Starting phenix.real_space_refine on Wed Jan 14 00:44:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgs_25120/01_2026/7sgs_25120.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgs_25120/01_2026/7sgs_25120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sgs_25120/01_2026/7sgs_25120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgs_25120/01_2026/7sgs_25120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sgs_25120/01_2026/7sgs_25120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgs_25120/01_2026/7sgs_25120.map" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= -0.050 sd= 1.469 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 70 5.16 5 C 6770 2.51 5 N 1865 2.21 5 O 2083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10798 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3430 Classifications: {'peptide': 439} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 417} Chain: "C" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "D" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3430 Classifications: {'peptide': 439} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 417} Chain: "A" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 493 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.73, per 1000 atoms: 0.25 Number of scatterers: 10798 At special positions: 0 Unit cell: (71.82, 75.24, 155.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 P 8 15.00 Mg 2 11.99 O 2083 8.00 N 1865 7.00 C 6770 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: 0.93 Conformation dependent library (CDL) restraints added in 465.0 milliseconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2516 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 55.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 71 through 80 removed outlier: 4.778A pdb=" N ILE B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 223 through 244 removed outlier: 4.316A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 4.323A pdb=" N GLN B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.537A pdb=" N CYS B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 6.204A pdb=" N ALA B 299 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 384 through 400 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 414 through 436 removed outlier: 4.099A pdb=" N PHE B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 40 through 44 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.894A pdb=" N PHE C 87 " --> pdb=" O GLY C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 109 through 127 removed outlier: 4.916A pdb=" N ASP C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.732A pdb=" N GLN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 4.004A pdb=" N THR C 239 " --> pdb=" O MET C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.857A pdb=" N ARG C 284 " --> pdb=" O GLN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 339 Processing helix chain 'C' and resid 340 through 343 Processing helix chain 'C' and resid 384 through 400 removed outlier: 3.566A pdb=" N PHE C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 414 through 434 Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 110 through 113 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 182 through 195 Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 223 through 244 removed outlier: 4.294A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 removed outlier: 4.043A pdb=" N GLN D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 260 " --> pdb=" O GLN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 282 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 296 through 301 removed outlier: 6.144A pdb=" N ALA D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN D 301 " --> pdb=" O PRO D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 338 Processing helix chain 'D' and resid 384 through 400 Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 415 through 436 removed outlier: 4.180A pdb=" N SER D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 139 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.179A pdb=" N ILE B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE B 67 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N VAL B 66 " --> pdb=" O CYS B 4 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER B 140 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS B 166 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE B 202 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU B 168 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL B 204 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER B 170 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 246 through 248 removed outlier: 6.427A pdb=" N ILE B 355 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LYS B 352 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY B 354 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 317 " --> pdb=" O GLY B 354 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASN B 356 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR B 319 " --> pdb=" O ASN B 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.335A pdb=" N VAL C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU C 67 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE C 66 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS C 6 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 68 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER C 140 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET C 166 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N TYR C 202 " --> pdb=" O MET C 166 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR C 168 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE C 204 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER C 170 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 201 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N CYS C 203 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 10.479A pdb=" N PHE C 272 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE C 267 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER C 381 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LYS C 352 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 315 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ALA C 354 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 317 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N CYS C 356 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE C 319 " --> pdb=" O CYS C 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 94 removed outlier: 8.271A pdb=" N ILE D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE D 67 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL D 66 " --> pdb=" O CYS D 4 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER D 6 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL D 68 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N HIS D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU D 3 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER D 140 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS D 166 " --> pdb=" O CYS D 200 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE D 202 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU D 168 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL D 204 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER D 170 " --> pdb=" O VAL D 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 246 through 248 removed outlier: 6.332A pdb=" N ILE D 355 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N LYS D 352 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N GLY D 354 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU D 317 " --> pdb=" O GLY D 354 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASN D 356 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR D 319 " --> pdb=" O ASN D 356 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN D 380 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N CYS D 315 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU D 378 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU D 317 " --> pdb=" O CYS D 376 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS D 376 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR D 319 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA D 374 " --> pdb=" O TYR D 319 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1608 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: 1.52 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2035 1.31 - 1.44: 3167 1.44 - 1.57: 5700 1.57 - 1.71: 30 1.71 - 1.84: 106 Bond restraints: 11038 Sorted by residual: bond pdb=" CB HIS C 229 " pdb=" CG HIS C 229 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.59e+01 bond pdb=" CB HIS D 197 " pdb=" CG HIS D 197 " ideal model delta sigma weight residual 1.497 1.422 0.075 1.40e-02 5.10e+03 2.87e+01 bond pdb=" CB HIS B 197 " pdb=" CG HIS B 197 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" CB HIS D 107 " pdb=" CG HIS D 107 " ideal model delta sigma weight residual 1.497 1.429 0.068 1.40e-02 5.10e+03 2.36e+01 bond pdb=" CB ASN B 206 " pdb=" CG ASN B 206 " ideal model delta sigma weight residual 1.516 1.395 0.121 2.50e-02 1.60e+03 2.36e+01 ... (remaining 11033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12135 1.89 - 3.78: 2349 3.78 - 5.67: 390 5.67 - 7.56: 82 7.56 - 9.45: 19 Bond angle restraints: 14975 Sorted by residual: angle pdb=" C ASP D 306 " pdb=" N PRO D 307 " pdb=" CA PRO D 307 " ideal model delta sigma weight residual 119.56 127.59 -8.03 1.02e+00 9.61e-01 6.19e+01 angle pdb=" CA ASN C 349 " pdb=" CB ASN C 349 " pdb=" CG ASN C 349 " ideal model delta sigma weight residual 112.60 104.78 7.82 1.00e+00 1.00e+00 6.12e+01 angle pdb=" C ILE C 358 " pdb=" N PRO C 359 " pdb=" CA PRO C 359 " ideal model delta sigma weight residual 120.38 128.06 -7.68 1.03e+00 9.43e-01 5.57e+01 angle pdb=" N THR B 73 " pdb=" CA THR B 73 " pdb=" C THR B 73 " ideal model delta sigma weight residual 111.07 118.68 -7.61 1.07e+00 8.73e-01 5.06e+01 angle pdb=" C ASP B 306 " pdb=" N PRO B 307 " pdb=" CA PRO B 307 " ideal model delta sigma weight residual 119.56 126.78 -7.22 1.02e+00 9.61e-01 5.01e+01 ... (remaining 14970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 6488 33.95 - 67.89: 82 67.89 - 101.84: 15 101.84 - 135.79: 1 135.79 - 169.74: 5 Dihedral angle restraints: 6591 sinusoidal: 2669 harmonic: 3922 Sorted by residual: dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -100.47 169.74 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP D 501 " pdb=" O5' GTP D 501 " pdb=" PA GTP D 501 " pdb=" O3A GTP D 501 " ideal model delta sinusoidal sigma weight residual 69.27 -123.62 -167.11 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O5' GTP B 501 " pdb=" O3A GTP B 501 " pdb=" PA GTP B 501 " pdb=" PB GTP B 501 " ideal model delta sinusoidal sigma weight residual 274.12 123.12 151.00 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 6588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1137 0.092 - 0.185: 413 0.185 - 0.277: 66 0.277 - 0.370: 9 0.370 - 0.462: 2 Chirality restraints: 1627 Sorted by residual: chirality pdb=" CA ASP B 47 " pdb=" N ASP B 47 " pdb=" C ASP B 47 " pdb=" CB ASP B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CB VAL A 87 " pdb=" CA VAL A 87 " pdb=" CG1 VAL A 87 " pdb=" CG2 VAL A 87 " both_signs ideal model delta sigma weight residual False -2.63 -3.05 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA ASN C 349 " pdb=" N ASN C 349 " pdb=" C ASN C 349 " pdb=" CB ASN C 349 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1624 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 61 " -0.051 2.00e-02 2.50e+03 2.64e-02 1.39e+01 pdb=" CG TYR C 61 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 61 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 61 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 61 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR C 61 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 61 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 61 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 251 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" CG ASP C 251 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASP C 251 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP C 251 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 99 " 0.042 2.00e-02 2.50e+03 2.13e-02 9.10e+00 pdb=" CG TYR A 99 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 99 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 99 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 99 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 99 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 99 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 99 " 0.025 2.00e-02 2.50e+03 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 6 2.41 - 3.03: 6876 3.03 - 3.66: 15279 3.66 - 4.28: 24976 4.28 - 4.90: 40658 Nonbonded interactions: 87795 Sorted by model distance: nonbonded pdb=" OD2 ASP D 98 " pdb="MG MG D 502 " model vdw 1.790 2.170 nonbonded pdb=" OD2 ASP B 98 " pdb="MG MG B 502 " model vdw 1.794 2.170 nonbonded pdb=" OE1 GLU B 71 " pdb="MG MG B 502 " model vdw 1.818 2.170 nonbonded pdb=" OE2 GLU D 71 " pdb="MG MG D 502 " model vdw 1.819 2.170 nonbonded pdb=" O1B GTP B 501 " pdb="MG MG B 502 " model vdw 1.850 2.170 ... (remaining 87790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } 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 individual isotropic 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: 0.160 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 10.260 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.021 0.121 11038 Z= 1.130 Angle : 1.596 9.450 14975 Z= 1.084 Chirality : 0.092 0.462 1627 Planarity : 0.008 0.035 1953 Dihedral : 12.722 169.736 4075 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.33 % Favored : 98.59 % Rotamer: Outliers : 0.78 % Allowed : 0.43 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.75 (0.21), residues: 1349 helix: 0.57 (0.18), residues: 603 sheet: 1.59 (0.37), residues: 205 loop : 0.15 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 105 TYR 0.051 0.007 TYR C 61 PHE 0.033 0.005 PHE C 20 TRP 0.036 0.008 TRP B 21 HIS 0.013 0.003 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.02070 (11038) covalent geometry : angle 1.59650 (14975) hydrogen bonds : bond 0.21226 ( 568) hydrogen bonds : angle 7.05024 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 298 time to evaluate : 0.367 Fit side-chains REVERT: B 221 ARG cc_start: 0.6199 (tpt170) cc_final: 0.3155 (mpt-90) REVERT: B 313 MET cc_start: 0.9048 (mtm) cc_final: 0.8843 (mtt) REVERT: B 335 ILE cc_start: 0.8978 (mm) cc_final: 0.8773 (mt) REVERT: C 110 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6880 (mm-30) REVERT: C 211 ASP cc_start: 0.7790 (t70) cc_final: 0.7491 (t0) REVERT: D 172 TYR cc_start: 0.8139 (t80) cc_final: 0.7575 (t80) REVERT: D 203 MET cc_start: 0.7865 (mmp) cc_final: 0.7518 (mmt) REVERT: D 214 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7842 (ttp80) REVERT: D 254 GLU cc_start: 0.4782 (mm-30) cc_final: 0.4565 (mt-10) REVERT: D 280 LYS cc_start: 0.8234 (mttp) cc_final: 0.7395 (tptt) REVERT: D 326 LYS cc_start: 0.5684 (mmtt) cc_final: 0.3871 (mttt) REVERT: D 352 LYS cc_start: 0.5250 (mmtt) cc_final: 0.4212 (tptt) outliers start: 9 outliers final: 1 residues processed: 304 average time/residue: 0.1356 time to fit residues: 54.2525 Evaluate side-chains 161 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 88 HIS B 133 GLN D 31 GLN D 300 ASN D 309 HIS A 139 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102133 restraints weight = 13902.255| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.99 r_work: 0.3067 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11038 Z= 0.206 Angle : 0.646 11.330 14975 Z= 0.352 Chirality : 0.047 0.284 1627 Planarity : 0.005 0.047 1953 Dihedral : 11.549 174.753 1523 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.56 % Allowed : 6.91 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 1.62 (0.22), residues: 1349 helix: 1.99 (0.21), residues: 619 sheet: 1.10 (0.35), residues: 223 loop : -0.02 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 284 TYR 0.014 0.002 TYR C 283 PHE 0.016 0.002 PHE C 20 TRP 0.014 0.002 TRP B 21 HIS 0.006 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00463 (11038) covalent geometry : angle 0.64591 (14975) hydrogen bonds : bond 0.06991 ( 568) hydrogen bonds : angle 5.00492 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.283 Fit side-chains REVERT: B 120 ASP cc_start: 0.8302 (t0) cc_final: 0.7854 (m-30) REVERT: B 123 ARG cc_start: 0.8309 (tmm-80) cc_final: 0.7792 (ttm-80) REVERT: B 221 ARG cc_start: 0.7008 (tpt170) cc_final: 0.2992 (mpt-90) REVERT: B 302 MET cc_start: 0.8471 (mmm) cc_final: 0.8001 (mmm) REVERT: B 377 MET cc_start: 0.8263 (ttp) cc_final: 0.7983 (ttt) REVERT: B 392 ASP cc_start: 0.8224 (m-30) cc_final: 0.7891 (m-30) REVERT: C 59 ASN cc_start: 0.8318 (m-40) cc_final: 0.7870 (t0) REVERT: C 71 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6659 (pt0) REVERT: C 75 MET cc_start: 0.8454 (mtm) cc_final: 0.8236 (mtt) REVERT: C 163 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8241 (p0) REVERT: C 176 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7964 (ptpp) REVERT: C 211 ASP cc_start: 0.8387 (t70) cc_final: 0.8102 (t0) REVERT: C 284 ARG cc_start: 0.7270 (ptm160) cc_final: 0.6695 (ptm-80) REVERT: C 314 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8867 (t) REVERT: C 330 GLU cc_start: 0.8589 (tp30) cc_final: 0.7990 (pt0) REVERT: D 172 TYR cc_start: 0.8085 (t80) cc_final: 0.7515 (t80) REVERT: D 211 ASP cc_start: 0.8351 (m-30) cc_final: 0.7765 (t0) REVERT: D 254 GLU cc_start: 0.5361 (mm-30) cc_final: 0.4599 (mt-10) REVERT: D 300 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7714 (t0) REVERT: D 326 LYS cc_start: 0.6289 (mmtt) cc_final: 0.4669 (tptt) REVERT: D 352 LYS cc_start: 0.6162 (mmtt) cc_final: 0.4429 (tptt) REVERT: A 109 ARG cc_start: 0.6928 (mtm110) cc_final: 0.6631 (ttp-110) outliers start: 18 outliers final: 11 residues processed: 215 average time/residue: 0.1236 time to fit residues: 36.0577 Evaluate side-chains 172 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 300 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 73 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN C 37 HIS D 128 GLN A 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.113047 restraints weight = 14058.796| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.32 r_work: 0.3553 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11038 Z= 0.166 Angle : 0.562 10.258 14975 Z= 0.304 Chirality : 0.045 0.263 1627 Planarity : 0.004 0.048 1953 Dihedral : 11.216 178.822 1522 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.16 % Allowed : 9.25 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 1.58 (0.22), residues: 1349 helix: 2.08 (0.21), residues: 621 sheet: 0.95 (0.35), residues: 217 loop : -0.15 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 214 TYR 0.014 0.001 TYR C 61 PHE 0.016 0.001 PHE C 20 TRP 0.011 0.001 TRP B 21 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00374 (11038) covalent geometry : angle 0.56208 (14975) hydrogen bonds : bond 0.05899 ( 568) hydrogen bonds : angle 4.68911 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.437 Fit side-chains REVERT: B 47 ASP cc_start: 0.6862 (m-30) cc_final: 0.6161 (t70) REVERT: B 123 ARG cc_start: 0.8142 (tmm-80) cc_final: 0.7597 (ttm-80) REVERT: B 154 MET cc_start: 0.8501 (mmm) cc_final: 0.8200 (mtp) REVERT: B 221 ARG cc_start: 0.6735 (tpt170) cc_final: 0.2771 (mpt-90) REVERT: B 290 GLU cc_start: 0.8146 (tp30) cc_final: 0.7749 (tt0) REVERT: B 377 MET cc_start: 0.7952 (ttp) cc_final: 0.7585 (ttt) REVERT: B 392 ASP cc_start: 0.8063 (m-30) cc_final: 0.7753 (m-30) REVERT: C 59 ASN cc_start: 0.8270 (m-40) cc_final: 0.7915 (t0) REVERT: C 75 MET cc_start: 0.8399 (mtm) cc_final: 0.8176 (mtt) REVERT: C 163 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8257 (p0) REVERT: C 176 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7889 (ptpp) REVERT: C 211 ASP cc_start: 0.8237 (t70) cc_final: 0.7919 (t0) REVERT: C 284 ARG cc_start: 0.6989 (ptm160) cc_final: 0.6630 (ptm-80) REVERT: C 330 GLU cc_start: 0.8459 (tp30) cc_final: 0.7926 (pt0) REVERT: C 417 GLU cc_start: 0.7942 (tt0) cc_final: 0.7641 (mt-10) REVERT: D 172 TYR cc_start: 0.8228 (t80) cc_final: 0.7616 (t80) REVERT: D 211 ASP cc_start: 0.8128 (m-30) cc_final: 0.7556 (t0) REVERT: D 251 ASP cc_start: 0.7304 (p0) cc_final: 0.6925 (p0) REVERT: D 254 GLU cc_start: 0.4977 (mm-30) cc_final: 0.4331 (mt-10) REVERT: D 326 LYS cc_start: 0.5788 (mmtt) cc_final: 0.3740 (mttt) REVERT: D 352 LYS cc_start: 0.5467 (mmtt) cc_final: 0.4022 (tptt) REVERT: A 109 ARG cc_start: 0.6962 (mtm110) cc_final: 0.6659 (ttp-110) outliers start: 25 outliers final: 18 residues processed: 193 average time/residue: 0.1150 time to fit residues: 30.5564 Evaluate side-chains 175 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 381 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 102 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS B 133 GLN B 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.154819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.134481 restraints weight = 14203.303| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.38 r_work: 0.3606 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11038 Z= 0.107 Angle : 0.493 7.569 14975 Z= 0.263 Chirality : 0.042 0.141 1627 Planarity : 0.004 0.046 1953 Dihedral : 10.838 179.877 1522 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.73 % Allowed : 10.80 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 1.81 (0.23), residues: 1349 helix: 2.31 (0.21), residues: 622 sheet: 0.99 (0.34), residues: 216 loop : -0.06 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 322 TYR 0.013 0.001 TYR B 24 PHE 0.016 0.001 PHE C 20 TRP 0.010 0.001 TRP D 21 HIS 0.009 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00213 (11038) covalent geometry : angle 0.49279 (14975) hydrogen bonds : bond 0.04511 ( 568) hydrogen bonds : angle 4.41547 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.452 Fit side-chains REVERT: B 47 ASP cc_start: 0.6766 (m-30) cc_final: 0.6141 (t70) REVERT: B 123 ARG cc_start: 0.8160 (tmm-80) cc_final: 0.7570 (ttm-80) REVERT: B 149 PHE cc_start: 0.8416 (t80) cc_final: 0.8079 (t80) REVERT: B 154 MET cc_start: 0.8378 (mmm) cc_final: 0.8083 (mtp) REVERT: B 221 ARG cc_start: 0.6562 (tpt170) cc_final: 0.2637 (mmt90) REVERT: B 290 GLU cc_start: 0.8196 (tp30) cc_final: 0.7790 (tt0) REVERT: B 302 MET cc_start: 0.8509 (mmm) cc_final: 0.8122 (mmm) REVERT: B 377 MET cc_start: 0.7933 (ttp) cc_final: 0.7638 (ttt) REVERT: B 392 ASP cc_start: 0.8212 (m-30) cc_final: 0.7902 (m-30) REVERT: C 59 ASN cc_start: 0.8244 (m-40) cc_final: 0.7930 (t0) REVERT: C 163 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8225 (p0) REVERT: C 176 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7815 (ptpp) REVERT: C 211 ASP cc_start: 0.8113 (t70) cc_final: 0.7777 (t0) REVERT: C 284 ARG cc_start: 0.6852 (ptm160) cc_final: 0.6507 (ptm-80) REVERT: C 330 GLU cc_start: 0.8388 (tp30) cc_final: 0.7883 (pt0) REVERT: D 47 ASP cc_start: 0.6455 (m-30) cc_final: 0.6081 (p0) REVERT: D 172 TYR cc_start: 0.8211 (t80) cc_final: 0.7600 (t80) REVERT: D 211 ASP cc_start: 0.8048 (m-30) cc_final: 0.7505 (t0) REVERT: D 254 GLU cc_start: 0.4633 (mm-30) cc_final: 0.4034 (mt-10) REVERT: D 326 LYS cc_start: 0.5571 (mmtt) cc_final: 0.3562 (mttt) REVERT: D 352 LYS cc_start: 0.5586 (mmtt) cc_final: 0.4142 (tptt) REVERT: D 414 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: A 109 ARG cc_start: 0.6931 (mtm110) cc_final: 0.6667 (ttp-110) outliers start: 20 outliers final: 10 residues processed: 199 average time/residue: 0.1224 time to fit residues: 33.0331 Evaluate side-chains 178 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 414 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103586 restraints weight = 14005.099| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.95 r_work: 0.3190 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11038 Z= 0.122 Angle : 0.498 7.413 14975 Z= 0.264 Chirality : 0.042 0.132 1627 Planarity : 0.004 0.044 1953 Dihedral : 10.631 179.563 1522 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.07 % Allowed : 11.06 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 1.86 (0.23), residues: 1349 helix: 2.40 (0.21), residues: 610 sheet: 0.96 (0.34), residues: 216 loop : -0.02 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 215 TYR 0.011 0.001 TYR B 24 PHE 0.015 0.001 PHE D 49 TRP 0.009 0.001 TRP C 21 HIS 0.002 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00263 (11038) covalent geometry : angle 0.49761 (14975) hydrogen bonds : bond 0.04635 ( 568) hydrogen bonds : angle 4.34960 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: B 123 ARG cc_start: 0.8366 (tmm-80) cc_final: 0.7819 (ttm-80) REVERT: B 149 PHE cc_start: 0.8573 (t80) cc_final: 0.8280 (t80) REVERT: B 154 MET cc_start: 0.8507 (mmm) cc_final: 0.8200 (mtp) REVERT: B 221 ARG cc_start: 0.6585 (tpt170) cc_final: 0.2747 (mmt180) REVERT: B 290 GLU cc_start: 0.8152 (tp30) cc_final: 0.7891 (tt0) REVERT: B 302 MET cc_start: 0.8535 (mmm) cc_final: 0.7987 (mmm) REVERT: B 377 MET cc_start: 0.8231 (ttp) cc_final: 0.7944 (ttt) REVERT: B 392 ASP cc_start: 0.8427 (m-30) cc_final: 0.8047 (m-30) REVERT: B 425 MET cc_start: 0.8413 (tpp) cc_final: 0.7935 (mmm) REVERT: C 59 ASN cc_start: 0.8208 (m-40) cc_final: 0.7963 (t0) REVERT: C 160 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: C 163 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8293 (p0) REVERT: C 176 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7780 (ptpp) REVERT: C 211 ASP cc_start: 0.8243 (t70) cc_final: 0.8015 (t0) REVERT: C 284 ARG cc_start: 0.7133 (ptm160) cc_final: 0.6684 (ptm-80) REVERT: C 330 GLU cc_start: 0.8711 (tp30) cc_final: 0.8143 (pt0) REVERT: D 172 TYR cc_start: 0.8224 (t80) cc_final: 0.7576 (t80) REVERT: D 211 ASP cc_start: 0.8198 (m-30) cc_final: 0.7824 (t0) REVERT: D 254 GLU cc_start: 0.5004 (mm-30) cc_final: 0.4345 (mt-10) REVERT: D 300 ASN cc_start: 0.8390 (t0) cc_final: 0.8021 (t0) REVERT: D 326 LYS cc_start: 0.6146 (mmtt) cc_final: 0.3855 (mttt) REVERT: D 352 LYS cc_start: 0.5894 (mmtt) cc_final: 0.4351 (tptt) REVERT: D 423 GLU cc_start: 0.8159 (mp0) cc_final: 0.7832 (mp0) REVERT: A 109 ARG cc_start: 0.6944 (mtm110) cc_final: 0.6653 (ttp-110) outliers start: 24 outliers final: 14 residues processed: 199 average time/residue: 0.1219 time to fit residues: 33.1077 Evaluate side-chains 180 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 367 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 60 optimal weight: 0.0570 chunk 98 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS B 300 ASN C 37 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.114226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.095151 restraints weight = 14584.260| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.99 r_work: 0.3070 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 11038 Z= 0.241 Angle : 0.614 11.776 14975 Z= 0.326 Chirality : 0.047 0.315 1627 Planarity : 0.005 0.052 1953 Dihedral : 10.897 178.508 1522 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.42 % Allowed : 11.50 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 1.34 (0.22), residues: 1349 helix: 2.01 (0.21), residues: 619 sheet: 0.61 (0.34), residues: 217 loop : -0.35 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 221 TYR 0.012 0.002 TYR B 272 PHE 0.020 0.002 PHE C 268 TRP 0.010 0.001 TRP C 21 HIS 0.005 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00573 (11038) covalent geometry : angle 0.61372 (14975) hydrogen bonds : bond 0.06351 ( 568) hydrogen bonds : angle 4.62837 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.399 Fit side-chains REVERT: B 47 ASP cc_start: 0.7054 (m-30) cc_final: 0.6326 (t70) REVERT: B 154 MET cc_start: 0.8601 (mmm) cc_final: 0.8221 (mtp) REVERT: B 221 ARG cc_start: 0.6643 (tpt170) cc_final: 0.2542 (mpt180) REVERT: B 290 GLU cc_start: 0.8336 (tp30) cc_final: 0.7988 (tt0) REVERT: B 377 MET cc_start: 0.8203 (ttp) cc_final: 0.7873 (ttt) REVERT: B 392 ASP cc_start: 0.8315 (m-30) cc_final: 0.8057 (m-30) REVERT: C 59 ASN cc_start: 0.8402 (m-40) cc_final: 0.8080 (t0) REVERT: C 71 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6478 (pt0) REVERT: C 75 MET cc_start: 0.8481 (mtt) cc_final: 0.8264 (mtt) REVERT: C 163 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8325 (p0) REVERT: C 176 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7756 (ptpp) REVERT: C 211 ASP cc_start: 0.8325 (t70) cc_final: 0.7911 (t0) REVERT: C 215 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7896 (ttm110) REVERT: C 284 ARG cc_start: 0.7171 (ptm160) cc_final: 0.6521 (ptm-80) REVERT: C 290 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7882 (tt0) REVERT: C 330 GLU cc_start: 0.8748 (tp30) cc_final: 0.8183 (pt0) REVERT: D 172 TYR cc_start: 0.8336 (t80) cc_final: 0.7786 (t80) REVERT: D 211 ASP cc_start: 0.8334 (m-30) cc_final: 0.7830 (t0) REVERT: D 254 GLU cc_start: 0.4416 (mm-30) cc_final: 0.3660 (mt-10) REVERT: D 300 ASN cc_start: 0.8450 (t0) cc_final: 0.8184 (t0) REVERT: D 326 LYS cc_start: 0.6535 (mmtt) cc_final: 0.4063 (mttt) REVERT: D 352 LYS cc_start: 0.6058 (mmtt) cc_final: 0.4379 (tptt) REVERT: D 423 GLU cc_start: 0.8037 (mp0) cc_final: 0.7755 (mp0) outliers start: 28 outliers final: 20 residues processed: 184 average time/residue: 0.1213 time to fit residues: 30.3290 Evaluate side-chains 179 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 381 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.090244 restraints weight = 14294.567| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.98 r_work: 0.3044 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11038 Z= 0.171 Angle : 0.551 8.694 14975 Z= 0.290 Chirality : 0.044 0.135 1627 Planarity : 0.004 0.044 1953 Dihedral : 10.778 179.711 1522 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.59 % Allowed : 11.93 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 1.37 (0.23), residues: 1349 helix: 2.15 (0.21), residues: 607 sheet: 0.59 (0.35), residues: 217 loop : -0.42 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 308 TYR 0.011 0.001 TYR B 24 PHE 0.015 0.001 PHE C 20 TRP 0.008 0.001 TRP B 21 HIS 0.003 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00396 (11038) covalent geometry : angle 0.55103 (14975) hydrogen bonds : bond 0.05436 ( 568) hydrogen bonds : angle 4.49170 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 ARG cc_start: 0.8286 (tmm-80) cc_final: 0.7772 (ttm-80) REVERT: B 154 MET cc_start: 0.8455 (mmm) cc_final: 0.8184 (mtp) REVERT: B 221 ARG cc_start: 0.6592 (tpt170) cc_final: 0.2643 (mpt180) REVERT: B 290 GLU cc_start: 0.8360 (tp30) cc_final: 0.8154 (tt0) REVERT: B 377 MET cc_start: 0.8240 (ttp) cc_final: 0.7925 (ttt) REVERT: B 392 ASP cc_start: 0.8397 (m-30) cc_final: 0.8124 (m-30) REVERT: C 160 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: C 163 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8294 (p0) REVERT: C 176 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7817 (ptpp) REVERT: C 211 ASP cc_start: 0.8349 (t70) cc_final: 0.8037 (t0) REVERT: C 284 ARG cc_start: 0.7086 (ptm160) cc_final: 0.6659 (ptm-80) REVERT: C 290 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7993 (tt0) REVERT: C 330 GLU cc_start: 0.8689 (tp30) cc_final: 0.8231 (pt0) REVERT: D 47 ASP cc_start: 0.6521 (m-30) cc_final: 0.6089 (p0) REVERT: D 211 ASP cc_start: 0.8258 (m-30) cc_final: 0.7771 (t0) REVERT: D 254 GLU cc_start: 0.5149 (mm-30) cc_final: 0.4433 (mt-10) REVERT: D 326 LYS cc_start: 0.6542 (mmtt) cc_final: 0.4089 (mttt) REVERT: D 352 LYS cc_start: 0.6200 (mmtt) cc_final: 0.4546 (tptt) REVERT: D 423 GLU cc_start: 0.7934 (mp0) cc_final: 0.7567 (mp0) outliers start: 30 outliers final: 21 residues processed: 192 average time/residue: 0.1213 time to fit residues: 31.7778 Evaluate side-chains 190 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 381 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN D 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.093897 restraints weight = 14147.383| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.97 r_work: 0.3180 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11038 Z= 0.120 Angle : 0.505 8.003 14975 Z= 0.265 Chirality : 0.042 0.133 1627 Planarity : 0.004 0.043 1953 Dihedral : 10.426 173.384 1522 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.33 % Allowed : 12.71 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 1.47 (0.23), residues: 1349 helix: 2.18 (0.21), residues: 632 sheet: 1.00 (0.38), residues: 186 loop : -0.51 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 123 TYR 0.012 0.001 TYR D 24 PHE 0.014 0.001 PHE C 20 TRP 0.009 0.001 TRP D 21 HIS 0.002 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00264 (11038) covalent geometry : angle 0.50544 (14975) hydrogen bonds : bond 0.04411 ( 568) hydrogen bonds : angle 4.29333 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 ARG cc_start: 0.8332 (tmm-80) cc_final: 0.7816 (ttm-80) REVERT: B 221 ARG cc_start: 0.6354 (tpt170) cc_final: 0.2695 (mmt180) REVERT: B 290 GLU cc_start: 0.8353 (tp30) cc_final: 0.8133 (tt0) REVERT: B 377 MET cc_start: 0.8185 (ttp) cc_final: 0.7910 (ttt) REVERT: B 392 ASP cc_start: 0.8418 (m-30) cc_final: 0.8140 (m-30) REVERT: C 163 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8360 (p0) REVERT: C 176 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7728 (ptpp) REVERT: C 211 ASP cc_start: 0.8198 (t70) cc_final: 0.7845 (t0) REVERT: C 284 ARG cc_start: 0.6964 (ptm160) cc_final: 0.6426 (ptm-80) REVERT: C 290 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7893 (tt0) REVERT: C 330 GLU cc_start: 0.8675 (tp30) cc_final: 0.8252 (pt0) REVERT: C 373 MET cc_start: 0.8594 (ptt) cc_final: 0.8198 (ptp) REVERT: D 211 ASP cc_start: 0.8144 (m-30) cc_final: 0.7694 (t0) REVERT: D 254 GLU cc_start: 0.5071 (mm-30) cc_final: 0.4327 (mt-10) REVERT: D 326 LYS cc_start: 0.6526 (mmtt) cc_final: 0.4097 (mttt) REVERT: D 352 LYS cc_start: 0.6354 (mmtt) cc_final: 0.4615 (tptt) outliers start: 27 outliers final: 20 residues processed: 193 average time/residue: 0.1257 time to fit residues: 33.1761 Evaluate side-chains 184 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 381 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 42 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN D 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.088600 restraints weight = 14419.087| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.98 r_work: 0.3009 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11038 Z= 0.229 Angle : 0.612 11.614 14975 Z= 0.323 Chirality : 0.046 0.291 1627 Planarity : 0.005 0.047 1953 Dihedral : 10.663 174.353 1522 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.90 % Allowed : 13.05 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 1.15 (0.23), residues: 1349 helix: 2.00 (0.21), residues: 620 sheet: 0.43 (0.36), residues: 203 loop : -0.59 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 215 TYR 0.011 0.002 TYR D 272 PHE 0.018 0.002 PHE C 20 TRP 0.009 0.001 TRP C 21 HIS 0.005 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00543 (11038) covalent geometry : angle 0.61221 (14975) hydrogen bonds : bond 0.06061 ( 568) hydrogen bonds : angle 4.54696 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 123 ARG cc_start: 0.8373 (tmm-80) cc_final: 0.7845 (ttm-80) REVERT: B 154 MET cc_start: 0.8387 (mtp) cc_final: 0.8052 (mtp) REVERT: B 221 ARG cc_start: 0.6567 (tpt170) cc_final: 0.2605 (mpt180) REVERT: B 290 GLU cc_start: 0.8356 (tp30) cc_final: 0.8143 (tt0) REVERT: B 377 MET cc_start: 0.8270 (ttp) cc_final: 0.7958 (ttt) REVERT: B 392 ASP cc_start: 0.8488 (m-30) cc_final: 0.8261 (m-30) REVERT: C 163 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8399 (p0) REVERT: C 176 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7881 (ptpp) REVERT: C 284 ARG cc_start: 0.7120 (ptm160) cc_final: 0.6503 (ptm-80) REVERT: C 290 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7869 (tt0) REVERT: C 330 GLU cc_start: 0.8744 (tp30) cc_final: 0.8296 (pt0) REVERT: C 373 MET cc_start: 0.8572 (ptt) cc_final: 0.8107 (ptp) REVERT: D 211 ASP cc_start: 0.8180 (m-30) cc_final: 0.7650 (t0) REVERT: D 254 GLU cc_start: 0.4546 (mm-30) cc_final: 0.3768 (mt-10) REVERT: D 326 LYS cc_start: 0.6374 (mmtt) cc_final: 0.3907 (mttt) REVERT: D 352 LYS cc_start: 0.6547 (mmtt) cc_final: 0.4674 (tptt) REVERT: D 423 GLU cc_start: 0.7942 (mp0) cc_final: 0.7557 (mp0) outliers start: 22 outliers final: 18 residues processed: 179 average time/residue: 0.1194 time to fit residues: 29.0004 Evaluate side-chains 176 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 381 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095002 restraints weight = 14099.842| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.95 r_work: 0.3224 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11038 Z= 0.111 Angle : 0.512 7.817 14975 Z= 0.270 Chirality : 0.042 0.133 1627 Planarity : 0.004 0.044 1953 Dihedral : 10.216 163.634 1522 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.38 % Allowed : 14.09 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 1.47 (0.23), residues: 1349 helix: 2.18 (0.21), residues: 632 sheet: 1.04 (0.38), residues: 184 loop : -0.53 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 2 TYR 0.012 0.001 TYR D 24 PHE 0.026 0.001 PHE D 49 TRP 0.010 0.001 TRP B 21 HIS 0.002 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00235 (11038) covalent geometry : angle 0.51155 (14975) hydrogen bonds : bond 0.04173 ( 568) hydrogen bonds : angle 4.26135 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 123 ARG cc_start: 0.8310 (tmm-80) cc_final: 0.7766 (ttm-80) REVERT: B 154 MET cc_start: 0.8305 (mtp) cc_final: 0.7978 (mtp) REVERT: B 221 ARG cc_start: 0.6276 (tpt170) cc_final: 0.2647 (mmt180) REVERT: B 290 GLU cc_start: 0.8369 (tp30) cc_final: 0.8098 (tt0) REVERT: B 377 MET cc_start: 0.8180 (ttp) cc_final: 0.7891 (ttt) REVERT: B 392 ASP cc_start: 0.8421 (m-30) cc_final: 0.8141 (m-30) REVERT: B 415 GLU cc_start: 0.7810 (mp0) cc_final: 0.7608 (mp0) REVERT: C 176 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7708 (ptpp) REVERT: C 283 TYR cc_start: 0.8074 (m-80) cc_final: 0.7835 (m-80) REVERT: C 284 ARG cc_start: 0.6958 (ptm160) cc_final: 0.6446 (ptm-80) REVERT: C 290 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7914 (tt0) REVERT: C 330 GLU cc_start: 0.8616 (tp30) cc_final: 0.8202 (pt0) REVERT: C 373 MET cc_start: 0.8611 (ptt) cc_final: 0.8247 (ptp) REVERT: D 47 ASP cc_start: 0.6458 (m-30) cc_final: 0.6055 (p0) REVERT: D 211 ASP cc_start: 0.8122 (m-30) cc_final: 0.7605 (t0) REVERT: D 254 GLU cc_start: 0.4932 (mm-30) cc_final: 0.4229 (mt-10) REVERT: D 326 LYS cc_start: 0.6259 (mmtt) cc_final: 0.3880 (mttt) REVERT: D 352 LYS cc_start: 0.6130 (mmtt) cc_final: 0.4444 (tptt) REVERT: D 423 GLU cc_start: 0.7990 (mp0) cc_final: 0.7577 (mp0) outliers start: 16 outliers final: 16 residues processed: 180 average time/residue: 0.1262 time to fit residues: 30.8847 Evaluate side-chains 182 residues out of total 1157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 300 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 128 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 0.0000 chunk 130 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 96 optimal weight: 0.0470 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN D 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095031 restraints weight = 14113.429| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.94 r_work: 0.3201 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11038 Z= 0.126 Angle : 0.800 59.199 14975 Z= 0.459 Chirality : 0.042 0.134 1627 Planarity : 0.004 0.043 1953 Dihedral : 10.208 163.414 1522 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.47 % Allowed : 14.26 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 1.49 (0.23), residues: 1349 helix: 2.19 (0.21), residues: 632 sheet: 1.05 (0.38), residues: 184 loop : -0.52 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 215 TYR 0.013 0.001 TYR B 24 PHE 0.014 0.001 PHE C 20 TRP 0.009 0.001 TRP B 21 HIS 0.003 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00276 (11038) covalent geometry : angle 0.79977 (14975) hydrogen bonds : bond 0.04207 ( 568) hydrogen bonds : angle 4.25844 ( 1608) =============================================================================== Job complete usr+sys time: 2329.38 seconds wall clock time: 40 minutes 44.54 seconds (2444.54 seconds total)