Starting phenix.real_space_refine on Tue Dec 31 03:01:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9emn_19821/12_2024/9emn_19821.cif Found real_map, /net/cci-nas-00/data/ceres_data/9emn_19821/12_2024/9emn_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_19821/12_2024/9emn_19821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9emn_19821/12_2024/9emn_19821.map" model { file = "/net/cci-nas-00/data/ceres_data/9emn_19821/12_2024/9emn_19821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9emn_19821/12_2024/9emn_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.95, per 1000 atoms: 0.61 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: 3.19 Conformation dependent library (CDL) restraints added in 1.9 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: 1.74 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: 4.68 Time building geometry restraints manager: 3.78 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: 0.010 Normalize map: mean=0, sd=1: 2.130 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.680 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.780 ------------------------------------------------------------------------------- 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= 0.194 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 *********************** 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 : 1.615 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: 0.3232 time to fit residues: 79.4014 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 : 1.686 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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= 0.327 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 *********************** 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 : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6341 (mp) REVERT: B 349 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: B 381 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6649 (tt0) REVERT: B 395 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7891 (mtt90) REVERT: B 415 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5631 (pp) REVERT: C 257 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7371 (tm130) REVERT: D 438 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6886 (t80) outliers start: 48 outliers final: 25 residues processed: 199 average time/residue: 0.3024 time to fit residues: 86.1648 Evaluate side-chains 189 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 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 90 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 163 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 131 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1097 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= 0.204 Angle : 0.574 9.041 20347 Z= 0.293 Chirality : 0.043 0.174 2181 Planarity : 0.005 0.050 2662 Dihedral : 4.364 55.161 2027 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.23 % Allowed : 24.48 % Favored : 72.29 % 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: -0.99 (0.26), residues: 422 sheet: -1.14 (0.26), residues: 371 loop : -1.70 (0.20), residues: 996 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 0.012 0.001 TYR A 308 ARG 0.002 0.000 ARG A 62 *********************** 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 212 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 349 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: B 381 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: B 395 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7860 (mtt90) REVERT: B 415 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5727 (pp) REVERT: C 184 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: C 208 MET cc_start: 0.8746 (mmp) cc_final: 0.8530 (mmp) REVERT: C 257 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7256 (tm130) REVERT: D 17 ARG cc_start: 0.4592 (OUTLIER) cc_final: 0.3734 (ptt-90) REVERT: D 438 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.6786 (t80) outliers start: 51 outliers final: 26 residues processed: 205 average time/residue: 0.3225 time to fit residues: 95.0177 Evaluate side-chains 193 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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 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 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 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 184 GLN 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 451 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 62 ARG 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 470 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 164 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1336 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= 0.316 Angle : 0.649 8.956 20347 Z= 0.330 Chirality : 0.046 0.151 2181 Planarity : 0.006 0.052 2662 Dihedral : 4.662 56.816 2027 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.99 % Allowed : 24.79 % 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: -2.15 (0.20), residues: 1789 helix: -0.85 (0.26), residues: 422 sheet: -1.19 (0.26), residues: 371 loop : -1.78 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 221 HIS 0.005 0.001 HIS D 228 PHE 0.012 0.002 PHE A 336 TYR 0.018 0.002 TYR A 308 ARG 0.003 0.000 ARG D 281 *********************** 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 224 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 161 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 377 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7495 (tp) REVERT: B 157 ASP cc_start: 0.6675 (OUTLIER) cc_final: 0.6419 (p0) REVERT: B 349 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: B 381 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6777 (tt0) REVERT: B 395 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8186 (mtt180) REVERT: B 415 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.5932 (pp) REVERT: B 474 ASP cc_start: 0.7708 (m-30) cc_final: 0.7304 (m-30) REVERT: C 184 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: C 208 MET cc_start: 0.8749 (mmp) cc_final: 0.8538 (mmp) REVERT: C 257 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7322 (tm130) REVERT: D 17 ARG cc_start: 0.4640 (OUTLIER) cc_final: 0.3681 (ptt-90) REVERT: D 438 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7326 (t80) outliers start: 63 outliers final: 42 residues processed: 215 average time/residue: 0.3225 time to fit residues: 99.9459 Evaluate side-chains 212 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 232 THR 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 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 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 184 GLN 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 156 optimal weight: 0.1980 chunk 43 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1353 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= 0.164 Angle : 0.547 8.821 20347 Z= 0.276 Chirality : 0.043 0.182 2181 Planarity : 0.005 0.045 2662 Dihedral : 4.286 51.835 2027 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % 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: -1.96 (0.20), residues: 1789 helix: -0.72 (0.26), residues: 432 sheet: -1.02 (0.26), residues: 369 loop : -1.68 (0.20), residues: 988 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 A 264 TYR 0.011 0.001 TYR C 134 ARG 0.002 0.000 ARG A 62 *********************** 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 213 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: B 157 ASP cc_start: 0.6662 (OUTLIER) cc_final: 0.6410 (p0) REVERT: B 349 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: B 381 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6836 (tt0) REVERT: B 395 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7986 (mtt90) REVERT: B 415 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5848 (pp) REVERT: B 474 ASP cc_start: 0.7654 (m-30) cc_final: 0.7223 (m-30) REVERT: C 257 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7243 (tm130) REVERT: D 17 ARG cc_start: 0.4632 (OUTLIER) cc_final: 0.3819 (ptt-90) REVERT: D 438 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7313 (t80) outliers start: 49 outliers final: 30 residues processed: 205 average time/residue: 0.2987 time to fit residues: 88.0300 Evaluate side-chains 200 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 A residue 454 THR 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 180 ASN Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 260 LEU 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 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 C residue 159 VAL 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 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 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 467 THR Chi-restraints excluded: chain D residue 470 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.0270 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 0.1980 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1464 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= 0.257 Angle : 0.605 8.641 20347 Z= 0.306 Chirality : 0.045 0.179 2181 Planarity : 0.005 0.049 2662 Dihedral : 4.516 59.671 2027 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.25 % Allowed : 24.92 % Favored : 70.83 % 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: -2.03 (0.20), residues: 1789 helix: -0.77 (0.26), residues: 436 sheet: -1.07 (0.26), residues: 371 loop : -1.74 (0.20), residues: 982 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 0.010 0.001 PHE D 406 TYR 0.017 0.001 TYR A 308 ARG 0.003 0.000 ARG D 281 *********************** 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 231 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 164 time to evaluate : 1.569 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8197 (t0) cc_final: 0.7711 (t0) REVERT: B 157 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6481 (p0) REVERT: B 349 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: B 381 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: B 395 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8185 (mtt90) REVERT: B 415 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.5931 (pp) REVERT: B 474 ASP cc_start: 0.7703 (m-30) cc_final: 0.7250 (m-30) REVERT: C 184 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: C 257 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7299 (tm130) REVERT: D 17 ARG cc_start: 0.4673 (OUTLIER) cc_final: 0.3792 (ptt-90) REVERT: D 38 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.6003 (mt) REVERT: D 438 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.7406 (t80) outliers start: 67 outliers final: 49 residues processed: 218 average time/residue: 0.2905 time to fit residues: 91.0287 Evaluate side-chains 218 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 159 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 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 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 458 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 184 GLN 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 428 SER 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 184 GLN 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 438 TYR Chi-restraints excluded: chain D residue 451 THR 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 167 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1535 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= 0.250 Angle : 0.603 8.961 20347 Z= 0.304 Chirality : 0.044 0.187 2181 Planarity : 0.005 0.050 2662 Dihedral : 4.562 59.406 2027 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.63 % Allowed : 24.73 % 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: -2.03 (0.20), residues: 1789 helix: -0.76 (0.26), residues: 439 sheet: -1.08 (0.26), residues: 371 loop : -1.74 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 221 HIS 0.004 0.001 HIS D 228 PHE 0.011 0.001 PHE A 336 TYR 0.015 0.001 TYR A 308 ARG 0.003 0.000 ARG D 281 *********************** 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 234 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8244 (t0) cc_final: 0.7786 (t0) REVERT: B 157 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.6487 (p0) REVERT: B 349 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: B 381 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6946 (tt0) REVERT: B 395 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8192 (mtt90) REVERT: B 415 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6050 (pp) REVERT: C 257 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7322 (tm130) REVERT: D 17 ARG cc_start: 0.4690 (OUTLIER) cc_final: 0.3792 (ptt-90) REVERT: D 38 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.6088 (mt) REVERT: D 438 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.7475 (t80) outliers start: 73 outliers final: 52 residues processed: 223 average time/residue: 0.2963 time to fit residues: 94.8543 Evaluate side-chains 221 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 160 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 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 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 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 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 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 335 THR Chi-restraints excluded: chain C residue 365 VAL 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 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 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 465 VAL Chi-restraints excluded: chain D residue 467 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 0.0980 chunk 85 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1564 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 : 0.560 8.616 20347 Z= 0.282 Chirality : 0.043 0.195 2181 Planarity : 0.005 0.047 2662 Dihedral : 4.411 59.314 2027 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.87 % Allowed : 24.98 % 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: -1.90 (0.20), residues: 1789 helix: -0.64 (0.26), residues: 439 sheet: -0.97 (0.26), residues: 371 loop : -1.67 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 221 HIS 0.003 0.001 HIS D 228 PHE 0.010 0.001 PHE A 264 TYR 0.011 0.001 TYR A 308 ARG 0.004 0.000 ARG A 62 *********************** 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 222 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 161 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8246 (t0) cc_final: 0.7778 (t0) REVERT: B 157 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6462 (p0) REVERT: B 349 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: B 381 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7019 (tt0) REVERT: B 395 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8223 (mtt90) REVERT: B 415 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.5969 (pp) REVERT: C 257 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7244 (tm130) REVERT: D 17 ARG cc_start: 0.4662 (OUTLIER) cc_final: 0.3823 (ptt-90) REVERT: D 38 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.6027 (mt) REVERT: D 438 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7454 (t80) outliers start: 61 outliers final: 43 residues processed: 213 average time/residue: 0.3000 time to fit residues: 92.1351 Evaluate side-chains 212 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 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 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 258 ASN Chi-restraints excluded: chain B residue 260 LEU 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 458 GLU 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 297 ASN Chi-restraints excluded: chain C residue 365 VAL 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 38 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 155 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 375 VAL Chi-restraints excluded: chain D residue 438 TYR Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 467 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.0970 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 49 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1609 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= 0.166 Angle : 0.549 10.265 20347 Z= 0.276 Chirality : 0.043 0.184 2181 Planarity : 0.005 0.045 2662 Dihedral : 4.256 57.574 2027 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.36 % Allowed : 25.62 % Favored : 71.02 % 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: -1.75 (0.20), residues: 1789 helix: -0.51 (0.26), residues: 439 sheet: -0.84 (0.26), residues: 369 loop : -1.59 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 221 HIS 0.002 0.001 HIS D 228 PHE 0.021 0.001 PHE A 70 TYR 0.011 0.001 TYR A 308 ARG 0.005 0.000 ARG A 62 *********************** 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 212 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8240 (t0) cc_final: 0.7805 (t0) REVERT: A 227 ASP cc_start: 0.8643 (t0) cc_final: 0.8206 (t0) REVERT: B 157 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6242 (p0) REVERT: B 349 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: B 381 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7063 (tt0) REVERT: B 395 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8236 (mtt90) REVERT: B 415 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.5966 (pp) REVERT: C 257 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7255 (tm130) REVERT: D 17 ARG cc_start: 0.4678 (OUTLIER) cc_final: 0.3896 (ptt-90) REVERT: D 38 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.6055 (mt) outliers start: 53 outliers final: 37 residues processed: 205 average time/residue: 0.2956 time to fit residues: 87.1974 Evaluate side-chains 204 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 38 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 375 VAL Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 467 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 165 optimal weight: 0.7980 chunk 142 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS D 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1674 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= 0.158 Angle : 0.541 9.972 20347 Z= 0.272 Chirality : 0.043 0.171 2181 Planarity : 0.005 0.045 2662 Dihedral : 4.140 54.122 2027 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.92 % Allowed : 26.00 % 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: -1.66 (0.20), residues: 1789 helix: -0.41 (0.26), residues: 439 sheet: -0.72 (0.27), residues: 366 loop : -1.58 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 221 HIS 0.003 0.001 HIS D 439 PHE 0.021 0.001 PHE A 70 TYR 0.014 0.001 TYR D 134 ARG 0.003 0.000 ARG A 62 ********************** 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: 46 poor density : 165 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8215 (t0) cc_final: 0.7791 (t0) REVERT: A 227 ASP cc_start: 0.8608 (t0) cc_final: 0.8155 (t0) REVERT: B 157 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.6450 (p0) REVERT: B 261 MET cc_start: 0.9105 (mmt) cc_final: 0.8505 (mmt) REVERT: B 349 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: B 381 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: B 395 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8161 (mtt90) REVERT: B 415 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5885 (pp) REVERT: C 257 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7192 (tm130) REVERT: D 17 ARG cc_start: 0.4662 (OUTLIER) cc_final: 0.3931 (ptt-90) outliers start: 46 outliers final: 34 residues processed: 206 average time/residue: 0.2969 time to fit residues: 87.5856 Evaluate side-chains 204 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 257 GLN Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 365 VAL 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 258 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 467 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 131 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 143 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.205615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.171609 restraints weight = 15153.913| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.11 r_work: 0.3571 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1705 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= 0.162 Angle : 0.543 9.939 20347 Z= 0.272 Chirality : 0.043 0.145 2181 Planarity : 0.005 0.044 2662 Dihedral : 4.104 54.806 2027 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.66 % Allowed : 26.44 % Favored : 70.89 % 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: -1.63 (0.20), residues: 1789 helix: -0.37 (0.26), residues: 439 sheet: -0.68 (0.27), residues: 366 loop : -1.58 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 221 HIS 0.002 0.000 HIS D 228 PHE 0.020 0.001 PHE A 70 TYR 0.011 0.001 TYR A 308 ARG 0.004 0.000 ARG A 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2838.85 seconds wall clock time: 53 minutes 21.80 seconds (3201.80 seconds total)