Starting phenix.real_space_refine on Thu May 22 20:18:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8enc_28270/05_2025/8enc_28270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8enc_28270/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8enc_28270/05_2025/8enc_28270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8enc_28270/05_2025/8enc_28270.map" model { file = "/net/cci-nas-00/data/ceres_data/8enc_28270/05_2025/8enc_28270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8enc_28270/05_2025/8enc_28270.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.35, per 1000 atoms: 0.62 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: 5.89 Conformation dependent library (CDL) restraints added in 2.9 seconds 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 2.97 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: 8.92 Time building geometry restraints manager: 6.84 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: 13.650 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 51.050 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (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 TRP 0.007 0.001 TRP B 340 HIS 0.010 0.001 HIS P 153 PHE 0.015 0.001 PHE E 223 TYR 0.020 0.001 TYR B 279 ARG 0.025 0.001 ARG P 182 Details of bonding type rmsd hydrogen bonds : bond 0.13703 ( 1268) hydrogen bonds : angle 5.45349 ( 3459) covalent geometry : bond 0.00252 (23671) covalent geometry : angle 0.56591 (31998) *********************** 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 : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8355 (ptp) cc_final: 0.8097 (pmm) REVERT: M 165 MET cc_start: 0.9242 (tmm) cc_final: 0.8845 (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: 0.8759 (mmt) REVERT: F 227 MET cc_start: 0.8972 (mmm) cc_final: 0.8710 (tpp) REVERT: O 105 ARG cc_start: 0.9103 (pmt170) cc_final: 0.8526 (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: 0.8947 (mmt) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.4113 time to fit residues: 126.8875 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 : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 138 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 264 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.066546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.042855 restraints weight = 99019.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.044263 restraints weight = 43275.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045163 restraints weight = 25157.384| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1069 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= 0.115 Angle : 0.563 7.880 31998 Z= 0.284 Chirality : 0.042 0.156 3536 Planarity : 0.004 0.043 4125 Dihedral : 5.351 102.608 3235 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 0.48 % Allowed : 5.02 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 2907 helix: 1.99 (0.15), residues: 1374 sheet: 0.24 (0.26), residues: 402 loop : 0.46 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 112 HIS 0.003 0.001 HIS O 153 PHE 0.022 0.001 PHE E 223 TYR 0.016 0.001 TYR B 279 ARG 0.007 0.000 ARG P 182 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 1268) hydrogen bonds : angle 4.41453 ( 3459) covalent geometry : bond 0.00245 (23671) covalent geometry : angle 0.56337 (31998) *********************** 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 187 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 2.631 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: 0.8639 (ptp) cc_final: 0.8197 (pmm) REVERT: M 165 MET cc_start: 0.9361 (tmm) cc_final: 0.9115 (tmm) REVERT: M 362 MET cc_start: 0.8989 (mmm) cc_final: 0.8757 (mmm) REVERT: M 493 MET cc_start: 0.8826 (ttp) cc_final: 0.8356 (tmm) REVERT: M 585 ILE cc_start: 0.9542 (mt) cc_final: 0.9136 (tp) REVERT: M 693 LEU cc_start: 0.9181 (tt) cc_final: 0.8977 (pp) REVERT: M 740 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8238 (pptt) REVERT: M 765 PHE cc_start: 0.8972 (m-80) cc_final: 0.8688 (m-80) REVERT: C 374 CYS cc_start: 0.6660 (p) cc_final: 0.6055 (m) REVERT: F 227 MET cc_start: 0.9083 (mmm) cc_final: 0.8803 (tpp) REVERT: O 127 MET cc_start: 0.8859 (ppp) cc_final: 0.8648 (ppp) REVERT: P 153 HIS cc_start: 0.8945 (m-70) cc_final: 0.8692 (m90) outliers start: 12 outliers final: 3 residues processed: 184 average time/residue: 0.4160 time to fit residues: 114.7263 Evaluate side-chains 163 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 159 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 740 LYS 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 8 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 213 optimal weight: 0.5980 chunk 234 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 153 optimal weight: 0.5980 chunk 199 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** D 162 ASN F 162 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.065579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.041841 restraints weight = 99044.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.043188 restraints weight = 44055.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.044037 restraints weight = 25977.389| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23671 Z= 0.114 Angle : 0.538 8.128 31998 Z= 0.269 Chirality : 0.041 0.156 3536 Planarity : 0.003 0.049 4125 Dihedral : 5.099 95.558 3235 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 0.60 % Allowed : 7.27 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.16), residues: 2907 helix: 2.06 (0.15), residues: 1362 sheet: 0.29 (0.25), residues: 427 loop : 0.49 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 593 HIS 0.006 0.001 HIS O 153 PHE 0.012 0.001 PHE M 488 TYR 0.011 0.001 TYR P 162 ARG 0.013 0.000 ARG P 125 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 1268) hydrogen bonds : angle 4.19640 ( 3459) covalent geometry : bond 0.00251 (23671) covalent geometry : angle 0.53819 (31998) *********************** 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 178 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 3.031 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: 0.8856 (ptp) cc_final: 0.8361 (pmm) REVERT: M 165 MET cc_start: 0.9385 (tmm) cc_final: 0.8538 (tpp) REVERT: M 357 MET cc_start: 0.8453 (tmm) cc_final: 0.8109 (tpt) REVERT: M 362 MET cc_start: 0.9057 (mmm) cc_final: 0.8804 (mmm) REVERT: M 433 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8842 (tm-30) REVERT: M 493 MET cc_start: 0.8916 (ttp) cc_final: 0.8346 (tmm) REVERT: M 740 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8387 (pptt) REVERT: M 765 PHE cc_start: 0.8923 (m-80) cc_final: 0.8701 (m-80) REVERT: B 283 MET cc_start: 0.8706 (mmm) cc_final: 0.8403 (mmm) REVERT: C 305 MET cc_start: 0.9544 (mmm) cc_final: 0.9284 (mmt) REVERT: C 374 CYS cc_start: 0.6802 (p) cc_final: 0.6123 (m) REVERT: E 283 MET cc_start: 0.8909 (mmt) cc_final: 0.8666 (mmt) REVERT: F 227 MET cc_start: 0.9136 (mmm) cc_final: 0.8819 (tpp) REVERT: F 305 MET cc_start: 0.9459 (mmm) cc_final: 0.9192 (tpp) REVERT: O 125 ARG cc_start: 0.8711 (tpp80) cc_final: 0.8464 (mmp80) outliers start: 15 outliers final: 6 residues processed: 173 average time/residue: 0.4079 time to fit residues: 106.6581 Evaluate side-chains 159 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 2.586 ------------------------------------------------------------------------------- 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 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 135 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 174 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 296 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 153 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.065537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.041791 restraints weight = 100059.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.043152 restraints weight = 44419.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.044013 restraints weight = 26082.569| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23671 Z= 0.107 Angle : 0.530 9.225 31998 Z= 0.263 Chirality : 0.041 0.170 3536 Planarity : 0.003 0.043 4125 Dihedral : 4.951 92.410 3235 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % Rotamer: Outliers : 0.56 % Allowed : 8.64 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.16), residues: 2907 helix: 2.09 (0.15), residues: 1363 sheet: 0.32 (0.25), residues: 427 loop : 0.55 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 593 HIS 0.013 0.001 HIS P 153 PHE 0.012 0.001 PHE B 223 TYR 0.011 0.001 TYR P 162 ARG 0.006 0.000 ARG P 160 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 1268) hydrogen bonds : angle 4.09811 ( 3459) covalent geometry : bond 0.00231 (23671) covalent geometry : angle 0.53025 (31998) *********************** 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 174 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 2.619 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: 0.8904 (ptp) cc_final: 0.8409 (pmm) REVERT: M 165 MET cc_start: 0.9369 (tmm) cc_final: 0.8496 (tpp) REVERT: M 357 MET cc_start: 0.8404 (tmm) cc_final: 0.7938 (tpt) REVERT: M 433 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8872 (tm-30) REVERT: M 493 MET cc_start: 0.8893 (ttp) cc_final: 0.8349 (ppp) REVERT: M 740 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8410 (pptt) REVERT: M 765 PHE cc_start: 0.8868 (m-80) cc_final: 0.8665 (m-80) REVERT: B 283 MET cc_start: 0.8757 (mmm) cc_final: 0.8529 (mmm) REVERT: C 305 MET cc_start: 0.9539 (mmm) cc_final: 0.9276 (mmt) REVERT: C 374 CYS cc_start: 0.6932 (p) cc_final: 0.6379 (m) REVERT: E 283 MET cc_start: 0.8909 (mmt) cc_final: 0.8682 (mmt) REVERT: F 227 MET cc_start: 0.9150 (mmm) cc_final: 0.8813 (tpp) REVERT: F 305 MET cc_start: 0.9457 (mmm) cc_final: 0.9183 (tpp) REVERT: O 127 MET cc_start: 0.8681 (ppp) cc_final: 0.8380 (ppp) REVERT: P 135 GLN cc_start: 0.9330 (mm-40) cc_final: 0.9045 (pp30) REVERT: P 160 ARG cc_start: 0.9191 (pmt-80) cc_final: 0.8970 (pmt-80) outliers start: 14 outliers final: 8 residues processed: 171 average time/residue: 0.3847 time to fit residues: 100.2289 Evaluate side-chains 161 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 102 LEU 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 107 optimal weight: 5.9990 chunk 50 optimal weight: 0.0770 chunk 11 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 276 optimal weight: 5.9990 chunk 217 optimal weight: 0.5980 chunk 165 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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 ** P 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 = 0.3490 r_free = 0.3490 target = 0.065384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.041620 restraints weight = 100047.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.042973 restraints weight = 44342.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.043833 restraints weight = 26082.741| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23671 Z= 0.104 Angle : 0.526 8.699 31998 Z= 0.260 Chirality : 0.041 0.159 3536 Planarity : 0.003 0.036 4125 Dihedral : 4.841 89.022 3235 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.59 % Rotamer: Outliers : 0.64 % Allowed : 9.44 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.16), residues: 2907 helix: 2.14 (0.14), residues: 1372 sheet: 0.45 (0.26), residues: 417 loop : 0.61 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 593 HIS 0.027 0.001 HIS P 153 PHE 0.015 0.001 PHE M 488 TYR 0.011 0.001 TYR P 162 ARG 0.004 0.000 ARG P 178 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 1268) hydrogen bonds : angle 4.01629 ( 3459) covalent geometry : bond 0.00225 (23671) covalent geometry : angle 0.52570 (31998) *********************** 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 171 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 3.081 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: M 77 MET cc_start: 0.8909 (ptp) cc_final: 0.8427 (pmm) REVERT: M 165 MET cc_start: 0.9368 (tmm) cc_final: 0.8484 (tpp) REVERT: M 357 MET cc_start: 0.8384 (tmm) cc_final: 0.7938 (tpt) REVERT: M 433 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8881 (tm-30) REVERT: M 493 MET cc_start: 0.8914 (ttp) cc_final: 0.8350 (ppp) REVERT: M 740 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8415 (pptt) REVERT: M 765 PHE cc_start: 0.8862 (m-80) cc_final: 0.8646 (m-80) REVERT: B 82 MET cc_start: 0.9278 (tpt) cc_final: 0.8843 (tpt) REVERT: C 305 MET cc_start: 0.9533 (mmm) cc_final: 0.9276 (mmt) REVERT: C 374 CYS cc_start: 0.6776 (p) cc_final: 0.6382 (m) REVERT: E 283 MET cc_start: 0.8924 (mmt) cc_final: 0.8672 (mmt) REVERT: F 227 MET cc_start: 0.9162 (mmm) cc_final: 0.8815 (tpp) REVERT: F 305 MET cc_start: 0.9454 (mmm) cc_final: 0.9158 (tpp) REVERT: O 127 MET cc_start: 0.8606 (ppp) cc_final: 0.8367 (ppp) outliers start: 16 outliers final: 10 residues processed: 166 average time/residue: 0.4199 time to fit residues: 106.8266 Evaluate side-chains 159 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 102 LEU 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 54 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 192 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 0.0570 chunk 1 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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 371 HIS ** 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 = 0.3490 r_free = 0.3490 target = 0.065278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.041562 restraints weight = 100216.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.042929 restraints weight = 44348.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.043789 restraints weight = 26028.774| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23671 Z= 0.102 Angle : 0.525 9.592 31998 Z= 0.259 Chirality : 0.040 0.157 3536 Planarity : 0.003 0.047 4125 Dihedral : 4.765 85.806 3235 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 0.76 % Allowed : 10.12 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.16), residues: 2907 helix: 2.17 (0.14), residues: 1372 sheet: 0.44 (0.26), residues: 417 loop : 0.66 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 593 HIS 0.010 0.001 HIS O 153 PHE 0.012 0.001 PHE E 223 TYR 0.015 0.001 TYR P 162 ARG 0.011 0.000 ARG P 160 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 1268) hydrogen bonds : angle 3.96230 ( 3459) covalent geometry : bond 0.00220 (23671) covalent geometry : angle 0.52478 (31998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 2.624 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: 0.8499 (pmm) REVERT: M 165 MET cc_start: 0.9343 (tmm) cc_final: 0.8435 (tpp) REVERT: M 357 MET cc_start: 0.8387 (tmm) cc_final: 0.7918 (tpt) REVERT: M 433 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8889 (tm-30) REVERT: M 493 MET cc_start: 0.8911 (ttp) cc_final: 0.8381 (ppp) REVERT: M 603 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: M 740 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8413 (pptt) REVERT: M 765 PHE cc_start: 0.8836 (m-80) cc_final: 0.8614 (m-80) REVERT: B 82 MET cc_start: 0.9314 (tpt) cc_final: 0.8842 (tpt) REVERT: C 305 MET cc_start: 0.9498 (mmm) cc_final: 0.9266 (mmt) REVERT: C 374 CYS cc_start: 0.6782 (p) cc_final: 0.6431 (m) REVERT: E 223 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: E 283 MET cc_start: 0.8923 (mmt) cc_final: 0.8657 (mmt) REVERT: F 227 MET cc_start: 0.9178 (mmm) cc_final: 0.8818 (tpp) REVERT: O 125 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8166 (mtm110) outliers start: 19 outliers final: 13 residues processed: 171 average time/residue: 0.4102 time to fit residues: 106.3037 Evaluate side-chains 167 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 603 GLU Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS 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 E residue 17 VAL 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 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 39 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 115 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 177 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 10 optimal weight: 20.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 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 = 0.3495 r_free = 0.3495 target = 0.065486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.041791 restraints weight = 99763.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.043161 restraints weight = 44178.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.044024 restraints weight = 25908.917| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23671 Z= 0.095 Angle : 0.538 10.697 31998 Z= 0.266 Chirality : 0.040 0.185 3536 Planarity : 0.003 0.040 4125 Dihedral : 4.685 82.766 3235 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.70 % Rotamer: Outliers : 0.72 % Allowed : 10.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.16), residues: 2907 helix: 2.15 (0.14), residues: 1373 sheet: 0.46 (0.26), residues: 417 loop : 0.69 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 593 HIS 0.009 0.001 HIS O 153 PHE 0.012 0.001 PHE E 223 TYR 0.011 0.001 TYR P 162 ARG 0.008 0.000 ARG P 160 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 1268) hydrogen bonds : angle 3.95606 ( 3459) covalent geometry : bond 0.00200 (23671) covalent geometry : angle 0.53782 (31998) *********************** 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 177 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 2.650 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: 0.8997 (ptp) cc_final: 0.8507 (pmm) REVERT: M 165 MET cc_start: 0.9331 (tmm) cc_final: 0.8406 (tpp) REVERT: M 493 MET cc_start: 0.8939 (ttp) cc_final: 0.8375 (ppp) REVERT: M 593 TRP cc_start: 0.8432 (m-10) cc_final: 0.7981 (m-10) REVERT: M 603 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: M 740 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8418 (pptt) REVERT: B 82 MET cc_start: 0.9354 (tpt) cc_final: 0.8961 (tpt) REVERT: C 47 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7669 (ptt) REVERT: C 374 CYS cc_start: 0.6776 (p) cc_final: 0.6370 (m) REVERT: E 223 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8529 (m-80) REVERT: F 227 MET cc_start: 0.9171 (mmm) cc_final: 0.8811 (tpp) REVERT: O 127 MET cc_start: 0.8505 (ppp) cc_final: 0.8231 (ppp) REVERT: O 141 MET cc_start: 0.8971 (mmt) cc_final: 0.8629 (mpp) REVERT: P 135 GLN cc_start: 0.9323 (mm-40) cc_final: 0.8968 (pp30) outliers start: 18 outliers final: 11 residues processed: 172 average time/residue: 0.4048 time to fit residues: 104.7505 Evaluate side-chains 166 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 603 GLU Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 152 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 210 optimal weight: 0.0170 chunk 106 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 280 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 29 optimal weight: 0.1980 chunk 270 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 269 optimal weight: 9.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.064643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.040940 restraints weight = 99994.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.042286 restraints weight = 44422.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.043147 restraints weight = 26160.784| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2102 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= 0.120 Angle : 0.564 11.851 31998 Z= 0.277 Chirality : 0.041 0.251 3536 Planarity : 0.003 0.036 4125 Dihedral : 4.652 78.175 3235 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 0.80 % Allowed : 10.89 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.16), residues: 2907 helix: 2.18 (0.15), residues: 1370 sheet: 0.45 (0.26), residues: 417 loop : 0.74 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 79 HIS 0.010 0.001 HIS O 153 PHE 0.018 0.001 PHE M 247 TYR 0.017 0.001 TYR P 162 ARG 0.011 0.000 ARG O 178 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1268) hydrogen bonds : angle 3.94705 ( 3459) covalent geometry : bond 0.00269 (23671) covalent geometry : angle 0.56411 (31998) *********************** 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 174 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 2.647 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: 0.9006 (ptp) cc_final: 0.8505 (pmm) REVERT: M 165 MET cc_start: 0.9333 (tmm) cc_final: 0.8393 (tpp) REVERT: M 357 MET cc_start: 0.8424 (tmm) cc_final: 0.7828 (tpp) REVERT: M 493 MET cc_start: 0.8951 (ttp) cc_final: 0.8385 (ppp) REVERT: M 593 TRP cc_start: 0.8604 (m-10) cc_final: 0.8150 (m-10) REVERT: M 740 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8429 (pptt) REVERT: B 82 MET cc_start: 0.9284 (tpt) cc_final: 0.8814 (tpt) REVERT: C 374 CYS cc_start: 0.6761 (p) cc_final: 0.6275 (m) REVERT: E 223 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8598 (m-80) REVERT: F 227 MET cc_start: 0.9173 (mmm) cc_final: 0.8795 (tpp) REVERT: O 101 ARG cc_start: 0.9418 (pmt-80) cc_final: 0.8874 (pmt-80) REVERT: O 125 ARG cc_start: 0.8541 (tpp80) cc_final: 0.8088 (mtm110) REVERT: O 127 MET cc_start: 0.8497 (ppp) cc_final: 0.8188 (ppp) outliers start: 20 outliers final: 13 residues processed: 169 average time/residue: 0.4066 time to fit residues: 102.8495 Evaluate side-chains 166 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 684 MET 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 D residue 34 ILE Chi-restraints excluded: chain E residue 17 VAL 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 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 159 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 199 optimal weight: 0.1980 chunk 239 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 245 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.064858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.041177 restraints weight = 99977.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.042527 restraints weight = 44363.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.043389 restraints weight = 26148.023| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23671 Z= 0.104 Angle : 0.566 11.792 31998 Z= 0.278 Chirality : 0.041 0.175 3536 Planarity : 0.003 0.043 4125 Dihedral : 4.617 76.965 3235 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 0.76 % Allowed : 11.17 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.16), residues: 2907 helix: 2.16 (0.15), residues: 1370 sheet: 0.45 (0.26), residues: 417 loop : 0.76 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 593 HIS 0.008 0.001 HIS O 153 PHE 0.015 0.001 PHE M 247 TYR 0.011 0.001 TYR M 142 ARG 0.013 0.000 ARG O 178 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 1268) hydrogen bonds : angle 3.93736 ( 3459) covalent geometry : bond 0.00227 (23671) covalent geometry : angle 0.56566 (31998) *********************** 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 171 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.9018 (ptp) cc_final: 0.8520 (pmm) REVERT: M 165 MET cc_start: 0.9334 (tmm) cc_final: 0.8528 (tpp) REVERT: M 357 MET cc_start: 0.8458 (tmm) cc_final: 0.7829 (tpp) REVERT: M 493 MET cc_start: 0.8946 (ttp) cc_final: 0.8381 (ppp) REVERT: M 593 TRP cc_start: 0.8600 (m-10) cc_final: 0.8122 (m-10) REVERT: M 740 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8439 (pptt) REVERT: B 82 MET cc_start: 0.9287 (tpt) cc_final: 0.8808 (tpt) REVERT: B 325 MET cc_start: 0.8550 (tpp) cc_final: 0.8319 (tpp) REVERT: C 374 CYS cc_start: 0.6746 (p) cc_final: 0.6263 (m) REVERT: E 223 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8633 (m-80) REVERT: O 125 ARG cc_start: 0.8534 (tpp80) cc_final: 0.8098 (mtm110) REVERT: O 127 MET cc_start: 0.8505 (ppp) cc_final: 0.8235 (ppp) REVERT: O 141 MET cc_start: 0.8950 (mmt) cc_final: 0.8550 (mpp) REVERT: P 135 GLN cc_start: 0.9320 (mm-40) cc_final: 0.9035 (pp30) outliers start: 19 outliers final: 15 residues processed: 165 average time/residue: 0.3984 time to fit residues: 98.6055 Evaluate side-chains 168 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 102 LEU 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 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 E residue 17 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 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 121 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 265 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 235 optimal weight: 0.6980 chunk 250 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** 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 = 0.3476 r_free = 0.3476 target = 0.064762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.041104 restraints weight = 99918.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.042435 restraints weight = 44389.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.043298 restraints weight = 26189.637| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23671 Z= 0.105 Angle : 0.573 11.177 31998 Z= 0.281 Chirality : 0.041 0.175 3536 Planarity : 0.003 0.061 4125 Dihedral : 4.580 74.955 3235 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.52 % Rotamer: Outliers : 0.72 % Allowed : 11.25 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.16), residues: 2907 helix: 2.19 (0.14), residues: 1371 sheet: 0.44 (0.26), residues: 417 loop : 0.77 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 593 HIS 0.009 0.001 HIS O 153 PHE 0.015 0.001 PHE E 223 TYR 0.012 0.001 TYR M 142 ARG 0.013 0.000 ARG O 178 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1268) hydrogen bonds : angle 3.92458 ( 3459) covalent geometry : bond 0.00230 (23671) covalent geometry : angle 0.57271 (31998) ********************** 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: 18 poor density : 152 time to evaluate : 2.627 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: 0.9019 (ptp) cc_final: 0.8527 (pmm) REVERT: M 165 MET cc_start: 0.9337 (tmm) cc_final: 0.8521 (tpp) REVERT: M 357 MET cc_start: 0.8461 (tmm) cc_final: 0.7830 (tpp) REVERT: M 493 MET cc_start: 0.8943 (ttp) cc_final: 0.8381 (ppp) REVERT: M 593 TRP cc_start: 0.8620 (m-10) cc_final: 0.8145 (m-10) REVERT: M 740 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8475 (pptt) REVERT: B 82 MET cc_start: 0.9339 (tpt) cc_final: 0.8837 (tpt) REVERT: C 374 CYS cc_start: 0.6762 (p) cc_final: 0.6259 (m) REVERT: E 223 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8656 (m-80) REVERT: O 125 ARG cc_start: 0.8589 (tpp80) cc_final: 0.8136 (ttp80) REVERT: O 127 MET cc_start: 0.8436 (ppp) cc_final: 0.8104 (ppp) REVERT: O 141 MET cc_start: 0.8864 (mmt) cc_final: 0.8497 (mpp) outliers start: 18 outliers final: 15 residues processed: 164 average time/residue: 0.3966 time to fit residues: 98.3555 Evaluate side-chains 168 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 102 LEU 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 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 E residue 17 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 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 167 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 1 optimal weight: 0.0370 chunk 61 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 282 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- 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 371 HIS ** 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 = 0.3445 r_free = 0.3445 target = 0.063570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.039932 restraints weight = 100104.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.041262 restraints weight = 44656.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.042115 restraints weight = 26350.396| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23671 Z= 0.152 Angle : 0.603 12.482 31998 Z= 0.296 Chirality : 0.042 0.202 3536 Planarity : 0.003 0.052 4125 Dihedral : 4.639 73.130 3235 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 0.76 % Allowed : 11.53 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.16), residues: 2907 helix: 2.15 (0.14), residues: 1390 sheet: 0.37 (0.26), residues: 402 loop : 0.75 (0.20), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 79 HIS 0.009 0.001 HIS O 153 PHE 0.018 0.001 PHE E 223 TYR 0.033 0.001 TYR P 162 ARG 0.015 0.001 ARG O 178 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 1268) hydrogen bonds : angle 3.97366 ( 3459) covalent geometry : bond 0.00347 (23671) covalent geometry : angle 0.60348 (31998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7610.77 seconds wall clock time: 134 minutes 35.06 seconds (8075.06 seconds total)