Starting phenix.real_space_refine on Thu Mar 5 15:00:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efi_28083/03_2026/8efi_28083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efi_28083/03_2026/8efi_28083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8efi_28083/03_2026/8efi_28083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efi_28083/03_2026/8efi_28083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8efi_28083/03_2026/8efi_28083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efi_28083/03_2026/8efi_28083.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 138 5.16 5 C 14666 2.51 5 N 3946 2.21 5 O 4491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23256 Number of models: 1 Model: "" Number of chains: 13 Chain: "M" Number of atoms: 5974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5974 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 28, 'TRANS': 713} Chain breaks: 3 Chain: "B" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "E" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "F" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "O" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "P" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.23, per 1000 atoms: 0.22 Number of scatterers: 23256 At special positions: 0 Unit cell: (142.296, 141.218, 247.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 10 15.00 Mg 5 11.99 O 4491 8.00 N 3946 7.00 C 14666 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5474 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 33 sheets defined 56.9% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'M' and resid 6 through 11 removed outlier: 6.467A pdb=" N ALA M 11 " --> pdb=" O VAL M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 17 Processing helix chain 'M' and resid 19 through 28 removed outlier: 4.030A pdb=" N THR M 28 " --> pdb=" O LEU M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 76 removed outlier: 3.773A pdb=" N GLN M 75 " --> pdb=" O LYS M 72 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL M 76 " --> pdb=" O GLU M 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 72 through 76' Processing helix chain 'M' and resid 81 through 85 Processing helix chain 'M' and resid 89 through 93 Processing helix chain 'M' and resid 97 through 111 removed outlier: 3.695A pdb=" N VAL M 101 " --> pdb=" O HIS M 97 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 134 removed outlier: 4.005A pdb=" N TYR M 134 " --> pdb=" O LEU M 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 131 through 134' Processing helix chain 'M' and resid 135 through 143 removed outlier: 3.688A pdb=" N VAL M 139 " --> pdb=" O THR M 135 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG M 143 " --> pdb=" O VAL M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 169 removed outlier: 3.752A pdb=" N ILE M 157 " --> pdb=" O HIS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 199 Processing helix chain 'M' and resid 217 through 231 Proline residue: M 225 - end of helix Processing helix chain 'M' and resid 270 through 275 removed outlier: 4.124A pdb=" N ILE M 274 " --> pdb=" O LYS M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 290 removed outlier: 4.341A pdb=" N TYR M 287 " --> pdb=" O TYR M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 302 removed outlier: 4.266A pdb=" N LEU M 298 " --> pdb=" O LYS M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 315 removed outlier: 3.933A pdb=" N GLN M 315 " --> pdb=" O ALA M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 338 removed outlier: 3.975A pdb=" N GLU M 328 " --> pdb=" O ASP M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 358 removed outlier: 3.857A pdb=" N LYS M 346 " --> pdb=" O THR M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 362 removed outlier: 3.674A pdb=" N MET M 362 " --> pdb=" O PHE M 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 359 through 362' Processing helix chain 'M' and resid 378 through 389 Processing helix chain 'M' and resid 391 through 401 Processing helix chain 'M' and resid 416 through 448 Processing helix chain 'M' and resid 472 through 505 Processing helix chain 'M' and resid 514 through 522 removed outlier: 4.742A pdb=" N CYS M 520 " --> pdb=" O ASP M 516 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE M 521 " --> pdb=" O LEU M 517 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 540 removed outlier: 3.858A pdb=" N MET M 539 " --> pdb=" O GLU M 535 " (cutoff:3.500A) Processing helix chain 'M' and resid 544 through 557 Processing helix chain 'M' and resid 592 through 598 removed outlier: 3.759A pdb=" N LYS M 596 " --> pdb=" O GLY M 592 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS M 598 " --> pdb=" O LEU M 594 " (cutoff:3.500A) Processing helix chain 'M' and resid 602 through 611 Processing helix chain 'M' and resid 615 through 620 removed outlier: 4.024A pdb=" N THR M 619 " --> pdb=" O LYS M 615 " (cutoff:3.500A) Processing helix chain 'M' and resid 646 through 663 removed outlier: 3.588A pdb=" N ASN M 661 " --> pdb=" O LYS M 657 " (cutoff:3.500A) Processing helix chain 'M' and resid 685 through 696 Processing helix chain 'M' and resid 697 through 708 removed outlier: 3.502A pdb=" N LYS M 707 " --> pdb=" O ARG M 703 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY M 708 " --> pdb=" O ILE M 704 " (cutoff:3.500A) Processing helix chain 'M' and resid 715 through 723 Processing helix chain 'M' and resid 724 through 726 No H-bonds generated for 'chain 'M' and resid 724 through 726' Processing helix chain 'M' and resid 739 through 748 Processing helix chain 'M' and resid 752 through 754 No H-bonds generated for 'chain 'M' and resid 752 through 754' Processing helix chain 'M' and resid 766 through 781 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.992A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 61' Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 4.005A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.721A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.749A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 4.021A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.519A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.703A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 257' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.642A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.986A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.833A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.790A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.859A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 61' Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.907A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.882A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.551A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.795A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.954A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.621A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.776A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.572A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.775A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.552A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.929A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 55 through 60' Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.737A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.657A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.748A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 4.049A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.743A pdb=" N GLU D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.582A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.682A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.572A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'E' and resid 56 through 62 removed outlier: 3.548A pdb=" N ARG E 62 " --> pdb=" O GLN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.511A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.714A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.618A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 217 removed outlier: 4.051A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 233 Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.580A pdb=" N PHE E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 285 removed outlier: 3.795A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.294A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 349 through 355 removed outlier: 3.620A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 removed outlier: 4.053A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.747A pdb=" N SER F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.572A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.841A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 202 through 217 removed outlier: 4.113A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 removed outlier: 3.510A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 255 removed outlier: 3.528A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 removed outlier: 4.290A pdb=" N PHE F 262 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 268 Processing helix chain 'F' and resid 273 through 285 removed outlier: 3.576A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.083A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 4.089A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 367 through 372 removed outlier: 3.549A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 210 removed outlier: 4.788A pdb=" N GLN O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 208 removed outlier: 3.604A pdb=" N ARG P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 39 through 40 removed outlier: 3.660A pdb=" N VAL M 39 " --> pdb=" O VAL M 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 49 through 55 removed outlier: 7.203A pdb=" N THR M 60 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG M 54 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS M 58 " --> pdb=" O ARG M 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 115 through 118 removed outlier: 6.012A pdb=" N CYS M 122 " --> pdb=" O ARG M 671 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE M 673 " --> pdb=" O CYS M 122 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR M 124 " --> pdb=" O ILE M 673 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER M 173 " --> pdb=" O HIS M 668 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL M 670 " --> pdb=" O SER M 173 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU M 175 " --> pdb=" O VAL M 670 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N CYS M 672 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR M 177 " --> pdb=" O CYS M 672 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN M 172 " --> pdb=" O PHE M 456 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER M 260 " --> pdb=" O HIS M 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'M' and resid 364 through 366 Processing sheet with id=AA6, first strand: chain 'M' and resid 403 through 406 Processing sheet with id=AA7, first strand: chain 'M' and resid 577 through 581 removed outlier: 3.924A pdb=" N PHE M 577 " --> pdb=" O TYR M 588 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 711 through 714 removed outlier: 3.991A pdb=" N ASN M 711 " --> pdb=" O PHE M 765 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.795A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.597A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 238 through 242 removed outlier: 4.870A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.869A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.514A pdb=" N VAL C 35 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.540A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 165 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 242 removed outlier: 4.360A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.671A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.518A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 240 Processing sheet with id=AC6, first strand: chain 'E' and resid 29 through 31 removed outlier: 4.038A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E 132 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.574A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.576A pdb=" N HIS E 161 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 238 through 240 Processing sheet with id=AD2, first strand: chain 'F' and resid 29 through 31 removed outlier: 6.914A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.694A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD5, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.365A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 238 through 242 removed outlier: 5.118A pdb=" N LEU F 242 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLN F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) 1274 hydrogen bonds defined for protein. 3432 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: 4.82 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5937 1.33 - 1.45: 4217 1.45 - 1.57: 13297 1.57 - 1.69: 15 1.69 - 1.81: 241 Bond restraints: 23707 Sorted by residual: bond pdb=" C ALA M 13 " pdb=" N PRO M 14 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.38e-02 5.25e+03 3.83e+00 bond pdb=" CG GLN P 103 " pdb=" CD GLN P 103 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" CG1 ILE B 212 " pdb=" CD1 ILE B 212 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.19e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 ... (remaining 23702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 31456 1.74 - 3.48: 451 3.48 - 5.22: 104 5.22 - 6.96: 31 6.96 - 8.70: 5 Bond angle restraints: 32047 Sorted by residual: angle pdb=" C GLU O 104 " pdb=" N ARG O 105 " pdb=" CA ARG O 105 " ideal model delta sigma weight residual 121.58 113.14 8.44 1.95e+00 2.63e-01 1.87e+01 angle pdb=" C ASP P 100 " pdb=" N ARG P 101 " pdb=" CA ARG P 101 " ideal model delta sigma weight residual 121.58 113.56 8.02 1.95e+00 2.63e-01 1.69e+01 angle pdb=" N GLN P 111 " pdb=" CA GLN P 111 " pdb=" CB GLN P 111 " ideal model delta sigma weight residual 110.28 116.16 -5.88 1.55e+00 4.16e-01 1.44e+01 angle pdb=" C GLU P 124 " pdb=" N ARG P 125 " pdb=" CA ARG P 125 " ideal model delta sigma weight residual 120.68 114.43 6.25 1.70e+00 3.46e-01 1.35e+01 angle pdb=" CA ARG O 105 " pdb=" CB ARG O 105 " pdb=" CG ARG O 105 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.30e+01 ... (remaining 32042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.04: 13569 23.04 - 46.08: 727 46.08 - 69.11: 93 69.11 - 92.15: 38 92.15 - 115.19: 2 Dihedral angle restraints: 14429 sinusoidal: 5922 harmonic: 8507 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 55.19 -115.19 1 2.00e+01 2.50e-03 3.42e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -172.06 112.05 1 2.00e+01 2.50e-03 3.30e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 20.96 -80.96 1 2.00e+01 2.50e-03 2.02e+01 ... (remaining 14426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2663 0.043 - 0.086: 640 0.086 - 0.129: 230 0.129 - 0.172: 10 0.172 - 0.215: 1 Chirality restraints: 3544 Sorted by residual: chirality pdb=" CA ARG O 105 " pdb=" N ARG O 105 " pdb=" C ARG O 105 " pdb=" CB ARG O 105 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE O 92 " pdb=" CA ILE O 92 " pdb=" CG1 ILE O 92 " pdb=" CG2 ILE O 92 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CG LEU P 176 " pdb=" CB LEU P 176 " pdb=" CD1 LEU P 176 " pdb=" CD2 LEU P 176 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 3541 not shown) Planarity restraints: 4130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 111 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO D 112 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 39 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO M 40 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO M 40 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 40 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN P 68 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C GLN P 68 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN P 68 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU P 69 " 0.009 2.00e-02 2.50e+03 ... (remaining 4127 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 213 2.63 - 3.20: 20970 3.20 - 3.77: 35388 3.77 - 4.33: 47263 4.33 - 4.90: 79763 Nonbonded interactions: 183597 Sorted by model distance: nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.065 2.170 nonbonded pdb=" O LYS P 140 " pdb=" NE2 GLN P 144 " model vdw 2.188 3.120 nonbonded pdb=" O LYS O 149 " pdb=" ND1 HIS O 153 " model vdw 2.234 3.120 nonbonded pdb=" O LEU O 64 " pdb=" NE2 GLN O 68 " model vdw 2.245 3.120 nonbonded pdb=" O THR E 304 " pdb=" NH1 ARG E 335 " model vdw 2.270 3.120 ... (remaining 183592 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.020 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 0.043 23707 Z= 0.133 Angle : 0.575 8.703 32047 Z= 0.303 Chirality : 0.042 0.215 3544 Planarity : 0.004 0.052 4130 Dihedral : 14.289 115.189 8955 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.04 % Allowed : 0.20 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.16), residues: 2907 helix: 1.71 (0.15), residues: 1350 sheet: 0.44 (0.28), residues: 390 loop : 0.32 (0.20), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 160 TYR 0.021 0.001 TYR O 60 PHE 0.014 0.001 PHE B 124 TRP 0.011 0.001 TRP F 79 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00292 (23707) covalent geometry : angle 0.57485 (32047) hydrogen bonds : bond 0.18154 ( 1266) hydrogen bonds : angle 5.94988 ( 3432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 101 ARG cc_start: 0.8763 (pmt-80) cc_final: 0.8543 (pmt-80) REVERT: O 127 MET cc_start: 0.8122 (ppp) cc_final: 0.7791 (ppp) REVERT: O 178 ARG cc_start: 0.9033 (pmt-80) cc_final: 0.8502 (pmt-80) REVERT: P 125 ARG cc_start: 0.9083 (pmt-80) cc_final: 0.8834 (pmt-80) REVERT: P 141 MET cc_start: 0.8792 (ptp) cc_final: 0.8372 (ptp) REVERT: P 160 ARG cc_start: 0.8839 (pmt-80) cc_final: 0.8634 (pmt-80) REVERT: P 162 TYR cc_start: 0.8637 (t80) cc_final: 0.8240 (t80) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1860 time to fit residues: 44.1835 Evaluate side-chains 136 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 172 GLN M 292 ASN ** M 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 668 HIS C 275 HIS D 161 HIS F 225 ASN O 68 GLN ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 144 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.075892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.047649 restraints weight = 76458.365| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.41 r_work: 0.2750 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23707 Z= 0.189 Angle : 0.594 8.479 32047 Z= 0.304 Chirality : 0.044 0.157 3544 Planarity : 0.004 0.045 4130 Dihedral : 5.391 97.735 3236 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.40 % Allowed : 5.21 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.16), residues: 2907 helix: 1.69 (0.14), residues: 1365 sheet: 0.12 (0.26), residues: 406 loop : 0.21 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 254 TYR 0.020 0.001 TYR M 350 PHE 0.019 0.001 PHE E 223 TRP 0.023 0.002 TRP M 130 HIS 0.005 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00441 (23707) covalent geometry : angle 0.59424 (32047) hydrogen bonds : bond 0.04622 ( 1266) hydrogen bonds : angle 4.70940 ( 3432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.5002 (ptt) cc_final: 0.4055 (ptt) REVERT: M 690 MET cc_start: 0.8881 (mmm) cc_final: 0.8626 (mmm) REVERT: D 375 PHE cc_start: 0.7742 (t80) cc_final: 0.7530 (t80) REVERT: E 223 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: O 127 MET cc_start: 0.8444 (ppp) cc_final: 0.7997 (ppp) REVERT: O 178 ARG cc_start: 0.9127 (pmt-80) cc_final: 0.8687 (pmt-80) REVERT: P 141 MET cc_start: 0.8925 (ptp) cc_final: 0.8388 (ptp) REVERT: P 162 TYR cc_start: 0.8822 (t80) cc_final: 0.8417 (t80) outliers start: 10 outliers final: 3 residues processed: 151 average time/residue: 0.1975 time to fit residues: 45.4573 Evaluate side-chains 141 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 695 CYS Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 208 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 chunk 143 optimal weight: 0.0770 chunk 91 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 623 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.077258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.048709 restraints weight = 77360.549| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.46 r_work: 0.2782 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23707 Z= 0.104 Angle : 0.529 9.671 32047 Z= 0.267 Chirality : 0.041 0.170 3544 Planarity : 0.004 0.040 4130 Dihedral : 5.067 85.647 3236 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.56 % Allowed : 6.69 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.16), residues: 2907 helix: 1.75 (0.15), residues: 1375 sheet: 0.19 (0.26), residues: 405 loop : 0.30 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 105 TYR 0.030 0.001 TYR O 60 PHE 0.011 0.001 PHE E 223 TRP 0.026 0.001 TRP M 130 HIS 0.003 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00219 (23707) covalent geometry : angle 0.52900 (32047) hydrogen bonds : bond 0.03910 ( 1266) hydrogen bonds : angle 4.41265 ( 3432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.4552 (ptt) cc_final: 0.3657 (ptt) REVERT: M 690 MET cc_start: 0.8895 (mmm) cc_final: 0.8643 (mmm) REVERT: B 132 MET cc_start: 0.9155 (ppp) cc_final: 0.8674 (ptm) REVERT: D 227 MET cc_start: 0.8918 (mmm) cc_final: 0.8569 (mmm) REVERT: E 223 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: O 127 MET cc_start: 0.8574 (ppp) cc_final: 0.8156 (ppp) REVERT: O 178 ARG cc_start: 0.9216 (pmt-80) cc_final: 0.8790 (pmt-80) REVERT: P 141 MET cc_start: 0.9010 (ptp) cc_final: 0.8378 (ptp) REVERT: P 162 TYR cc_start: 0.8792 (t80) cc_final: 0.8363 (t80) REVERT: P 178 ARG cc_start: 0.8584 (ppt170) cc_final: 0.8172 (ppt170) outliers start: 14 outliers final: 10 residues processed: 155 average time/residue: 0.1750 time to fit residues: 41.7295 Evaluate side-chains 147 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 695 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain O residue 122 GLU Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 86 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 123 optimal weight: 0.0060 chunk 55 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN F 353 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.075403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.046735 restraints weight = 77750.097| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.44 r_work: 0.2719 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23707 Z= 0.191 Angle : 0.577 6.785 32047 Z= 0.291 Chirality : 0.043 0.162 3544 Planarity : 0.004 0.037 4130 Dihedral : 5.022 64.082 3236 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.92 % Allowed : 8.65 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.16), residues: 2907 helix: 1.82 (0.14), residues: 1351 sheet: 0.11 (0.26), residues: 408 loop : 0.26 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG O 105 TYR 0.013 0.001 TYR E 143 PHE 0.017 0.001 PHE E 223 TRP 0.030 0.002 TRP M 130 HIS 0.006 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00449 (23707) covalent geometry : angle 0.57730 (32047) hydrogen bonds : bond 0.04143 ( 1266) hydrogen bonds : angle 4.31318 ( 3432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.4760 (ptt) cc_final: 0.4002 (ptt) REVERT: M 539 MET cc_start: 0.8220 (tpp) cc_final: 0.7881 (tpt) REVERT: M 690 MET cc_start: 0.8915 (mmm) cc_final: 0.8679 (mmm) REVERT: B 283 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8589 (mtp) REVERT: D 227 MET cc_start: 0.8935 (mmm) cc_final: 0.8534 (mmm) REVERT: E 223 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8284 (m-80) REVERT: O 127 MET cc_start: 0.8573 (ppp) cc_final: 0.8111 (ppp) REVERT: P 141 MET cc_start: 0.9135 (ptp) cc_final: 0.8574 (ptp) REVERT: P 150 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.9132 (mp0) REVERT: P 162 TYR cc_start: 0.8709 (t80) cc_final: 0.8316 (t80) REVERT: P 178 ARG cc_start: 0.8544 (ppt170) cc_final: 0.8189 (ppt170) outliers start: 23 outliers final: 16 residues processed: 156 average time/residue: 0.1640 time to fit residues: 39.2505 Evaluate side-chains 157 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 695 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain O residue 122 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 235 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 5 optimal weight: 40.0000 chunk 142 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.075999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.047838 restraints weight = 76028.336| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.40 r_work: 0.2756 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23707 Z= 0.108 Angle : 0.528 7.474 32047 Z= 0.265 Chirality : 0.041 0.163 3544 Planarity : 0.003 0.040 4130 Dihedral : 4.785 54.010 3236 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.84 % Allowed : 9.70 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.16), residues: 2907 helix: 1.81 (0.14), residues: 1376 sheet: 0.11 (0.26), residues: 408 loop : 0.26 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG O 105 TYR 0.012 0.001 TYR M 350 PHE 0.014 0.001 PHE M 230 TRP 0.029 0.002 TRP M 130 HIS 0.003 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00238 (23707) covalent geometry : angle 0.52778 (32047) hydrogen bonds : bond 0.03686 ( 1266) hydrogen bonds : angle 4.19014 ( 3432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.4711 (ptt) cc_final: 0.3993 (ptt) REVERT: M 690 MET cc_start: 0.8916 (mmm) cc_final: 0.8697 (mmm) REVERT: B 132 MET cc_start: 0.9152 (ppp) cc_final: 0.8745 (ppp) REVERT: D 132 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8496 (tmm) REVERT: D 227 MET cc_start: 0.8932 (mmm) cc_final: 0.8505 (mmm) REVERT: E 223 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: O 127 MET cc_start: 0.8615 (ppp) cc_final: 0.8149 (ppp) REVERT: P 141 MET cc_start: 0.9114 (ptp) cc_final: 0.8545 (ptp) REVERT: P 150 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9093 (mp0) REVERT: P 162 TYR cc_start: 0.8697 (t80) cc_final: 0.8113 (t80) REVERT: P 178 ARG cc_start: 0.8531 (ppt170) cc_final: 0.8207 (ppt170) outliers start: 21 outliers final: 13 residues processed: 158 average time/residue: 0.1703 time to fit residues: 41.6623 Evaluate side-chains 153 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 695 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain O residue 122 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 194 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 48 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 75 GLN C 280 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.074887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.046616 restraints weight = 77079.061| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.41 r_work: 0.2717 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23707 Z= 0.178 Angle : 0.570 10.865 32047 Z= 0.287 Chirality : 0.043 0.179 3544 Planarity : 0.004 0.044 4130 Dihedral : 4.824 67.088 3236 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.20 % Allowed : 10.22 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 2907 helix: 1.88 (0.14), residues: 1360 sheet: 0.06 (0.26), residues: 408 loop : 0.26 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG O 105 TYR 0.012 0.001 TYR P 162 PHE 0.016 0.001 PHE E 223 TRP 0.030 0.002 TRP M 130 HIS 0.005 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00419 (23707) covalent geometry : angle 0.57033 (32047) hydrogen bonds : bond 0.03906 ( 1266) hydrogen bonds : angle 4.18708 ( 3432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.5267 (ptt) cc_final: 0.4430 (ptt) REVERT: M 690 MET cc_start: 0.8934 (mmm) cc_final: 0.8732 (mmm) REVERT: B 132 MET cc_start: 0.9167 (ppp) cc_final: 0.8782 (ppp) REVERT: D 132 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8513 (tmm) REVERT: D 227 MET cc_start: 0.8964 (mmm) cc_final: 0.8510 (mmm) REVERT: E 223 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: O 127 MET cc_start: 0.8616 (ppp) cc_final: 0.8139 (ppp) REVERT: O 167 ARG cc_start: 0.9234 (mmp80) cc_final: 0.8837 (mmp80) REVERT: P 141 MET cc_start: 0.9108 (ptp) cc_final: 0.8528 (ptp) REVERT: P 150 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9124 (mp0) REVERT: P 162 TYR cc_start: 0.8655 (t80) cc_final: 0.8118 (t80) REVERT: P 178 ARG cc_start: 0.8568 (ppt170) cc_final: 0.8283 (ppt170) outliers start: 30 outliers final: 17 residues processed: 166 average time/residue: 0.1734 time to fit residues: 44.3868 Evaluate side-chains 158 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 695 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain O residue 122 GLU Chi-restraints excluded: chain O residue 153 HIS Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 88 optimal weight: 0.0270 chunk 47 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 overall best weight: 2.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 HIS ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.075321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.046668 restraints weight = 77466.386| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.44 r_work: 0.2720 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23707 Z= 0.160 Angle : 0.559 9.971 32047 Z= 0.282 Chirality : 0.043 0.205 3544 Planarity : 0.004 0.043 4130 Dihedral : 4.826 62.072 3236 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.20 % Allowed : 10.94 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.16), residues: 2907 helix: 1.88 (0.14), residues: 1360 sheet: 0.04 (0.25), residues: 416 loop : 0.25 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG O 105 TYR 0.014 0.001 TYR O 60 PHE 0.015 0.001 PHE E 223 TRP 0.030 0.002 TRP M 130 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00375 (23707) covalent geometry : angle 0.55898 (32047) hydrogen bonds : bond 0.03814 ( 1266) hydrogen bonds : angle 4.14832 ( 3432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.5316 (ptt) cc_final: 0.4518 (ptt) REVERT: M 539 MET cc_start: 0.7932 (tpt) cc_final: 0.7705 (tpt) REVERT: B 132 MET cc_start: 0.9172 (ppp) cc_final: 0.8826 (ppp) REVERT: D 132 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8470 (tmm) REVERT: E 223 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: O 127 MET cc_start: 0.8645 (ppp) cc_final: 0.8161 (ppp) REVERT: O 178 ARG cc_start: 0.9126 (ppt170) cc_final: 0.8613 (pmt-80) REVERT: P 141 MET cc_start: 0.9136 (ptp) cc_final: 0.8563 (ptp) REVERT: P 150 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9113 (mp0) REVERT: P 162 TYR cc_start: 0.8684 (t80) cc_final: 0.8129 (t80) REVERT: P 178 ARG cc_start: 0.8576 (ppt170) cc_final: 0.8295 (ppt170) outliers start: 30 outliers final: 21 residues processed: 163 average time/residue: 0.1734 time to fit residues: 43.4972 Evaluate side-chains 162 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 695 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain O residue 122 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 10 optimal weight: 7.9990 chunk 274 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN F 371 HIS ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.074785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.046082 restraints weight = 77200.513| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.43 r_work: 0.2703 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23707 Z= 0.187 Angle : 0.582 8.580 32047 Z= 0.292 Chirality : 0.043 0.216 3544 Planarity : 0.004 0.052 4130 Dihedral : 4.884 58.039 3236 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.28 % Allowed : 11.14 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.16), residues: 2907 helix: 1.86 (0.14), residues: 1359 sheet: 0.04 (0.26), residues: 408 loop : 0.19 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG O 105 TYR 0.014 0.001 TYR O 60 PHE 0.017 0.001 PHE E 223 TRP 0.028 0.002 TRP M 130 HIS 0.005 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00443 (23707) covalent geometry : angle 0.58177 (32047) hydrogen bonds : bond 0.03946 ( 1266) hydrogen bonds : angle 4.17418 ( 3432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.5485 (ptt) cc_final: 0.4677 (ptt) REVERT: M 539 MET cc_start: 0.8009 (tpt) cc_final: 0.7791 (tpt) REVERT: D 132 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8558 (tmm) REVERT: D 227 MET cc_start: 0.8968 (mmm) cc_final: 0.8346 (mmm) REVERT: E 223 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: O 127 MET cc_start: 0.8643 (ppp) cc_final: 0.8156 (ppp) REVERT: P 105 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8025 (ppt170) REVERT: P 141 MET cc_start: 0.9068 (ptp) cc_final: 0.8476 (ptp) REVERT: P 150 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.9096 (mp0) REVERT: P 162 TYR cc_start: 0.8707 (t80) cc_final: 0.7648 (t80) REVERT: P 178 ARG cc_start: 0.8557 (ppt170) cc_final: 0.8246 (ppt170) outliers start: 32 outliers final: 25 residues processed: 168 average time/residue: 0.1914 time to fit residues: 48.6688 Evaluate side-chains 167 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 695 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain O residue 122 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 160 ARG Chi-restraints excluded: chain P residue 204 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 9 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 176 optimal weight: 0.0070 chunk 29 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 135 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.076048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.047548 restraints weight = 77372.720| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.44 r_work: 0.2746 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23707 Z= 0.106 Angle : 0.550 13.303 32047 Z= 0.276 Chirality : 0.042 0.255 3544 Planarity : 0.004 0.175 4130 Dihedral : 4.761 53.929 3236 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.16 % Allowed : 11.50 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.16), residues: 2907 helix: 1.80 (0.14), residues: 1382 sheet: 0.07 (0.26), residues: 418 loop : 0.26 (0.20), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG O 105 TYR 0.017 0.001 TYR O 60 PHE 0.013 0.001 PHE E 223 TRP 0.032 0.002 TRP M 130 HIS 0.003 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00233 (23707) covalent geometry : angle 0.55035 (32047) hydrogen bonds : bond 0.03587 ( 1266) hydrogen bonds : angle 4.09714 ( 3432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.5268 (ptt) cc_final: 0.4506 (ptt) REVERT: M 539 MET cc_start: 0.7961 (tpt) cc_final: 0.7750 (tpt) REVERT: M 684 MET cc_start: 0.5975 (mtm) cc_final: 0.5695 (mtt) REVERT: B 132 MET cc_start: 0.9148 (ppp) cc_final: 0.8826 (ppp) REVERT: D 132 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8463 (tmm) REVERT: D 227 MET cc_start: 0.8986 (mmm) cc_final: 0.8663 (tpp) REVERT: E 223 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: O 105 ARG cc_start: 0.8862 (pmt-80) cc_final: 0.8536 (pmt-80) REVERT: O 178 ARG cc_start: 0.9081 (ppt170) cc_final: 0.8544 (pmt-80) REVERT: P 105 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8029 (ppt170) REVERT: P 141 MET cc_start: 0.9084 (ptp) cc_final: 0.8464 (ptp) REVERT: P 150 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.9117 (mp0) REVERT: P 178 ARG cc_start: 0.8541 (ppt170) cc_final: 0.8231 (ppt170) outliers start: 29 outliers final: 17 residues processed: 159 average time/residue: 0.1758 time to fit residues: 43.0133 Evaluate side-chains 159 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 695 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain O residue 122 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 160 ARG Chi-restraints excluded: chain P residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 226 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 180 optimal weight: 0.0070 chunk 234 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.075594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.047531 restraints weight = 76547.990| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.39 r_work: 0.2745 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23707 Z= 0.117 Angle : 0.577 20.989 32047 Z= 0.287 Chirality : 0.042 0.235 3544 Planarity : 0.004 0.157 4130 Dihedral : 4.698 51.229 3236 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.88 % Allowed : 11.70 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 2907 helix: 1.83 (0.14), residues: 1385 sheet: 0.05 (0.26), residues: 418 loop : 0.30 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG O 105 TYR 0.017 0.001 TYR O 60 PHE 0.016 0.001 PHE M 230 TRP 0.034 0.002 TRP M 130 HIS 0.003 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00263 (23707) covalent geometry : angle 0.57670 (32047) hydrogen bonds : bond 0.03616 ( 1266) hydrogen bonds : angle 4.09779 ( 3432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.5390 (ptt) cc_final: 0.4626 (ptt) REVERT: M 684 MET cc_start: 0.5993 (mtm) cc_final: 0.5711 (mtt) REVERT: B 132 MET cc_start: 0.9114 (ppp) cc_final: 0.8825 (ppp) REVERT: D 123 MET cc_start: 0.9329 (tpp) cc_final: 0.9042 (tpt) REVERT: D 132 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8455 (tmm) REVERT: D 227 MET cc_start: 0.8983 (mmm) cc_final: 0.8666 (tpp) REVERT: E 223 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: P 105 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8134 (ppt170) REVERT: P 141 MET cc_start: 0.9019 (ptp) cc_final: 0.8474 (ptp) REVERT: P 150 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9115 (mp0) REVERT: P 178 ARG cc_start: 0.8529 (ppt170) cc_final: 0.8221 (ppt170) outliers start: 22 outliers final: 18 residues processed: 156 average time/residue: 0.1777 time to fit residues: 42.1306 Evaluate side-chains 161 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 695 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain O residue 122 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 150 GLU Chi-restraints excluded: chain P residue 160 ARG Chi-restraints excluded: chain P residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 283 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 152 optimal weight: 0.0370 chunk 121 optimal weight: 0.5980 chunk 204 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 274 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 287 optimal weight: 10.0000 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.076903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.048540 restraints weight = 77031.102| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.43 r_work: 0.2776 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 23707 Z= 0.099 Angle : 0.569 18.557 32047 Z= 0.285 Chirality : 0.042 0.245 3544 Planarity : 0.004 0.141 4130 Dihedral : 4.542 46.396 3236 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.84 % Allowed : 11.78 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.16), residues: 2907 helix: 1.87 (0.14), residues: 1385 sheet: 0.06 (0.25), residues: 418 loop : 0.43 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG O 105 TYR 0.018 0.001 TYR O 60 PHE 0.011 0.001 PHE E 223 TRP 0.034 0.002 TRP M 130 HIS 0.002 0.001 HIS M 153 Details of bonding type rmsd covalent geometry : bond 0.00207 (23707) covalent geometry : angle 0.56944 (32047) hydrogen bonds : bond 0.03437 ( 1266) hydrogen bonds : angle 4.07352 ( 3432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7290.38 seconds wall clock time: 125 minutes 3.43 seconds (7503.43 seconds total)