Starting phenix.real_space_refine on Tue Sep 15 07:33:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i7t_4428/09_2026/6i7t_4428.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i7t_4428/09_2026/6i7t_4428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6i7t_4428/09_2026/6i7t_4428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i7t_4428/09_2026/6i7t_4428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i7t_4428/09_2026/6i7t_4428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i7t_4428/09_2026/6i7t_4428.map" } resolution = 4.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 23570 2.51 5 N 6300 2.21 5 O 6966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37004 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2393 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "C" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2677 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "D" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2677 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "E" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2797 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3265 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 395} Chain: "I" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2187 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Chain: "J" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2187 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain breaks: 3 Chain: "B" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2393 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "F" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2797 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "H" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3265 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 395} Chain: "K" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain breaks: 2 Chain: "M" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "O" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3034 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain breaks: 2 Chain: "N" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "P" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3034 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 8.76, per 1000 atoms: 0.24 Number of scatterers: 37004 At special positions: 0 Unit cell: (176.88, 270.68, 123.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 6966 8.00 N 6300 7.00 C 23570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.5 seconds 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8904 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 44 sheets defined 33.0% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 removed outlier: 3.631A pdb=" N ARG A 12 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 37 removed outlier: 3.692A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 60 removed outlier: 3.689A pdb=" N MET A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 82 removed outlier: 4.310A pdb=" N MET A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.676A pdb=" N ASN A 97 " --> pdb=" O HIS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 removed outlier: 3.705A pdb=" N LYS A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.861A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 4.077A pdb=" N GLN A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.734A pdb=" N VAL A 184 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY A 185 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.594A pdb=" N ASN A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.568A pdb=" N LEU A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N MET A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 283 removed outlier: 3.728A pdb=" N LEU C 275 " --> pdb=" O HIS C 271 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 306 removed outlier: 3.730A pdb=" N LEU C 297 " --> pdb=" O CYS C 293 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 removed outlier: 3.767A pdb=" N LEU C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 326 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 329 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 353 removed outlier: 4.212A pdb=" N ALA C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 378 removed outlier: 3.705A pdb=" N GLU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 375 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.507A pdb=" N ILE C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'C' and resid 436 through 447 removed outlier: 4.017A pdb=" N MET C 440 " --> pdb=" O GLU C 436 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 464 removed outlier: 3.662A pdb=" N PHE C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 499 removed outlier: 4.454A pdb=" N LEU C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 512 Processing helix chain 'C' and resid 528 through 533 removed outlier: 4.081A pdb=" N LEU C 532 " --> pdb=" O PRO C 529 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 533 " --> pdb=" O ASN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 643 removed outlier: 3.646A pdb=" N VAL C 640 " --> pdb=" O PRO C 637 " (cutoff:3.500A) Proline residue: C 641 - end of helix Processing helix chain 'D' and resid 271 through 283 removed outlier: 3.728A pdb=" N LEU D 275 " --> pdb=" O HIS D 271 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 306 removed outlier: 3.730A pdb=" N LEU D 297 " --> pdb=" O CYS D 293 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 305 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 334 removed outlier: 3.767A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR D 320 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN D 326 " --> pdb=" O TYR D 322 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 330 " --> pdb=" O GLN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 353 removed outlier: 4.214A pdb=" N ALA D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP D 346 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 378 removed outlier: 3.704A pdb=" N GLU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA D 375 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.507A pdb=" N ILE D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP D 388 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 418 Processing helix chain 'D' and resid 436 through 447 removed outlier: 4.017A pdb=" N MET D 440 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 464 removed outlier: 3.662A pdb=" N PHE D 463 " --> pdb=" O LEU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 499 removed outlier: 4.454A pdb=" N LEU D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 497 " --> pdb=" O ALA D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 512 Processing helix chain 'D' and resid 528 through 533 removed outlier: 4.081A pdb=" N LEU D 532 " --> pdb=" O PRO D 529 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 533 " --> pdb=" O ASN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 643 removed outlier: 3.646A pdb=" N VAL D 640 " --> pdb=" O PRO D 637 " (cutoff:3.500A) Proline residue: D 641 - end of helix Processing helix chain 'E' and resid 17 through 29 removed outlier: 3.515A pdb=" N THR E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 54 removed outlier: 3.616A pdb=" N LEU E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 73 removed outlier: 3.733A pdb=" N ILE E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 107 removed outlier: 3.914A pdb=" N LEU E 95 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 98 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 removed outlier: 4.520A pdb=" N LEU E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 166 removed outlier: 3.867A pdb=" N GLN E 152 " --> pdb=" O THR E 148 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU E 161 " --> pdb=" O GLY E 157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE E 162 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 removed outlier: 4.081A pdb=" N ILE E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE E 177 " --> pdb=" O GLN E 173 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP E 178 " --> pdb=" O GLN E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 206 removed outlier: 4.216A pdb=" N ILE E 201 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 202 " --> pdb=" O LYS E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 236 removed outlier: 3.657A pdb=" N HIS E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS E 231 " --> pdb=" O HIS E 227 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 249 removed outlier: 3.740A pdb=" N VAL E 248 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE E 249 " --> pdb=" O SER E 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 245 through 249' Processing helix chain 'E' and resid 277 through 288 removed outlier: 4.072A pdb=" N VAL E 281 " --> pdb=" O GLY E 277 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE E 288 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 342 through 346 Processing helix chain 'E' and resid 360 through 366 removed outlier: 3.915A pdb=" N ILE E 364 " --> pdb=" O PHE E 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 71 removed outlier: 4.139A pdb=" N THR G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 92 removed outlier: 4.237A pdb=" N ASN G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP G 88 " --> pdb=" O ASN G 84 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR G 89 " --> pdb=" O GLN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 126 removed outlier: 3.509A pdb=" N ASP G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 159 removed outlier: 3.670A pdb=" N LEU G 149 " --> pdb=" O PHE G 145 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 218 removed outlier: 3.799A pdb=" N LEU G 217 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 249 removed outlier: 3.926A pdb=" N LEU G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU G 248 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN G 249 " --> pdb=" O ILE G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 Processing helix chain 'G' and resid 287 through 300 removed outlier: 3.796A pdb=" N SER G 295 " --> pdb=" O TYR G 291 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN G 296 " --> pdb=" O ASP G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 304 removed outlier: 3.706A pdb=" N TYR G 304 " --> pdb=" O ARG G 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 301 through 304' Processing helix chain 'G' and resid 307 through 311 removed outlier: 3.660A pdb=" N SER G 310 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 81 removed outlier: 3.951A pdb=" N VAL I 80 " --> pdb=" O ILE I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 128 removed outlier: 4.248A pdb=" N TYR I 123 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA I 125 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU I 126 " --> pdb=" O ILE I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 157 removed outlier: 3.914A pdb=" N GLN I 156 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS I 157 " --> pdb=" O GLU I 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 152 through 157' Processing helix chain 'I' and resid 180 through 189 removed outlier: 3.972A pdb=" N ASN I 189 " --> pdb=" O ASP I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 261 Processing helix chain 'I' and resid 403 through 411 removed outlier: 3.616A pdb=" N VAL I 408 " --> pdb=" O ALA I 404 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU I 409 " --> pdb=" O ASN I 405 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS I 410 " --> pdb=" O ARG I 406 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE I 411 " --> pdb=" O PHE I 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 81 removed outlier: 3.950A pdb=" N VAL J 80 " --> pdb=" O ILE J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 128 removed outlier: 4.248A pdb=" N TYR J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 125 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU J 126 " --> pdb=" O ILE J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 157 removed outlier: 3.913A pdb=" N GLN J 156 " --> pdb=" O GLY J 152 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS J 157 " --> pdb=" O GLU J 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 152 through 157' Processing helix chain 'J' and resid 180 through 189 removed outlier: 3.972A pdb=" N ASN J 189 " --> pdb=" O ASP J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 403 through 411 removed outlier: 3.616A pdb=" N VAL J 408 " --> pdb=" O ALA J 404 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU J 409 " --> pdb=" O ASN J 405 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS J 410 " --> pdb=" O ARG J 406 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE J 411 " --> pdb=" O PHE J 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.630A pdb=" N ARG B 12 " --> pdb=" O THR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.693A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 60 removed outlier: 3.689A pdb=" N MET B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 82 removed outlier: 4.309A pdb=" N MET B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG B 79 " --> pdb=" O ARG B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.675A pdb=" N ASN B 97 " --> pdb=" O HIS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 removed outlier: 3.705A pdb=" N LYS B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 146 removed outlier: 3.861A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 4.078A pdb=" N GLN B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 171 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.732A pdb=" N VAL B 184 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 185 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.594A pdb=" N ASN B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.569A pdb=" N LEU B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N MET B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 29 removed outlier: 3.514A pdb=" N THR F 21 " --> pdb=" O ASP F 17 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP F 23 " --> pdb=" O ASN F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 54 removed outlier: 3.616A pdb=" N LEU F 42 " --> pdb=" O TYR F 38 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 73 removed outlier: 3.733A pdb=" N ILE F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU F 70 " --> pdb=" O GLN F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 107 removed outlier: 3.915A pdb=" N LEU F 95 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU F 98 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 removed outlier: 4.519A pdb=" N LEU F 124 " --> pdb=" O SER F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 166 removed outlier: 3.867A pdb=" N GLN F 152 " --> pdb=" O THR F 148 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU F 161 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE F 162 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 removed outlier: 4.080A pdb=" N ILE F 175 " --> pdb=" O GLY F 171 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE F 177 " --> pdb=" O GLN F 173 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP F 178 " --> pdb=" O GLN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 removed outlier: 4.217A pdb=" N ILE F 201 " --> pdb=" O LEU F 197 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR F 202 " --> pdb=" O LYS F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 236 removed outlier: 3.658A pdb=" N HIS F 227 " --> pdb=" O THR F 223 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 228 " --> pdb=" O LYS F 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS F 231 " --> pdb=" O HIS F 227 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 249 removed outlier: 3.741A pdb=" N VAL F 248 " --> pdb=" O ASP F 245 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE F 249 " --> pdb=" O SER F 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 245 through 249' Processing helix chain 'F' and resid 277 through 288 removed outlier: 4.072A pdb=" N VAL F 281 " --> pdb=" O GLY F 277 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE F 288 " --> pdb=" O CYS F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 342 through 346 Processing helix chain 'F' and resid 360 through 366 removed outlier: 3.915A pdb=" N ILE F 364 " --> pdb=" O PHE F 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 71 removed outlier: 4.138A pdb=" N THR H 63 " --> pdb=" O LEU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 removed outlier: 4.236A pdb=" N ASN H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP H 88 " --> pdb=" O ASN H 84 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR H 89 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 126 removed outlier: 3.510A pdb=" N ASP H 121 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 159 removed outlier: 3.670A pdb=" N LEU H 149 " --> pdb=" O PHE H 145 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 218 removed outlier: 3.800A pdb=" N LEU H 217 " --> pdb=" O ASP H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 249 removed outlier: 3.926A pdb=" N LEU H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU H 248 " --> pdb=" O LEU H 244 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN H 249 " --> pdb=" O ILE H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 287 through 300 removed outlier: 3.796A pdb=" N SER H 295 " --> pdb=" O TYR H 291 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN H 296 " --> pdb=" O ASP H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 304 removed outlier: 3.705A pdb=" N TYR H 304 " --> pdb=" O ARG H 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 301 through 304' Processing helix chain 'H' and resid 307 through 311 removed outlier: 3.660A pdb=" N SER H 310 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 57 through 62 Processing helix chain 'K' and resid 63 through 65 No H-bonds generated for 'chain 'K' and resid 63 through 65' Processing helix chain 'K' and resid 92 through 115 removed outlier: 3.876A pdb=" N ILE K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU K 99 " --> pdb=" O ILE K 95 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU K 100 " --> pdb=" O ILE K 96 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL K 108 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS K 109 " --> pdb=" O SER K 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG K 113 " --> pdb=" O HIS K 109 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS K 115 " --> pdb=" O ILE K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 135 Processing helix chain 'K' and resid 141 through 146 Processing helix chain 'K' and resid 163 through 173 removed outlier: 3.639A pdb=" N ASP K 167 " --> pdb=" O LYS K 163 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS K 170 " --> pdb=" O LEU K 166 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN K 171 " --> pdb=" O ASP K 167 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR K 172 " --> pdb=" O GLU K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 209 removed outlier: 3.603A pdb=" N SER K 207 " --> pdb=" O ASP K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 240 through 257 removed outlier: 3.560A pdb=" N GLU K 245 " --> pdb=" O ILE K 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER K 246 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR K 256 " --> pdb=" O THR K 252 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS K 257 " --> pdb=" O GLU K 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'O' and resid 130 through 135 removed outlier: 4.010A pdb=" N ARG O 134 " --> pdb=" O ASP O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 201 through 209 Processing helix chain 'O' and resid 226 through 239 Processing helix chain 'O' and resid 257 through 270 Processing helix chain 'O' and resid 290 through 301 removed outlier: 4.242A pdb=" N VAL O 294 " --> pdb=" O ASN O 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 57 through 62 Processing helix chain 'L' and resid 63 through 65 No H-bonds generated for 'chain 'L' and resid 63 through 65' Processing helix chain 'L' and resid 92 through 115 removed outlier: 3.876A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU L 99 " --> pdb=" O ILE L 95 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU L 100 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL L 108 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG L 113 " --> pdb=" O HIS L 109 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 135 Processing helix chain 'L' and resid 141 through 146 Processing helix chain 'L' and resid 163 through 173 removed outlier: 3.638A pdb=" N ASP L 167 " --> pdb=" O LYS L 163 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS L 170 " --> pdb=" O LEU L 166 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN L 171 " --> pdb=" O ASP L 167 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR L 172 " --> pdb=" O GLU L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 209 removed outlier: 3.602A pdb=" N SER L 207 " --> pdb=" O ASP L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 257 removed outlier: 3.560A pdb=" N GLU L 245 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER L 246 " --> pdb=" O GLU L 242 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR L 256 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 141 Processing helix chain 'P' and resid 112 through 121 Processing helix chain 'P' and resid 130 through 135 removed outlier: 4.012A pdb=" N ARG P 134 " --> pdb=" O ASP P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 209 Processing helix chain 'P' and resid 226 through 239 Processing helix chain 'P' and resid 257 through 270 Processing helix chain 'P' and resid 290 through 301 removed outlier: 4.243A pdb=" N VAL P 294 " --> pdb=" O ASN P 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 178 removed outlier: 5.897A pdb=" N ILE A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE A 125 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE A 195 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 127 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL A 194 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A 230 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 196 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE A 227 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ILE A 284 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL A 229 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 398 through 403 removed outlier: 4.320A pdb=" N ASN C 450 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 430 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 470 through 472 removed outlier: 6.242A pdb=" N VAL C 470 " --> pdb=" O LEU C 504 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS C 506 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU C 472 " --> pdb=" O CYS C 506 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 503 " --> pdb=" O LYS C 627 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE C 629 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C 505 " --> pdb=" O ILE C 629 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 476 through 477 Processing sheet with id=AA5, first strand: chain 'D' and resid 398 through 403 removed outlier: 4.320A pdb=" N ASN D 450 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP D 430 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 470 through 472 removed outlier: 6.242A pdb=" N VAL D 470 " --> pdb=" O LEU D 504 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS D 506 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU D 472 " --> pdb=" O CYS D 506 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL D 503 " --> pdb=" O LYS D 627 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE D 629 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL D 505 " --> pdb=" O ILE D 629 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 476 through 477 Processing sheet with id=AA8, first strand: chain 'E' and resid 185 through 188 removed outlier: 6.403A pdb=" N LEU E 186 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL E 213 " --> pdb=" O LEU E 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 258 through 261 removed outlier: 6.547A pdb=" N VAL E 258 " --> pdb=" O PHE E 293 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL E 295 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE E 260 " --> pdb=" O VAL E 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 264 through 265 Processing sheet with id=AB2, first strand: chain 'G' and resid 30 through 31 removed outlier: 4.666A pdb=" N ILE G 235 " --> pdb=" O CYS G 167 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE G 237 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR G 165 " --> pdb=" O ILE G 237 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N HIS G 162 " --> pdb=" O HIS G 272 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR G 274 " --> pdb=" O HIS G 162 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER G 164 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR G 276 " --> pdb=" O SER G 164 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N MET G 166 " --> pdb=" O TYR G 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 139 through 141 Processing sheet with id=AB4, first strand: chain 'G' and resid 194 through 199 removed outlier: 7.025A pdb=" N VAL G 186 " --> pdb=" O ILE G 195 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TYR G 197 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA G 184 " --> pdb=" O TYR G 197 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 211 through 212 Processing sheet with id=AB6, first strand: chain 'G' and resid 319 through 321 removed outlier: 6.131A pdb=" N TYR G 326 " --> pdb=" O ILE G 345 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA G 344 " --> pdb=" O ILE G 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 338 through 339 removed outlier: 6.445A pdb=" N LYS G 338 " --> pdb=" O ILE G 357 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS G 356 " --> pdb=" O ILE G 374 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 367 through 368 removed outlier: 7.311A pdb=" N GLN G 367 " --> pdb=" O ILE G 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 279 through 280 removed outlier: 6.439A pdb=" N ALA I 196 " --> pdb=" O ASN I 388 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR I 390 " --> pdb=" O ALA I 196 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR I 198 " --> pdb=" O THR I 390 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 221 through 222 removed outlier: 3.942A pdb=" N GLN I 221 " --> pdb=" O ASP I 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 254 through 255 Processing sheet with id=AC3, first strand: chain 'I' and resid 266 through 269 removed outlier: 7.694A pdb=" N ALA H 184 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR H 197 " --> pdb=" O ALA H 184 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL H 186 " --> pdb=" O ILE H 195 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 279 through 280 removed outlier: 6.439A pdb=" N ALA J 196 " --> pdb=" O ASN J 388 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR J 390 " --> pdb=" O ALA J 196 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N THR J 198 " --> pdb=" O THR J 390 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 221 through 222 removed outlier: 3.943A pdb=" N GLN J 221 " --> pdb=" O ASP J 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 176 through 178 removed outlier: 5.897A pdb=" N ILE B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 125 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE B 195 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B 127 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL B 194 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 230 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 196 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE B 227 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ILE B 284 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL B 229 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 185 through 188 removed outlier: 6.404A pdb=" N LEU F 186 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL F 213 " --> pdb=" O LEU F 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 258 through 261 removed outlier: 6.547A pdb=" N VAL F 258 " --> pdb=" O PHE F 293 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL F 295 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE F 260 " --> pdb=" O VAL F 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 264 through 265 Processing sheet with id=AD1, first strand: chain 'H' and resid 30 through 31 removed outlier: 4.665A pdb=" N ILE H 235 " --> pdb=" O CYS H 167 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE H 237 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR H 165 " --> pdb=" O ILE H 237 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N HIS H 162 " --> pdb=" O HIS H 272 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR H 274 " --> pdb=" O HIS H 162 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER H 164 " --> pdb=" O TYR H 274 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR H 276 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N MET H 166 " --> pdb=" O TYR H 276 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 139 through 141 Processing sheet with id=AD3, first strand: chain 'H' and resid 319 through 321 removed outlier: 6.132A pdb=" N TYR H 326 " --> pdb=" O ILE H 345 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA H 344 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 338 through 339 removed outlier: 6.445A pdb=" N LYS H 338 " --> pdb=" O ILE H 357 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS H 356 " --> pdb=" O ILE H 374 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 367 through 368 removed outlier: 7.311A pdb=" N GLN H 367 " --> pdb=" O ILE H 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 35 through 36 removed outlier: 3.686A pdb=" N LYS K 35 " --> pdb=" O ASN K 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN K 23 " --> pdb=" O LYS K 35 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 219 through 222 Processing sheet with id=AD8, first strand: chain 'O' and resid 144 through 149 removed outlier: 5.732A pdb=" N LYS O 149 " --> pdb=" O LEU O 185 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU O 185 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 385 through 387 removed outlier: 4.248A pdb=" N ALA O 382 " --> pdb=" O ASN O 385 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU O 387 " --> pdb=" O LEU O 380 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU O 380 " --> pdb=" O LEU O 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY O 394 " --> pdb=" O ILE O 342 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL O 337 " --> pdb=" O SER O 320 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER O 320 " --> pdb=" O VAL O 337 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY O 339 " --> pdb=" O ILE O 318 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU O 343 " --> pdb=" O ARG O 314 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG O 314 " --> pdb=" O LEU O 343 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL O 416 " --> pdb=" O ARG O 356 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LYS O 371 " --> pdb=" O PRO O 357 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 347 through 348 Processing sheet with id=AE2, first strand: chain 'O' and resid 425 through 441 removed outlier: 9.812A pdb=" N ILE O 426 " --> pdb=" O SER O 489 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N SER O 489 " --> pdb=" O ILE O 426 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR O 428 " --> pdb=" O LEU O 487 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET O 482 " --> pdb=" O VAL O 478 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL O 478 " --> pdb=" O MET O 482 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG O 484 " --> pdb=" O VAL O 476 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLY O 472 " --> pdb=" O THR O 488 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ALA O 470 " --> pdb=" O PRO O 490 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL O 461 " --> pdb=" O ARG O 504 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG O 504 " --> pdb=" O VAL O 461 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE O 499 " --> pdb=" O TRP O 514 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP O 514 " --> pdb=" O ILE O 499 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU O 501 " --> pdb=" O ILE O 512 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE O 512 " --> pdb=" O LEU O 501 " (cutoff:3.500A) removed outlier: 11.530A pdb=" N ARG O 510 " --> pdb=" O ARG O 439 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ARG O 439 " --> pdb=" O ARG O 510 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ILE O 512 " --> pdb=" O LEU O 437 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 35 through 36 removed outlier: 3.686A pdb=" N LYS L 35 " --> pdb=" O ASN L 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN L 23 " --> pdb=" O LYS L 35 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 219 through 222 Processing sheet with id=AE5, first strand: chain 'P' and resid 144 through 149 removed outlier: 5.732A pdb=" N LYS P 149 " --> pdb=" O LEU P 185 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU P 185 " --> pdb=" O LYS P 149 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 385 through 387 removed outlier: 4.248A pdb=" N ALA P 382 " --> pdb=" O ASN P 385 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU P 387 " --> pdb=" O LEU P 380 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU P 380 " --> pdb=" O LEU P 387 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY P 394 " --> pdb=" O ILE P 342 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL P 337 " --> pdb=" O SER P 320 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER P 320 " --> pdb=" O VAL P 337 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY P 339 " --> pdb=" O ILE P 318 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU P 343 " --> pdb=" O ARG P 314 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG P 314 " --> pdb=" O LEU P 343 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL P 416 " --> pdb=" O ARG P 356 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS P 371 " --> pdb=" O PRO P 357 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 347 through 348 Processing sheet with id=AE8, first strand: chain 'P' and resid 425 through 441 removed outlier: 9.812A pdb=" N ILE P 426 " --> pdb=" O SER P 489 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N SER P 489 " --> pdb=" O ILE P 426 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR P 428 " --> pdb=" O LEU P 487 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET P 482 " --> pdb=" O VAL P 478 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL P 478 " --> pdb=" O MET P 482 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG P 484 " --> pdb=" O VAL P 476 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLY P 472 " --> pdb=" O THR P 488 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ALA P 470 " --> pdb=" O PRO P 490 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL P 461 " --> pdb=" O ARG P 504 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG P 504 " --> pdb=" O VAL P 461 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE P 499 " --> pdb=" O TRP P 514 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP P 514 " --> pdb=" O ILE P 499 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU P 501 " --> pdb=" O ILE P 512 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE P 512 " --> pdb=" O LEU P 501 " (cutoff:3.500A) removed outlier: 11.530A pdb=" N ARG P 510 " --> pdb=" O ARG P 439 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ARG P 439 " --> pdb=" O ARG P 510 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ILE P 512 " --> pdb=" O LEU P 437 " (cutoff:3.500A) 1042 hydrogen bonds defined for protein. 2922 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: 7.86 Time building geometry restraints manager: 4.29 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: 11255 1.34 - 1.46: 5951 1.46 - 1.58: 20182 1.58 - 1.70: 0 1.70 - 1.82: 254 Bond restraints: 37642 Sorted by residual: bond pdb=" C ILE J 144 " pdb=" N PRO J 145 " ideal model delta sigma weight residual 1.340 1.425 -0.085 2.76e-02 1.31e+03 9.45e+00 bond pdb=" CZ ARG P 503 " pdb=" NH1 ARG P 503 " ideal model delta sigma weight residual 1.323 1.366 -0.043 1.40e-02 5.10e+03 9.37e+00 bond pdb=" C ILE I 144 " pdb=" N PRO I 145 " ideal model delta sigma weight residual 1.340 1.424 -0.084 2.76e-02 1.31e+03 9.29e+00 bond pdb=" CA VAL P 453 " pdb=" CB VAL P 453 " ideal model delta sigma weight residual 1.530 1.562 -0.031 1.05e-02 9.07e+03 8.94e+00 bond pdb=" CZ ARG O 503 " pdb=" NH1 ARG O 503 " ideal model delta sigma weight residual 1.323 1.365 -0.042 1.40e-02 5.10e+03 8.91e+00 ... (remaining 37637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 49411 2.93 - 5.87: 1289 5.87 - 8.80: 208 8.80 - 11.74: 22 11.74 - 14.67: 8 Bond angle restraints: 50938 Sorted by residual: angle pdb=" N SER K 194 " pdb=" CA SER K 194 " pdb=" C SER K 194 " ideal model delta sigma weight residual 108.07 117.24 -9.17 1.38e+00 5.25e-01 4.41e+01 angle pdb=" N SER L 194 " pdb=" CA SER L 194 " pdb=" C SER L 194 " ideal model delta sigma weight residual 108.07 117.19 -9.12 1.38e+00 5.25e-01 4.37e+01 angle pdb=" N ARG O 356 " pdb=" CA ARG O 356 " pdb=" C ARG O 356 " ideal model delta sigma weight residual 109.81 123.18 -13.37 2.21e+00 2.05e-01 3.66e+01 angle pdb=" N ARG P 356 " pdb=" CA ARG P 356 " pdb=" C ARG P 356 " ideal model delta sigma weight residual 109.81 123.17 -13.36 2.21e+00 2.05e-01 3.65e+01 angle pdb=" N ILE O 430 " pdb=" CA ILE O 430 " pdb=" C ILE O 430 " ideal model delta sigma weight residual 108.48 116.75 -8.27 1.44e+00 4.82e-01 3.30e+01 ... (remaining 50933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 20845 16.19 - 32.38: 1621 32.38 - 48.57: 464 48.57 - 64.76: 74 64.76 - 80.95: 52 Dihedral angle restraints: 23056 sinusoidal: 9364 harmonic: 13692 Sorted by residual: dihedral pdb=" CA HIS K 140 " pdb=" C HIS K 140 " pdb=" N ALA K 141 " pdb=" CA ALA K 141 " ideal model delta harmonic sigma weight residual -180.00 -144.91 -35.09 0 5.00e+00 4.00e-02 4.93e+01 dihedral pdb=" CA HIS L 140 " pdb=" C HIS L 140 " pdb=" N ALA L 141 " pdb=" CA ALA L 141 " ideal model delta harmonic sigma weight residual 180.00 -144.94 -35.06 0 5.00e+00 4.00e-02 4.92e+01 dihedral pdb=" CA ARG H 178 " pdb=" C ARG H 178 " pdb=" N THR H 179 " pdb=" CA THR H 179 " ideal model delta harmonic sigma weight residual 180.00 -147.96 -32.04 0 5.00e+00 4.00e-02 4.11e+01 ... (remaining 23053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 5522 0.122 - 0.244: 396 0.244 - 0.367: 38 0.367 - 0.489: 0 0.489 - 0.611: 2 Chirality restraints: 5958 Sorted by residual: chirality pdb=" CA ARG O 356 " pdb=" N ARG O 356 " pdb=" C ARG O 356 " pdb=" CB ARG O 356 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.33e+00 chirality pdb=" CA ARG P 356 " pdb=" N ARG P 356 " pdb=" C ARG P 356 " pdb=" CB ARG P 356 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 chirality pdb=" CA ASP O 130 " pdb=" N ASP O 130 " pdb=" C ASP O 130 " pdb=" CB ASP O 130 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 5955 not shown) Planarity restraints: 6490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 303 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO I 304 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO I 304 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 304 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 303 " 0.052 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO J 304 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO J 304 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO J 304 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 291 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO I 292 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I 292 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO I 292 " -0.039 5.00e-02 4.00e+02 ... (remaining 6487 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 6397 2.78 - 3.31: 35232 3.31 - 3.84: 62030 3.84 - 4.37: 72400 4.37 - 4.90: 116550 Nonbonded interactions: 292609 Sorted by model distance: nonbonded pdb=" O ALA E 264 " pdb=" OG1 THR E 271 " model vdw 2.245 3.040 nonbonded pdb=" O ALA F 264 " pdb=" OG1 THR F 271 " model vdw 2.245 3.040 nonbonded pdb=" O GLY F 269 " pdb=" OH TYR F 349 " model vdw 2.269 3.040 nonbonded pdb=" O GLY E 269 " pdb=" OH TYR E 349 " model vdw 2.270 3.040 nonbonded pdb=" OG SER H 80 " pdb=" O PRO H 110 " model vdw 2.280 3.040 ... (remaining 292604 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints Number of NCS constrained groups: 8 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'O' selection = chain 'P' } Set refine NCS operators NCS operators will be refined. 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 35.050 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5887 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 : 0.006 0.085 37642 Z= 0.371 Angle : 1.172 14.669 50938 Z= 0.678 Chirality : 0.069 0.611 5958 Planarity : 0.007 0.078 6490 Dihedral : 13.627 80.951 14152 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.02 % Favored : 87.55 % Rotamer: Outliers : 2.54 % Allowed : 7.91 % Favored : 89.54 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.10), residues: 4610 helix: -3.10 (0.10), residues: 1360 sheet: -2.15 (0.19), residues: 618 loop : -3.01 (0.10), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 157 TYR 0.035 0.003 TYR K 9 PHE 0.040 0.003 PHE I 119 TRP 0.017 0.002 TRP E 366 HIS 0.015 0.002 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.37 (37642) covalent geometry : angle 1.17152 / 0.68 (50938) hydrogen bonds : bond 0.27642 / 17.95 ( 1042) hydrogen bonds : angle 9.61994 / 6.70 ( 2922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.8662 (t80) cc_final: 0.8263 (t80) REVERT: A 199 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 221 HIS cc_start: 0.9013 (t-90) cc_final: 0.8548 (t70) REVERT: A 285 THR cc_start: 0.9424 (p) cc_final: 0.8820 (p) REVERT: A 302 MET cc_start: 0.8378 (ptm) cc_final: 0.8043 (mpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0968 time to fit residues: 5.4726 Evaluate side-chains 26 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.094 Evaluate side-chains 66 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 296 MET cc_start: 0.9131 (tmm) cc_final: 0.8527 (tmm) REVERT: C 300 PHE cc_start: 0.9077 (m-10) cc_final: 0.8280 (m-10) REVERT: C 322 TYR cc_start: 0.8155 (t80) cc_final: 0.7913 (t80) REVERT: C 378 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8911 (tppt) REVERT: C 457 THR cc_start: 0.8701 (p) cc_final: 0.8461 (t) REVERT: C 465 MET cc_start: 0.7205 (mtm) cc_final: 0.6569 (ttt) REVERT: C 472 LEU cc_start: 0.9612 (mt) cc_final: 0.9411 (mm) REVERT: C 504 LEU cc_start: 0.9266 (mp) cc_final: 0.9016 (mt) REVERT: C 523 PHE cc_start: 0.9101 (t80) cc_final: 0.8215 (t80) REVERT: C 528 ASP cc_start: 0.8296 (t0) cc_final: 0.7686 (t0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0688 time to fit residues: 5.4119 Evaluate side-chains 37 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.107 Evaluate side-chains 50 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: E 65 GLU cc_start: 0.9268 (tp30) cc_final: 0.8875 (tm-30) REVERT: E 69 ASP cc_start: 0.8420 (p0) cc_final: 0.8210 (p0) REVERT: E 84 CYS cc_start: 0.7982 (p) cc_final: 0.7709 (p) REVERT: E 88 ILE cc_start: 0.9507 (pt) cc_final: 0.8953 (tt) REVERT: E 158 ILE cc_start: 0.8598 (mm) cc_final: 0.8161 (mm) REVERT: E 344 GLU cc_start: 0.9073 (mp0) cc_final: 0.8738 (tm-30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0989 time to fit residues: 5.6857 Evaluate side-chains 19 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.113 Evaluate side-chains 60 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: G 52 LEU cc_start: 0.9592 (mt) cc_final: 0.9362 (mt) REVERT: G 108 MET cc_start: 0.8122 (pmm) cc_final: 0.6943 (ppp) REVERT: G 306 LEU cc_start: 0.9568 (tm) cc_final: 0.9292 (tt) REVERT: G 391 ILE cc_start: 0.9564 (mt) cc_final: 0.9108 (tp) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.0856 time to fit residues: 6.1506 Evaluate side-chains 25 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.133 Evaluate side-chains 37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 224 THR cc_start: 0.9002 (m) cc_final: 0.8770 (m) REVERT: I 230 GLU cc_start: 0.8653 (tt0) cc_final: 0.7632 (mm-30) REVERT: I 295 MET cc_start: 0.7386 (ttp) cc_final: 0.6918 (ttt) outliers start: 2 outliers final: 0 residues processed: 37 average time/residue: 0.0774 time to fit residues: 3.3286 Evaluate side-chains 16 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.091 Evaluate side-chains 43 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.074 Fit side-chains REVERT: K 45 MET cc_start: 0.8406 (ptm) cc_final: 0.8027 (ppp) REVERT: K 63 ILE cc_start: 0.9156 (tt) cc_final: 0.8955 (tp) REVERT: K 78 LYS cc_start: 0.9423 (tttt) cc_final: 0.9089 (tppt) REVERT: K 171 ASN cc_start: 0.8832 (t0) cc_final: 0.8624 (m-40) REVERT: K 185 ARG cc_start: 0.3409 (OUTLIER) cc_final: 0.3040 (ptt-90) REVERT: K 235 LEU cc_start: -0.4104 (OUTLIER) cc_final: -0.4325 (tp) outliers start: 11 outliers final: 1 residues processed: 43 average time/residue: 0.0809 time to fit residues: 3.9142 Evaluate side-chains 17 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.081 Evaluate side-chains 1 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0213 time to fit residues: 0.0328 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 77 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 39 time to evaluate : 0.097 Fit side-chains REVERT: O 239 MET cc_start: -0.0056 (mtp) cc_final: -0.0811 (mmt) REVERT: O 307 ARG cc_start: -0.2756 (OUTLIER) cc_final: -0.3398 (mtt90) REVERT: O 512 ILE cc_start: 0.1506 (OUTLIER) cc_final: 0.1296 (mm) outliers start: 38 outliers final: 5 residues processed: 75 average time/residue: 0.0755 time to fit residues: 6.8036 Evaluate side-chains 24 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 0.4980 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0370 chunk 401 optimal weight: 1.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS C 271 HIS C 301 GLN C 342 ASN ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN G 82 HIS G 85 GLN G 96 ASN G 324 HIS G 376 ASN G 423 ASN I 131 HIS I 186 GLN I 244 GLN I 258 HIS O 98 GLN O 221 ASN O 422 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.041018 restraints weight = 15737.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.042341 restraints weight = 10060.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.043310 restraints weight = 7085.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.044032 restraints weight = 5301.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.044568 restraints weight = 4170.730| |-----------------------------------------------------------------------------| r_work (final): 0.2916 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.042241 restraints weight = 16983.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.043465 restraints weight = 11095.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044296 restraints weight = 8014.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045032 restraints weight = 6254.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.045551 restraints weight = 5068.920| |-----------------------------------------------------------------------------| r_work (final): 0.2965 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.039597 restraints weight = 19005.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.040700 restraints weight = 12480.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.041535 restraints weight = 9127.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042078 restraints weight = 7174.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.042547 restraints weight = 6024.195| |-----------------------------------------------------------------------------| r_work (final): 0.2883 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.043179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036758 restraints weight = 25442.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.037957 restraints weight = 15654.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.038828 restraints weight = 10754.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.039516 restraints weight = 7948.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.040011 restraints weight = 6085.627| |-----------------------------------------------------------------------------| r_work (final): 0.2935 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.068120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.059420 restraints weight = 19500.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.060469 restraints weight = 14597.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.061132 restraints weight = 11721.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.061712 restraints weight = 10027.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.061969 restraints weight = 8791.214| |-----------------------------------------------------------------------------| r_work (final): 0.3619 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.088943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.060748 restraints weight = 21029.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.061782 restraints weight = 13650.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.062647 restraints weight = 9402.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.063124 restraints weight = 7014.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.063535 restraints weight = 5484.185| |-----------------------------------------------------------------------------| r_work (final): 0.3594 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.100787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.097916 restraints weight = 1764.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.098522 restraints weight = 1275.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.098979 restraints weight = 953.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.099318 restraints weight = 708.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.099585 restraints weight = 535.918| |-----------------------------------------------------------------------------| r_work (final): 0.3854 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.078530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.075877 restraints weight = 50209.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.076310 restraints weight = 37918.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.076566 restraints weight = 30384.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.076782 restraints weight = 25732.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.076968 restraints weight = 22302.798| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37642 Z= 0.150 Angle : 0.761 10.112 50938 Z= 0.401 Chirality : 0.049 0.341 5958 Planarity : 0.006 0.102 6490 Dihedral : 7.018 61.340 5022 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.28 % Favored : 90.63 % Rotamer: Outliers : 0.29 % Allowed : 4.84 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.11), residues: 4610 helix: -2.24 (0.12), residues: 1406 sheet: -1.95 (0.19), residues: 722 loop : -2.69 (0.11), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 31 TYR 0.030 0.002 TYR K 82 PHE 0.019 0.002 PHE G 145 TRP 0.038 0.002 TRP K 132 HIS 0.006 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (37642) covalent geometry : angle 0.76099 / 0.40 (50938) hydrogen bonds : bond 0.05301 / 3.49 ( 1042) hydrogen bonds : angle 6.38470 / 4.34 ( 2922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 GLN cc_start: 0.9162 (pm20) cc_final: 0.8796 (pp30) REVERT: B 153 VAL cc_start: 0.8572 (t) cc_final: 0.8338 (p) REVERT: B 166 TYR cc_start: 0.8934 (t80) cc_final: 0.8584 (t80) REVERT: B 199 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 208 ILE cc_start: 0.9078 (mt) cc_final: 0.8436 (pt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0482 time to fit residues: 2.3970 Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.091 Evaluate side-chains 49 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 296 MET cc_start: 0.8775 (tmm) cc_final: 0.8207 (tmm) REVERT: C 300 PHE cc_start: 0.9067 (m-10) cc_final: 0.8730 (m-10) REVERT: C 439 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8751 (tptt) REVERT: C 465 MET cc_start: 0.7555 (mtm) cc_final: 0.6774 (ttt) REVERT: C 523 PHE cc_start: 0.9156 (t80) cc_final: 0.8294 (t80) REVERT: C 528 ASP cc_start: 0.8145 (t0) cc_final: 0.7880 (t0) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.0929 time to fit residues: 5.2520 Evaluate side-chains 32 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.105 Evaluate side-chains 26 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: E 63 LEU cc_start: 0.9675 (tp) cc_final: 0.9307 (pp) REVERT: E 65 GLU cc_start: 0.9309 (tp30) cc_final: 0.8995 (tm-30) REVERT: E 104 MET cc_start: 0.8675 (mmp) cc_final: 0.8332 (tpp) REVERT: E 315 PHE cc_start: 0.8442 (m-10) cc_final: 0.8019 (p90) REVERT: E 344 GLU cc_start: 0.9219 (mp0) cc_final: 0.8854 (tm-30) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0409 time to fit residues: 1.5345 Evaluate side-chains 17 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.106 Evaluate side-chains 39 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: H 52 LEU cc_start: 0.9578 (mt) cc_final: 0.9314 (mt) REVERT: H 108 MET cc_start: 0.8262 (pmm) cc_final: 0.6961 (ppp) REVERT: H 155 MET cc_start: 0.8463 (ptm) cc_final: 0.8221 (ppp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0583 time to fit residues: 2.9662 Evaluate side-chains 22 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.133 Evaluate side-chains 22 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 221 GLN cc_start: 0.7851 (mp10) cc_final: 0.7196 (mp10) REVERT: I 230 GLU cc_start: 0.8861 (tt0) cc_final: 0.7838 (mm-30) REVERT: I 295 MET cc_start: 0.7291 (ttp) cc_final: 0.6717 (ttt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0720 time to fit residues: 1.8875 Evaluate side-chains 15 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.093 Evaluate side-chains 24 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.083 Fit side-chains REVERT: L 54 ARG cc_start: 0.8919 (mtm180) cc_final: 0.8682 (ptm-80) outliers start: 2 outliers final: 0 residues processed: 23 average time/residue: 0.1241 time to fit residues: 3.1831 Evaluate side-chains 9 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.081 Evaluate side-chains 3 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1647 time to fit residues: 0.5076 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 22 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 239 MET cc_start: 0.0073 (mtp) cc_final: -0.0902 (mmt) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.1001 time to fit residues: 2.6689 Evaluate side-chains 15 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 331 optimal weight: 6.9990 chunk 287 optimal weight: 3.9990 chunk 429 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 328 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN H 124 ASN H 324 HIS H 371 ASN ** H 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 ASN ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.038884 restraints weight = 16755.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.040053 restraints weight = 10776.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.040973 restraints weight = 7671.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.041567 restraints weight = 5705.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.042114 restraints weight = 4540.359| |-----------------------------------------------------------------------------| r_work (final): 0.2842 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.039870 restraints weight = 18138.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.040948 restraints weight = 12172.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.041753 restraints weight = 8913.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.042361 restraints weight = 6954.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.042828 restraints weight = 5681.476| |-----------------------------------------------------------------------------| r_work (final): 0.2879 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.046317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.037040 restraints weight = 19969.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.038103 restraints weight = 13004.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.038907 restraints weight = 9472.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.039496 restraints weight = 7424.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.039803 restraints weight = 6136.618| |-----------------------------------------------------------------------------| r_work (final): 0.2802 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.040058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033997 restraints weight = 26721.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.035098 restraints weight = 16252.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.035932 restraints weight = 11184.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.036547 restraints weight = 8193.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.037008 restraints weight = 6346.930| |-----------------------------------------------------------------------------| r_work (final): 0.2823 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.063557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.055111 restraints weight = 21115.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.056134 restraints weight = 15624.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.056875 restraints weight = 12406.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.057388 restraints weight = 10389.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057772 restraints weight = 9047.596| |-----------------------------------------------------------------------------| r_work (final): 0.3526 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.084897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.057517 restraints weight = 20373.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.058319 restraints weight = 13215.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.058973 restraints weight = 9386.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.059381 restraints weight = 7324.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.059591 restraints weight = 5530.708| |-----------------------------------------------------------------------------| r_work (final): 0.3480 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.092710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.091722 restraints weight = 1469.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.092079 restraints weight = 850.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.092341 restraints weight = 512.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.092464 restraints weight = 303.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.092567 restraints weight = 176.917| |-----------------------------------------------------------------------------| r_work (final): 0.3823 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.078748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.076747 restraints weight = 40272.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.077082 restraints weight = 32252.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.077299 restraints weight = 25019.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.077472 restraints weight = 20573.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.077565 restraints weight = 17645.315| |-----------------------------------------------------------------------------| r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 37642 Z= 0.241 Angle : 0.771 10.791 50938 Z= 0.408 Chirality : 0.048 0.290 5958 Planarity : 0.006 0.113 6490 Dihedral : 6.760 62.813 5022 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.63 % Favored : 88.29 % Rotamer: Outliers : 0.24 % Allowed : 4.80 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.12), residues: 4610 helix: -1.58 (0.13), residues: 1424 sheet: -1.76 (0.20), residues: 610 loop : -2.40 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG P 408 TYR 0.021 0.002 TYR G 174 PHE 0.022 0.002 PHE D 251 TRP 0.017 0.002 TRP L 132 HIS 0.009 0.002 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.24 (37642) covalent geometry : angle 0.77074 / 0.41 (50938) hydrogen bonds : bond 0.04949 / 3.24 ( 1042) hydrogen bonds : angle 5.89365 / 4.03 ( 2922) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9292 (mtp) cc_final: 0.8999 (mtt) REVERT: A 99 GLN cc_start: 0.9300 (pm20) cc_final: 0.8917 (pp30) REVERT: A 153 VAL cc_start: 0.8885 (t) cc_final: 0.8676 (p) REVERT: A 166 TYR cc_start: 0.9252 (t80) cc_final: 0.8918 (t80) REVERT: A 199 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7969 (mt-10) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0610 time to fit residues: 2.1602 Evaluate side-chains 23 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.116 Evaluate side-chains 37 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 439 LYS cc_start: 0.9265 (mtpp) cc_final: 0.8825 (mmtm) REVERT: C 465 MET cc_start: 0.7671 (mtm) cc_final: 0.7020 (ttt) REVERT: C 523 PHE cc_start: 0.9120 (t80) cc_final: 0.8188 (t80) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0900 time to fit residues: 3.9055 Evaluate side-chains 21 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.141 Evaluate side-chains 21 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: E 65 GLU cc_start: 0.9451 (tp30) cc_final: 0.9230 (tm-30) REVERT: E 104 MET cc_start: 0.8533 (mmp) cc_final: 0.8189 (tpp) REVERT: E 122 PHE cc_start: 0.8149 (t80) cc_final: 0.7846 (t80) REVERT: E 252 MET cc_start: 0.9110 (tpt) cc_final: 0.8696 (tpt) REVERT: E 266 PHE cc_start: 0.8770 (m-10) cc_final: 0.8565 (m-80) REVERT: E 310 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8941 (tm-30) REVERT: E 375 HIS cc_start: 0.8611 (t-90) cc_final: 0.8343 (t-90) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0486 time to fit residues: 1.4333 Evaluate side-chains 14 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.141 Evaluate side-chains 31 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: H 52 LEU cc_start: 0.9634 (mt) cc_final: 0.9413 (mt) REVERT: H 108 MET cc_start: 0.8427 (pmm) cc_final: 0.7124 (tmm) REVERT: H 140 LEU cc_start: 0.9578 (tp) cc_final: 0.9345 (tp) REVERT: H 155 MET cc_start: 0.8783 (ptm) cc_final: 0.8184 (ppp) REVERT: H 424 MET cc_start: 0.2643 (mmm) cc_final: 0.2285 (mmm) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.0473 time to fit residues: 2.0801 Evaluate side-chains 19 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.134 Evaluate side-chains 20 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 228 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8661 (mm-30) REVERT: I 230 GLU cc_start: 0.8938 (tt0) cc_final: 0.7989 (mm-30) REVERT: I 295 MET cc_start: 0.7514 (ttp) cc_final: 0.6834 (ttp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0739 time to fit residues: 1.7950 Evaluate side-chains 13 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.088 Evaluate side-chains 14 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.087 Fit side-chains REVERT: L 54 ARG cc_start: 0.8871 (mtm180) cc_final: 0.8309 (tmt170) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0874 time to fit residues: 1.4800 Evaluate side-chains 9 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.086 Evaluate side-chains 1 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0218 time to fit residues: 0.0340 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 18 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.124 Fit side-chains REVERT: O 239 MET cc_start: 0.0259 (mtp) cc_final: -0.0972 (mmt) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1102 time to fit residues: 2.3852 Evaluate side-chains 14 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 402 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 301 optimal weight: 0.0050 chunk 248 optimal weight: 3.9990 chunk 359 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 396 optimal weight: 0.0270 chunk 63 optimal weight: 2.9990 chunk 348 optimal weight: 0.3980 overall best weight: 1.0856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 97 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 ASN ** E 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS H 85 GLN O 98 GLN ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.040154 restraints weight = 16152.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.041319 restraints weight = 10487.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.042267 restraints weight = 7604.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.042956 restraints weight = 5700.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.043530 restraints weight = 4500.531| |-----------------------------------------------------------------------------| r_work (final): 0.2888 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.050134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041732 restraints weight = 17378.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.042898 restraints weight = 11695.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.043739 restraints weight = 8571.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044392 restraints weight = 6640.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044879 restraints weight = 5391.202| |-----------------------------------------------------------------------------| r_work (final): 0.2951 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.047984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.038444 restraints weight = 19100.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.039564 restraints weight = 12384.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.040375 restraints weight = 8938.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.040990 restraints weight = 6970.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.041331 restraints weight = 5737.638| |-----------------------------------------------------------------------------| r_work (final): 0.2848 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.035077 restraints weight = 26336.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.036245 restraints weight = 16156.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.037067 restraints weight = 11090.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037711 restraints weight = 8170.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.038198 restraints weight = 6310.554| |-----------------------------------------------------------------------------| r_work (final): 0.2876 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.065588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.057217 restraints weight = 19317.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.058130 restraints weight = 14636.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.058758 restraints weight = 11956.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.059186 restraints weight = 10239.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.059508 restraints weight = 9121.281| |-----------------------------------------------------------------------------| r_work (final): 0.3554 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.086053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.058804 restraints weight = 20233.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.059555 restraints weight = 12932.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.059980 restraints weight = 9246.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.060281 restraints weight = 7271.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.060872 restraints weight = 5736.659| |-----------------------------------------------------------------------------| r_work (final): 0.3526 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.093376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.092481 restraints weight = 1486.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.092852 restraints weight = 814.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.093050 restraints weight = 456.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.093166 restraints weight = 261.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.093255 restraints weight = 156.186| |-----------------------------------------------------------------------------| r_work (final): 0.3876 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.079167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.076874 restraints weight = 47751.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.077133 restraints weight = 39825.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.077253 restraints weight = 32690.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.077253 restraints weight = 29144.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.077253 restraints weight = 29144.490| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37642 Z= 0.129 Angle : 0.668 10.760 50938 Z= 0.347 Chirality : 0.047 0.250 5958 Planarity : 0.005 0.067 6490 Dihedral : 6.333 59.553 5022 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.63 % Favored : 90.28 % Rotamer: Outliers : 0.05 % Allowed : 3.69 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.12), residues: 4610 helix: -1.35 (0.13), residues: 1434 sheet: -1.67 (0.21), residues: 588 loop : -2.26 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG D 498 TYR 0.029 0.002 TYR I 252 PHE 0.017 0.001 PHE B 4 TRP 0.010 0.001 TRP F 366 HIS 0.005 0.001 HIS G 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (37642) covalent geometry : angle 0.66813 / 0.35 (50938) hydrogen bonds : bond 0.04219 / 2.75 ( 1042) hydrogen bonds : angle 5.63823 / 3.86 ( 2922) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.9259 (ptp) cc_final: 0.9020 (ptp) REVERT: A 74 MET cc_start: 0.9267 (mtp) cc_final: 0.8940 (mtt) REVERT: A 99 GLN cc_start: 0.9253 (pm20) cc_final: 0.8947 (pp30) REVERT: A 166 TYR cc_start: 0.9105 (t80) cc_final: 0.8784 (t80) REVERT: A 199 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 228 TYR cc_start: 0.9281 (m-80) cc_final: 0.9042 (m-10) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0589 time to fit residues: 1.9821 Evaluate side-chains 24 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.096 Evaluate side-chains 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 296 MET cc_start: 0.8648 (tmm) cc_final: 0.8162 (tmm) REVERT: C 300 PHE cc_start: 0.9054 (m-10) cc_final: 0.8840 (m-10) REVERT: C 439 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8544 (tptt) REVERT: C 465 MET cc_start: 0.7557 (mtm) cc_final: 0.6919 (ttt) REVERT: C 523 PHE cc_start: 0.9019 (t80) cc_final: 0.8111 (t80) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.0769 time to fit residues: 3.5852 Evaluate side-chains 25 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.131 Evaluate side-chains 23 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 104 MET cc_start: 0.8598 (mmp) cc_final: 0.8366 (tpp) REVERT: E 122 PHE cc_start: 0.7930 (t80) cc_final: 0.7497 (t80) REVERT: E 252 MET cc_start: 0.8957 (tpt) cc_final: 0.8650 (tpt) REVERT: E 266 PHE cc_start: 0.8706 (m-10) cc_final: 0.8461 (m-80) REVERT: E 310 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8864 (tm-30) REVERT: E 344 GLU cc_start: 0.9207 (mp0) cc_final: 0.8856 (tm-30) REVERT: E 375 HIS cc_start: 0.8679 (t-90) cc_final: 0.8397 (t-90) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0821 time to fit residues: 2.3458 Evaluate side-chains 15 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.111 Evaluate side-chains 31 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: H 108 MET cc_start: 0.8191 (pmm) cc_final: 0.6859 (tmm) REVERT: H 140 LEU cc_start: 0.9614 (tp) cc_final: 0.9404 (tp) REVERT: H 155 MET cc_start: 0.8754 (ptm) cc_final: 0.8107 (ppp) REVERT: H 301 ARG cc_start: 0.7334 (mmt180) cc_final: 0.6500 (ppt170) REVERT: H 306 LEU cc_start: 0.9510 (tp) cc_final: 0.9229 (tt) REVERT: H 424 MET cc_start: 0.2622 (mmm) cc_final: 0.2278 (mmm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0815 time to fit residues: 3.1379 Evaluate side-chains 18 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.137 Evaluate side-chains 20 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: J 76 MET cc_start: 0.5243 (ptt) cc_final: 0.4403 (ptp) REVERT: J 224 THR cc_start: 0.8711 (m) cc_final: 0.8428 (m) REVERT: J 228 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8411 (pm20) REVERT: J 230 GLU cc_start: 0.8386 (tt0) cc_final: 0.7315 (mm-30) REVERT: J 295 MET cc_start: 0.7514 (ttp) cc_final: 0.7013 (ttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0490 time to fit residues: 1.2845 Evaluate side-chains 12 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.082 Evaluate side-chains 18 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.078 Fit side-chains REVERT: L 54 ARG cc_start: 0.9001 (mtm180) cc_final: 0.8744 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0750 time to fit residues: 1.6154 Evaluate side-chains 9 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.080 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0106 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 17 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.119 Fit side-chains REVERT: O 239 MET cc_start: 0.0257 (mtp) cc_final: -0.0927 (mmt) REVERT: O 310 MET cc_start: 0.2913 (ttt) cc_final: 0.2679 (ttt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1026 time to fit residues: 2.1426 Evaluate side-chains 12 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 163 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 325 optimal weight: 0.0040 chunk 388 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 391 optimal weight: 7.9990 chunk 66 optimal weight: 0.0060 chunk 238 optimal weight: 9.9990 chunk 338 optimal weight: 0.4980 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 HIS ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.040977 restraints weight = 15598.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.042157 restraints weight = 10170.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.043118 restraints weight = 7383.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043841 restraints weight = 5611.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.044407 restraints weight = 4421.859| |-----------------------------------------------------------------------------| r_work (final): 0.2915 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.050662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.042111 restraints weight = 17137.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.043235 restraints weight = 11563.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.044077 restraints weight = 8486.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.044645 restraints weight = 6604.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.045199 restraints weight = 5450.135| |-----------------------------------------------------------------------------| r_work (final): 0.2965 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.047923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.038480 restraints weight = 18843.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.039599 restraints weight = 12009.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.040410 restraints weight = 8672.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.040879 restraints weight = 6800.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041362 restraints weight = 5747.549| |-----------------------------------------------------------------------------| r_work (final): 0.2860 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.042884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.036741 restraints weight = 26307.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.037879 restraints weight = 16454.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038726 restraints weight = 11389.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.039357 restraints weight = 8435.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039855 restraints weight = 6529.273| |-----------------------------------------------------------------------------| r_work (final): 0.2913 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.067134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.057988 restraints weight = 19188.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.059070 restraints weight = 14288.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.059848 restraints weight = 11490.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.060414 restraints weight = 9697.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.060820 restraints weight = 8552.356| |-----------------------------------------------------------------------------| r_work (final): 0.3591 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.087464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.064057 restraints weight = 17984.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.064861 restraints weight = 12559.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.065376 restraints weight = 9499.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.065776 restraints weight = 7233.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.066180 restraints weight = 5675.553| |-----------------------------------------------------------------------------| r_work (final): 0.3579 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.091467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.089645 restraints weight = 1944.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.090145 restraints weight = 1184.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.090470 restraints weight = 758.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.090670 restraints weight = 525.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.090802 restraints weight = 371.697| |-----------------------------------------------------------------------------| r_work (final): 0.3818 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5475 r_free = 0.5475 target = 0.144001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.107943 restraints weight = 20991.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.107932 restraints weight = 26672.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.107932 restraints weight = 24957.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.107932 restraints weight = 24890.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.107932 restraints weight = 24885.060| |-----------------------------------------------------------------------------| r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 37642 Z= 0.123 Angle : 0.660 11.339 50938 Z= 0.339 Chirality : 0.048 0.410 5958 Planarity : 0.005 0.063 6490 Dihedral : 6.041 54.789 5022 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.72 % Favored : 90.20 % Rotamer: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.12), residues: 4610 helix: -1.19 (0.13), residues: 1414 sheet: -1.39 (0.21), residues: 564 loop : -2.14 (0.12), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG B 224 TYR 0.021 0.001 TYR K 82 PHE 0.034 0.001 PHE I 222 TRP 0.044 0.002 TRP K 132 HIS 0.004 0.001 HIS H 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (37642) covalent geometry : angle 0.66018 / 0.34 (50938) hydrogen bonds : bond 0.04107 / 2.68 ( 1042) hydrogen bonds : angle 5.49690 / 3.77 ( 2922) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.9265 (ptp) cc_final: 0.9026 (ptp) REVERT: A 74 MET cc_start: 0.9237 (mtp) cc_final: 0.8914 (mtt) REVERT: A 99 GLN cc_start: 0.9260 (pm20) cc_final: 0.8947 (pp30) REVERT: A 166 TYR cc_start: 0.9240 (t80) cc_final: 0.8872 (t80) REVERT: A 199 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7830 (mt-10) REVERT: A 249 MET cc_start: 0.7850 (mpp) cc_final: 0.7252 (mmp) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.0830 time to fit residues: 2.4807 Evaluate side-chains 24 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.097 Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.099 Fit side-chains REVERT: D 296 MET cc_start: 0.8745 (tmm) cc_final: 0.8314 (tmm) REVERT: D 439 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8629 (tptt) REVERT: D 465 MET cc_start: 0.7398 (mtm) cc_final: 0.6786 (ttt) REVERT: D 469 TYR cc_start: 0.8303 (m-80) cc_final: 0.7948 (m-80) REVERT: D 523 PHE cc_start: 0.9102 (t80) cc_final: 0.8303 (t80) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0546 time to fit residues: 2.9551 Evaluate side-chains 25 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.108 Evaluate side-chains 22 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 104 MET cc_start: 0.8601 (mmp) cc_final: 0.8320 (tpp) REVERT: E 252 MET cc_start: 0.8997 (tpt) cc_final: 0.8772 (tpt) REVERT: E 310 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8848 (tm-30) REVERT: E 344 GLU cc_start: 0.9248 (mp0) cc_final: 0.8867 (tm-30) REVERT: E 349 TYR cc_start: 0.8704 (m-80) cc_final: 0.8165 (m-80) REVERT: E 375 HIS cc_start: 0.8647 (t-90) cc_final: 0.8394 (t-90) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0893 time to fit residues: 2.4083 Evaluate side-chains 18 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.124 Evaluate side-chains 34 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 108 MET cc_start: 0.8077 (pmm) cc_final: 0.7152 (ppp) REVERT: G 140 LEU cc_start: 0.9650 (tp) cc_final: 0.9408 (tp) REVERT: G 306 LEU cc_start: 0.9633 (tp) cc_final: 0.9379 (tt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0798 time to fit residues: 3.3862 Evaluate side-chains 21 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.134 Evaluate side-chains 19 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: I 76 MET cc_start: 0.4470 (ptt) cc_final: 0.3889 (ptp) REVERT: I 230 GLU cc_start: 0.8823 (tt0) cc_final: 0.7782 (mm-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0503 time to fit residues: 1.2704 Evaluate side-chains 13 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.092 Evaluate side-chains 16 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.083 Fit side-chains REVERT: L 54 ARG cc_start: 0.8967 (mtm180) cc_final: 0.8763 (pmt-80) REVERT: L 78 LYS cc_start: 0.9152 (tttt) cc_final: 0.8797 (tppt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0959 time to fit residues: 1.7996 Evaluate side-chains 9 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.083 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0105 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 15 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.123 Fit side-chains REVERT: O 239 MET cc_start: -0.0872 (mtp) cc_final: -0.1871 (mmt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0782 time to fit residues: 1.5628 Evaluate side-chains 11 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 375 optimal weight: 0.9990 chunk 395 optimal weight: 3.9990 chunk 243 optimal weight: 0.0070 chunk 274 optimal weight: 0.0010 chunk 100 optimal weight: 6.9990 chunk 97 optimal weight: 0.2980 chunk 127 optimal weight: 8.9990 chunk 354 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 305 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 388 ASN ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.041340 restraints weight = 15875.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.042622 restraints weight = 10290.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.043441 restraints weight = 7303.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044191 restraints weight = 5614.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044743 restraints weight = 4415.878| |-----------------------------------------------------------------------------| r_work (final): 0.2925 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.042712 restraints weight = 17114.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.043874 restraints weight = 11169.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044730 restraints weight = 7964.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045374 restraints weight = 6079.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.045844 restraints weight = 4883.409| |-----------------------------------------------------------------------------| r_work (final): 0.2998 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.040483 restraints weight = 18763.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.041522 restraints weight = 12499.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042312 restraints weight = 9325.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.042891 restraints weight = 7413.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043214 restraints weight = 6214.870| |-----------------------------------------------------------------------------| r_work (final): 0.2908 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.037258 restraints weight = 26069.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.038355 restraints weight = 16217.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.039212 restraints weight = 11156.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.039854 restraints weight = 8095.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.040353 restraints weight = 6150.193| |-----------------------------------------------------------------------------| r_work (final): 0.2952 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.067638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.059145 restraints weight = 19597.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.060160 restraints weight = 14782.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.060905 restraints weight = 11910.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.061426 restraints weight = 10065.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.061834 restraints weight = 8879.801| |-----------------------------------------------------------------------------| r_work (final): 0.3607 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.085883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.060800 restraints weight = 19444.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.061794 restraints weight = 13379.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.062384 restraints weight = 9911.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.063078 restraints weight = 7753.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.063419 restraints weight = 6312.106| |-----------------------------------------------------------------------------| r_work (final): 0.3547 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.093167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.091273 restraints weight = 1772.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.091816 restraints weight = 1115.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.092111 restraints weight = 752.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.092319 restraints weight = 531.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.092450 restraints weight = 382.193| |-----------------------------------------------------------------------------| r_work (final): 0.3831 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5422 r_free = 0.5422 target = 0.140184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.108339 restraints weight = 20952.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.108337 restraints weight = 24918.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.108337 restraints weight = 24385.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.108337 restraints weight = 24380.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.108337 restraints weight = 24380.826| |-----------------------------------------------------------------------------| r_work (final): 0.4597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 37642 Z= 0.120 Angle : 0.669 11.697 50938 Z= 0.340 Chirality : 0.047 0.217 5958 Planarity : 0.007 0.281 6490 Dihedral : 5.892 49.773 5022 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.63 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.12), residues: 4610 helix: -1.11 (0.13), residues: 1414 sheet: -1.42 (0.21), residues: 562 loop : -2.03 (0.12), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 289 TYR 0.025 0.001 TYR I 242 PHE 0.037 0.001 PHE G 145 TRP 0.051 0.002 TRP G 302 HIS 0.005 0.001 HIS G 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (37642) covalent geometry : angle 0.66945 / 0.34 (50938) hydrogen bonds : bond 0.03928 / 2.57 ( 1042) hydrogen bonds : angle 5.38437 / 3.72 ( 2922) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9283 (mtp) cc_final: 0.8937 (mtt) REVERT: A 99 GLN cc_start: 0.9221 (pm20) cc_final: 0.8965 (pp30) REVERT: A 166 TYR cc_start: 0.9275 (t80) cc_final: 0.8854 (t80) REVERT: A 199 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 249 MET cc_start: 0.7857 (mpp) cc_final: 0.7522 (mmp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0584 time to fit residues: 1.9920 Evaluate side-chains 20 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.101 Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.9024 (m-10) cc_final: 0.8216 (m-80) REVERT: C 361 LYS cc_start: 0.9007 (pttt) cc_final: 0.8436 (tptt) REVERT: C 439 LYS cc_start: 0.9072 (mtpp) cc_final: 0.8492 (tptt) REVERT: C 465 MET cc_start: 0.7581 (mtm) cc_final: 0.6866 (ttt) REVERT: C 469 TYR cc_start: 0.8232 (m-80) cc_final: 0.7979 (m-80) REVERT: C 523 PHE cc_start: 0.8830 (t80) cc_final: 0.8083 (t80) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0647 time to fit residues: 3.3425 Evaluate side-chains 26 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.104 Evaluate side-chains 23 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 63 LEU cc_start: 0.9664 (tp) cc_final: 0.9308 (pp) REVERT: E 104 MET cc_start: 0.8522 (mmp) cc_final: 0.8293 (tpp) REVERT: E 310 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8779 (tm-30) REVERT: E 344 GLU cc_start: 0.9206 (mp0) cc_final: 0.8832 (tm-30) REVERT: E 349 TYR cc_start: 0.8546 (m-80) cc_final: 0.8039 (m-80) REVERT: E 375 HIS cc_start: 0.8698 (t-90) cc_final: 0.8446 (t-90) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0821 time to fit residues: 2.2780 Evaluate side-chains 18 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.110 Evaluate side-chains 28 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: H 52 LEU cc_start: 0.9612 (mt) cc_final: 0.9345 (mt) REVERT: H 108 MET cc_start: 0.7902 (pmm) cc_final: 0.6762 (ppp) REVERT: H 119 MET cc_start: 0.8718 (ppp) cc_final: 0.8510 (ppp) REVERT: H 140 LEU cc_start: 0.9560 (tp) cc_final: 0.9266 (tp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0439 time to fit residues: 1.7585 Evaluate side-chains 21 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.121 Evaluate side-chains 16 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.083 Fit side-chains REVERT: I 76 MET cc_start: 0.4526 (ptt) cc_final: 0.3957 (ptp) REVERT: I 230 GLU cc_start: 0.8794 (tt0) cc_final: 0.7752 (mm-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0516 time to fit residues: 1.1000 Evaluate side-chains 13 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.094 Evaluate side-chains 12 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.078 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0819 time to fit residues: 1.2044 Evaluate side-chains 8 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.082 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0062 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 25 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: P 310 MET cc_start: 0.2794 (ttt) cc_final: 0.2468 (pmm) REVERT: P 435 PHE cc_start: 0.4619 (m-80) cc_final: 0.4339 (t80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0993 time to fit residues: 2.9772 Evaluate side-chains 15 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 0.0570 chunk 27 optimal weight: 0.0570 chunk 346 optimal weight: 0.0370 chunk 423 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 379 optimal weight: 0.3980 chunk 242 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS C 271 HIS ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 171 ASN P 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.041467 restraints weight = 15972.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.042651 restraints weight = 10557.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.043626 restraints weight = 7732.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.044364 restraints weight = 5907.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044916 restraints weight = 4707.785| |-----------------------------------------------------------------------------| r_work (final): 0.2926 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.051714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043069 restraints weight = 17252.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.044154 restraints weight = 11763.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044966 restraints weight = 8709.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045584 restraints weight = 6836.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046020 restraints weight = 5628.601| |-----------------------------------------------------------------------------| r_work (final): 0.2992 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.042060 restraints weight = 18653.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043240 restraints weight = 11887.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044067 restraints weight = 8531.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044747 restraints weight = 6672.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045224 restraints weight = 5484.355| |-----------------------------------------------------------------------------| r_work (final): 0.2944 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.043366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037526 restraints weight = 26415.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.038681 restraints weight = 16245.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.039532 restraints weight = 11069.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.040172 restraints weight = 8049.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040655 restraints weight = 6137.245| |-----------------------------------------------------------------------------| r_work (final): 0.2984 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.072040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.064102 restraints weight = 20544.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.065344 restraints weight = 13956.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.066232 restraints weight = 10496.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.066857 restraints weight = 8408.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.067277 restraints weight = 7072.874| |-----------------------------------------------------------------------------| r_work (final): 0.3647 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.087366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.059692 restraints weight = 19758.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.060560 restraints weight = 12525.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.061047 restraints weight = 8823.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.061625 restraints weight = 6618.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.061893 restraints weight = 5153.067| |-----------------------------------------------------------------------------| r_work (final): 0.3564 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.093636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.091684 restraints weight = 1739.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.092262 restraints weight = 1047.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.092590 restraints weight = 673.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.092831 restraints weight = 476.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.092990 restraints weight = 329.925| |-----------------------------------------------------------------------------| r_work (final): 0.3828 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.074648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.073492 restraints weight = 44880.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.073663 restraints weight = 36046.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.073736 restraints weight = 29196.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.073878 restraints weight = 25578.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.073974 restraints weight = 21836.085| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5689 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37642 Z= 0.116 Angle : 0.680 12.305 50938 Z= 0.344 Chirality : 0.047 0.235 5958 Planarity : 0.006 0.194 6490 Dihedral : 5.732 44.644 5022 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.11 % Favored : 90.80 % Rotamer: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.12), residues: 4610 helix: -1.08 (0.13), residues: 1430 sheet: -1.35 (0.20), residues: 620 loop : -2.00 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 301 TYR 0.020 0.001 TYR L 82 PHE 0.028 0.001 PHE F 307 TRP 0.033 0.002 TRP B 87 HIS 0.004 0.001 HIS G 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (37642) covalent geometry : angle 0.67997 / 0.34 (50938) hydrogen bonds : bond 0.03889 / 2.57 ( 1042) hydrogen bonds : angle 5.26706 / 3.63 ( 2922) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9125 (mtp) cc_final: 0.8861 (mtt) REVERT: A 99 GLN cc_start: 0.9272 (pm20) cc_final: 0.9063 (pp30) REVERT: A 166 TYR cc_start: 0.9241 (t80) cc_final: 0.8816 (t80) REVERT: A 199 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 249 MET cc_start: 0.7679 (mpp) cc_final: 0.7476 (mmp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0419 time to fit residues: 1.4900 Evaluate side-chains 22 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.107 Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: D 296 MET cc_start: 0.8607 (tmm) cc_final: 0.8387 (tmm) REVERT: D 300 PHE cc_start: 0.8935 (m-10) cc_final: 0.8425 (m-80) REVERT: D 439 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8569 (tptt) REVERT: D 462 ILE cc_start: 0.9079 (pt) cc_final: 0.8840 (pt) REVERT: D 464 ASN cc_start: 0.9036 (t0) cc_final: 0.8742 (p0) REVERT: D 465 MET cc_start: 0.7236 (mtm) cc_final: 0.6984 (ttt) REVERT: D 469 TYR cc_start: 0.8232 (m-80) cc_final: 0.7974 (m-80) REVERT: D 523 PHE cc_start: 0.8856 (t80) cc_final: 0.8246 (t80) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0572 time to fit residues: 3.0921 Evaluate side-chains 25 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.114 Evaluate side-chains 25 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 63 LEU cc_start: 0.9668 (tp) cc_final: 0.9310 (pp) REVERT: E 344 GLU cc_start: 0.9269 (mp0) cc_final: 0.8915 (tm-30) REVERT: E 349 TYR cc_start: 0.8662 (m-80) cc_final: 0.8002 (m-80) REVERT: E 375 HIS cc_start: 0.8669 (t-90) cc_final: 0.8434 (t-90) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.0617 time to fit residues: 2.0156 Evaluate side-chains 18 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.117 Evaluate side-chains 32 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.139 Fit side-chains REVERT: H 52 LEU cc_start: 0.9587 (mt) cc_final: 0.9307 (mt) REVERT: H 108 MET cc_start: 0.7879 (pmm) cc_final: 0.6683 (tmm) REVERT: H 119 MET cc_start: 0.8751 (ppp) cc_final: 0.8523 (ppp) REVERT: H 140 LEU cc_start: 0.9576 (tp) cc_final: 0.9331 (tp) REVERT: H 155 MET cc_start: 0.8066 (ppp) cc_final: 0.7708 (ppp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0553 time to fit residues: 2.4029 Evaluate side-chains 19 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.129 Evaluate side-chains 19 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.094 Fit side-chains REVERT: I 76 MET cc_start: 0.4412 (ptt) cc_final: 0.3802 (ptp) REVERT: I 224 THR cc_start: 0.8599 (m) cc_final: 0.8102 (m) REVERT: I 230 GLU cc_start: 0.8707 (tt0) cc_final: 0.7640 (mm-30) REVERT: I 266 LEU cc_start: 0.6124 (pt) cc_final: 0.5864 (mp) REVERT: I 295 MET cc_start: 0.5691 (ttt) cc_final: 0.5199 (tmm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0676 time to fit residues: 1.6031 Evaluate side-chains 13 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.094 Evaluate side-chains 14 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0819 time to fit residues: 1.3665 Evaluate side-chains 7 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.082 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0101 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 18 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.125 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0529 time to fit residues: 1.3758 Evaluate side-chains 13 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 54 optimal weight: 5.9990 chunk 91 optimal weight: 0.0040 chunk 188 optimal weight: 0.0980 chunk 209 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 chunk 333 optimal weight: 1.9990 chunk 350 optimal weight: 0.0000 chunk 205 optimal weight: 10.0000 chunk 315 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS D 271 HIS D 280 HIS ** D 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.042073 restraints weight = 15641.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.043356 restraints weight = 10111.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.044347 restraints weight = 7190.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.044953 restraints weight = 5420.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045523 restraints weight = 4394.416| |-----------------------------------------------------------------------------| r_work (final): 0.2952 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.051979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.043404 restraints weight = 16808.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044521 restraints weight = 11334.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045363 restraints weight = 8333.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.045969 restraints weight = 6522.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.046381 restraints weight = 5364.977| |-----------------------------------------------------------------------------| r_work (final): 0.3002 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.050669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.040967 restraints weight = 18778.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.042108 restraints weight = 12180.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.042936 restraints weight = 8842.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.043572 restraints weight = 6927.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.044015 restraints weight = 5730.629| |-----------------------------------------------------------------------------| r_work (final): 0.2935 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.043201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.037187 restraints weight = 25585.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038387 restraints weight = 15759.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.039259 restraints weight = 10778.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.039905 restraints weight = 7882.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040393 restraints weight = 6027.461| |-----------------------------------------------------------------------------| r_work (final): 0.2983 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.067624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.057382 restraints weight = 18464.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.058413 restraints weight = 14046.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.059155 restraints weight = 11633.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.059631 restraints weight = 10044.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.060033 restraints weight = 9091.019| |-----------------------------------------------------------------------------| r_work (final): 0.3595 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.085501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.066075 restraints weight = 19751.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.066980 restraints weight = 13017.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.067538 restraints weight = 9091.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.067931 restraints weight = 6596.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.068119 restraints weight = 5087.220| |-----------------------------------------------------------------------------| r_work (final): 0.3585 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.092551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.089788 restraints weight = 1279.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.090300 restraints weight = 789.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.090637 restraints weight = 512.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.090842 restraints weight = 343.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.091011 restraints weight = 239.091| |-----------------------------------------------------------------------------| r_work (final): 0.3884 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5432 r_free = 0.5432 target = 0.142522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.102177 restraints weight = 20146.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.102174 restraints weight = 22850.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.102174 restraints weight = 22655.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.102174 restraints weight = 22655.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.102174 restraints weight = 22655.489| |-----------------------------------------------------------------------------| r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 37642 Z= 0.116 Angle : 0.668 11.318 50938 Z= 0.340 Chirality : 0.047 0.239 5958 Planarity : 0.006 0.194 6490 Dihedral : 5.574 38.408 5022 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.37 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.12), residues: 4610 helix: -0.94 (0.13), residues: 1414 sheet: -1.39 (0.19), residues: 724 loop : -1.97 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 224 TYR 0.022 0.001 TYR L 82 PHE 0.021 0.001 PHE J 222 TRP 0.030 0.002 TRP L 132 HIS 0.004 0.001 HIS G 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (37642) covalent geometry : angle 0.66803 / 0.34 (50938) hydrogen bonds : bond 0.03838 / 2.56 ( 1042) hydrogen bonds : angle 5.05057 / 3.47 ( 2922) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 166 TYR cc_start: 0.9232 (t80) cc_final: 0.8818 (t80) REVERT: A 199 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7645 (mt-10) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0428 time to fit residues: 1.6944 Evaluate side-chains 21 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.095 Evaluate side-chains 38 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 300 PHE cc_start: 0.8986 (m-10) cc_final: 0.8614 (m-80) REVERT: D 340 MET cc_start: 0.8816 (ptp) cc_final: 0.8310 (ptp) REVERT: D 439 LYS cc_start: 0.9080 (mtpp) cc_final: 0.8518 (tptt) REVERT: D 465 MET cc_start: 0.7401 (mtm) cc_final: 0.6749 (ttt) REVERT: D 469 TYR cc_start: 0.8304 (m-80) cc_final: 0.8013 (m-80) REVERT: D 523 PHE cc_start: 0.8850 (t80) cc_final: 0.8249 (t80) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0662 time to fit residues: 3.1166 Evaluate side-chains 24 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.115 Evaluate side-chains 22 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 63 LEU cc_start: 0.9665 (tp) cc_final: 0.9309 (pp) REVERT: E 344 GLU cc_start: 0.9281 (mp0) cc_final: 0.8920 (tm-30) REVERT: E 349 TYR cc_start: 0.8752 (m-80) cc_final: 0.8450 (m-80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0655 time to fit residues: 1.8762 Evaluate side-chains 14 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.115 Evaluate side-chains 29 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.133 Fit side-chains REVERT: H 52 LEU cc_start: 0.9587 (mt) cc_final: 0.9323 (mt) REVERT: H 108 MET cc_start: 0.7877 (pmm) cc_final: 0.6693 (tmm) REVERT: H 119 MET cc_start: 0.8762 (ppp) cc_final: 0.8551 (ppp) REVERT: H 140 LEU cc_start: 0.9579 (tp) cc_final: 0.9338 (tp) REVERT: H 155 MET cc_start: 0.8049 (ppp) cc_final: 0.7722 (ppp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0651 time to fit residues: 2.4765 Evaluate side-chains 20 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.121 Evaluate side-chains 21 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.089 Fit side-chains REVERT: I 224 THR cc_start: 0.8673 (m) cc_final: 0.8228 (m) REVERT: I 230 GLU cc_start: 0.8687 (tt0) cc_final: 0.7519 (mm-30) REVERT: I 266 LEU cc_start: 0.6248 (pt) cc_final: 0.5882 (mt) REVERT: I 295 MET cc_start: 0.6295 (ttt) cc_final: 0.5737 (tmm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0462 time to fit residues: 1.2989 Evaluate side-chains 15 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.095 Evaluate side-chains 12 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.084 Fit side-chains REVERT: K 85 LEU cc_start: 0.8918 (mp) cc_final: 0.8714 (tp) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0609 time to fit residues: 0.9547 Evaluate side-chains 7 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.084 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0107 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 15 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.130 Fit side-chains REVERT: O 211 MET cc_start: 0.0482 (tmm) cc_final: 0.0041 (tmm) REVERT: O 271 ARG cc_start: -0.0034 (ppt170) cc_final: -0.0354 (mmt-90) REVERT: O 482 MET cc_start: 0.1670 (pmm) cc_final: 0.1205 (mtt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0758 time to fit residues: 1.4812 Evaluate side-chains 10 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 122 optimal weight: 10.0000 chunk 205 optimal weight: 0.0870 chunk 417 optimal weight: 0.0570 chunk 347 optimal weight: 0.2980 chunk 230 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 270 optimal weight: 5.9990 chunk 324 optimal weight: 0.0770 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 HIS H 56 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.043764 restraints weight = 15789.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045074 restraints weight = 10472.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.046027 restraints weight = 7567.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046762 restraints weight = 5833.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.047353 restraints weight = 4633.843| |-----------------------------------------------------------------------------| r_work (final): 0.2989 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.043980 restraints weight = 17117.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045101 restraints weight = 11584.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045946 restraints weight = 8527.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.046503 restraints weight = 6633.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047083 restraints weight = 5472.339| |-----------------------------------------------------------------------------| r_work (final): 0.3027 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.041989 restraints weight = 18234.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.043153 restraints weight = 12091.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.044019 restraints weight = 8926.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.044644 restraints weight = 7051.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045104 restraints weight = 5879.269| |-----------------------------------------------------------------------------| r_work (final): 0.2966 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.043488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.037645 restraints weight = 25772.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.038796 restraints weight = 16003.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.039626 restraints weight = 10972.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.040278 restraints weight = 8043.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.040763 restraints weight = 6141.809| |-----------------------------------------------------------------------------| r_work (final): 0.2994 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.068573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.058897 restraints weight = 19636.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.060026 restraints weight = 14676.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.060813 restraints weight = 11822.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.061338 restraints weight = 10140.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.061674 restraints weight = 9076.200| |-----------------------------------------------------------------------------| r_work (final): 0.3603 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.086479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.064894 restraints weight = 18386.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.065735 restraints weight = 12550.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.066169 restraints weight = 8987.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.066289 restraints weight = 6815.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.066824 restraints weight = 5766.511| |-----------------------------------------------------------------------------| r_work (final): 0.3604 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.091861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.089274 restraints weight = 1524.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.089861 restraints weight = 1073.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.090246 restraints weight = 784.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.090532 restraints weight = 587.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.090718 restraints weight = 450.980| |-----------------------------------------------------------------------------| r_work (final): 0.3886 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.078612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.074696 restraints weight = 344913.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.075454 restraints weight = 267231.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.075767 restraints weight = 203421.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.075911 restraints weight = 176902.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.075954 restraints weight = 162935.292| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37642 Z= 0.119 Angle : 0.673 11.953 50938 Z= 0.342 Chirality : 0.047 0.269 5958 Planarity : 0.006 0.186 6490 Dihedral : 5.472 32.909 5022 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.98 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.12), residues: 4610 helix: -0.90 (0.13), residues: 1414 sheet: -1.33 (0.20), residues: 608 loop : -1.84 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 324 TYR 0.021 0.001 TYR C 624 PHE 0.041 0.001 PHE G 145 TRP 0.026 0.002 TRP H 302 HIS 0.004 0.001 HIS O 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (37642) covalent geometry : angle 0.67340 / 0.34 (50938) hydrogen bonds : bond 0.03849 / 2.56 ( 1042) hydrogen bonds : angle 5.03787 / 3.47 ( 2922) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.182 Fit side-chains REVERT: A 74 MET cc_start: 0.9042 (mtm) cc_final: 0.8636 (mtt) REVERT: A 166 TYR cc_start: 0.9237 (t80) cc_final: 0.8782 (t80) REVERT: A 199 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 249 MET cc_start: 0.7792 (mmp) cc_final: 0.7577 (mmp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0418 time to fit residues: 1.6315 Evaluate side-chains 18 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.097 Evaluate side-chains 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 300 PHE cc_start: 0.9074 (m-10) cc_final: 0.8713 (m-80) REVERT: C 340 MET cc_start: 0.8707 (ptp) cc_final: 0.8490 (ptp) REVERT: C 439 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8358 (tptt) REVERT: C 465 MET cc_start: 0.7058 (mtm) cc_final: 0.6620 (ttt) REVERT: C 469 TYR cc_start: 0.8303 (m-80) cc_final: 0.8018 (m-80) REVERT: C 472 LEU cc_start: 0.9535 (mm) cc_final: 0.9315 (mp) REVERT: C 523 PHE cc_start: 0.8701 (t80) cc_final: 0.8070 (t80) REVERT: C 528 ASP cc_start: 0.7746 (t0) cc_final: 0.7396 (t0) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0517 time to fit residues: 2.6759 Evaluate side-chains 25 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.108 Evaluate side-chains 23 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 63 LEU cc_start: 0.9650 (tp) cc_final: 0.9311 (pp) REVERT: E 320 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7788 (mmp80) REVERT: E 344 GLU cc_start: 0.9254 (mp0) cc_final: 0.8894 (tm-30) REVERT: E 349 TYR cc_start: 0.8618 (m-80) cc_final: 0.8349 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0769 time to fit residues: 2.2057 Evaluate side-chains 16 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.121 Evaluate side-chains 30 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.132 Fit side-chains REVERT: H 52 LEU cc_start: 0.9572 (mt) cc_final: 0.9306 (mt) REVERT: H 108 MET cc_start: 0.7949 (pmm) cc_final: 0.6830 (tmm) REVERT: H 119 MET cc_start: 0.8776 (ppp) cc_final: 0.8563 (ppp) REVERT: H 140 LEU cc_start: 0.9606 (tp) cc_final: 0.9377 (tp) REVERT: H 155 MET cc_start: 0.8106 (ppp) cc_final: 0.7807 (ppp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0617 time to fit residues: 2.3902 Evaluate side-chains 20 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.134 Evaluate side-chains 20 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.091 Fit side-chains REVERT: I 224 THR cc_start: 0.8685 (m) cc_final: 0.8173 (m) REVERT: I 230 GLU cc_start: 0.7767 (tt0) cc_final: 0.6989 (mm-30) REVERT: I 295 MET cc_start: 0.5766 (ttt) cc_final: 0.5375 (tmm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0519 time to fit residues: 1.3704 Evaluate side-chains 16 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.087 Evaluate side-chains 12 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.083 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0614 time to fit residues: 0.9561 Evaluate side-chains 8 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.080 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0101 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 17 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: P 201 MET cc_start: 0.1939 (pmm) cc_final: -0.0701 (ppp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0521 time to fit residues: 1.2762 Evaluate side-chains 13 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 455 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 355 optimal weight: 9.9990 chunk 309 optimal weight: 0.0980 chunk 118 optimal weight: 1.9990 chunk 404 optimal weight: 0.0170 chunk 296 optimal weight: 4.9990 chunk 319 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 ASN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 HIS ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN ** P 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.042343 restraints weight = 15572.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.043595 restraints weight = 10079.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044556 restraints weight = 7219.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.045253 restraints weight = 5431.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045764 restraints weight = 4292.759| |-----------------------------------------------------------------------------| r_work (final): 0.2961 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.051807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.043068 restraints weight = 17684.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.044170 restraints weight = 12169.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.044993 restraints weight = 9033.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045648 restraints weight = 7090.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046101 restraints weight = 5811.288| |-----------------------------------------------------------------------------| r_work (final): 0.2996 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.051130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.041175 restraints weight = 18307.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.042339 restraints weight = 12035.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043181 restraints weight = 8828.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.043779 restraints weight = 6975.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.044239 restraints weight = 5847.923| |-----------------------------------------------------------------------------| r_work (final): 0.2936 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.037333 restraints weight = 25604.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.038462 restraints weight = 15969.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.039274 restraints weight = 11028.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.039887 restraints weight = 8148.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.040378 restraints weight = 6294.830| |-----------------------------------------------------------------------------| r_work (final): 0.2950 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.066898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.057071 restraints weight = 19101.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.058142 restraints weight = 14384.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.058920 restraints weight = 11714.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.059497 restraints weight = 10065.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.059854 restraints weight = 8956.831| |-----------------------------------------------------------------------------| r_work (final): 0.3569 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.086346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.062109 restraints weight = 18625.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.062763 restraints weight = 12445.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.063357 restraints weight = 9007.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.063472 restraints weight = 7001.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.063786 restraints weight = 5980.679| |-----------------------------------------------------------------------------| r_work (final): 0.3565 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.092666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.090397 restraints weight = 1730.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.090953 restraints weight = 1206.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.091370 restraints weight = 875.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.091657 restraints weight = 658.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.091847 restraints weight = 504.825| |-----------------------------------------------------------------------------| r_work (final): 0.3837 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.079238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.077120 restraints weight = 48703.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.077417 restraints weight = 38932.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.077575 restraints weight = 32914.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.077575 restraints weight = 28398.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.077575 restraints weight = 28040.021| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37642 Z= 0.122 Angle : 0.664 11.465 50938 Z= 0.339 Chirality : 0.047 0.293 5958 Planarity : 0.006 0.191 6490 Dihedral : 5.399 30.251 5022 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.59 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.12), residues: 4610 helix: -0.77 (0.14), residues: 1418 sheet: -1.27 (0.20), residues: 634 loop : -1.76 (0.13), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 301 TYR 0.017 0.001 TYR L 82 PHE 0.020 0.001 PHE E 122 TRP 0.028 0.002 TRP K 132 HIS 0.005 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (37642) covalent geometry : angle 0.66395 / 0.34 (50938) hydrogen bonds : bond 0.03842 / 2.51 ( 1042) hydrogen bonds : angle 5.00299 / 3.44 ( 2922) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9220 Ramachandran restraints generated. 4610 Oldfield, 0 Emsley, 4610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.101 Fit side-chains REVERT: A 74 MET cc_start: 0.9042 (mtm) cc_final: 0.8535 (mtt) REVERT: A 166 TYR cc_start: 0.9205 (t80) cc_final: 0.8748 (t80) REVERT: A 199 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7807 (mt-10) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0398 time to fit residues: 1.3461 Evaluate side-chains 19 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.098 Evaluate side-chains 37 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: C 296 MET cc_start: 0.8481 (tmm) cc_final: 0.8278 (tmm) REVERT: C 300 PHE cc_start: 0.9177 (m-10) cc_final: 0.8812 (m-80) REVERT: C 340 MET cc_start: 0.8675 (ptp) cc_final: 0.8445 (ptp) REVERT: C 436 GLU cc_start: 0.8107 (pt0) cc_final: 0.7371 (pt0) REVERT: C 439 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8443 (tptt) REVERT: C 465 MET cc_start: 0.7219 (mtm) cc_final: 0.6788 (ttt) REVERT: C 469 TYR cc_start: 0.8388 (m-80) cc_final: 0.8037 (m-80) REVERT: C 472 LEU cc_start: 0.9532 (mm) cc_final: 0.9300 (mp) REVERT: C 523 PHE cc_start: 0.8751 (t80) cc_final: 0.8072 (t80) REVERT: C 528 ASP cc_start: 0.7829 (t0) cc_final: 0.7516 (t0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0563 time to fit residues: 2.6596 Evaluate side-chains 25 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.111 Evaluate side-chains 21 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 320 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7856 (mmp80) REVERT: E 325 MET cc_start: 0.7520 (ttm) cc_final: 0.6924 (mmt) REVERT: E 344 GLU cc_start: 0.9258 (mp0) cc_final: 0.8881 (tm-30) REVERT: E 349 TYR cc_start: 0.8662 (m-80) cc_final: 0.8337 (m-80) REVERT: E 375 HIS cc_start: 0.8662 (t-90) cc_final: 0.8435 (t-90) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0846 time to fit residues: 2.1945 Evaluate side-chains 16 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.138 Evaluate side-chains 29 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.164 Fit side-chains REVERT: H 52 LEU cc_start: 0.9609 (mt) cc_final: 0.9351 (mt) REVERT: H 108 MET cc_start: 0.7861 (pmm) cc_final: 0.6777 (tmm) REVERT: H 140 LEU cc_start: 0.9560 (tp) cc_final: 0.9263 (tp) REVERT: H 166 MET cc_start: 0.8896 (mmt) cc_final: 0.8398 (mmm) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0675 time to fit residues: 2.5837 Evaluate side-chains 18 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.145 Evaluate side-chains 19 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.089 Fit side-chains REVERT: I 224 THR cc_start: 0.8519 (m) cc_final: 0.7950 (m) REVERT: I 230 GLU cc_start: 0.8295 (tt0) cc_final: 0.7393 (mm-30) REVERT: I 295 MET cc_start: 0.6182 (ttt) cc_final: 0.5694 (tmm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0505 time to fit residues: 1.2963 Evaluate side-chains 16 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.107 Evaluate side-chains 12 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0648 time to fit residues: 1.0300 Evaluate side-chains 7 residues out of total 224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.098 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0122 Evaluate side-chains 0 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Evaluate side-chains 14 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.122 Fit side-chains REVERT: O 271 ARG cc_start: -0.0749 (ppt170) cc_final: -0.1789 (mmt180) REVERT: O 482 MET cc_start: -0.1295 (pmm) cc_final: -0.1501 (mtt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1148 time to fit residues: 1.9685 Evaluate side-chains 10 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 336 optimal weight: 2.9990 chunk 168 optimal weight: 0.0670 chunk 278 optimal weight: 6.9990 chunk 287 optimal weight: 0.9990 chunk 435 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 194 optimal weight: 0.0170 chunk 102 optimal weight: 7.9990 chunk 447 optimal weight: 5.9990 chunk 418 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 HIS ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 HIS O 98 GLN ** O 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.042511 restraints weight = 15364.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.043838 restraints weight = 9926.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.044837 restraints weight = 7019.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045553 restraints weight = 5274.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046085 restraints weight = 4148.879| |-----------------------------------------------------------------------------| r_work (final): 0.2966 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.043496 restraints weight = 17158.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044655 restraints weight = 11470.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045546 restraints weight = 8334.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046189 restraints weight = 6438.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.046691 restraints weight = 5226.567| |-----------------------------------------------------------------------------| r_work (final): 0.3018 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.041261 restraints weight = 18565.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042478 restraints weight = 12042.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.043336 restraints weight = 8761.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044045 restraints weight = 6912.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.044537 restraints weight = 5690.770| |-----------------------------------------------------------------------------| r_work (final): 0.2940 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.043550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.037601 restraints weight = 25551.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.038754 restraints weight = 15754.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039597 restraints weight = 10784.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.040248 restraints weight = 7895.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.040747 restraints weight = 6026.558| |-----------------------------------------------------------------------------| r_work (final): 0.2966 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.067639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.056920 restraints weight = 18237.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.057912 restraints weight = 14121.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.058606 restraints weight = 11788.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.059072 restraints weight = 10376.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.059316 restraints weight = 9477.925| |-----------------------------------------------------------------------------| r_work (final): 0.3573 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.084581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.060187 restraints weight = 21167.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.060970 restraints weight = 14989.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.061377 restraints weight = 10833.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.061910 restraints weight = 8352.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.062116 restraints weight = 6568.172| |-----------------------------------------------------------------------------| r_work (final): 0.3564 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.125640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.122389 restraints weight = 887.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.123732 restraints weight = 511.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.124583 restraints weight = 291.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.124974 restraints weight = 161.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.125357 restraints weight = 99.616| |-----------------------------------------------------------------------------| r_work (final): 0.4264 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.078912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.075490 restraints weight = 384076.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.076084 restraints weight = 283805.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.076403 restraints weight = 219095.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.076537 restraints weight = 190160.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.076639 restraints weight = 182199.198| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 37642 Z= 0.113 Angle : 0.658 14.265 50938 Z= 0.336 Chirality : 0.047 0.260 5958 Planarity : 0.005 0.139 6490 Dihedral : 5.316 29.122 5022 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.12), residues: 4610 helix: -0.73 (0.13), residues: 1446 sheet: -1.29 (0.20), residues: 612 loop : -1.77 (0.13), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG G 301 TYR 0.019 0.001 TYR L 82 PHE 0.026 0.001 PHE G 145 TRP 0.025 0.001 TRP K 132 HIS 0.007 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (37642) covalent geometry : angle 0.65835 / 0.34 (50938) hydrogen bonds : bond 0.03788 / 2.51 ( 1042) hydrogen bonds : angle 5.02556 / 3.43 ( 2922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3712.56 seconds wall clock time: 66 minutes 40.01 seconds (4000.01 seconds total)