Starting phenix.real_space_refine on Fri Sep 11 16:22:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6iww_9743/09_2026/6iww_9743.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iww_9743/09_2026/6iww_9743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6iww_9743/09_2026/6iww_9743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iww_9743/09_2026/6iww_9743.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6iww_9743/09_2026/6iww_9743.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6iww_9743/09_2026/6iww_9743.cif" model { file = "/net/cci-nas-00/data/ceres_data/6iww_9743/09_2026/6iww_9743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iww_9743/09_2026/6iww_9743.cif" } resolution = 3.9 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= 0.022 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 69 5.16 5 C 6741 2.51 5 N 1653 2.21 5 O 1764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 10227 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3054 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397} Chain: "B" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 320 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3054 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397} Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 320 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "E" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3054 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397} Chain: "F" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 320 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.40, per 1000 atoms: 0.23 Number of scatterers: 10227 At special positions: 0 Unit cell: (104.304, 106.944, 85.8195, 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 69 16.00 O 1764 8.00 N 1653 7.00 C 6741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 444.9 milliseconds 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2484 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 0 sheets defined 82.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.765A pdb=" N ILE A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.682A pdb=" N ASN A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.671A pdb=" N HIS A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 93 through 100 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.527A pdb=" N ILE A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.682A pdb=" N PHE A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.510A pdb=" N ALA A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 183 removed outlier: 3.963A pdb=" N PHE A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 198 removed outlier: 3.934A pdb=" N ALA A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 202 Processing helix chain 'A' and resid 203 through 214 removed outlier: 4.217A pdb=" N TYR A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 245 Proline residue: A 238 - end of helix removed outlier: 3.524A pdb=" N THR A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 261 through 279 Proline residue: A 269 - end of helix Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 283 through 300 removed outlier: 3.661A pdb=" N MET A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.694A pdb=" N GLN A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 327 removed outlier: 5.055A pdb=" N ILE A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 336 through 363 removed outlier: 3.984A pdb=" N LEU A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.745A pdb=" N VAL A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 3.647A pdb=" N SER A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 3.936A pdb=" N ASN A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 43 removed outlier: 3.915A pdb=" N ALA B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 37 removed outlier: 3.742A pdb=" N ILE C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 55 removed outlier: 3.570A pdb=" N LEU C 45 " --> pdb=" O PRO C 41 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.724A pdb=" N ASN C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 73 removed outlier: 3.684A pdb=" N HIS C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 93 through 100 removed outlier: 3.536A pdb=" N LEU C 100 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 121 through 130 Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.700A pdb=" N PHE C 141 " --> pdb=" O PRO C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 155 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 167 through 183 removed outlier: 3.898A pdb=" N PHE C 171 " --> pdb=" O GLN C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 198 removed outlier: 4.195A pdb=" N ALA C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 196 " --> pdb=" O GLN C 192 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 202 Processing helix chain 'C' and resid 203 through 214 removed outlier: 4.228A pdb=" N TYR C 209 " --> pdb=" O PRO C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 218 through 228 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 232 through 245 Proline residue: C 238 - end of helix removed outlier: 3.559A pdb=" N THR C 245 " --> pdb=" O MET C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 removed outlier: 3.505A pdb=" N ARG C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 279 Proline residue: C 269 - end of helix Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 283 through 300 removed outlier: 3.670A pdb=" N MET C 289 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY C 300 " --> pdb=" O MET C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.717A pdb=" N GLN C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 327 removed outlier: 4.993A pdb=" N ILE C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'C' and resid 336 through 364 removed outlier: 4.015A pdb=" N LEU C 340 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 355 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.735A pdb=" N VAL C 381 " --> pdb=" O SER C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 399 removed outlier: 3.580A pdb=" N SER C 398 " --> pdb=" O VAL C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 431 removed outlier: 3.969A pdb=" N ASN C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 420 " --> pdb=" O VAL C 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 43 removed outlier: 3.915A pdb=" N ALA D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 37 removed outlier: 3.689A pdb=" N ILE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 24 " --> pdb=" O GLN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 55 removed outlier: 3.594A pdb=" N LEU E 45 " --> pdb=" O PRO E 41 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.725A pdb=" N ASN E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 removed outlier: 3.700A pdb=" N HIS E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.667A pdb=" N PHE E 141 " --> pdb=" O PRO E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 156 through 160 Processing helix chain 'E' and resid 161 through 166 removed outlier: 3.697A pdb=" N ALA E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 183 removed outlier: 3.857A pdb=" N PHE E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 198 removed outlier: 3.547A pdb=" N ALA E 195 " --> pdb=" O PRO E 191 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 202 Processing helix chain 'E' and resid 203 through 214 removed outlier: 4.292A pdb=" N TYR E 209 " --> pdb=" O PRO E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 218 through 228 Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'E' and resid 232 through 245 Proline residue: E 238 - end of helix removed outlier: 3.546A pdb=" N THR E 245 " --> pdb=" O MET E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 261 through 279 Proline residue: E 269 - end of helix Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 283 through 299 removed outlier: 3.649A pdb=" N MET E 289 " --> pdb=" O PRO E 285 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 293 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 313 through 327 removed outlier: 5.044A pdb=" N ILE E 319 " --> pdb=" O ASN E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 336 through 364 removed outlier: 3.965A pdb=" N LEU E 340 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL E 347 " --> pdb=" O LEU E 343 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE E 348 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E 350 " --> pdb=" O GLY E 346 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA E 355 " --> pdb=" O GLY E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.538A pdb=" N GLY E 380 " --> pdb=" O GLY E 377 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 381 " --> pdb=" O SER E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 399 removed outlier: 3.584A pdb=" N SER E 398 " --> pdb=" O VAL E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 431 removed outlier: 3.855A pdb=" N ASN E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA E 420 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 43 removed outlier: 3.914A pdb=" N ALA F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 2004 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: 1.88 Time building geometry restraints manager: 1.41 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: 3146 1.34 - 1.46: 1606 1.46 - 1.57: 5520 1.57 - 1.69: 0 1.69 - 1.81: 129 Bond restraints: 10401 Sorted by residual: bond pdb=" C6' LMT E1000 " pdb=" O6' LMT E1000 " ideal model delta sigma weight residual 1.407 1.364 0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C8 LMT E1000 " pdb=" C9 LMT E1000 " ideal model delta sigma weight residual 1.531 1.490 0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C6' LMT C1000 " pdb=" O6' LMT C1000 " ideal model delta sigma weight residual 1.407 1.367 0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C8 LMT A1000 " pdb=" C9 LMT A1000 " ideal model delta sigma weight residual 1.531 1.491 0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb=" C8 LMT C1000 " pdb=" C9 LMT C1000 " ideal model delta sigma weight residual 1.531 1.491 0.040 2.00e-02 2.50e+03 4.02e+00 ... (remaining 10396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 13147 1.88 - 3.77: 768 3.77 - 5.65: 138 5.65 - 7.53: 44 7.53 - 9.42: 21 Bond angle restraints: 14118 Sorted by residual: angle pdb=" N PRO E 238 " pdb=" CA PRO E 238 " pdb=" C PRO E 238 " ideal model delta sigma weight residual 110.70 115.58 -4.88 1.22e+00 6.72e-01 1.60e+01 angle pdb=" N PRO A 238 " pdb=" CA PRO A 238 " pdb=" C PRO A 238 " ideal model delta sigma weight residual 110.70 115.49 -4.79 1.22e+00 6.72e-01 1.54e+01 angle pdb=" N PRO C 238 " pdb=" CA PRO C 238 " pdb=" C PRO C 238 " ideal model delta sigma weight residual 110.70 115.32 -4.62 1.22e+00 6.72e-01 1.43e+01 angle pdb=" CA PRO E 238 " pdb=" C PRO E 238 " pdb=" N PRO E 239 " ideal model delta sigma weight residual 117.93 122.31 -4.38 1.20e+00 6.94e-01 1.33e+01 angle pdb=" CA PRO A 238 " pdb=" C PRO A 238 " pdb=" N PRO A 239 " ideal model delta sigma weight residual 117.93 122.30 -4.37 1.20e+00 6.94e-01 1.33e+01 ... (remaining 14113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.89: 5591 11.89 - 23.78: 489 23.78 - 35.67: 75 35.67 - 47.56: 19 47.56 - 59.45: 9 Dihedral angle restraints: 6183 sinusoidal: 2298 harmonic: 3885 Sorted by residual: dihedral pdb=" CA ALA A 130 " pdb=" C ALA A 130 " pdb=" N ILE A 131 " pdb=" CA ILE A 131 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA C 130 " pdb=" C ALA C 130 " pdb=" N ILE C 131 " pdb=" CA ILE C 131 " ideal model delta harmonic sigma weight residual 180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ALA A 231 " pdb=" C ALA A 231 " pdb=" N LEU A 232 " pdb=" CA LEU A 232 " ideal model delta harmonic sigma weight residual 180.00 160.75 19.25 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 6180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1202 0.055 - 0.109: 451 0.109 - 0.164: 99 0.164 - 0.219: 16 0.219 - 0.273: 11 Chirality restraints: 1779 Sorted by residual: chirality pdb=" CB ILE C 131 " pdb=" CA ILE C 131 " pdb=" CG1 ILE C 131 " pdb=" CG2 ILE C 131 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE A 131 " pdb=" CA ILE A 131 " pdb=" CG1 ILE A 131 " pdb=" CG2 ILE A 131 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE E 131 " pdb=" CA ILE E 131 " pdb=" CG1 ILE E 131 " pdb=" CG2 ILE E 131 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1776 not shown) Planarity restraints: 1737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 151 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO A 152 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 151 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO E 152 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 152 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 151 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO C 152 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " -0.033 5.00e-02 4.00e+02 ... (remaining 1734 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3030 2.82 - 3.34: 10086 3.34 - 3.86: 17001 3.86 - 4.38: 20139 4.38 - 4.90: 33674 Nonbonded interactions: 83930 Sorted by model distance: nonbonded pdb=" O GLY C 201 " pdb=" OG SER C 382 " model vdw 2.301 3.040 nonbonded pdb=" O VAL A 144 " pdb=" OG1 THR A 148 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR A 229 " pdb=" O LEU A 343 " model vdw 2.317 3.040 nonbonded pdb=" O GLY A 201 " pdb=" OG SER A 382 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR E 229 " pdb=" O LEU E 343 " model vdw 2.321 3.040 ... (remaining 83925 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.008 0.064 10401 Z= 0.333 Angle : 1.088 9.417 14118 Z= 0.547 Chirality : 0.060 0.273 1779 Planarity : 0.009 0.061 1737 Dihedral : 9.806 59.450 3699 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -4.19 (0.17), residues: 1374 helix: -2.71 (0.12), residues: 1038 sheet: None (None), residues: 0 loop : -2.14 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 242 TYR 0.015 0.003 TYR E 118 PHE 0.025 0.003 PHE A 141 TRP 0.005 0.002 TRP A 32 HIS 0.009 0.002 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.33 (10401) covalent geometry : angle 1.08842 / 0.55 (14118) hydrogen bonds : bond 0.16987 / 11.87 ( 682) hydrogen bonds : angle 7.19375 / 4.89 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.356 Fit side-chains REVERT: A 149 ASP cc_start: 0.8614 (t0) cc_final: 0.8349 (t0) REVERT: A 264 GLU cc_start: 0.7728 (tt0) cc_final: 0.6947 (tp30) REVERT: A 289 MET cc_start: 0.8341 (tpp) cc_final: 0.7949 (tpp) REVERT: A 429 TYR cc_start: 0.7884 (t80) cc_final: 0.7640 (t80) REVERT: C 161 LEU cc_start: 0.8925 (tp) cc_final: 0.8684 (tp) REVERT: C 264 GLU cc_start: 0.7558 (tt0) cc_final: 0.6712 (tp30) REVERT: C 338 GLN cc_start: 0.8762 (mp10) cc_final: 0.8413 (mp10) REVERT: C 429 TYR cc_start: 0.7987 (t80) cc_final: 0.7563 (t80) REVERT: D 7 LEU cc_start: 0.8545 (mt) cc_final: 0.8217 (mt) REVERT: E 115 ASP cc_start: 0.8360 (m-30) cc_final: 0.8048 (m-30) REVERT: E 175 LEU cc_start: 0.8791 (mp) cc_final: 0.8527 (mt) REVERT: E 253 ARG cc_start: 0.7682 (mmt-90) cc_final: 0.7197 (mmt-90) REVERT: E 264 GLU cc_start: 0.7925 (tt0) cc_final: 0.7056 (tp30) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.1004 time to fit residues: 55.6095 Evaluate side-chains 235 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN A 72 HIS A 77 GLN A 106 GLN C 72 HIS C 106 GLN C 192 GLN E 20 GLN E 72 HIS ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102908 restraints weight = 16258.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104364 restraints weight = 10943.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.105719 restraints weight = 8620.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.106224 restraints weight = 7324.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106321 restraints weight = 6728.592| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10401 Z= 0.148 Angle : 0.685 6.641 14118 Z= 0.339 Chirality : 0.043 0.166 1779 Planarity : 0.006 0.051 1737 Dihedral : 6.944 58.919 1467 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.30 % Allowed : 9.96 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.21), residues: 1374 helix: -1.00 (0.15), residues: 1053 sheet: None (None), residues: 0 loop : -1.65 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.019 0.002 TYR A 182 PHE 0.014 0.002 PHE A 268 TRP 0.014 0.002 TRP E 32 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (10401) covalent geometry : angle 0.68497 / 0.34 (14118) hydrogen bonds : bond 0.04025 / 2.71 ( 682) hydrogen bonds : angle 4.82505 / 3.29 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 291 time to evaluate : 0.354 Fit side-chains REVERT: A 111 ASN cc_start: 0.8194 (t0) cc_final: 0.7831 (t0) REVERT: A 173 THR cc_start: 0.9149 (m) cc_final: 0.8676 (p) REVERT: A 245 THR cc_start: 0.8090 (m) cc_final: 0.7761 (t) REVERT: A 248 LYS cc_start: 0.8191 (tppt) cc_final: 0.7976 (ttpt) REVERT: A 292 PHE cc_start: 0.8987 (t80) cc_final: 0.8625 (t80) REVERT: B 15 MET cc_start: 0.6779 (ttp) cc_final: 0.6549 (ttp) REVERT: B 42 ARG cc_start: 0.4803 (tmt-80) cc_final: 0.4195 (mtm180) REVERT: C 109 MET cc_start: 0.7687 (mmm) cc_final: 0.7476 (mmp) REVERT: C 159 THR cc_start: 0.8745 (p) cc_final: 0.8366 (p) REVERT: C 248 LYS cc_start: 0.8261 (tppt) cc_final: 0.7963 (tmmt) REVERT: C 429 TYR cc_start: 0.7990 (t80) cc_final: 0.7601 (t80) REVERT: E 23 MET cc_start: 0.8577 (tpp) cc_final: 0.8207 (tpp) REVERT: E 110 GLU cc_start: 0.7907 (tm-30) cc_final: 0.6905 (tm-30) REVERT: E 111 ASN cc_start: 0.8273 (t0) cc_final: 0.7885 (t0) REVERT: E 248 LYS cc_start: 0.8271 (tppt) cc_final: 0.7924 (tmmt) REVERT: E 264 GLU cc_start: 0.8010 (tt0) cc_final: 0.7010 (tp30) REVERT: F 10 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6589 (mt-10) outliers start: 24 outliers final: 14 residues processed: 302 average time/residue: 0.0964 time to fit residues: 41.8772 Evaluate side-chains 258 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 244 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 384 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 0.0670 chunk 106 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 114 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 167 GLN E 77 GLN E 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.101682 restraints weight = 16391.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.103523 restraints weight = 10633.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.104729 restraints weight = 8129.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.105561 restraints weight = 6842.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.105935 restraints weight = 6126.436| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10401 Z= 0.140 Angle : 0.640 7.801 14118 Z= 0.314 Chirality : 0.042 0.178 1779 Planarity : 0.006 0.047 1737 Dihedral : 6.415 58.355 1467 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.39 % Allowed : 13.31 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.78 (0.22), residues: 1374 helix: -0.11 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.50 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 389 TYR 0.016 0.002 TYR C 127 PHE 0.015 0.001 PHE A 292 TRP 0.010 0.002 TRP E 32 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10401) covalent geometry : angle 0.64040 / 0.31 (14118) hydrogen bonds : bond 0.03647 / 2.46 ( 682) hydrogen bonds : angle 4.53922 / 3.11 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 281 time to evaluate : 0.377 Fit side-chains REVERT: A 56 ILE cc_start: 0.9154 (mm) cc_final: 0.8828 (mm) REVERT: A 111 ASN cc_start: 0.8163 (t0) cc_final: 0.7917 (t0) REVERT: A 147 MET cc_start: 0.7721 (mtp) cc_final: 0.7251 (mtp) REVERT: A 173 THR cc_start: 0.9112 (m) cc_final: 0.8583 (p) REVERT: B 15 MET cc_start: 0.6810 (ttp) cc_final: 0.6492 (ttp) REVERT: B 42 ARG cc_start: 0.4837 (tmt-80) cc_final: 0.4180 (mtm180) REVERT: C 110 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7093 (tm-30) REVERT: C 149 ASP cc_start: 0.8109 (t70) cc_final: 0.7898 (t0) REVERT: C 173 THR cc_start: 0.9314 (m) cc_final: 0.9085 (p) REVERT: C 406 MET cc_start: 0.7667 (tpp) cc_final: 0.7316 (tpp) REVERT: C 429 TYR cc_start: 0.8032 (t80) cc_final: 0.7606 (t80) REVERT: E 23 MET cc_start: 0.8520 (tpp) cc_final: 0.8302 (tpp) REVERT: E 110 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7028 (tm-30) REVERT: E 111 ASN cc_start: 0.8277 (t0) cc_final: 0.7996 (t0) REVERT: E 254 MET cc_start: 0.6358 (mmm) cc_final: 0.6109 (mmm) REVERT: E 264 GLU cc_start: 0.7989 (tt0) cc_final: 0.7052 (tp30) REVERT: E 375 LEU cc_start: 0.8786 (mp) cc_final: 0.8538 (mt) REVERT: F 10 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6660 (mt-10) outliers start: 25 outliers final: 20 residues processed: 293 average time/residue: 0.0894 time to fit residues: 38.1880 Evaluate side-chains 256 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain E residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 127 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 96 optimal weight: 0.0970 chunk 114 optimal weight: 0.8980 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102835 restraints weight = 16584.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.104304 restraints weight = 11197.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.105480 restraints weight = 8777.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106048 restraints weight = 7497.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106051 restraints weight = 6844.348| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10401 Z= 0.129 Angle : 0.615 6.687 14118 Z= 0.302 Chirality : 0.041 0.185 1779 Planarity : 0.005 0.047 1737 Dihedral : 6.111 55.861 1467 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.07 % Allowed : 16.38 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.20 (0.23), residues: 1374 helix: 0.30 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -1.31 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 389 TYR 0.015 0.002 TYR E 429 PHE 0.015 0.001 PHE A 292 TRP 0.007 0.001 TRP E 32 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10401) covalent geometry : angle 0.61500 / 0.30 (14118) hydrogen bonds : bond 0.03414 / 2.29 ( 682) hydrogen bonds : angle 4.37421 / 3.00 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 0.373 Fit side-chains REVERT: A 111 ASN cc_start: 0.8025 (t0) cc_final: 0.7815 (t0) REVERT: A 147 MET cc_start: 0.7676 (mtp) cc_final: 0.7259 (mtp) REVERT: A 173 THR cc_start: 0.9077 (m) cc_final: 0.8581 (p) REVERT: A 248 LYS cc_start: 0.8133 (tppt) cc_final: 0.7867 (pttp) REVERT: B 42 ARG cc_start: 0.4966 (tmt-80) cc_final: 0.4188 (mtm180) REVERT: C 147 MET cc_start: 0.7247 (mtp) cc_final: 0.6997 (mtp) REVERT: C 173 THR cc_start: 0.9324 (m) cc_final: 0.9111 (p) REVERT: C 406 MET cc_start: 0.7602 (tpp) cc_final: 0.7341 (tpp) REVERT: C 429 TYR cc_start: 0.7997 (t80) cc_final: 0.7536 (t80) REVERT: E 111 ASN cc_start: 0.8134 (t0) cc_final: 0.7908 (t0) REVERT: E 248 LYS cc_start: 0.8371 (tppt) cc_final: 0.7843 (pttp) REVERT: E 264 GLU cc_start: 0.7964 (tt0) cc_final: 0.7064 (tp30) REVERT: F 10 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6814 (mt-10) outliers start: 32 outliers final: 19 residues processed: 283 average time/residue: 0.0884 time to fit residues: 36.8504 Evaluate side-chains 258 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 110 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 0.0770 chunk 128 optimal weight: 5.9990 chunk 31 optimal weight: 0.0270 chunk 86 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS C 370 ASN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.104269 restraints weight = 16421.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.105854 restraints weight = 11188.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106968 restraints weight = 8797.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.107313 restraints weight = 7547.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.107825 restraints weight = 7064.660| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10401 Z= 0.119 Angle : 0.598 8.574 14118 Z= 0.295 Chirality : 0.041 0.180 1779 Planarity : 0.005 0.047 1737 Dihedral : 5.859 57.821 1467 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.26 % Allowed : 18.01 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.15 (0.23), residues: 1374 helix: 0.56 (0.17), residues: 1050 sheet: None (None), residues: 0 loop : -1.18 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 389 TYR 0.018 0.002 TYR E 429 PHE 0.019 0.001 PHE A 292 TRP 0.006 0.001 TRP C 32 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10401) covalent geometry : angle 0.59841 / 0.29 (14118) hydrogen bonds : bond 0.03284 / 2.21 ( 682) hydrogen bonds : angle 4.25620 / 2.92 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 0.379 Fit side-chains REVERT: A 56 ILE cc_start: 0.8939 (mm) cc_final: 0.8675 (mm) REVERT: A 147 MET cc_start: 0.7642 (mtp) cc_final: 0.7198 (mtp) REVERT: A 173 THR cc_start: 0.8937 (m) cc_final: 0.8507 (p) REVERT: A 248 LYS cc_start: 0.8183 (tppt) cc_final: 0.7930 (ttpt) REVERT: B 42 ARG cc_start: 0.4867 (tmt-80) cc_final: 0.4114 (mtm180) REVERT: C 69 LEU cc_start: 0.9335 (tt) cc_final: 0.9088 (tt) REVERT: C 147 MET cc_start: 0.7287 (mtp) cc_final: 0.7006 (mtp) REVERT: C 208 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.8989 (mt) REVERT: C 219 LEU cc_start: 0.9442 (tp) cc_final: 0.9214 (tp) REVERT: C 264 GLU cc_start: 0.7265 (tt0) cc_final: 0.6738 (tp30) REVERT: C 375 LEU cc_start: 0.8777 (mm) cc_final: 0.8471 (mt) REVERT: C 406 MET cc_start: 0.7510 (tpp) cc_final: 0.7290 (tpp) REVERT: C 429 TYR cc_start: 0.7932 (t80) cc_final: 0.7429 (t80) REVERT: E 23 MET cc_start: 0.8612 (tpp) cc_final: 0.8380 (tpp) REVERT: E 43 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8502 (tt) REVERT: E 111 ASN cc_start: 0.7972 (t0) cc_final: 0.7767 (t0) REVERT: E 115 ASP cc_start: 0.7983 (m-30) cc_final: 0.7761 (m-30) REVERT: E 147 MET cc_start: 0.7537 (mtp) cc_final: 0.7296 (mtp) REVERT: E 264 GLU cc_start: 0.7902 (tt0) cc_final: 0.6966 (tp30) REVERT: F 10 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6830 (mt-10) REVERT: F 15 MET cc_start: 0.7183 (tpp) cc_final: 0.6407 (ttt) outliers start: 34 outliers final: 21 residues processed: 275 average time/residue: 0.0811 time to fit residues: 33.4461 Evaluate side-chains 254 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 63 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 407 HIS C 370 ASN C 407 HIS ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.104576 restraints weight = 16488.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.106132 restraints weight = 11377.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107023 restraints weight = 8989.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.107842 restraints weight = 7781.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108019 restraints weight = 7055.672| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10401 Z= 0.126 Angle : 0.612 10.883 14118 Z= 0.298 Chirality : 0.041 0.167 1779 Planarity : 0.005 0.048 1737 Dihedral : 5.733 57.426 1467 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.54 % Allowed : 19.35 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.49 (0.23), residues: 1374 helix: 0.80 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -0.92 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 389 TYR 0.019 0.002 TYR E 429 PHE 0.017 0.001 PHE A 292 TRP 0.005 0.001 TRP C 32 HIS 0.006 0.001 HIS C 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10401) covalent geometry : angle 0.61156 / 0.30 (14118) hydrogen bonds : bond 0.03266 / 2.19 ( 682) hydrogen bonds : angle 4.26463 / 2.94 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 0.368 Fit side-chains REVERT: A 173 THR cc_start: 0.9028 (m) cc_final: 0.8548 (p) REVERT: A 218 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8058 (tt) REVERT: A 376 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8980 (mm) REVERT: B 42 ARG cc_start: 0.4804 (tmt-80) cc_final: 0.4061 (mtm180) REVERT: C 69 LEU cc_start: 0.9322 (tt) cc_final: 0.9116 (tt) REVERT: C 147 MET cc_start: 0.7313 (mtp) cc_final: 0.7056 (mtp) REVERT: C 173 THR cc_start: 0.9255 (p) cc_final: 0.9021 (p) REVERT: C 208 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.8966 (mt) REVERT: C 219 LEU cc_start: 0.9425 (tp) cc_final: 0.9194 (tp) REVERT: C 264 GLU cc_start: 0.7370 (tt0) cc_final: 0.6660 (tp30) REVERT: C 375 LEU cc_start: 0.8848 (mm) cc_final: 0.8516 (mt) REVERT: E 23 MET cc_start: 0.8654 (tpp) cc_final: 0.8353 (tpp) REVERT: E 115 ASP cc_start: 0.8002 (m-30) cc_final: 0.7798 (m-30) REVERT: E 147 MET cc_start: 0.7588 (mtp) cc_final: 0.7341 (mtp) REVERT: E 248 LYS cc_start: 0.8436 (tppt) cc_final: 0.7927 (pttp) REVERT: E 264 GLU cc_start: 0.7857 (tt0) cc_final: 0.6963 (tp30) REVERT: F 10 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6804 (mt-10) REVERT: F 15 MET cc_start: 0.7185 (tpp) cc_final: 0.6779 (ttt) outliers start: 37 outliers final: 26 residues processed: 282 average time/residue: 0.0829 time to fit residues: 35.1758 Evaluate side-chains 262 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain E residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 137 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS C 370 ASN C 407 HIS E 370 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.104196 restraints weight = 16371.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.105948 restraints weight = 10772.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.107140 restraints weight = 8273.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107812 restraints weight = 7010.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107812 restraints weight = 6334.301| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10401 Z= 0.128 Angle : 0.634 11.736 14118 Z= 0.308 Chirality : 0.042 0.197 1779 Planarity : 0.005 0.046 1737 Dihedral : 5.665 58.331 1467 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.54 % Allowed : 19.92 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.54 (0.24), residues: 1374 helix: 0.81 (0.17), residues: 1056 sheet: None (None), residues: 0 loop : -0.95 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.021 0.002 TYR A 429 PHE 0.011 0.001 PHE A 49 TRP 0.005 0.001 TRP C 32 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10401) covalent geometry : angle 0.63420 / 0.31 (14118) hydrogen bonds : bond 0.03288 / 2.23 ( 682) hydrogen bonds : angle 4.33564 / 2.99 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 0.376 Fit side-chains REVERT: A 105 VAL cc_start: 0.8498 (t) cc_final: 0.8148 (t) REVERT: A 173 THR cc_start: 0.8961 (m) cc_final: 0.8611 (p) REVERT: A 218 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8066 (tt) REVERT: A 426 MET cc_start: 0.8155 (ttm) cc_final: 0.7909 (mtp) REVERT: C 69 LEU cc_start: 0.9312 (tt) cc_final: 0.9056 (tt) REVERT: C 147 MET cc_start: 0.7411 (mtp) cc_final: 0.7175 (mtp) REVERT: C 173 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8961 (p) REVERT: C 208 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9001 (mt) REVERT: C 375 LEU cc_start: 0.8857 (mm) cc_final: 0.8546 (mt) REVERT: E 23 MET cc_start: 0.8655 (tpp) cc_final: 0.8360 (tpp) REVERT: E 147 MET cc_start: 0.7581 (mtp) cc_final: 0.7331 (mtp) REVERT: E 264 GLU cc_start: 0.7920 (tt0) cc_final: 0.7054 (tp30) REVERT: F 10 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6828 (mt-10) REVERT: F 15 MET cc_start: 0.7212 (tpp) cc_final: 0.6819 (ttt) outliers start: 37 outliers final: 27 residues processed: 266 average time/residue: 0.0829 time to fit residues: 32.8120 Evaluate side-chains 258 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 0.0030 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 ASN A 407 HIS C 370 ASN C 407 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106162 restraints weight = 16283.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107715 restraints weight = 11414.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108532 restraints weight = 9063.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109257 restraints weight = 7911.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109843 restraints weight = 7149.840| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10401 Z= 0.125 Angle : 0.638 10.514 14118 Z= 0.311 Chirality : 0.042 0.210 1779 Planarity : 0.005 0.045 1737 Dihedral : 5.576 59.861 1467 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.16 % Allowed : 21.74 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.74 (0.24), residues: 1374 helix: 0.93 (0.17), residues: 1053 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 158 TYR 0.022 0.002 TYR E 429 PHE 0.011 0.001 PHE A 49 TRP 0.006 0.001 TRP C 32 HIS 0.005 0.001 HIS C 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10401) covalent geometry : angle 0.63766 / 0.31 (14118) hydrogen bonds : bond 0.03296 / 2.24 ( 682) hydrogen bonds : angle 4.34332 / 3.00 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.398 Fit side-chains REVERT: A 105 VAL cc_start: 0.8487 (t) cc_final: 0.8150 (t) REVERT: A 173 THR cc_start: 0.8992 (m) cc_final: 0.8665 (p) REVERT: A 218 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8112 (tt) REVERT: C 147 MET cc_start: 0.7455 (mtp) cc_final: 0.7249 (mtp) REVERT: C 173 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8980 (p) REVERT: C 208 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9022 (mt) REVERT: C 360 MET cc_start: 0.7584 (ttp) cc_final: 0.7304 (ttp) REVERT: C 375 LEU cc_start: 0.8864 (mm) cc_final: 0.8544 (mt) REVERT: E 92 HIS cc_start: 0.6589 (m170) cc_final: 0.6212 (m-70) REVERT: E 147 MET cc_start: 0.7552 (mtp) cc_final: 0.7261 (mtp) REVERT: E 219 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8998 (tp) REVERT: E 264 GLU cc_start: 0.7899 (tt0) cc_final: 0.7027 (tp30) REVERT: F 10 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6641 (mt-10) REVERT: F 15 MET cc_start: 0.7071 (tpp) cc_final: 0.6721 (ttt) outliers start: 33 outliers final: 20 residues processed: 260 average time/residue: 0.0809 time to fit residues: 31.8363 Evaluate side-chains 251 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain E residue 384 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN A 237 GLN A 407 HIS C 370 ASN C 407 HIS E 370 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.121154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.104376 restraints weight = 16372.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.105671 restraints weight = 11476.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.106750 restraints weight = 9211.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107555 restraints weight = 7938.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.107916 restraints weight = 7232.218| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10401 Z= 0.138 Angle : 0.665 10.891 14118 Z= 0.318 Chirality : 0.043 0.208 1779 Planarity : 0.005 0.044 1737 Dihedral : 5.671 59.528 1467 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.16 % Allowed : 22.32 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.62 (0.23), residues: 1374 helix: 0.96 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -1.19 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 158 TYR 0.025 0.002 TYR C 429 PHE 0.016 0.001 PHE C 292 TRP 0.005 0.001 TRP E 32 HIS 0.007 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (10401) covalent geometry : angle 0.66455 / 0.32 (14118) hydrogen bonds : bond 0.03375 / 2.29 ( 682) hydrogen bonds : angle 4.43042 / 3.06 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.407 Fit side-chains REVERT: A 105 VAL cc_start: 0.8519 (t) cc_final: 0.8159 (t) REVERT: A 173 THR cc_start: 0.9017 (m) cc_final: 0.8685 (p) REVERT: A 218 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8074 (tt) REVERT: C 147 MET cc_start: 0.7593 (mtp) cc_final: 0.7362 (mtp) REVERT: C 173 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8998 (p) REVERT: C 208 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.8995 (mt) REVERT: C 375 LEU cc_start: 0.8977 (mm) cc_final: 0.8675 (mt) REVERT: E 254 MET cc_start: 0.5845 (mmt) cc_final: 0.5622 (mmt) REVERT: F 10 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6781 (mt-10) REVERT: F 15 MET cc_start: 0.7157 (tpp) cc_final: 0.6459 (ttt) outliers start: 33 outliers final: 24 residues processed: 251 average time/residue: 0.0850 time to fit residues: 32.1967 Evaluate side-chains 247 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 HIS C 370 ASN C 407 HIS ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.120822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.104171 restraints weight = 16323.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.105460 restraints weight = 11498.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.106507 restraints weight = 9274.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107107 restraints weight = 8035.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107624 restraints weight = 7321.103| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10401 Z= 0.137 Angle : 0.662 12.304 14118 Z= 0.319 Chirality : 0.043 0.236 1779 Planarity : 0.005 0.045 1737 Dihedral : 5.634 58.789 1467 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.68 % Allowed : 23.28 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.65 (0.23), residues: 1374 helix: 0.93 (0.16), residues: 1050 sheet: None (None), residues: 0 loop : -1.05 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 389 TYR 0.026 0.002 TYR A 429 PHE 0.014 0.001 PHE C 292 TRP 0.004 0.001 TRP C 32 HIS 0.004 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (10401) covalent geometry : angle 0.66158 / 0.32 (14118) hydrogen bonds : bond 0.03331 / 2.25 ( 682) hydrogen bonds : angle 4.43271 / 3.07 ( 2004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8496 (t) cc_final: 0.8125 (t) REVERT: A 173 THR cc_start: 0.9005 (m) cc_final: 0.8677 (p) REVERT: A 218 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8113 (tt) REVERT: A 254 MET cc_start: 0.5593 (mmt) cc_final: 0.5363 (mmt) REVERT: A 426 MET cc_start: 0.8283 (ttm) cc_final: 0.7820 (mtp) REVERT: B 42 ARG cc_start: 0.5680 (ptm160) cc_final: 0.3916 (ptp-110) REVERT: C 147 MET cc_start: 0.7610 (mtp) cc_final: 0.7393 (mtp) REVERT: C 173 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8994 (p) REVERT: C 375 LEU cc_start: 0.9011 (mm) cc_final: 0.8710 (mt) REVERT: D 33 ILE cc_start: 0.7585 (mm) cc_final: 0.7238 (mt) REVERT: D 36 MET cc_start: 0.7622 (mmp) cc_final: 0.7176 (mmp) REVERT: E 254 MET cc_start: 0.5673 (mmt) cc_final: 0.5406 (mmt) REVERT: F 10 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6773 (mt-10) REVERT: F 15 MET cc_start: 0.7112 (tpp) cc_final: 0.6765 (ttt) outliers start: 28 outliers final: 22 residues processed: 253 average time/residue: 0.0832 time to fit residues: 31.5981 Evaluate side-chains 251 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 61 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 HIS C 370 ASN C 407 HIS ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.104212 restraints weight = 16464.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.105665 restraints weight = 11531.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.106736 restraints weight = 9141.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107284 restraints weight = 7906.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.107783 restraints weight = 7242.446| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10401 Z= 0.134 Angle : 0.677 11.894 14118 Z= 0.322 Chirality : 0.043 0.193 1779 Planarity : 0.005 0.048 1737 Dihedral : 5.579 57.435 1467 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.68 % Allowed : 23.66 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.63 (0.23), residues: 1374 helix: 0.91 (0.16), residues: 1059 sheet: None (None), residues: 0 loop : -1.05 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 158 TYR 0.028 0.002 TYR C 429 PHE 0.011 0.001 PHE C 292 TRP 0.005 0.001 TRP C 32 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (10401) covalent geometry : angle 0.67669 / 0.32 (14118) hydrogen bonds : bond 0.03364 / 2.29 ( 682) hydrogen bonds : angle 4.47340 / 3.09 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1596.57 seconds wall clock time: 28 minutes 24.10 seconds (1704.10 seconds total)