Starting phenix.real_space_refine on Sun Aug 24 22:10:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8enc_28270/08_2025/8enc_28270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8enc_28270/08_2025/8enc_28270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8enc_28270/08_2025/8enc_28270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8enc_28270/08_2025/8enc_28270.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8enc_28270/08_2025/8enc_28270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8enc_28270/08_2025/8enc_28270.map" } resolution = 3.6 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= 0.002 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 14642 2.51 5 N 3940 2.21 5 O 4485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23220 Number of models: 1 Model: "" Number of chains: 13 Chain: "M" Number of atoms: 5938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5938 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: 6.01, per 1000 atoms: 0.26 Number of scatterers: 23220 At special positions: 0 Unit cell: (159.544, 108.878, 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 4485 8.00 N 3940 7.00 C 14642 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: 2.15 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 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: 5460 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 33 sheets defined 57.4% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'M' and resid 6 through 11 removed outlier: 6.480A 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: 3.971A pdb=" N THR M 28 " --> pdb=" O LEU M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 76 removed outlier: 3.660A pdb=" N GLN M 75 " --> pdb=" O LYS M 72 " (cutoff:3.500A) removed outlier: 3.988A 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: 3.517A pdb=" N VAL M 101 " --> pdb=" O HIS M 97 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 134 removed outlier: 4.098A 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: 3.637A pdb=" N VAL M 139 " --> pdb=" O THR M 135 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG M 143 " --> pdb=" O VAL M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 168 removed outlier: 3.835A 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: 4.157A pdb=" N ILE M 274 " --> pdb=" O LYS M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 290 removed outlier: 4.258A pdb=" N TYR M 287 " --> pdb=" O TYR M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 302 removed outlier: 3.973A pdb=" N LEU M 298 " --> pdb=" O LYS M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 315 removed outlier: 3.727A pdb=" N SER M 314 " --> pdb=" O TYR M 310 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN M 315 " --> pdb=" O ALA M 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 310 through 315' Processing helix chain 'M' and resid 324 through 338 removed outlier: 3.678A pdb=" N GLU M 328 " --> pdb=" O ASP M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 359 removed outlier: 3.765A pdb=" N LYS M 346 " --> pdb=" O THR M 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE M 359 " --> pdb=" O ALA M 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 360 through 362 No H-bonds generated for 'chain 'M' and resid 360 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: 4.822A pdb=" N CYS M 520 " --> pdb=" O ASP M 516 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE M 521 " --> pdb=" O LEU M 517 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 540 removed outlier: 3.642A 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: 3.538A pdb=" N LYS M 596 " --> pdb=" O GLY M 592 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS M 598 " --> pdb=" O LEU M 594 " (cutoff:3.500A) Processing helix chain 'M' and resid 602 through 612 Processing helix chain 'M' and resid 615 through 620 removed outlier: 4.071A pdb=" N THR M 619 " --> pdb=" O LYS M 615 " (cutoff:3.500A) Processing helix chain 'M' and resid 646 through 663 removed outlier: 3.532A pdb=" N LEU M 650 " --> pdb=" O THR M 646 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN M 661 " --> pdb=" O LYS M 657 " (cutoff:3.500A) Processing helix chain 'M' and resid 685 through 697 Processing helix chain 'M' and resid 697 through 707 removed outlier: 3.510A pdb=" N LYS M 707 " --> pdb=" O ARG M 703 " (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: 3.875A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 4.036A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.672A 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: 3.720A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.631A 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: 3.857A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.604A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.644A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.778A 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 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.554A 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: 4.043A 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: 3.750A 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: 3.785A 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: 3.672A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.933A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.671A 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: 3.871A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.889A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.968A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.623A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.803A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.230A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.525A 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: 3.822A 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 349 through 355 removed outlier: 4.080A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.753A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.768A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.562A 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: 3.841A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.598A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.772A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.547A pdb=" N ARG D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.642A pdb=" N GLU D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.596A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.290A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.674A 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: 3.512A 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: 3.529A 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: 3.506A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.909A 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: 3.665A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.621A pdb=" N GLY E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.610A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 204 through 217 removed outlier: 4.026A 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 252 through 260 removed outlier: 3.664A pdb=" N ARG E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix No H-bonds generated for 'chain 'E' and resid 252 through 260' Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 285 removed outlier: 3.816A 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: 4.356A 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 350 through 356 removed outlier: 3.586A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 removed outlier: 4.072A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.944A pdb=" N GLN F 59 " --> pdb=" O GLY F 55 " (cutoff:3.500A) removed outlier: 3.674A 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: 3.579A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.538A 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: 3.858A 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 removed outlier: 3.503A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 217 removed outlier: 4.042A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 removed outlier: 3.504A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.623A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 removed outlier: 4.314A 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: 3.529A 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: 4.172A 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: 4.002A 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: 3.682A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 210 removed outlier: 4.658A pdb=" N GLN O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 208 removed outlier: 3.556A 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: 3.610A 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: 7.226A pdb=" N THR M 60 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ARG M 54 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 6.330A 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: 6.039A pdb=" N CYS M 122 " --> pdb=" O ARG M 671 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE M 673 " --> pdb=" O CYS M 122 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR M 124 " --> pdb=" O ILE M 673 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER M 173 " --> pdb=" O HIS M 668 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL M 670 " --> pdb=" O SER M 173 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU M 175 " --> pdb=" O VAL M 670 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N CYS M 672 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR M 177 " --> pdb=" O CYS M 672 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN M 172 " --> pdb=" O PHE M 456 " (cutoff:3.500A) removed outlier: 3.627A 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 563 through 564 removed outlier: 3.598A 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: 3.805A 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: 3.564A pdb=" N GLY B 20 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.501A 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: 6.848A 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: 4.906A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 5.715A 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: 6.808A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 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: 6.414A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 7.015A 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: 4.387A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.373A 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: 6.727A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.419A 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: 6.813A 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: 4.121A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.615A 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: 6.217A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.867A 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: 6.812A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.456A 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: 3.633A 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: 6.275A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.880A 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: 5.048A pdb=" N LEU F 242 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLN F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) 1276 hydrogen bonds defined for protein. 3459 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: 5.01 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7504 1.34 - 1.46: 3004 1.46 - 1.57: 12907 1.57 - 1.69: 15 1.69 - 1.81: 241 Bond restraints: 23671 Sorted by residual: bond pdb=" N LYS M 640 " pdb=" CA LYS M 640 " ideal model delta sigma weight residual 1.456 1.476 -0.019 1.21e-02 6.83e+03 2.56e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.55e+00 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.39e+00 ... (remaining 23666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 31473 1.76 - 3.52: 411 3.52 - 5.28: 82 5.28 - 7.04: 28 7.04 - 8.79: 4 Bond angle restraints: 31998 Sorted by residual: angle pdb=" CA ARG O 105 " pdb=" CB ARG O 105 " pdb=" CG ARG O 105 " ideal model delta sigma weight residual 114.10 122.43 -8.33 2.00e+00 2.50e-01 1.74e+01 angle pdb=" C LEU P 110 " pdb=" N GLN P 111 " pdb=" CA GLN P 111 " ideal model delta sigma weight residual 120.29 114.60 5.69 1.42e+00 4.96e-01 1.61e+01 angle pdb=" N GLN P 111 " pdb=" CA GLN P 111 " pdb=" CB GLN P 111 " ideal model delta sigma weight residual 110.16 115.87 -5.71 1.48e+00 4.57e-01 1.49e+01 angle pdb=" C GLU O 104 " pdb=" N ARG O 105 " pdb=" CA ARG O 105 " ideal model delta sigma weight residual 121.58 114.11 7.47 1.95e+00 2.63e-01 1.47e+01 angle pdb=" N LYS M 640 " pdb=" CA LYS M 640 " pdb=" C LYS M 640 " ideal model delta sigma weight residual 109.07 115.10 -6.03 1.61e+00 3.86e-01 1.40e+01 ... (remaining 31993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 13574 23.62 - 47.24: 695 47.24 - 70.86: 94 70.86 - 94.48: 26 94.48 - 118.10: 3 Dihedral angle restraints: 14392 sinusoidal: 5899 harmonic: 8493 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.11 118.10 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -174.39 114.39 1 2.00e+01 2.50e-03 3.39e+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 -168.86 108.86 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 14389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2640 0.037 - 0.074: 597 0.074 - 0.111: 234 0.111 - 0.148: 63 0.148 - 0.186: 2 Chirality restraints: 3536 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 2.32 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CA ILE M 174 " pdb=" N ILE M 174 " pdb=" C ILE M 174 " pdb=" CB ILE M 174 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE M 585 " pdb=" N ILE M 585 " pdb=" C ILE M 585 " pdb=" CB ILE M 585 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 3533 not shown) Planarity restraints: 4125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN M 80 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO M 81 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO M 81 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO M 81 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 182 " 0.031 9.50e-02 1.11e+02 1.89e-02 2.14e+00 pdb=" NE ARG P 182 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG P 182 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG P 182 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG P 182 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG O 105 " 0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C ARG O 105 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG O 105 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU O 106 " 0.008 2.00e-02 2.50e+03 ... (remaining 4122 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 99 2.48 - 3.08: 16678 3.08 - 3.69: 35059 3.69 - 4.29: 49451 4.29 - 4.90: 84238 Nonbonded interactions: 185525 Sorted by model distance: nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.869 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 1.990 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.004 2.170 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.080 3.040 nonbonded pdb=" O CYS M 538 " pdb=" NZ LYS M 598 " model vdw 2.119 3.120 ... (remaining 185520 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.060 Find NCS groups from input model: 0.370 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 0.035 23671 Z= 0.129 Angle : 0.566 8.794 31998 Z= 0.305 Chirality : 0.039 0.186 3536 Planarity : 0.003 0.037 4125 Dihedral : 14.184 118.104 8932 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 0.08 % Allowed : 0.28 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.17), residues: 2907 helix: 2.16 (0.15), residues: 1357 sheet: 0.22 (0.25), residues: 414 loop : 0.49 (0.20), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG P 182 TYR 0.020 0.001 TYR B 279 PHE 0.015 0.001 PHE E 223 TRP 0.007 0.001 TRP B 340 HIS 0.010 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00252 (23671) covalent geometry : angle 0.56591 (31998) hydrogen bonds : bond 0.13703 ( 1268) hydrogen bonds : angle 5.45349 ( 3459) *********************** 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 208 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 0.830 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: 0.8355 (ptp) cc_final: 0.8097 (pmm) REVERT: M 165 MET cc_start: 0.9242 (tmm) cc_final: 0.8844 (tmm) REVERT: M 362 MET cc_start: 0.8776 (mmm) cc_final: 0.8526 (mmm) REVERT: M 493 MET cc_start: 0.8839 (ttp) cc_final: 0.8458 (ppp) REVERT: M 585 ILE cc_start: 0.9564 (mt) cc_final: 0.9183 (tp) REVERT: M 690 MET cc_start: 0.9180 (mmm) cc_final: 0.8579 (mmm) REVERT: M 693 LEU cc_start: 0.9190 (tt) cc_final: 0.8912 (pp) REVERT: M 765 PHE cc_start: 0.8706 (m-80) cc_final: 0.8375 (m-10) REVERT: B 82 MET cc_start: 0.8986 (tpt) cc_final: 0.8607 (tpt) REVERT: C 374 CYS cc_start: 0.6436 (p) cc_final: 0.5832 (m) REVERT: E 283 MET cc_start: 0.9015 (mmt) cc_final: 0.8760 (mmt) REVERT: F 227 MET cc_start: 0.8972 (mmm) cc_final: 0.8709 (tpp) REVERT: O 105 ARG cc_start: 0.9103 (pmt170) cc_final: 0.8525 (pmt170) REVERT: O 178 ARG cc_start: 0.8793 (pmt-80) cc_final: 0.8552 (pmt-80) REVERT: P 127 MET cc_start: 0.9150 (ptp) cc_final: 0.8948 (mmt) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.1993 time to fit residues: 61.6185 Evaluate side-chains 158 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 104 ASN M 172 GLN ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.066279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.042499 restraints weight = 99527.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.043899 restraints weight = 43541.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.044803 restraints weight = 25280.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.045345 restraints weight = 17661.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.045660 restraints weight = 14165.676| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23671 Z= 0.126 Angle : 0.569 8.079 31998 Z= 0.288 Chirality : 0.042 0.159 3536 Planarity : 0.004 0.042 4125 Dihedral : 5.375 102.708 3235 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 0.52 % Allowed : 5.14 % Favored : 94.34 % 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 aren not related in a simple way. whole: 1.66 (0.16), residues: 2907 helix: 1.98 (0.15), residues: 1373 sheet: 0.24 (0.26), residues: 402 loop : 0.46 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 101 TYR 0.016 0.001 TYR B 279 PHE 0.023 0.001 PHE E 223 TRP 0.007 0.001 TRP F 79 HIS 0.006 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00278 (23671) covalent geometry : angle 0.56930 (31998) hydrogen bonds : bond 0.04101 ( 1268) hydrogen bonds : angle 4.44390 ( 3459) *********************** 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 185 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 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: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8617 (ptp) cc_final: 0.8179 (pmm) REVERT: M 165 MET cc_start: 0.9362 (tmm) cc_final: 0.9113 (tmm) REVERT: M 362 MET cc_start: 0.8996 (mmm) cc_final: 0.8762 (mmm) REVERT: M 493 MET cc_start: 0.8839 (ttp) cc_final: 0.8347 (ppp) REVERT: M 585 ILE cc_start: 0.9539 (mt) cc_final: 0.9125 (tp) REVERT: M 693 LEU cc_start: 0.9183 (tt) cc_final: 0.8977 (pp) REVERT: M 740 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8295 (pptt) REVERT: M 765 PHE cc_start: 0.8943 (m-80) cc_final: 0.8666 (m-80) REVERT: C 374 CYS cc_start: 0.6466 (p) cc_final: 0.5842 (m) REVERT: F 227 MET cc_start: 0.9067 (mmm) cc_final: 0.8788 (tpp) REVERT: P 153 HIS cc_start: 0.8940 (m-70) cc_final: 0.8674 (m90) outliers start: 13 outliers final: 4 residues processed: 182 average time/residue: 0.1724 time to fit residues: 47.3786 Evaluate side-chains 163 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 139 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 289 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 219 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** 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 = 0.3517 r_free = 0.3517 target = 0.066191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.042351 restraints weight = 99439.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.043760 restraints weight = 43427.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.044656 restraints weight = 25076.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045203 restraints weight = 17550.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.045509 restraints weight = 14084.899| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23671 Z= 0.116 Angle : 0.542 8.438 31998 Z= 0.271 Chirality : 0.041 0.155 3536 Planarity : 0.004 0.054 4125 Dihedral : 5.146 96.130 3235 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 0.64 % Allowed : 7.39 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.16), residues: 2907 helix: 2.03 (0.15), residues: 1362 sheet: 0.27 (0.25), residues: 427 loop : 0.47 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 125 TYR 0.041 0.001 TYR O 60 PHE 0.012 0.001 PHE M 488 TRP 0.007 0.001 TRP F 79 HIS 0.008 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00251 (23671) covalent geometry : angle 0.54151 (31998) hydrogen bonds : bond 0.03687 ( 1268) hydrogen bonds : angle 4.20026 ( 3459) *********************** 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 181 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.688 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: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8763 (ptp) cc_final: 0.8306 (pmm) REVERT: M 165 MET cc_start: 0.9372 (tmm) cc_final: 0.8525 (tpp) REVERT: M 357 MET cc_start: 0.8381 (tmm) cc_final: 0.8005 (tpp) REVERT: M 362 MET cc_start: 0.9037 (mmm) cc_final: 0.8786 (mmm) REVERT: M 433 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8846 (tm-30) REVERT: M 493 MET cc_start: 0.8927 (ttp) cc_final: 0.8349 (tmm) REVERT: M 740 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8369 (pptt) REVERT: M 765 PHE cc_start: 0.8756 (m-80) cc_final: 0.8552 (m-80) REVERT: C 305 MET cc_start: 0.9514 (mmm) cc_final: 0.9267 (mmt) REVERT: C 374 CYS cc_start: 0.6518 (p) cc_final: 0.5843 (m) REVERT: E 82 MET cc_start: 0.9376 (tpp) cc_final: 0.9162 (tpt) REVERT: E 283 MET cc_start: 0.8872 (mmt) cc_final: 0.8654 (mmt) REVERT: F 227 MET cc_start: 0.9104 (mmm) cc_final: 0.8803 (tpp) REVERT: F 305 MET cc_start: 0.9430 (mmm) cc_final: 0.9164 (tpp) REVERT: O 127 MET cc_start: 0.8944 (ppp) cc_final: 0.8662 (ppp) outliers start: 16 outliers final: 7 residues processed: 176 average time/residue: 0.1734 time to fit residues: 46.0707 Evaluate side-chains 161 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 95 optimal weight: 0.2980 chunk 268 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 289 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 171 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 296 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 153 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.065345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.041555 restraints weight = 99505.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.042915 restraints weight = 44249.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.043770 restraints weight = 25950.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.044305 restraints weight = 18303.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.044622 restraints weight = 14706.542| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23671 Z= 0.109 Angle : 0.535 9.376 31998 Z= 0.265 Chirality : 0.041 0.169 3536 Planarity : 0.003 0.036 4125 Dihedral : 4.964 92.001 3235 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.59 % Rotamer: Outliers : 0.68 % Allowed : 8.72 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.16), residues: 2907 helix: 2.08 (0.15), residues: 1363 sheet: 0.30 (0.25), residues: 427 loop : 0.55 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 125 TYR 0.042 0.001 TYR O 60 PHE 0.010 0.001 PHE E 223 TRP 0.012 0.001 TRP M 593 HIS 0.013 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00238 (23671) covalent geometry : angle 0.53484 (31998) hydrogen bonds : bond 0.03548 ( 1268) hydrogen bonds : angle 4.07392 ( 3459) *********************** 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 178 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.768 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8827 (ptp) cc_final: 0.8406 (pmm) REVERT: M 165 MET cc_start: 0.9363 (tmm) cc_final: 0.8479 (tpp) REVERT: M 357 MET cc_start: 0.8388 (tmm) cc_final: 0.7926 (tpt) REVERT: M 433 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8882 (tm-30) REVERT: M 493 MET cc_start: 0.8905 (ttp) cc_final: 0.8358 (tmm) REVERT: M 740 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8379 (pptt) REVERT: C 305 MET cc_start: 0.9548 (mmm) cc_final: 0.9286 (mmt) REVERT: C 374 CYS cc_start: 0.6729 (p) cc_final: 0.6192 (m) REVERT: E 283 MET cc_start: 0.8914 (mmt) cc_final: 0.8702 (mmt) REVERT: F 227 MET cc_start: 0.9138 (mmm) cc_final: 0.8803 (tpp) REVERT: P 135 GLN cc_start: 0.9298 (mm-40) cc_final: 0.9048 (pp30) outliers start: 17 outliers final: 8 residues processed: 173 average time/residue: 0.1664 time to fit residues: 43.7849 Evaluate side-chains 160 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 66 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 223 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 247 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 371 HIS ** P 153 HIS ** 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 = 0.3450 r_free = 0.3450 target = 0.063631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.039830 restraints weight = 99630.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.041165 restraints weight = 44069.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.042044 restraints weight = 25843.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.042573 restraints weight = 18166.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.042846 restraints weight = 14605.837| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23671 Z= 0.187 Angle : 0.591 10.909 31998 Z= 0.294 Chirality : 0.042 0.188 3536 Planarity : 0.004 0.034 4125 Dihedral : 5.016 84.465 3235 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 1.21 % Allowed : 9.64 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.16), residues: 2907 helix: 2.00 (0.15), residues: 1378 sheet: 0.21 (0.26), residues: 412 loop : 0.59 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 125 TYR 0.038 0.001 TYR O 60 PHE 0.020 0.001 PHE E 223 TRP 0.011 0.001 TRP M 593 HIS 0.023 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00425 (23671) covalent geometry : angle 0.59089 (31998) hydrogen bonds : bond 0.03803 ( 1268) hydrogen bonds : angle 4.10954 ( 3459) *********************** 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 182 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.951 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: 0.8911 (ptp) cc_final: 0.8424 (pmm) REVERT: M 90 MET cc_start: 0.8505 (mmm) cc_final: 0.8192 (mmp) REVERT: M 165 MET cc_start: 0.9327 (tmm) cc_final: 0.8377 (tpp) REVERT: M 357 MET cc_start: 0.8466 (tmm) cc_final: 0.8002 (tpt) REVERT: M 493 MET cc_start: 0.8937 (ttp) cc_final: 0.8417 (tmm) REVERT: M 593 TRP cc_start: 0.8676 (m-10) cc_final: 0.8212 (m-10) REVERT: M 690 MET cc_start: 0.9306 (mmm) cc_final: 0.9015 (mmm) REVERT: M 740 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8438 (pptt) REVERT: C 374 CYS cc_start: 0.6308 (p) cc_final: 0.5533 (m) REVERT: E 82 MET cc_start: 0.9437 (tpp) cc_final: 0.9229 (tpt) REVERT: E 223 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: E 283 MET cc_start: 0.8931 (mmt) cc_final: 0.8728 (mmt) REVERT: F 227 MET cc_start: 0.9158 (mmm) cc_final: 0.8810 (tpp) REVERT: O 127 MET cc_start: 0.8903 (ppp) cc_final: 0.8476 (ppp) outliers start: 30 outliers final: 15 residues processed: 174 average time/residue: 0.1770 time to fit residues: 46.9091 Evaluate side-chains 166 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain M residue 530 ILE Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 202 ASN Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 276 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.064001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.040224 restraints weight = 99356.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.041592 restraints weight = 43761.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.042469 restraints weight = 25517.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.042985 restraints weight = 17917.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.043333 restraints weight = 14446.212| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23671 Z= 0.135 Angle : 0.559 9.365 31998 Z= 0.279 Chirality : 0.041 0.202 3536 Planarity : 0.003 0.041 4125 Dihedral : 4.956 84.673 3235 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.52 % Rotamer: Outliers : 0.68 % Allowed : 10.57 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.16), residues: 2907 helix: 2.02 (0.15), residues: 1384 sheet: 0.19 (0.26), residues: 412 loop : 0.63 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 160 TYR 0.043 0.001 TYR O 60 PHE 0.019 0.001 PHE E 223 TRP 0.008 0.001 TRP F 79 HIS 0.006 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00305 (23671) covalent geometry : angle 0.55882 (31998) hydrogen bonds : bond 0.03565 ( 1268) hydrogen bonds : angle 4.05240 ( 3459) *********************** 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 171 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.798 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: 0.8943 (ptp) cc_final: 0.8497 (pmm) REVERT: M 165 MET cc_start: 0.9335 (tmm) cc_final: 0.8361 (tpp) REVERT: M 493 MET cc_start: 0.8960 (ttp) cc_final: 0.8410 (tmm) REVERT: M 593 TRP cc_start: 0.8614 (m-10) cc_final: 0.8129 (m-10) REVERT: M 690 MET cc_start: 0.9289 (mmm) cc_final: 0.9015 (mmm) REVERT: M 740 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8436 (pptt) REVERT: C 374 CYS cc_start: 0.6479 (p) cc_final: 0.5877 (m) REVERT: E 223 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: F 227 MET cc_start: 0.9167 (mmm) cc_final: 0.8810 (tpp) REVERT: O 127 MET cc_start: 0.8686 (ppp) cc_final: 0.8401 (ppp) REVERT: P 135 GLN cc_start: 0.9285 (mm-40) cc_final: 0.9051 (pp30) outliers start: 17 outliers final: 14 residues processed: 165 average time/residue: 0.1931 time to fit residues: 47.9453 Evaluate side-chains 166 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 3 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS O 103 GLN ** O 153 HIS ** 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 = 0.3458 r_free = 0.3458 target = 0.063865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.040118 restraints weight = 99328.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.041482 restraints weight = 43755.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.042362 restraints weight = 25504.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.042842 restraints weight = 17905.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.043215 restraints weight = 14534.563| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23671 Z= 0.133 Angle : 0.563 10.298 31998 Z= 0.279 Chirality : 0.041 0.174 3536 Planarity : 0.003 0.038 4125 Dihedral : 4.897 81.272 3235 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 0.88 % Allowed : 10.89 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.16), residues: 2907 helix: 2.03 (0.15), residues: 1378 sheet: 0.19 (0.25), residues: 449 loop : 0.67 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 105 TYR 0.043 0.001 TYR O 60 PHE 0.019 0.001 PHE E 223 TRP 0.008 0.001 TRP F 79 HIS 0.008 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00300 (23671) covalent geometry : angle 0.56279 (31998) hydrogen bonds : bond 0.03560 ( 1268) hydrogen bonds : angle 4.00658 ( 3459) *********************** 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 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.874 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: 0.8892 (ptp) cc_final: 0.8598 (pmm) REVERT: M 165 MET cc_start: 0.9339 (tmm) cc_final: 0.8357 (tpp) REVERT: M 357 MET cc_start: 0.8545 (tmm) cc_final: 0.7895 (tpp) REVERT: M 493 MET cc_start: 0.8972 (ttp) cc_final: 0.8409 (tmm) REVERT: M 593 TRP cc_start: 0.8694 (m-10) cc_final: 0.8181 (m-10) REVERT: M 690 MET cc_start: 0.9304 (mmm) cc_final: 0.9029 (mmm) REVERT: M 740 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8455 (pptt) REVERT: C 374 CYS cc_start: 0.6431 (p) cc_final: 0.5789 (m) REVERT: E 223 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: F 107 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: F 227 MET cc_start: 0.9177 (mmm) cc_final: 0.8821 (tpp) REVERT: O 127 MET cc_start: 0.8755 (ppp) cc_final: 0.8519 (ppp) REVERT: O 141 MET cc_start: 0.8887 (mmt) cc_final: 0.8487 (mpp) outliers start: 22 outliers final: 16 residues processed: 167 average time/residue: 0.1821 time to fit residues: 46.3519 Evaluate side-chains 166 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 30 optimal weight: 0.9990 chunk 280 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 290 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS F 111 ASN ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 HIS ** 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 = 0.3460 r_free = 0.3460 target = 0.063890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.040209 restraints weight = 99133.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.041567 restraints weight = 43596.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.042450 restraints weight = 25423.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.042970 restraints weight = 17844.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.043248 restraints weight = 14367.054| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23671 Z= 0.124 Angle : 0.560 10.696 31998 Z= 0.277 Chirality : 0.041 0.169 3536 Planarity : 0.003 0.034 4125 Dihedral : 4.851 78.977 3235 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.52 % Rotamer: Outliers : 0.96 % Allowed : 11.21 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.16), residues: 2907 helix: 2.02 (0.15), residues: 1389 sheet: 0.24 (0.26), residues: 414 loop : 0.71 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG O 178 TYR 0.045 0.001 TYR O 60 PHE 0.019 0.001 PHE E 223 TRP 0.008 0.001 TRP F 79 HIS 0.008 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00278 (23671) covalent geometry : angle 0.55961 (31998) hydrogen bonds : bond 0.03517 ( 1268) hydrogen bonds : angle 3.98604 ( 3459) *********************** 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 175 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.005 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: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.9024 (ptp) cc_final: 0.8726 (pmm) REVERT: M 90 MET cc_start: 0.8371 (mmm) cc_final: 0.8071 (mmp) REVERT: M 165 MET cc_start: 0.9332 (tmm) cc_final: 0.8328 (tpp) REVERT: M 357 MET cc_start: 0.8568 (tmm) cc_final: 0.8145 (tpp) REVERT: M 493 MET cc_start: 0.8966 (ttp) cc_final: 0.8409 (tmm) REVERT: M 593 TRP cc_start: 0.8728 (m-10) cc_final: 0.8198 (m-10) REVERT: M 690 MET cc_start: 0.9321 (mmm) cc_final: 0.9025 (mmm) REVERT: M 740 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8493 (pptt) REVERT: C 374 CYS cc_start: 0.6426 (p) cc_final: 0.5871 (m) REVERT: D 132 MET cc_start: 0.8614 (tmm) cc_final: 0.8374 (tmm) REVERT: E 47 MET cc_start: 0.8054 (tpp) cc_final: 0.7682 (tpp) REVERT: E 223 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: F 107 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8462 (tm-30) REVERT: F 227 MET cc_start: 0.9179 (mmm) cc_final: 0.8656 (tpp) REVERT: O 127 MET cc_start: 0.8803 (ppp) cc_final: 0.8577 (ppp) outliers start: 24 outliers final: 16 residues processed: 169 average time/residue: 0.2033 time to fit residues: 51.8225 Evaluate side-chains 167 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 83 optimal weight: 0.0470 chunk 148 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 GLN ** O 153 HIS ** 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 = 0.3466 r_free = 0.3466 target = 0.064128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.040522 restraints weight = 99360.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.041902 restraints weight = 43605.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.042785 restraints weight = 25328.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.043296 restraints weight = 17738.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.043656 restraints weight = 14290.278| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23671 Z= 0.107 Angle : 0.568 12.509 31998 Z= 0.278 Chirality : 0.041 0.175 3536 Planarity : 0.003 0.044 4125 Dihedral : 4.764 77.413 3235 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 0.84 % Allowed : 11.49 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.16), residues: 2907 helix: 2.05 (0.14), residues: 1388 sheet: 0.26 (0.26), residues: 414 loop : 0.76 (0.20), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG P 160 TYR 0.046 0.001 TYR O 60 PHE 0.019 0.001 PHE E 223 TRP 0.008 0.001 TRP F 79 HIS 0.008 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00235 (23671) covalent geometry : angle 0.56774 (31998) hydrogen bonds : bond 0.03450 ( 1268) hydrogen bonds : angle 3.95745 ( 3459) *********************** 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 172 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.924 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: 0.8945 (ptp) cc_final: 0.8712 (pmm) REVERT: M 90 MET cc_start: 0.8364 (mmm) cc_final: 0.8035 (mmp) REVERT: M 165 MET cc_start: 0.9322 (tmm) cc_final: 0.8316 (tpp) REVERT: M 357 MET cc_start: 0.8553 (tmm) cc_final: 0.8115 (tpp) REVERT: M 493 MET cc_start: 0.8977 (ttp) cc_final: 0.8418 (tmm) REVERT: M 593 TRP cc_start: 0.8708 (m-10) cc_final: 0.8147 (m-10) REVERT: M 690 MET cc_start: 0.9331 (mmm) cc_final: 0.9070 (mmm) REVERT: M 740 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8471 (pptt) REVERT: C 374 CYS cc_start: 0.6534 (p) cc_final: 0.6061 (m) REVERT: E 223 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: F 107 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8457 (tm-30) REVERT: F 227 MET cc_start: 0.9174 (mmm) cc_final: 0.8652 (tpp) REVERT: O 127 MET cc_start: 0.8754 (ppp) cc_final: 0.8502 (ppp) REVERT: O 141 MET cc_start: 0.8852 (mmt) cc_final: 0.8478 (mpp) outliers start: 21 outliers final: 13 residues processed: 165 average time/residue: 0.1986 time to fit residues: 49.4608 Evaluate side-chains 164 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 206 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 115 optimal weight: 0.3980 chunk 146 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 HIS ** 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 = 0.3453 r_free = 0.3453 target = 0.063600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.039995 restraints weight = 99806.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.041360 restraints weight = 43835.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.042233 restraints weight = 25550.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.042770 restraints weight = 17970.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.043075 restraints weight = 14440.541| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23671 Z= 0.135 Angle : 0.581 11.462 31998 Z= 0.285 Chirality : 0.041 0.181 3536 Planarity : 0.004 0.068 4125 Dihedral : 4.777 75.097 3235 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 0.84 % Allowed : 11.49 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.17), residues: 2907 helix: 2.06 (0.15), residues: 1388 sheet: 0.22 (0.26), residues: 414 loop : 0.79 (0.20), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG O 125 TYR 0.047 0.001 TYR O 60 PHE 0.020 0.001 PHE E 223 TRP 0.010 0.001 TRP E 86 HIS 0.008 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00306 (23671) covalent geometry : angle 0.58147 (31998) hydrogen bonds : bond 0.03547 ( 1268) hydrogen bonds : angle 3.97872 ( 3459) ********************** 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 170 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.130 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: 0.8983 (ptp) cc_final: 0.8728 (pmm) REVERT: M 90 MET cc_start: 0.8381 (mmm) cc_final: 0.8053 (mmp) REVERT: M 165 MET cc_start: 0.9323 (tmm) cc_final: 0.8828 (tmm) REVERT: M 493 MET cc_start: 0.8982 (ttp) cc_final: 0.8423 (tmm) REVERT: M 593 TRP cc_start: 0.8781 (m-10) cc_final: 0.8216 (m-10) REVERT: M 690 MET cc_start: 0.9355 (mmm) cc_final: 0.9102 (mmm) REVERT: M 740 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8503 (pptt) REVERT: C 374 CYS cc_start: 0.6210 (p) cc_final: 0.5402 (m) REVERT: E 223 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: F 107 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8452 (tm-30) REVERT: F 227 MET cc_start: 0.9183 (mmm) cc_final: 0.8654 (tpp) REVERT: O 127 MET cc_start: 0.8793 (ppp) cc_final: 0.8553 (ppp) outliers start: 21 outliers final: 16 residues processed: 164 average time/residue: 0.1961 time to fit residues: 48.7015 Evaluate side-chains 167 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 286 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 256 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 GLN ** O 153 HIS ** 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 = 0.3454 r_free = 0.3454 target = 0.063685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.040133 restraints weight = 99399.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.041501 restraints weight = 43719.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.042373 restraints weight = 25498.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.042919 restraints weight = 17895.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.043231 restraints weight = 14329.014| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23671 Z= 0.123 Angle : 0.589 15.001 31998 Z= 0.288 Chirality : 0.041 0.190 3536 Planarity : 0.003 0.054 4125 Dihedral : 4.761 74.682 3235 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 1.00 % Allowed : 11.17 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.17), residues: 2907 helix: 2.08 (0.15), residues: 1383 sheet: 0.29 (0.25), residues: 439 loop : 0.78 (0.21), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG P 101 TYR 0.047 0.001 TYR O 60 PHE 0.021 0.001 PHE E 223 TRP 0.008 0.001 TRP F 79 HIS 0.008 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00276 (23671) covalent geometry : angle 0.58856 (31998) hydrogen bonds : bond 0.03531 ( 1268) hydrogen bonds : angle 3.97273 ( 3459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4439.99 seconds wall clock time: 77 minutes 26.68 seconds (4646.68 seconds total)