Starting phenix.real_space_refine on Wed Jun 11 09:20:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ndy_0443/06_2025/6ndy_0443.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ndy_0443/06_2025/6ndy_0443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ndy_0443/06_2025/6ndy_0443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ndy_0443/06_2025/6ndy_0443.map" model { file = "/net/cci-nas-00/data/ceres_data/6ndy_0443/06_2025/6ndy_0443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ndy_0443/06_2025/6ndy_0443.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 45 5.16 5 Be 3 3.05 5 C 7846 2.51 5 N 2143 2.21 5 O 2471 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12531 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2427 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "E" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2360 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 287} Chain breaks: 1 Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.83, per 1000 atoms: 0.62 Number of scatterers: 12531 At special positions: 0 Unit cell: (79.57, 141.7, 156.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 45 16.00 P 10 15.00 Mg 4 11.99 F 9 9.00 O 2471 8.00 N 2143 7.00 C 7846 6.00 Be 3 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.6 seconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 11 sheets defined 50.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.783A pdb=" N LEU A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 121 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 122' Processing helix chain 'A' and resid 138 through 155 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 208 through 224 removed outlier: 4.004A pdb=" N VAL A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 245 through 260 removed outlier: 4.709A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 335 through 356 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.891A pdb=" N LEU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 178 through 190 Processing helix chain 'B' and resid 208 through 224 removed outlier: 4.313A pdb=" N VAL B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 261 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.584A pdb=" N GLY B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 335 through 356 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 402 through 413 removed outlier: 3.998A pdb=" N PHE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 138 through 155 Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 209 through 224 removed outlier: 3.608A pdb=" N LEU C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 removed outlier: 4.056A pdb=" N ASN C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 335 through 356 Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 402 through 413 removed outlier: 3.967A pdb=" N PHE C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.569A pdb=" N VAL D 135 " --> pdb=" O TRP D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 155 Proline residue: D 152 - end of helix Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.736A pdb=" N LEU D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.659A pdb=" N ASN D 224 " --> pdb=" O MET D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 245 through 261 removed outlier: 4.202A pdb=" N ASN D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 335 through 356 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 402 through 413 removed outlier: 3.944A pdb=" N PHE D 406 " --> pdb=" O THR D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'E' and resid 138 through 155 Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 178 through 190 Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.755A pdb=" N VAL E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 224 removed outlier: 3.592A pdb=" N ASN E 224 " --> pdb=" O MET E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 removed outlier: 3.718A pdb=" N THR E 238 " --> pdb=" O VAL E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 261 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 300 through 313 removed outlier: 4.147A pdb=" N GLY E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 331 Processing helix chain 'E' and resid 335 through 356 Proline residue: E 350 - end of helix removed outlier: 3.557A pdb=" N GLN E 355 " --> pdb=" O ILE E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 413 removed outlier: 3.966A pdb=" N PHE E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 432 removed outlier: 3.643A pdb=" N LEU E 423 " --> pdb=" O GLU E 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 removed outlier: 8.619A pdb=" N THR A 276 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 171 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 170 " --> pdb=" O ILE A 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 363 removed outlier: 4.037A pdb=" N LYS A 372 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 197 removed outlier: 6.363A pdb=" N THR B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE B 230 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE B 195 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 232 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 197 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 275 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 170 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 360 through 362 Processing sheet with id=AA6, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.503A pdb=" N ILE C 228 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 232 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 275 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLY C 168 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE C 294 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU C 170 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG C 293 " --> pdb=" O GLN C 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AA8, first strand: chain 'D' and resid 193 through 197 removed outlier: 6.447A pdb=" N THR D 193 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE D 195 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP D 232 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 197 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU D 273 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE D 229 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA D 275 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 231 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 372 through 375 removed outlier: 4.222A pdb=" N LYS D 372 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 363 " --> pdb=" O LYS D 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.672A pdb=" N THR E 193 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE E 230 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE E 195 " --> pdb=" O PHE E 230 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP E 232 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER E 227 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU E 273 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE E 229 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA E 275 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 231 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 372 through 375 removed outlier: 4.255A pdb=" N LYS E 372 " --> pdb=" O VAL E 363 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1614 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: 3.17 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4106 1.34 - 1.46: 2151 1.46 - 1.58: 6385 1.58 - 1.69: 15 1.69 - 1.81: 80 Bond restraints: 12737 Sorted by residual: bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C5 ADP C 501 " pdb=" C6 ADP C 501 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C5 ADP A 501 " pdb=" C6 ADP A 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 12732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 16962 2.99 - 5.98: 190 5.98 - 8.96: 54 8.96 - 11.95: 14 11.95 - 14.94: 3 Bond angle restraints: 17223 Sorted by residual: angle pdb=" C ASN E 265 " pdb=" N ASP E 266 " pdb=" CA ASP E 266 " ideal model delta sigma weight residual 122.46 130.35 -7.89 1.41e+00 5.03e-01 3.13e+01 angle pdb=" C GLY B 239 " pdb=" N THR B 240 " pdb=" CA THR B 240 " ideal model delta sigma weight residual 121.54 131.26 -9.72 1.91e+00 2.74e-01 2.59e+01 angle pdb=" O1B ADP A 501 " pdb=" PB ADP A 501 " pdb=" O3B ADP A 501 " ideal model delta sigma weight residual 119.90 104.96 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" O2B ADP B 501 " pdb=" PB ADP B 501 " pdb=" O3B ADP B 501 " ideal model delta sigma weight residual 119.90 104.96 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" O2B ADP C 501 " pdb=" PB ADP C 501 " pdb=" O3B ADP C 501 " ideal model delta sigma weight residual 119.90 105.52 14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 17218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.41: 7581 32.41 - 64.82: 196 64.82 - 97.23: 14 97.23 - 129.63: 3 129.63 - 162.04: 2 Dihedral angle restraints: 7796 sinusoidal: 3213 harmonic: 4583 Sorted by residual: dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 102.04 -162.04 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 73.34 -133.34 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 178.17 121.83 1 2.00e+01 2.50e-03 3.67e+01 ... (remaining 7793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1612 0.056 - 0.113: 272 0.113 - 0.169: 62 0.169 - 0.225: 9 0.225 - 0.282: 2 Chirality restraints: 1957 Sorted by residual: chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE C 278 " pdb=" CA ILE C 278 " pdb=" CG1 ILE C 278 " pdb=" CG2 ILE C 278 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE A 228 " pdb=" CA ILE A 228 " pdb=" CG1 ILE A 228 " pdb=" CG2 ILE A 228 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1954 not shown) Planarity restraints: 2206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 147 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C GLU C 147 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU C 147 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 148 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 349 " -0.038 5.00e-02 4.00e+02 5.60e-02 5.03e+00 pdb=" N PRO C 350 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 350 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 350 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 374 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO D 375 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 375 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 375 " 0.030 5.00e-02 4.00e+02 ... (remaining 2203 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 166 2.61 - 3.18: 9937 3.18 - 3.75: 19375 3.75 - 4.33: 25287 4.33 - 4.90: 43033 Nonbonded interactions: 97798 Sorted by model distance: nonbonded pdb=" OG SER A 180 " pdb="MG MG A 503 " model vdw 2.037 2.170 nonbonded pdb=" OG SER C 180 " pdb="MG MG C 503 " model vdw 2.038 2.170 nonbonded pdb=" F1 BEF C 502 " pdb="MG MG C 503 " model vdw 2.038 2.120 nonbonded pdb=" OG SER B 180 " pdb="MG MG B 503 " model vdw 2.038 2.170 nonbonded pdb=" O2B ADP A 501 " pdb="MG MG A 503 " model vdw 2.038 2.170 ... (remaining 97793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 126 through 433) selection = (chain 'B' and resid 126 through 433) selection = (chain 'C' and resid 126 through 433) selection = (chain 'D' and resid 126 through 433) selection = (chain 'E' and resid 126 through 433) } 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: 1.220 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.370 Find NCS groups from input model: 0.690 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 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 : 0.012 0.709 12740 Z= 1.112 Angle : 0.892 14.941 17223 Z= 0.451 Chirality : 0.048 0.282 1957 Planarity : 0.006 0.056 2206 Dihedral : 14.707 162.042 4830 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.16), residues: 1574 helix: -2.38 (0.12), residues: 751 sheet: -2.34 (0.39), residues: 160 loop : -2.54 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 280 HIS 0.001 0.000 HIS A 359 PHE 0.011 0.001 PHE A 308 TYR 0.008 0.001 TYR C 181 ARG 0.002 0.000 ARG E 251 Details of bonding type rmsd hydrogen bonds : bond 0.09906 ( 553) hydrogen bonds : angle 6.39954 ( 1614) covalent geometry : bond 0.00467 (12737) covalent geometry : angle 0.89200 (17223) Misc. bond : bond 0.70646 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.6605 (mt0) cc_final: 0.6379 (tt0) REVERT: A 343 VAL cc_start: 0.7244 (t) cc_final: 0.6741 (t) REVERT: A 351 ILE cc_start: 0.6725 (mp) cc_final: 0.6227 (mm) REVERT: B 162 ASN cc_start: 0.6193 (m110) cc_final: 0.5772 (t0) REVERT: C 289 ARG cc_start: 0.4564 (mmt90) cc_final: 0.3295 (mmt90) REVERT: C 373 LEU cc_start: 0.7974 (mp) cc_final: 0.7663 (tp) REVERT: D 355 GLN cc_start: 0.6696 (mt0) cc_final: 0.6204 (tt0) REVERT: D 425 GLN cc_start: 0.5833 (mm-40) cc_final: 0.5472 (mt0) REVERT: E 157 HIS cc_start: 0.5602 (p90) cc_final: 0.5375 (p-80) REVERT: E 233 GLU cc_start: 0.7046 (mp0) cc_final: 0.6580 (mp0) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.3109 time to fit residues: 180.2704 Evaluate side-chains 207 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.0270 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 355 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 311 ASN B 427 GLN C 281 GLN C 311 ASN C 437 ASN D 216 GLN D 265 ASN E 281 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.117490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.093660 restraints weight = 29305.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094228 restraints weight = 21402.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095521 restraints weight = 17323.994| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12740 Z= 0.154 Angle : 0.741 11.753 17223 Z= 0.359 Chirality : 0.044 0.254 1957 Planarity : 0.006 0.046 2206 Dihedral : 9.138 157.988 1756 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.37 % Allowed : 14.42 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1574 helix: -0.77 (0.17), residues: 796 sheet: -1.55 (0.41), residues: 156 loop : -2.23 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 206 HIS 0.004 0.001 HIS C 359 PHE 0.014 0.002 PHE B 406 TYR 0.025 0.002 TYR C 181 ARG 0.006 0.001 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 553) hydrogen bonds : angle 5.24095 ( 1614) covalent geometry : bond 0.00331 (12737) covalent geometry : angle 0.74135 (17223) Misc. bond : bond 0.00063 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.7746 (tpp) cc_final: 0.7003 (tpp) REVERT: B 431 ASP cc_start: 0.6774 (m-30) cc_final: 0.6516 (m-30) REVERT: D 425 GLN cc_start: 0.6545 (mm-40) cc_final: 0.6323 (mt0) REVERT: E 233 GLU cc_start: 0.7133 (mp0) cc_final: 0.6659 (mp0) REVERT: E 386 MET cc_start: 0.5037 (OUTLIER) cc_final: 0.4760 (mtm) REVERT: E 425 GLN cc_start: 0.6104 (mm110) cc_final: 0.5854 (mm-40) outliers start: 32 outliers final: 16 residues processed: 256 average time/residue: 0.2169 time to fit residues: 82.2516 Evaluate side-chains 191 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 61 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 162 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN B 425 GLN C 349 GLN D 359 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.117547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.093116 restraints weight = 30185.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093325 restraints weight = 21537.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093892 restraints weight = 17811.544| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.8718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12740 Z= 0.237 Angle : 0.851 8.009 17223 Z= 0.424 Chirality : 0.050 0.279 1957 Planarity : 0.006 0.059 2206 Dihedral : 8.795 128.730 1756 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.62 % Allowed : 17.01 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.21), residues: 1574 helix: -0.41 (0.18), residues: 769 sheet: -1.42 (0.44), residues: 148 loop : -1.67 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D 206 HIS 0.006 0.002 HIS A 157 PHE 0.032 0.003 PHE C 432 TYR 0.033 0.003 TYR D 324 ARG 0.010 0.001 ARG D 288 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 553) hydrogen bonds : angle 5.59894 ( 1614) covalent geometry : bond 0.00519 (12737) covalent geometry : angle 0.85063 (17223) Misc. bond : bond 0.00315 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8225 (tp) REVERT: C 351 ILE cc_start: 0.8028 (mt) cc_final: 0.7808 (mm) REVERT: D 123 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7952 (mt) REVERT: D 235 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.7072 (p0) REVERT: D 386 MET cc_start: 0.4812 (pmm) cc_final: 0.4499 (pmm) REVERT: D 421 ASP cc_start: 0.7743 (t0) cc_final: 0.7503 (t70) REVERT: E 388 TRP cc_start: 0.6785 (p90) cc_final: 0.6388 (p90) outliers start: 49 outliers final: 19 residues processed: 209 average time/residue: 0.2437 time to fit residues: 73.4145 Evaluate side-chains 130 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 88 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 216 GLN A 355 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 355 GLN E 281 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.115895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.091287 restraints weight = 29167.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091395 restraints weight = 20409.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092187 restraints weight = 17622.324| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.9121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12740 Z= 0.132 Angle : 0.670 7.955 17223 Z= 0.324 Chirality : 0.044 0.333 1957 Planarity : 0.004 0.043 2206 Dihedral : 8.170 133.137 1756 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.22 % Allowed : 18.86 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1574 helix: 0.30 (0.19), residues: 751 sheet: -1.32 (0.43), residues: 160 loop : -1.35 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 206 HIS 0.005 0.001 HIS D 359 PHE 0.026 0.001 PHE C 432 TYR 0.014 0.001 TYR D 295 ARG 0.005 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 553) hydrogen bonds : angle 5.04458 ( 1614) covalent geometry : bond 0.00291 (12737) covalent geometry : angle 0.66986 (17223) Misc. bond : bond 0.00040 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 386 MET cc_start: 0.3243 (ppp) cc_final: 0.1835 (ptt) REVERT: C 113 LYS cc_start: 0.6272 (pttm) cc_final: 0.5759 (mtmm) REVERT: C 348 MET cc_start: 0.8006 (mmm) cc_final: 0.7777 (tpt) REVERT: D 386 MET cc_start: 0.4415 (pmm) cc_final: 0.4071 (pmm) REVERT: D 421 ASP cc_start: 0.7813 (t0) cc_final: 0.7353 (t0) REVERT: E 388 TRP cc_start: 0.6938 (p90) cc_final: 0.6288 (p-90) outliers start: 30 outliers final: 15 residues processed: 164 average time/residue: 0.2251 time to fit residues: 56.8832 Evaluate side-chains 127 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.112224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086213 restraints weight = 29144.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.086076 restraints weight = 19166.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.087195 restraints weight = 15040.665| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.9728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12740 Z= 0.149 Angle : 0.657 8.880 17223 Z= 0.319 Chirality : 0.045 0.371 1957 Planarity : 0.004 0.040 2206 Dihedral : 7.948 137.390 1756 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.00 % Allowed : 19.67 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1574 helix: 0.50 (0.19), residues: 757 sheet: -1.40 (0.41), residues: 162 loop : -1.14 (0.26), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 280 HIS 0.005 0.001 HIS D 359 PHE 0.019 0.001 PHE C 360 TYR 0.015 0.001 TYR D 295 ARG 0.006 0.001 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 553) hydrogen bonds : angle 4.97880 ( 1614) covalent geometry : bond 0.00328 (12737) covalent geometry : angle 0.65702 (17223) Misc. bond : bond 0.00044 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 386 MET cc_start: 0.3563 (ppp) cc_final: 0.2340 (ptt) REVERT: C 113 LYS cc_start: 0.6312 (pttm) cc_final: 0.5997 (mtmm) REVERT: C 348 MET cc_start: 0.8354 (mmm) cc_final: 0.8153 (tpt) REVERT: D 386 MET cc_start: 0.4387 (pmm) cc_final: 0.4097 (pmm) REVERT: E 149 VAL cc_start: 0.7727 (t) cc_final: 0.7512 (t) REVERT: E 388 TRP cc_start: 0.7008 (p90) cc_final: 0.6406 (p-90) outliers start: 27 outliers final: 14 residues processed: 145 average time/residue: 0.2412 time to fit residues: 54.3126 Evaluate side-chains 121 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 16 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.112113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.087076 restraints weight = 29469.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086377 restraints weight = 18791.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.087294 restraints weight = 16350.581| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 1.0097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12740 Z= 0.123 Angle : 0.651 11.526 17223 Z= 0.310 Chirality : 0.044 0.389 1957 Planarity : 0.004 0.058 2206 Dihedral : 7.761 134.308 1756 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.00 % Allowed : 20.78 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1574 helix: 0.50 (0.19), residues: 777 sheet: -1.33 (0.41), residues: 164 loop : -1.00 (0.27), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 280 HIS 0.004 0.001 HIS D 359 PHE 0.018 0.001 PHE C 360 TYR 0.013 0.001 TYR D 295 ARG 0.011 0.001 ARG E 251 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 553) hydrogen bonds : angle 4.90096 ( 1614) covalent geometry : bond 0.00275 (12737) covalent geometry : angle 0.65082 (17223) Misc. bond : bond 0.00035 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 386 MET cc_start: 0.3937 (ppp) cc_final: 0.2681 (ptt) REVERT: C 113 LYS cc_start: 0.6216 (pttm) cc_final: 0.5597 (mtmm) REVERT: C 348 MET cc_start: 0.8477 (mmm) cc_final: 0.8270 (tpt) REVERT: D 233 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7523 (mm-30) REVERT: D 386 MET cc_start: 0.4466 (pmm) cc_final: 0.4102 (pmm) REVERT: E 348 MET cc_start: 0.6452 (mmt) cc_final: 0.5868 (ppp) REVERT: E 388 TRP cc_start: 0.6922 (p90) cc_final: 0.6339 (p-90) outliers start: 27 outliers final: 21 residues processed: 143 average time/residue: 0.2131 time to fit residues: 46.3613 Evaluate side-chains 129 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 148 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 143 optimal weight: 0.0870 chunk 88 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** B 265 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 = 0.3752 r_free = 0.3752 target = 0.111301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.086343 restraints weight = 28948.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.086024 restraints weight = 22358.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.087307 restraints weight = 19978.173| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 1.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12740 Z= 0.145 Angle : 0.664 10.833 17223 Z= 0.320 Chirality : 0.044 0.388 1957 Planarity : 0.004 0.035 2206 Dihedral : 7.748 134.460 1756 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.51 % Allowed : 20.64 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1574 helix: 0.70 (0.19), residues: 759 sheet: -1.18 (0.43), residues: 157 loop : -0.86 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 280 HIS 0.004 0.001 HIS D 359 PHE 0.017 0.001 PHE C 360 TYR 0.010 0.001 TYR D 295 ARG 0.007 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 553) hydrogen bonds : angle 4.93105 ( 1614) covalent geometry : bond 0.00327 (12737) covalent geometry : angle 0.66438 (17223) Misc. bond : bond 0.00040 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 260 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8076 (ttt) REVERT: B 386 MET cc_start: 0.4041 (ppp) cc_final: 0.2801 (ptt) REVERT: B 420 ASP cc_start: 0.6825 (m-30) cc_final: 0.6553 (t0) REVERT: C 348 MET cc_start: 0.8545 (mmm) cc_final: 0.8094 (tpt) REVERT: E 149 VAL cc_start: 0.8174 (t) cc_final: 0.7893 (t) REVERT: E 288 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7763 (ptt90) REVERT: E 388 TRP cc_start: 0.6932 (p90) cc_final: 0.6367 (p-90) outliers start: 34 outliers final: 23 residues processed: 146 average time/residue: 0.2746 time to fit residues: 60.2933 Evaluate side-chains 126 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 288 ARG Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085408 restraints weight = 29133.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.085425 restraints weight = 22438.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.086802 restraints weight = 19056.264| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 1.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12740 Z= 0.148 Angle : 0.686 11.770 17223 Z= 0.329 Chirality : 0.045 0.415 1957 Planarity : 0.004 0.035 2206 Dihedral : 7.771 135.274 1756 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.22 % Allowed : 21.75 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1574 helix: 0.76 (0.19), residues: 758 sheet: -1.18 (0.44), residues: 154 loop : -0.77 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 280 HIS 0.003 0.001 HIS D 359 PHE 0.017 0.001 PHE C 360 TYR 0.011 0.001 TYR D 295 ARG 0.004 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 553) hydrogen bonds : angle 4.98144 ( 1614) covalent geometry : bond 0.00337 (12737) covalent geometry : angle 0.68613 (17223) Misc. bond : bond 0.00046 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 286 ILE cc_start: 0.7440 (pt) cc_final: 0.7180 (mt) REVERT: B 260 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8240 (ttt) REVERT: C 348 MET cc_start: 0.8520 (mmm) cc_final: 0.8302 (tpt) REVERT: D 386 MET cc_start: 0.4294 (pmm) cc_final: 0.3465 (ptp) REVERT: E 149 VAL cc_start: 0.8264 (t) cc_final: 0.7944 (t) REVERT: E 288 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7931 (ptt90) REVERT: E 388 TRP cc_start: 0.6622 (p90) cc_final: 0.6353 (p-90) outliers start: 30 outliers final: 21 residues processed: 133 average time/residue: 0.2251 time to fit residues: 46.8210 Evaluate side-chains 124 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 288 ARG Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 138 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN E 191 ASN ** E 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.111127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086413 restraints weight = 28923.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.086160 restraints weight = 21993.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.086994 restraints weight = 19688.119| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 1.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12740 Z= 0.121 Angle : 0.669 13.189 17223 Z= 0.318 Chirality : 0.044 0.431 1957 Planarity : 0.004 0.037 2206 Dihedral : 7.594 134.465 1756 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.85 % Allowed : 22.26 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1574 helix: 0.74 (0.19), residues: 776 sheet: -0.98 (0.44), residues: 154 loop : -0.71 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 206 HIS 0.004 0.001 HIS D 359 PHE 0.016 0.001 PHE C 360 TYR 0.011 0.001 TYR C 181 ARG 0.003 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 553) hydrogen bonds : angle 4.90183 ( 1614) covalent geometry : bond 0.00269 (12737) covalent geometry : angle 0.66869 (17223) Misc. bond : bond 0.00029 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.402 Fit side-chains REVERT: A 349 GLN cc_start: 0.8401 (tp40) cc_final: 0.8065 (tm-30) REVERT: B 260 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8291 (ttt) REVERT: D 386 MET cc_start: 0.3823 (pmm) cc_final: 0.3081 (ptp) REVERT: E 149 VAL cc_start: 0.8231 (t) cc_final: 0.7917 (t) REVERT: E 288 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7670 (ptt90) REVERT: E 388 TRP cc_start: 0.6530 (p90) cc_final: 0.6283 (p-90) outliers start: 25 outliers final: 17 residues processed: 126 average time/residue: 0.2087 time to fit residues: 40.7704 Evaluate side-chains 121 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 288 ARG Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 120 optimal weight: 0.0270 chunk 83 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 124 optimal weight: 50.0000 chunk 93 optimal weight: 0.0670 chunk 1 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.110967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.086259 restraints weight = 28837.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.086363 restraints weight = 22059.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.087942 restraints weight = 18750.796| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 1.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12740 Z= 0.121 Angle : 0.678 13.421 17223 Z= 0.322 Chirality : 0.044 0.452 1957 Planarity : 0.004 0.036 2206 Dihedral : 7.508 133.293 1756 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.48 % Allowed : 22.63 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1574 helix: 0.74 (0.19), residues: 776 sheet: -0.94 (0.44), residues: 154 loop : -0.67 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 206 HIS 0.002 0.000 HIS D 359 PHE 0.017 0.001 PHE D 406 TYR 0.011 0.001 TYR D 295 ARG 0.004 0.000 ARG D 414 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 553) hydrogen bonds : angle 4.92026 ( 1614) covalent geometry : bond 0.00266 (12737) covalent geometry : angle 0.67755 (17223) Misc. bond : bond 0.00020 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.616 Fit side-chains REVERT: B 250 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7497 (mmm-85) REVERT: B 260 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8304 (ttt) REVERT: D 386 MET cc_start: 0.4377 (pmm) cc_final: 0.3674 (ptp) REVERT: E 149 VAL cc_start: 0.8206 (t) cc_final: 0.7880 (t) REVERT: E 196 SER cc_start: 0.7944 (t) cc_final: 0.7654 (t) REVERT: E 288 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7709 (ptt90) REVERT: E 388 TRP cc_start: 0.6505 (p90) cc_final: 0.6280 (p-90) outliers start: 20 outliers final: 15 residues processed: 121 average time/residue: 0.2976 time to fit residues: 56.4088 Evaluate side-chains 124 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 288 ARG Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 147 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083816 restraints weight = 28877.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.083713 restraints weight = 22384.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084459 restraints weight = 19420.470| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 1.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12740 Z= 0.152 Angle : 0.702 13.905 17223 Z= 0.336 Chirality : 0.045 0.464 1957 Planarity : 0.004 0.035 2206 Dihedral : 7.654 136.372 1756 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.41 % Allowed : 22.49 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1574 helix: 0.81 (0.19), residues: 759 sheet: -0.85 (0.45), residues: 155 loop : -0.65 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS D 359 PHE 0.015 0.001 PHE C 360 TYR 0.011 0.001 TYR D 295 ARG 0.003 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 553) hydrogen bonds : angle 5.04211 ( 1614) covalent geometry : bond 0.00349 (12737) covalent geometry : angle 0.70190 (17223) Misc. bond : bond 0.00027 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4308.83 seconds wall clock time: 78 minutes 59.78 seconds (4739.78 seconds total)