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 448 removed outlier: 3.943A pdb=" N CYS C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 466 removed outlier: 3.565A pdb=" N VAL C 459 " --> pdb=" O ARG C 455 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.524A pdb=" N SER C 481 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 478 through 482' Processing helix chain 'C' and resid 492 through 495 Processing helix chain 'C' and resid 496 through 501 removed outlier: 3.581A pdb=" N ASN C 500 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 501 " --> pdb=" O TRP C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 501' Processing helix chain 'D' and resid 37 through 48 Processing helix chain 'D' and resid 66 through 82 removed outlier: 3.543A pdb=" N PHE D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 114 removed outlier: 4.144A pdb=" N TYR D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D 112 " --> pdb=" O PRO D 108 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS D 113 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 114' Processing helix chain 'D' and resid 141 through 153 removed outlier: 3.726A pdb=" N GLY D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.614A pdb=" N LEU D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 200 through 213 removed outlier: 3.676A pdb=" N VAL D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 249 through 254 removed outlier: 4.038A pdb=" N ARG D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 267 removed outlier: 3.532A pdb=" N PHE D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 removed outlier: 4.362A pdb=" N GLU D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 286 " --> pdb=" O ASN D 282 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 445 removed outlier: 3.636A pdb=" N CYS D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 466 removed outlier: 3.833A pdb=" N VAL D 459 " --> pdb=" O ARG D 455 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 475 removed outlier: 3.537A pdb=" N ALA D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 removed outlier: 3.764A pdb=" N GLU D 496 " --> pdb=" O PRO D 492 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TRP D 497 " --> pdb=" O ALA D 493 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.680A pdb=" N ILE A 23 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 293 removed outlier: 7.175A pdb=" N GLN A 371 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL A 229 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 369 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE A 231 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU A 367 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 391 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 403 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 395 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 401 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 406 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.558A pdb=" N PHE A 336 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 306 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR A 485 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN A 307 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.548A pdb=" N GLY A 311 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 100 removed outlier: 8.141A pdb=" N PHE B 99 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 57 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU B 22 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N VAL B 58 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B 24 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 291 through 293 removed outlier: 7.149A pdb=" N GLN B 371 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL B 229 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA B 369 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE B 231 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU B 367 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 391 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 403 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 395 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 401 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 291 through 293 removed outlier: 7.663A pdb=" N TYR B 485 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN B 307 " --> pdb=" O TYR B 485 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AA9, first strand: chain 'C' and resid 55 through 58 removed outlier: 3.997A pdb=" N TYR C 134 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 164 " --> pdb=" O PHE C 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 292 through 293 removed outlier: 3.872A pdb=" N PHE C 336 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 306 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 292 through 293 removed outlier: 3.612A pdb=" N GLY C 358 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLN C 371 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL C 229 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA C 369 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE C 231 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU C 367 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL C 391 " --> pdb=" O ARG C 405 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 403 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 395 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 401 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 406 " --> pdb=" O VAL C 420 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AB4, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.552A pdb=" N GLY C 311 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.512A pdb=" N THR D 56 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE D 26 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR D 134 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D 164 " --> pdb=" O PHE D 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.651A pdb=" N GLY D 358 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLN D 371 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL D 229 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA D 369 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE D 231 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU D 367 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 368 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL D 391 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 395 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 401 " --> pdb=" O ARG D 395 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 406 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.597A pdb=" N PHE D 336 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 306 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 311 through 313 removed outlier: 3.698A pdb=" N GLY D 311 " --> pdb=" O VAL D 318 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2423 1.31 - 1.44: 4025 1.44 - 1.56: 8440 1.56 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 15024 Sorted by residual: bond pdb=" C VAL D 391 " pdb=" O VAL D 391 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.08e-02 8.57e+03 1.70e+01 bond pdb=" C GLY B 401 " pdb=" O GLY B 401 " ideal model delta sigma weight residual 1.232 1.189 0.043 1.16e-02 7.43e+03 1.39e+01 bond pdb=" C ARG B 395 " pdb=" O ARG B 395 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.23e-02 6.61e+03 1.05e+01 bond pdb=" N GLN B 397 " pdb=" CA GLN B 397 " ideal model delta sigma weight residual 1.461 1.491 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" N GLN D 397 " pdb=" CA GLN D 397 " ideal model delta sigma weight residual 1.461 1.490 -0.028 9.20e-03 1.18e+04 9.56e+00 ... (remaining 15019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 19925 1.83 - 3.66: 359 3.66 - 5.49: 54 5.49 - 7.32: 5 7.32 - 9.14: 4 Bond angle restraints: 20347 Sorted by residual: angle pdb=" N ILE B 275 " pdb=" CA ILE B 275 " pdb=" C ILE B 275 " ideal model delta sigma weight residual 111.91 106.60 5.31 8.90e-01 1.26e+00 3.56e+01 angle pdb=" CA VAL D 391 " pdb=" C VAL D 391 " pdb=" O VAL D 391 " ideal model delta sigma weight residual 121.67 116.28 5.39 1.05e+00 9.07e-01 2.64e+01 angle pdb=" C ARG D 395 " pdb=" CA ARG D 395 " pdb=" CB ARG D 395 " ideal model delta sigma weight residual 109.46 118.60 -9.14 1.84e+00 2.95e-01 2.47e+01 angle pdb=" CA GLY B 401 " pdb=" C GLY B 401 " pdb=" O GLY B 401 " ideal model delta sigma weight residual 121.41 116.79 4.62 9.50e-01 1.11e+00 2.37e+01 angle pdb=" CA ARG D 395 " pdb=" C ARG D 395 " pdb=" O ARG D 395 " ideal model delta sigma weight residual 121.47 116.45 5.02 1.15e+00 7.56e-01 1.90e+01 ... (remaining 20342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7648 17.83 - 35.66: 1091 35.66 - 53.49: 294 53.49 - 71.32: 42 71.32 - 89.15: 18 Dihedral angle restraints: 9093 sinusoidal: 3810 harmonic: 5283 Sorted by residual: dihedral pdb=" CA VAL C 159 " pdb=" C VAL C 159 " pdb=" N LYS C 160 " pdb=" CA LYS C 160 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ARG B 211 " pdb=" C ARG B 211 " pdb=" N PHE B 212 " pdb=" CA PHE B 212 " ideal model delta harmonic sigma weight residual -180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP A 328 " pdb=" CB ASP A 328 " pdb=" CG ASP A 328 " pdb=" OD1 ASP A 328 " ideal model delta sinusoidal sigma weight residual -30.00 -86.28 56.28 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 9090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1534 0.040 - 0.080: 469 0.080 - 0.120: 148 0.120 - 0.159: 22 0.159 - 0.199: 8 Chirality restraints: 2181 Sorted by residual: chirality pdb=" CA LEU D 392 " pdb=" N LEU D 392 " pdb=" C LEU D 392 " pdb=" CB LEU D 392 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CB VAL D 391 " pdb=" CA VAL D 391 " pdb=" CG1 VAL D 391 " pdb=" CG2 VAL D 391 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA ILE D 402 " pdb=" N ILE D 402 " pdb=" C ILE D 402 " pdb=" CB ILE D 402 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 2178 not shown) Planarity restraints: 2662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 143 " 0.058 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO A 144 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 316 " 0.047 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO C 317 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 317 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 317 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 107 " 0.040 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO C 108 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 108 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 108 " 0.034 5.00e-02 4.00e+02 ... (remaining 2659 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2546 2.77 - 3.30: 12070 3.30 - 3.83: 21627 3.83 - 4.37: 24791 4.37 - 4.90: 45984 Nonbonded interactions: 107018 Sorted by model distance: nonbonded pdb=" O ASN D 140 " pdb=" ND2 ASN D 140 " model vdw 2.236 3.120 nonbonded pdb=" O SER C 428 " pdb=" OG SER C 428 " model vdw 2.250 3.040 nonbonded pdb=" O ASP B 478 " pdb=" OD1 ASP B 478 " model vdw 2.260 3.040 nonbonded pdb=" NH2 ARG A 47 " pdb=" O GLY A 84 " model vdw 2.276 3.120 nonbonded pdb=" OH TYR C 134 " pdb=" OH TYR C 438 " model vdw 2.278 3.040 ... (remaining 107013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 17 through 428 or resid 437 through 509)) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.640 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.003 0.045 15024 Z= 0.181 Angle : 0.589 9.145 20347 Z= 0.333 Chirality : 0.044 0.199 2181 Planarity : 0.006 0.088 2662 Dihedral : 17.622 89.152 5675 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.38 % Allowed : 27.20 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.43 (0.19), residues: 1789 helix: -1.55 (0.26), residues: 382 sheet: -1.19 (0.26), residues: 389 loop : -1.81 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.002 0.001 HIS C 228 PHE 0.011 0.001 PHE B 142 TYR 0.010 0.001 TYR A 308 ARG 0.005 0.000 ARG B 395 Details of bonding type rmsd hydrogen bonds : bond 0.30379 ( 389) hydrogen bonds : angle 8.39721 ( 1131) covalent geometry : bond 0.00300 (15024) covalent geometry : angle 0.58884 (20347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 167 time to evaluate : 1.708 Fit side-chains revert: symmetry clash REVERT: B 395 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8273 (mtt90) outliers start: 6 outliers final: 3 residues processed: 173 average time/residue: 0.3059 time to fit residues: 74.9662 Evaluate side-chains 165 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 395 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 85 optimal weight: 0.0470 chunk 105 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN C 399 ASN D 140 ASN D 399 ASN D 450 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.201309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.172596 restraints weight = 15106.558| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.12 r_work: 0.3546 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15024 Z= 0.198 Angle : 0.669 8.985 20347 Z= 0.343 Chirality : 0.046 0.169 2181 Planarity : 0.006 0.064 2662 Dihedral : 4.665 59.991 2031 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.04 % Allowed : 25.49 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.42 (0.20), residues: 1789 helix: -1.31 (0.25), residues: 416 sheet: -1.41 (0.26), residues: 389 loop : -1.82 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 221 HIS 0.006 0.001 HIS D 228 PHE 0.015 0.002 PHE B 142 TYR 0.019 0.002 TYR D 308 ARG 0.003 0.000 ARG C 281 Details of bonding type rmsd hydrogen bonds : bond 0.06505 ( 389) hydrogen bonds : angle 5.76948 ( 1131) covalent geometry : bond 0.00500 (15024) covalent geometry : angle 0.66916 (20347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6262 (mp) REVERT: B 349 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: B 381 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6735 (tt0) REVERT: B 395 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8022 (mtt90) REVERT: B 415 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5680 (pp) REVERT: C 257 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7364 (tm130) REVERT: C 399 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7982 (p0) REVERT: D 162 ARG cc_start: 0.6956 (mtt-85) cc_final: 0.6729 (mpt-90) REVERT: D 184 GLN cc_start: 0.7626 (tt0) cc_final: 0.7284 (tp40) REVERT: D 438 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7015 (t80) outliers start: 48 outliers final: 25 residues processed: 199 average time/residue: 0.3226 time to fit residues: 92.5471 Evaluate side-chains 189 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 438 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 163 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN C 399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.200950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139895 restraints weight = 15036.813| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.55 r_work: 0.3207 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15024 Z= 0.141 Angle : 0.594 9.126 20347 Z= 0.303 Chirality : 0.044 0.169 2181 Planarity : 0.005 0.050 2662 Dihedral : 4.455 57.772 2027 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.49 % Allowed : 24.54 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.12 (0.20), residues: 1789 helix: -0.95 (0.26), residues: 425 sheet: -1.16 (0.26), residues: 371 loop : -1.72 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 221 HIS 0.004 0.001 HIS D 228 PHE 0.011 0.001 PHE B 142 TYR 0.014 0.001 TYR A 308 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 389) hydrogen bonds : angle 5.33121 ( 1131) covalent geometry : bond 0.00350 (15024) covalent geometry : angle 0.59359 (20347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 246 TYR cc_start: 0.8721 (t80) cc_final: 0.8493 (t80) REVERT: B 349 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: B 381 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: B 395 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8040 (mtt90) REVERT: B 415 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5663 (pp) REVERT: C 257 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7102 (tm130) REVERT: C 399 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7769 (p0) REVERT: D 17 ARG cc_start: 0.4614 (OUTLIER) cc_final: 0.3639 (ptt-90) REVERT: D 184 GLN cc_start: 0.7348 (tt0) cc_final: 0.7045 (tp40) REVERT: D 438 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.6989 (t80) outliers start: 55 outliers final: 31 residues processed: 207 average time/residue: 0.2936 time to fit residues: 87.4058 Evaluate side-chains 199 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 438 TYR Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 470 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 96 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN C 399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.200016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.165844 restraints weight = 15147.709| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.17 r_work: 0.3445 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15024 Z= 0.215 Angle : 0.677 9.193 20347 Z= 0.345 Chirality : 0.047 0.157 2181 Planarity : 0.006 0.053 2662 Dihedral : 4.752 56.152 2027 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.50 % Allowed : 24.35 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.23 (0.20), residues: 1789 helix: -0.93 (0.26), residues: 422 sheet: -1.25 (0.26), residues: 371 loop : -1.83 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 221 HIS 0.006 0.001 HIS D 228 PHE 0.013 0.002 PHE B 380 TYR 0.019 0.002 TYR A 308 ARG 0.004 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.05745 ( 389) hydrogen bonds : angle 5.24732 ( 1131) covalent geometry : bond 0.00550 (15024) covalent geometry : angle 0.67677 (20347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 164 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: A 377 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7691 (tp) REVERT: A 457 ASP cc_start: 0.8450 (t0) cc_final: 0.8198 (t0) REVERT: B 157 ASP cc_start: 0.6363 (OUTLIER) cc_final: 0.6045 (p0) REVERT: B 349 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: B 381 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.6878 (tt0) REVERT: B 395 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8341 (mtt180) REVERT: B 415 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6058 (pp) REVERT: B 474 ASP cc_start: 0.8026 (m-30) cc_final: 0.7490 (m-30) REVERT: C 257 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7356 (tm130) REVERT: C 399 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8047 (p0) REVERT: D 17 ARG cc_start: 0.4783 (OUTLIER) cc_final: 0.3732 (ptt-90) REVERT: D 438 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7248 (t80) outliers start: 71 outliers final: 46 residues processed: 227 average time/residue: 0.2740 time to fit residues: 90.6346 Evaluate side-chains 218 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 438 TYR Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 467 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 25 optimal weight: 3.9990 chunk 155 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 72 optimal weight: 0.0170 chunk 101 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167541 restraints weight = 15238.724| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.12 r_work: 0.3466 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15024 Z= 0.152 Angle : 0.617 9.248 20347 Z= 0.312 Chirality : 0.045 0.175 2181 Planarity : 0.005 0.052 2662 Dihedral : 4.661 59.071 2027 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.19 % Allowed : 24.60 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.19 (0.20), residues: 1789 helix: -0.89 (0.26), residues: 433 sheet: -1.20 (0.26), residues: 371 loop : -1.82 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 221 HIS 0.004 0.001 HIS D 228 PHE 0.011 0.001 PHE A 264 TYR 0.015 0.001 TYR A 308 ARG 0.002 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 389) hydrogen bonds : angle 5.03470 ( 1131) covalent geometry : bond 0.00381 (15024) covalent geometry : angle 0.61653 (20347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 159 time to evaluate : 1.724 Fit side-chains revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8218 (t0) cc_final: 0.7937 (m-30) REVERT: A 470 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7415 (tp) REVERT: B 157 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.6184 (p0) REVERT: B 349 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: B 381 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: B 395 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8204 (mtt90) REVERT: B 415 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5909 (pp) REVERT: C 257 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7207 (tm130) REVERT: C 399 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7572 (p0) REVERT: D 17 ARG cc_start: 0.4744 (OUTLIER) cc_final: 0.3751 (ptt-90) REVERT: D 438 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7185 (t80) outliers start: 66 outliers final: 48 residues processed: 217 average time/residue: 0.3024 time to fit residues: 95.3511 Evaluate side-chains 214 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 438 TYR Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 465 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.200105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141643 restraints weight = 15109.562| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 6.27 r_work: 0.3200 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15024 Z= 0.171 Angle : 0.632 9.218 20347 Z= 0.319 Chirality : 0.045 0.173 2181 Planarity : 0.005 0.053 2662 Dihedral : 4.709 58.285 2027 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.01 % Allowed : 24.03 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.20 (0.20), residues: 1789 helix: -0.86 (0.26), residues: 433 sheet: -1.21 (0.26), residues: 371 loop : -1.84 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 221 HIS 0.005 0.001 HIS D 228 PHE 0.011 0.001 PHE A 264 TYR 0.018 0.001 TYR B 100 ARG 0.003 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.04854 ( 389) hydrogen bonds : angle 4.98136 ( 1131) covalent geometry : bond 0.00435 (15024) covalent geometry : angle 0.63174 (20347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 158 time to evaluate : 2.436 Fit side-chains revert: symmetry clash REVERT: A 457 ASP cc_start: 0.8300 (t0) cc_final: 0.7947 (m-30) REVERT: A 470 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7340 (tp) REVERT: B 157 ASP cc_start: 0.6326 (OUTLIER) cc_final: 0.5989 (p0) REVERT: B 349 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: B 381 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: B 395 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8263 (mtt90) REVERT: B 415 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6076 (pp) REVERT: C 257 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7137 (tm130) REVERT: C 399 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7467 (p0) REVERT: C 438 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.6581 (t80) REVERT: D 17 ARG cc_start: 0.4829 (OUTLIER) cc_final: 0.3760 (ptt-90) REVERT: D 38 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5722 (mt) REVERT: D 438 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7367 (t80) outliers start: 79 outliers final: 61 residues processed: 228 average time/residue: 0.3339 time to fit residues: 112.0204 Evaluate side-chains 228 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 155 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 439 HIS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 438 TYR Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 467 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 104 optimal weight: 0.0980 chunk 59 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 3 optimal weight: 0.0070 chunk 165 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 151 optimal weight: 0.0060 chunk 120 optimal weight: 0.8980 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN C 399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.203567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.163277 restraints weight = 15066.628| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.35 r_work: 0.3446 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15024 Z= 0.095 Angle : 0.536 8.928 20347 Z= 0.270 Chirality : 0.043 0.189 2181 Planarity : 0.005 0.046 2662 Dihedral : 4.329 58.897 2027 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.30 % Allowed : 25.62 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.92 (0.20), residues: 1789 helix: -0.65 (0.26), residues: 436 sheet: -0.99 (0.26), residues: 369 loop : -1.68 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 221 HIS 0.003 0.000 HIS B 197 PHE 0.011 0.001 PHE B 336 TYR 0.008 0.001 TYR B 485 ARG 0.005 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 389) hydrogen bonds : angle 4.75140 ( 1131) covalent geometry : bond 0.00220 (15024) covalent geometry : angle 0.53610 (20347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 1.661 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8236 (t0) cc_final: 0.7695 (t0) REVERT: A 457 ASP cc_start: 0.8244 (t0) cc_final: 0.8009 (m-30) REVERT: B 157 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.5908 (p0) REVERT: B 349 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: B 381 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7015 (tt0) REVERT: B 395 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8166 (mtt90) REVERT: B 415 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5912 (pp) REVERT: C 257 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7207 (tm130) REVERT: C 287 VAL cc_start: 0.8762 (t) cc_final: 0.8548 (p) REVERT: C 399 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7502 (p0) REVERT: D 17 ARG cc_start: 0.4719 (OUTLIER) cc_final: 0.3818 (ptt-90) REVERT: D 38 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.6004 (mt) REVERT: D 134 TYR cc_start: 0.6563 (t80) cc_final: 0.6112 (t80) REVERT: D 438 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7503 (t80) outliers start: 52 outliers final: 27 residues processed: 206 average time/residue: 0.3009 time to fit residues: 89.6847 Evaluate side-chains 196 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 438 TYR Chi-restraints excluded: chain D residue 470 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 ASN D 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162799 restraints weight = 15007.951| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.26 r_work: 0.3418 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15024 Z= 0.138 Angle : 0.585 8.710 20347 Z= 0.295 Chirality : 0.044 0.182 2181 Planarity : 0.005 0.048 2662 Dihedral : 4.440 57.671 2027 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.42 % Allowed : 25.36 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.93 (0.20), residues: 1789 helix: -0.70 (0.26), residues: 434 sheet: -0.99 (0.26), residues: 371 loop : -1.67 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 221 HIS 0.004 0.001 HIS D 228 PHE 0.010 0.001 PHE A 264 TYR 0.015 0.001 TYR A 308 ARG 0.004 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 389) hydrogen bonds : angle 4.79320 ( 1131) covalent geometry : bond 0.00345 (15024) covalent geometry : angle 0.58525 (20347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8344 (t0) cc_final: 0.7781 (t0) REVERT: B 157 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6482 (p0) REVERT: B 286 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8798 (tttt) REVERT: B 349 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: B 381 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: B 395 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8196 (mtt90) REVERT: B 415 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.5935 (pp) REVERT: C 257 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7224 (tm130) REVERT: C 399 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7217 (p0) REVERT: D 17 ARG cc_start: 0.4608 (OUTLIER) cc_final: 0.3783 (ptt-90) REVERT: D 134 TYR cc_start: 0.6848 (t80) cc_final: 0.6360 (t80) outliers start: 54 outliers final: 38 residues processed: 203 average time/residue: 0.2910 time to fit residues: 84.5843 Evaluate side-chains 206 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 465 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 101 optimal weight: 0.0060 chunk 50 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 133 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.204553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142741 restraints weight = 15024.453| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 4.37 r_work: 0.3174 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15024 Z= 0.107 Angle : 0.552 8.767 20347 Z= 0.278 Chirality : 0.043 0.188 2181 Planarity : 0.005 0.046 2662 Dihedral : 4.306 55.232 2027 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.11 % Allowed : 25.81 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.85 (0.20), residues: 1789 helix: -0.59 (0.26), residues: 433 sheet: -0.92 (0.26), residues: 371 loop : -1.65 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 221 HIS 0.003 0.001 HIS B 197 PHE 0.011 0.001 PHE B 336 TYR 0.016 0.001 TYR D 134 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 389) hydrogen bonds : angle 4.68870 ( 1131) covalent geometry : bond 0.00257 (15024) covalent geometry : angle 0.55201 (20347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8258 (t0) cc_final: 0.7811 (t0) REVERT: A 241 GLU cc_start: 0.8482 (mp0) cc_final: 0.8263 (mp0) REVERT: B 157 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5564 (p0) REVERT: B 286 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8744 (tttt) REVERT: B 349 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: B 381 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6910 (tt0) REVERT: B 395 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8246 (mtt90) REVERT: B 415 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5932 (pp) REVERT: C 257 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7102 (tm130) REVERT: C 287 VAL cc_start: 0.8680 (t) cc_final: 0.8410 (p) REVERT: C 399 ASN cc_start: 0.7455 (OUTLIER) cc_final: 0.6842 (p0) REVERT: D 17 ARG cc_start: 0.4786 (OUTLIER) cc_final: 0.3867 (ptt-90) REVERT: D 220 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8714 (mt) outliers start: 49 outliers final: 36 residues processed: 203 average time/residue: 0.2907 time to fit residues: 84.5154 Evaluate side-chains 206 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 168 optimal weight: 0.0980 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 174 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 ASN D 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.202613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171108 restraints weight = 15155.384| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.14 r_work: 0.3495 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15024 Z= 0.152 Angle : 0.609 10.203 20347 Z= 0.307 Chirality : 0.044 0.181 2181 Planarity : 0.005 0.048 2662 Dihedral : 4.446 59.223 2027 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.36 % Allowed : 25.87 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.20), residues: 1789 helix: -0.66 (0.26), residues: 434 sheet: -0.96 (0.26), residues: 371 loop : -1.68 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 221 HIS 0.004 0.001 HIS D 228 PHE 0.025 0.001 PHE A 70 TYR 0.016 0.001 TYR A 308 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 389) hydrogen bonds : angle 4.78659 ( 1131) covalent geometry : bond 0.00384 (15024) covalent geometry : angle 0.60866 (20347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 158 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8270 (t0) cc_final: 0.7798 (t0) REVERT: B 157 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.6212 (p0) REVERT: B 286 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8792 (tttt) REVERT: B 349 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: B 381 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: B 395 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8268 (mtt90) REVERT: B 415 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.5996 (pp) REVERT: C 257 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7191 (tm130) REVERT: C 399 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7022 (p0) REVERT: D 17 ARG cc_start: 0.4760 (OUTLIER) cc_final: 0.3827 (ptt-90) REVERT: D 220 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8829 (mt) outliers start: 53 outliers final: 42 residues processed: 203 average time/residue: 0.2837 time to fit residues: 82.4591 Evaluate side-chains 209 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 157 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 399 ASN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 8 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.202870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.173385 restraints weight = 15169.177| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.15 r_work: 0.3524 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15024 Z= 0.140 Angle : 0.597 10.047 20347 Z= 0.302 Chirality : 0.044 0.178 2181 Planarity : 0.005 0.047 2662 Dihedral : 4.427 59.925 2027 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.42 % Allowed : 25.94 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.90 (0.20), residues: 1789 helix: -0.65 (0.26), residues: 433 sheet: -0.96 (0.26), residues: 371 loop : -1.67 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 221 HIS 0.003 0.001 HIS D 228 PHE 0.023 0.001 PHE A 70 TYR 0.014 0.001 TYR A 308 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 389) hydrogen bonds : angle 4.76254 ( 1131) covalent geometry : bond 0.00349 (15024) covalent geometry : angle 0.59687 (20347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7383.73 seconds wall clock time: 127 minutes 43.57 seconds (7663.57 seconds total)