Starting phenix.real_space_refine on Sat Jul 4 03:23:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xde_33145/07_2026/7xde_33145.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xde_33145/07_2026/7xde_33145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xde_33145/07_2026/7xde_33145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xde_33145/07_2026/7xde_33145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xde_33145/07_2026/7xde_33145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xde_33145/07_2026/7xde_33145.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xde_33145/07_2026/7xde_33145.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xde_33145/07_2026/7xde_33145.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.228 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 92 5.16 5 C 11420 2.51 5 N 3048 2.21 5 O 3328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17896 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4430 Classifications: {'peptide': 562} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 528} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 3.82, per 1000 atoms: 0.21 Number of scatterers: 17896 At special positions: 0 Unit cell: (134.747, 134.747, 79.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 8 15.00 O 3328 8.00 N 3048 7.00 C 11420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 701.7 milliseconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 12 sheets defined 53.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.672A pdb=" N MET A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.740A pdb=" N PHE A 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 60 through 75 removed outlier: 3.707A pdb=" N MET A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 92 Processing helix chain 'A' and resid 92 through 103 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.527A pdb=" N LEU A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 142 through 149 removed outlier: 3.590A pdb=" N ILE A 146 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.738A pdb=" N VAL A 181 " --> pdb=" O MET A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 228 through 247 removed outlier: 4.020A pdb=" N ASP A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.511A pdb=" N ALA A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 Processing helix chain 'A' and resid 333 through 339 Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 466 through 469 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 488 through 501 removed outlier: 3.605A pdb=" N LEU A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 518 through 537 removed outlier: 3.793A pdb=" N ILE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 555 Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.672A pdb=" N MET B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.740A pdb=" N PHE B 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 60 through 75 removed outlier: 3.707A pdb=" N MET B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.527A pdb=" N LEU B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 142 through 149 removed outlier: 3.590A pdb=" N ILE B 146 " --> pdb=" O HIS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.738A pdb=" N VAL B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 228 through 247 removed outlier: 4.020A pdb=" N ASP B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 280 through 298 removed outlier: 3.511A pdb=" N ALA B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 330 Processing helix chain 'B' and resid 333 through 339 Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 466 through 469 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 488 through 501 removed outlier: 3.605A pdb=" N LEU B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 509 Processing helix chain 'B' and resid 515 through 517 No H-bonds generated for 'chain 'B' and resid 515 through 517' Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.793A pdb=" N ILE B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.672A pdb=" N MET C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.740A pdb=" N PHE C 40 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.706A pdb=" N MET C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 92 Processing helix chain 'C' and resid 92 through 103 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.528A pdb=" N LEU C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 142 through 149 removed outlier: 3.590A pdb=" N ILE C 146 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.739A pdb=" N VAL C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 228 through 247 removed outlier: 4.020A pdb=" N ASP C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 270 Processing helix chain 'C' and resid 280 through 298 removed outlier: 3.511A pdb=" N ALA C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 330 Processing helix chain 'C' and resid 333 through 339 Processing helix chain 'C' and resid 376 through 385 Processing helix chain 'C' and resid 400 through 411 Processing helix chain 'C' and resid 422 through 426 Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 466 through 469 Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 488 through 501 removed outlier: 3.605A pdb=" N LEU C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 509 Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 518 through 537 removed outlier: 3.794A pdb=" N ILE C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 555 Processing helix chain 'D' and resid 25 through 31 removed outlier: 3.672A pdb=" N MET D 29 " --> pdb=" O GLY D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.740A pdb=" N PHE D 40 " --> pdb=" O GLY D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 60 through 75 removed outlier: 3.708A pdb=" N MET D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 92 through 103 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 114 through 124 removed outlier: 3.527A pdb=" N LEU D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 142 through 149 removed outlier: 3.590A pdb=" N ILE D 146 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 190 removed outlier: 3.739A pdb=" N VAL D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 228 through 247 removed outlier: 4.020A pdb=" N ASP D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 270 Processing helix chain 'D' and resid 280 through 298 removed outlier: 3.511A pdb=" N ALA D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 330 Processing helix chain 'D' and resid 333 through 339 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 400 through 411 Processing helix chain 'D' and resid 422 through 426 Processing helix chain 'D' and resid 429 through 436 Processing helix chain 'D' and resid 466 through 469 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 488 through 501 removed outlier: 3.605A pdb=" N LEU D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 509 Processing helix chain 'D' and resid 515 through 517 No H-bonds generated for 'chain 'D' and resid 515 through 517' Processing helix chain 'D' and resid 518 through 537 removed outlier: 3.793A pdb=" N ILE D 524 " --> pdb=" O GLN D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 555 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 136 removed outlier: 6.843A pdb=" N ALA A 157 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL A 201 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 159 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A 203 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR A 161 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 158 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU A 255 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL A 160 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 344 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 136 removed outlier: 6.842A pdb=" N ALA B 157 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL B 201 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 159 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE B 203 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR B 161 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 158 " --> pdb=" O GLN B 253 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU B 255 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL B 160 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 341 through 344 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.843A pdb=" N ALA C 157 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL C 201 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 159 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE C 203 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 161 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL C 158 " --> pdb=" O GLN C 253 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU C 255 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL C 160 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 341 through 344 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'D' and resid 133 through 136 removed outlier: 6.843A pdb=" N ALA D 157 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL D 201 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 159 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE D 203 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR D 161 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 158 " --> pdb=" O GLN D 253 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU D 255 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL D 160 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 341 through 344 Processing sheet with id=AB3, first strand: chain 'D' and resid 452 through 453 796 hydrogen bonds defined for protein. 2280 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: 2.41 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2972 1.31 - 1.43: 4680 1.43 - 1.56: 10460 1.56 - 1.68: 40 1.68 - 1.80: 148 Bond restraints: 18300 Sorted by residual: bond pdb=" C2D NAD C 601 " pdb=" C3D NAD C 601 " ideal model delta sigma weight residual 1.531 1.243 0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.243 0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C2D NAD D 601 " pdb=" C3D NAD D 601 " ideal model delta sigma weight residual 1.531 1.244 0.287 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C2D NAD B 601 " pdb=" C3D NAD B 601 " ideal model delta sigma weight residual 1.531 1.244 0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C1B NAD D 601 " pdb=" C2B NAD D 601 " ideal model delta sigma weight residual 1.534 1.279 0.255 2.00e-02 2.50e+03 1.62e+02 ... (remaining 18295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 24375 2.74 - 5.47: 369 5.47 - 8.21: 48 8.21 - 10.94: 20 10.94 - 13.68: 8 Bond angle restraints: 24820 Sorted by residual: angle pdb=" O1A NAD B 601 " pdb=" PA NAD B 601 " pdb=" O2A NAD B 601 " ideal model delta sigma weight residual 122.64 108.96 13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" O1A NAD D 601 " pdb=" PA NAD D 601 " pdb=" O2A NAD D 601 " ideal model delta sigma weight residual 122.64 108.98 13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" O1A NAD C 601 " pdb=" PA NAD C 601 " pdb=" O2A NAD C 601 " ideal model delta sigma weight residual 122.64 109.00 13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.03 13.61 3.00e+00 1.11e-01 2.06e+01 angle pdb=" N ARG C 197 " pdb=" CA ARG C 197 " pdb=" C ARG C 197 " ideal model delta sigma weight residual 113.15 117.96 -4.81 1.19e+00 7.06e-01 1.63e+01 ... (remaining 24815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 9966 17.01 - 34.01: 870 34.01 - 51.02: 164 51.02 - 68.03: 12 68.03 - 85.03: 16 Dihedral angle restraints: 11028 sinusoidal: 4512 harmonic: 6516 Sorted by residual: dihedral pdb=" CG ARG A 70 " pdb=" CD ARG A 70 " pdb=" NE ARG A 70 " pdb=" CZ ARG A 70 " ideal model delta sinusoidal sigma weight residual 90.00 4.97 85.03 2 1.50e+01 4.44e-03 2.12e+01 dihedral pdb=" CG ARG D 70 " pdb=" CD ARG D 70 " pdb=" NE ARG D 70 " pdb=" CZ ARG D 70 " ideal model delta sinusoidal sigma weight residual 90.00 4.97 85.03 2 1.50e+01 4.44e-03 2.12e+01 dihedral pdb=" CG ARG B 70 " pdb=" CD ARG B 70 " pdb=" NE ARG B 70 " pdb=" CZ ARG B 70 " ideal model delta sinusoidal sigma weight residual 90.00 5.00 85.00 2 1.50e+01 4.44e-03 2.12e+01 ... (remaining 11025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2368 0.070 - 0.141: 338 0.141 - 0.211: 38 0.211 - 0.281: 4 0.281 - 0.351: 4 Chirality restraints: 2752 Sorted by residual: chirality pdb=" C3D NAD D 601 " pdb=" C2D NAD D 601 " pdb=" C4D NAD D 601 " pdb=" O3D NAD D 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C3D NAD A 601 " pdb=" C2D NAD A 601 " pdb=" C4D NAD A 601 " pdb=" O3D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C3D NAD C 601 " pdb=" C2D NAD C 601 " pdb=" C4D NAD C 601 " pdb=" O3D NAD C 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 2749 not shown) Planarity restraints: 3196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 460 " -0.012 2.00e-02 2.50e+03 1.74e-02 5.30e+00 pdb=" CG PHE D 460 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE D 460 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE D 460 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 460 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE D 460 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 460 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 460 " -0.012 2.00e-02 2.50e+03 1.73e-02 5.25e+00 pdb=" CG PHE B 460 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 460 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE B 460 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 460 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 460 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 460 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 460 " 0.011 2.00e-02 2.50e+03 1.72e-02 5.15e+00 pdb=" CG PHE A 460 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 460 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 460 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 460 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 460 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 460 " -0.001 2.00e-02 2.50e+03 ... (remaining 3193 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 252 2.67 - 3.23: 17067 3.23 - 3.78: 28619 3.78 - 4.34: 41008 4.34 - 4.90: 67278 Nonbonded interactions: 154224 Sorted by model distance: nonbonded pdb=" OD1 ASP D 236 " pdb=" OH TYR D 269 " model vdw 2.110 3.040 nonbonded pdb=" OD1 ASP A 236 " pdb=" OH TYR A 269 " model vdw 2.110 3.040 nonbonded pdb=" OD1 ASP C 236 " pdb=" OH TYR C 269 " model vdw 2.111 3.040 nonbonded pdb=" OD1 ASP B 236 " pdb=" OH TYR B 269 " model vdw 2.111 3.040 nonbonded pdb=" OD1 ASP B 139 " pdb=" OH TYR C 570 " model vdw 2.153 3.040 ... (remaining 154219 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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=0.00 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: 1.120 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.780 Find NCS groups from input model: 0.160 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:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.011 0.288 18300 Z= 0.530 Angle : 0.824 13.680 24820 Z= 0.404 Chirality : 0.053 0.351 2752 Planarity : 0.004 0.032 3196 Dihedral : 13.032 85.035 6852 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.63 % Allowed : 0.00 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 2240 helix: 0.18 (0.16), residues: 1032 sheet: 0.70 (0.35), residues: 208 loop : 0.46 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 70 TYR 0.033 0.002 TYR D 231 PHE 0.036 0.003 PHE D 460 TRP 0.012 0.002 TRP A 572 HIS 0.005 0.002 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.01122 / 0.53 (18300) covalent geometry : angle 0.82374 / 0.40 (24820) hydrogen bonds : bond 0.16754 / 10.86 ( 796) hydrogen bonds : angle 7.26325 / 5.17 ( 2280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 252 time to evaluate : 0.707 Fit side-chains REVERT: A 239 MET cc_start: 0.8637 (mmm) cc_final: 0.8350 (mmm) REVERT: A 384 LEU cc_start: 0.8122 (mt) cc_final: 0.7896 (mt) REVERT: B 239 MET cc_start: 0.8629 (mmm) cc_final: 0.8344 (mmm) REVERT: B 384 LEU cc_start: 0.8155 (mt) cc_final: 0.7926 (mt) REVERT: B 551 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8362 (ttpp) REVERT: C 239 MET cc_start: 0.8636 (mmm) cc_final: 0.8341 (mmm) REVERT: C 384 LEU cc_start: 0.8123 (mt) cc_final: 0.7896 (mt) REVERT: C 551 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8365 (ttpp) REVERT: D 239 MET cc_start: 0.8631 (mmm) cc_final: 0.8340 (mmm) REVERT: D 384 LEU cc_start: 0.8118 (mt) cc_final: 0.7901 (mt) REVERT: D 551 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8367 (ttpp) outliers start: 12 outliers final: 0 residues processed: 252 average time/residue: 0.6375 time to fit residues: 178.3311 Evaluate side-chains 182 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 ASN B 382 ASN C 382 ASN D 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101421 restraints weight = 19025.112| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.91 r_work: 0.2976 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18300 Z= 0.158 Angle : 0.574 7.035 24820 Z= 0.291 Chirality : 0.045 0.180 2752 Planarity : 0.004 0.033 3196 Dihedral : 4.922 36.214 2484 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.26 % Allowed : 10.64 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 2240 helix: 0.88 (0.17), residues: 1048 sheet: 0.84 (0.36), residues: 208 loop : 0.61 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.013 0.001 TYR B 222 PHE 0.023 0.002 PHE A 471 TRP 0.005 0.001 TRP D 558 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (18300) covalent geometry : angle 0.57408 / 0.29 (24820) hydrogen bonds : bond 0.04795 / 3.18 ( 796) hydrogen bonds : angle 5.04105 / 3.58 ( 2280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.693 Fit side-chains REVERT: A 70 ARG cc_start: 0.7549 (ptm-80) cc_final: 0.7256 (ppt170) REVERT: A 219 MET cc_start: 0.8407 (mtm) cc_final: 0.8176 (mtt) REVERT: A 222 TYR cc_start: 0.8759 (m-80) cc_final: 0.8422 (m-80) REVERT: A 239 MET cc_start: 0.8519 (mmm) cc_final: 0.8202 (mmm) REVERT: A 384 LEU cc_start: 0.7443 (mt) cc_final: 0.7189 (mt) REVERT: A 559 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.7719 (mpp-170) REVERT: A 561 GLU cc_start: 0.8289 (mp0) cc_final: 0.8005 (mp0) REVERT: B 70 ARG cc_start: 0.7554 (ptm-80) cc_final: 0.7250 (ppt170) REVERT: B 222 TYR cc_start: 0.8772 (m-80) cc_final: 0.8421 (m-80) REVERT: B 239 MET cc_start: 0.8527 (mmm) cc_final: 0.8209 (mmm) REVERT: B 384 LEU cc_start: 0.7425 (mt) cc_final: 0.7155 (mt) REVERT: B 551 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7729 (ttpp) REVERT: B 561 GLU cc_start: 0.8207 (mp0) cc_final: 0.7972 (mp0) REVERT: C 70 ARG cc_start: 0.7539 (ptm-80) cc_final: 0.7248 (ppt170) REVERT: C 219 MET cc_start: 0.8428 (mtm) cc_final: 0.8196 (mtt) REVERT: C 222 TYR cc_start: 0.8753 (m-80) cc_final: 0.8410 (m-80) REVERT: C 239 MET cc_start: 0.8537 (mmm) cc_final: 0.8221 (mmm) REVERT: C 384 LEU cc_start: 0.7458 (mt) cc_final: 0.7205 (mt) REVERT: C 551 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7749 (ttpp) REVERT: C 561 GLU cc_start: 0.8222 (mp0) cc_final: 0.7981 (mp0) REVERT: D 70 ARG cc_start: 0.7547 (ptm-80) cc_final: 0.7258 (ppt170) REVERT: D 239 MET cc_start: 0.8515 (mmm) cc_final: 0.8194 (mmm) REVERT: D 384 LEU cc_start: 0.7458 (mt) cc_final: 0.7206 (mt) REVERT: D 551 LYS cc_start: 0.7963 (ttpp) cc_final: 0.7747 (ttpp) REVERT: D 559 ARG cc_start: 0.7911 (mmt-90) cc_final: 0.7704 (mpp-170) REVERT: D 561 GLU cc_start: 0.8282 (mp0) cc_final: 0.7999 (mp0) outliers start: 24 outliers final: 8 residues processed: 222 average time/residue: 0.7137 time to fit residues: 174.4418 Evaluate side-chains 212 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 181 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101237 restraints weight = 19162.703| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.93 r_work: 0.2975 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18300 Z= 0.167 Angle : 0.557 7.163 24820 Z= 0.282 Chirality : 0.045 0.187 2752 Planarity : 0.004 0.031 3196 Dihedral : 4.892 37.079 2484 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.04 % Allowed : 11.95 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.18), residues: 2240 helix: 1.05 (0.17), residues: 1048 sheet: 0.80 (0.36), residues: 208 loop : 0.59 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 70 TYR 0.017 0.001 TYR D 222 PHE 0.025 0.002 PHE B 471 TRP 0.006 0.001 TRP D 558 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (18300) covalent geometry : angle 0.55678 / 0.28 (24820) hydrogen bonds : bond 0.04310 / 2.86 ( 796) hydrogen bonds : angle 4.75908 / 3.37 ( 2280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.641 Fit side-chains REVERT: A 70 ARG cc_start: 0.7587 (ptm-80) cc_final: 0.7355 (ppt170) REVERT: A 219 MET cc_start: 0.8453 (mtm) cc_final: 0.8157 (mtt) REVERT: A 384 LEU cc_start: 0.7681 (mt) cc_final: 0.7423 (mt) REVERT: A 559 ARG cc_start: 0.7890 (mmt-90) cc_final: 0.7635 (mpp-170) REVERT: A 561 GLU cc_start: 0.8216 (mp0) cc_final: 0.7949 (mp0) REVERT: B 70 ARG cc_start: 0.7584 (ptm-80) cc_final: 0.7350 (ppt170) REVERT: B 384 LEU cc_start: 0.7504 (mt) cc_final: 0.7232 (mt) REVERT: B 561 GLU cc_start: 0.8137 (mp0) cc_final: 0.7832 (mp0) REVERT: C 70 ARG cc_start: 0.7588 (ptm-80) cc_final: 0.7360 (ppt170) REVERT: C 219 MET cc_start: 0.8447 (mtm) cc_final: 0.8117 (mtt) REVERT: C 384 LEU cc_start: 0.7645 (mt) cc_final: 0.7376 (mt) REVERT: C 561 GLU cc_start: 0.8163 (mp0) cc_final: 0.7850 (mp0) REVERT: D 70 ARG cc_start: 0.7590 (ptm-80) cc_final: 0.7364 (ppt170) REVERT: D 384 LEU cc_start: 0.7638 (mt) cc_final: 0.7370 (mt) REVERT: D 559 ARG cc_start: 0.7896 (mmt-90) cc_final: 0.7641 (mpp-170) REVERT: D 561 GLU cc_start: 0.8210 (mp0) cc_final: 0.7941 (mp0) outliers start: 39 outliers final: 12 residues processed: 220 average time/residue: 0.6617 time to fit residues: 161.5456 Evaluate side-chains 208 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 220 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 211 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 99 optimal weight: 0.2980 chunk 202 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.140343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103856 restraints weight = 19052.011| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.83 r_work: 0.3022 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18300 Z= 0.127 Angle : 0.510 6.736 24820 Z= 0.259 Chirality : 0.043 0.183 2752 Planarity : 0.004 0.031 3196 Dihedral : 4.760 37.553 2484 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.46 % Allowed : 11.90 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.18), residues: 2240 helix: 1.22 (0.17), residues: 1048 sheet: 0.69 (0.35), residues: 208 loop : 0.63 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 70 TYR 0.015 0.001 TYR D 222 PHE 0.022 0.002 PHE D 471 TRP 0.005 0.001 TRP C 558 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (18300) covalent geometry : angle 0.51035 / 0.26 (24820) hydrogen bonds : bond 0.03707 / 2.47 ( 796) hydrogen bonds : angle 4.52090 / 3.21 ( 2280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.660 Fit side-chains REVERT: A 70 ARG cc_start: 0.7399 (ptm-80) cc_final: 0.7173 (ppt170) REVERT: A 219 MET cc_start: 0.8437 (mtm) cc_final: 0.8053 (mtt) REVERT: A 343 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8608 (mmm) REVERT: A 384 LEU cc_start: 0.7586 (mt) cc_final: 0.7328 (mt) REVERT: A 559 ARG cc_start: 0.7793 (mmt-90) cc_final: 0.7489 (mpp-170) REVERT: A 561 GLU cc_start: 0.8094 (mp0) cc_final: 0.7808 (mp0) REVERT: B 70 ARG cc_start: 0.7392 (ptm-80) cc_final: 0.7174 (ppt170) REVERT: B 343 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8604 (mmm) REVERT: B 384 LEU cc_start: 0.7561 (mt) cc_final: 0.7302 (mt) REVERT: B 561 GLU cc_start: 0.8029 (mp0) cc_final: 0.7749 (mp0) REVERT: C 219 MET cc_start: 0.8448 (mtm) cc_final: 0.8113 (mtt) REVERT: C 343 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8593 (mmm) REVERT: C 384 LEU cc_start: 0.7585 (mt) cc_final: 0.7319 (mt) REVERT: C 561 GLU cc_start: 0.8057 (mp0) cc_final: 0.7777 (mp0) REVERT: D 343 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8593 (mmm) REVERT: D 384 LEU cc_start: 0.7571 (mt) cc_final: 0.7304 (mt) REVERT: D 559 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7478 (mpp-170) REVERT: D 561 GLU cc_start: 0.8113 (mp0) cc_final: 0.7829 (mp0) outliers start: 47 outliers final: 20 residues processed: 224 average time/residue: 0.6677 time to fit residues: 166.3438 Evaluate side-chains 206 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 204 optimal weight: 8.9990 chunk 75 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 131 optimal weight: 0.0980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.099666 restraints weight = 19034.221| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.92 r_work: 0.2906 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18300 Z= 0.240 Angle : 0.601 6.575 24820 Z= 0.304 Chirality : 0.048 0.217 2752 Planarity : 0.004 0.034 3196 Dihedral : 4.985 36.811 2484 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.30 % Allowed : 11.90 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.18), residues: 2240 helix: 1.10 (0.16), residues: 1040 sheet: 0.58 (0.35), residues: 208 loop : 0.47 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 70 TYR 0.013 0.002 TYR B 97 PHE 0.031 0.002 PHE C 471 TRP 0.006 0.001 TRP C 558 HIS 0.006 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.24 (18300) covalent geometry : angle 0.60140 / 0.30 (24820) hydrogen bonds : bond 0.04580 / 3.03 ( 796) hydrogen bonds : angle 4.73090 / 3.36 ( 2280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.706 Fit side-chains REVERT: A 75 MET cc_start: 0.7490 (mtt) cc_final: 0.7087 (mtp) REVERT: A 219 MET cc_start: 0.8493 (mtm) cc_final: 0.8193 (mtt) REVERT: A 239 MET cc_start: 0.8619 (mmm) cc_final: 0.8328 (mmm) REVERT: A 384 LEU cc_start: 0.7682 (mt) cc_final: 0.7417 (mt) REVERT: A 559 ARG cc_start: 0.7927 (mmt-90) cc_final: 0.7654 (mpp-170) REVERT: A 561 GLU cc_start: 0.8140 (mp0) cc_final: 0.7839 (mp0) REVERT: B 75 MET cc_start: 0.7471 (mtt) cc_final: 0.7063 (mtp) REVERT: B 239 MET cc_start: 0.8577 (mmm) cc_final: 0.8222 (mmm) REVERT: B 384 LEU cc_start: 0.7611 (mt) cc_final: 0.7340 (mt) REVERT: B 561 GLU cc_start: 0.8146 (mp0) cc_final: 0.7823 (mp0) REVERT: C 219 MET cc_start: 0.8492 (mtm) cc_final: 0.8196 (mtt) REVERT: C 239 MET cc_start: 0.8595 (mmm) cc_final: 0.8238 (mmm) REVERT: C 384 LEU cc_start: 0.7684 (mt) cc_final: 0.7419 (mt) REVERT: C 561 GLU cc_start: 0.8168 (mp0) cc_final: 0.7842 (mp0) REVERT: D 75 MET cc_start: 0.7471 (mtt) cc_final: 0.7071 (mtp) REVERT: D 239 MET cc_start: 0.8601 (mmm) cc_final: 0.8310 (mmm) REVERT: D 384 LEU cc_start: 0.7662 (mt) cc_final: 0.7398 (mt) REVERT: D 559 ARG cc_start: 0.7938 (mmt-90) cc_final: 0.7660 (mpp-170) REVERT: D 561 GLU cc_start: 0.8131 (mp0) cc_final: 0.7828 (mp0) outliers start: 63 outliers final: 36 residues processed: 226 average time/residue: 0.5845 time to fit residues: 148.5587 Evaluate side-chains 219 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103408 restraints weight = 18820.000| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.92 r_work: 0.2987 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18300 Z= 0.117 Angle : 0.506 7.529 24820 Z= 0.257 Chirality : 0.043 0.180 2752 Planarity : 0.004 0.036 3196 Dihedral : 4.812 41.224 2484 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.67 % Allowed : 12.95 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 2240 helix: 1.27 (0.17), residues: 1048 sheet: 0.84 (0.35), residues: 200 loop : 0.53 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 70 TYR 0.008 0.001 TYR D 543 PHE 0.020 0.001 PHE A 471 TRP 0.006 0.001 TRP D 558 HIS 0.002 0.000 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (18300) covalent geometry : angle 0.50615 / 0.26 (24820) hydrogen bonds : bond 0.03537 / 2.36 ( 796) hydrogen bonds : angle 4.44907 / 3.16 ( 2280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 0.576 Fit side-chains REVERT: A 75 MET cc_start: 0.7504 (mtt) cc_final: 0.7113 (mtp) REVERT: A 219 MET cc_start: 0.8548 (mtm) cc_final: 0.8233 (mtt) REVERT: A 384 LEU cc_start: 0.7691 (mt) cc_final: 0.7422 (mt) REVERT: A 548 ASP cc_start: 0.7405 (p0) cc_final: 0.7054 (t0) REVERT: A 551 LYS cc_start: 0.7878 (ttpp) cc_final: 0.7634 (tttm) REVERT: A 559 ARG cc_start: 0.7890 (mmt-90) cc_final: 0.7593 (mpp-170) REVERT: A 561 GLU cc_start: 0.8229 (mp0) cc_final: 0.7917 (mp0) REVERT: B 75 MET cc_start: 0.7473 (mtt) cc_final: 0.7080 (mtp) REVERT: B 384 LEU cc_start: 0.7681 (mt) cc_final: 0.7392 (mt) REVERT: B 548 ASP cc_start: 0.7403 (p0) cc_final: 0.7025 (t0) REVERT: B 561 GLU cc_start: 0.8162 (mp0) cc_final: 0.7870 (mp0) REVERT: C 219 MET cc_start: 0.8541 (mtm) cc_final: 0.8213 (mtt) REVERT: C 384 LEU cc_start: 0.7775 (mt) cc_final: 0.7511 (mt) REVERT: C 548 ASP cc_start: 0.7389 (p0) cc_final: 0.7028 (t0) REVERT: C 561 GLU cc_start: 0.8198 (mp0) cc_final: 0.7905 (mp0) REVERT: D 75 MET cc_start: 0.7466 (mtt) cc_final: 0.7070 (mtp) REVERT: D 384 LEU cc_start: 0.7675 (mt) cc_final: 0.7409 (mt) REVERT: D 548 ASP cc_start: 0.7365 (p0) cc_final: 0.7021 (t0) REVERT: D 559 ARG cc_start: 0.7899 (mmt-90) cc_final: 0.7604 (mpp-170) REVERT: D 561 GLU cc_start: 0.8216 (mp0) cc_final: 0.7899 (mp0) outliers start: 51 outliers final: 27 residues processed: 232 average time/residue: 0.6083 time to fit residues: 158.2120 Evaluate side-chains 214 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 200 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 HIS C 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.140463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103949 restraints weight = 18922.352| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.83 r_work: 0.2976 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18300 Z= 0.132 Angle : 0.515 7.287 24820 Z= 0.259 Chirality : 0.043 0.191 2752 Planarity : 0.004 0.030 3196 Dihedral : 4.757 41.524 2484 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.04 % Allowed : 13.16 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.18), residues: 2240 helix: 1.32 (0.17), residues: 1048 sheet: 0.57 (0.32), residues: 224 loop : 0.57 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 70 TYR 0.009 0.001 TYR D 97 PHE 0.024 0.002 PHE A 471 TRP 0.005 0.001 TRP D 558 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (18300) covalent geometry : angle 0.51542 / 0.26 (24820) hydrogen bonds : bond 0.03634 / 2.42 ( 796) hydrogen bonds : angle 4.41175 / 3.14 ( 2280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.677 Fit side-chains REVERT: A 75 MET cc_start: 0.7141 (mtt) cc_final: 0.6740 (mtp) REVERT: A 219 MET cc_start: 0.8419 (mtm) cc_final: 0.8073 (mtt) REVERT: A 384 LEU cc_start: 0.7431 (mt) cc_final: 0.7173 (mt) REVERT: A 548 ASP cc_start: 0.7100 (p0) cc_final: 0.6844 (t0) REVERT: A 551 LYS cc_start: 0.7558 (ttpp) cc_final: 0.7274 (tttm) REVERT: A 559 ARG cc_start: 0.7635 (mmt-90) cc_final: 0.7309 (mpp-170) REVERT: A 561 GLU cc_start: 0.7957 (mp0) cc_final: 0.7632 (mp0) REVERT: B 75 MET cc_start: 0.7117 (mtt) cc_final: 0.6718 (mtp) REVERT: B 219 MET cc_start: 0.8767 (mtt) cc_final: 0.8453 (mtt) REVERT: B 239 MET cc_start: 0.8330 (mmm) cc_final: 0.7982 (mmm) REVERT: B 384 LEU cc_start: 0.7431 (mt) cc_final: 0.7173 (mt) REVERT: B 548 ASP cc_start: 0.7158 (p0) cc_final: 0.6813 (t0) REVERT: B 561 GLU cc_start: 0.7925 (mp0) cc_final: 0.7582 (mp0) REVERT: C 219 MET cc_start: 0.8363 (mtm) cc_final: 0.8012 (mtt) REVERT: C 239 MET cc_start: 0.8338 (mmm) cc_final: 0.7989 (mmm) REVERT: C 384 LEU cc_start: 0.7471 (mt) cc_final: 0.7218 (mt) REVERT: C 548 ASP cc_start: 0.7144 (p0) cc_final: 0.6806 (t0) REVERT: C 561 GLU cc_start: 0.7957 (mp0) cc_final: 0.7618 (mp0) REVERT: D 75 MET cc_start: 0.7128 (mtt) cc_final: 0.6720 (mtp) REVERT: D 384 LEU cc_start: 0.7439 (mt) cc_final: 0.7180 (mt) REVERT: D 548 ASP cc_start: 0.7138 (p0) cc_final: 0.6804 (t0) REVERT: D 559 ARG cc_start: 0.7656 (mmt-90) cc_final: 0.7323 (mpp-170) REVERT: D 561 GLU cc_start: 0.7948 (mp0) cc_final: 0.7620 (mp0) outliers start: 39 outliers final: 29 residues processed: 247 average time/residue: 0.5726 time to fit residues: 159.0103 Evaluate side-chains 221 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 112 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 147 optimal weight: 0.0980 chunk 156 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104436 restraints weight = 18902.563| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.93 r_work: 0.3000 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18300 Z= 0.113 Angle : 0.502 7.492 24820 Z= 0.252 Chirality : 0.042 0.174 2752 Planarity : 0.004 0.031 3196 Dihedral : 4.708 42.776 2484 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.99 % Allowed : 13.94 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.18), residues: 2240 helix: 1.40 (0.17), residues: 1048 sheet: 0.39 (0.32), residues: 236 loop : 0.62 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 70 TYR 0.009 0.001 TYR D 533 PHE 0.019 0.001 PHE A 471 TRP 0.005 0.001 TRP D 558 HIS 0.002 0.000 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (18300) covalent geometry : angle 0.50159 / 0.25 (24820) hydrogen bonds : bond 0.03393 / 2.26 ( 796) hydrogen bonds : angle 4.33188 / 3.08 ( 2280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.602 Fit side-chains REVERT: A 75 MET cc_start: 0.7394 (mtt) cc_final: 0.7003 (mtp) REVERT: A 219 MET cc_start: 0.8538 (mtm) cc_final: 0.8231 (mtt) REVERT: A 384 LEU cc_start: 0.7684 (mt) cc_final: 0.7415 (mt) REVERT: A 551 LYS cc_start: 0.7846 (ttpp) cc_final: 0.7585 (tttm) REVERT: A 561 GLU cc_start: 0.8147 (mp0) cc_final: 0.7920 (mp0) REVERT: B 75 MET cc_start: 0.7372 (mtt) cc_final: 0.6980 (mtp) REVERT: B 219 MET cc_start: 0.8911 (mtt) cc_final: 0.8596 (mtt) REVERT: B 384 LEU cc_start: 0.7712 (mt) cc_final: 0.7432 (mt) REVERT: B 548 ASP cc_start: 0.7270 (p0) cc_final: 0.7020 (t0) REVERT: B 561 GLU cc_start: 0.8143 (mp0) cc_final: 0.7840 (mp0) REVERT: C 219 MET cc_start: 0.8519 (mtm) cc_final: 0.8204 (mtt) REVERT: C 384 LEU cc_start: 0.7701 (mt) cc_final: 0.7443 (mt) REVERT: C 548 ASP cc_start: 0.7320 (p0) cc_final: 0.7070 (t0) REVERT: C 561 GLU cc_start: 0.8151 (mp0) cc_final: 0.7849 (mp0) REVERT: D 75 MET cc_start: 0.7398 (mtt) cc_final: 0.7003 (mtp) REVERT: D 384 LEU cc_start: 0.7652 (mt) cc_final: 0.7382 (mt) REVERT: D 548 ASP cc_start: 0.7237 (p0) cc_final: 0.7013 (t0) REVERT: D 561 GLU cc_start: 0.8143 (mp0) cc_final: 0.7914 (mp0) outliers start: 38 outliers final: 29 residues processed: 233 average time/residue: 0.5860 time to fit residues: 153.3784 Evaluate side-chains 224 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 210 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104052 restraints weight = 19011.145| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.93 r_work: 0.2989 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18300 Z= 0.123 Angle : 0.512 7.351 24820 Z= 0.256 Chirality : 0.043 0.176 2752 Planarity : 0.004 0.041 3196 Dihedral : 4.700 42.755 2484 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.68 % Allowed : 14.78 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.18), residues: 2240 helix: 1.43 (0.17), residues: 1048 sheet: 0.02 (0.32), residues: 216 loop : 0.61 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 559 TYR 0.008 0.001 TYR A 543 PHE 0.020 0.001 PHE C 471 TRP 0.004 0.001 TRP B 558 HIS 0.002 0.000 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 (18300) covalent geometry : angle 0.51201 / 0.26 (24820) hydrogen bonds : bond 0.03446 / 2.29 ( 796) hydrogen bonds : angle 4.32886 / 3.08 ( 2280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.553 Fit side-chains REVERT: A 75 MET cc_start: 0.7325 (mtt) cc_final: 0.6935 (mtp) REVERT: A 219 MET cc_start: 0.8512 (mtm) cc_final: 0.8196 (mtt) REVERT: A 384 LEU cc_start: 0.7659 (mt) cc_final: 0.7394 (mt) REVERT: A 561 GLU cc_start: 0.8186 (mp0) cc_final: 0.7963 (mp0) REVERT: B 75 MET cc_start: 0.7318 (mtt) cc_final: 0.6931 (mtp) REVERT: B 384 LEU cc_start: 0.7689 (mt) cc_final: 0.7435 (mt) REVERT: B 548 ASP cc_start: 0.7227 (p0) cc_final: 0.7000 (t0) REVERT: B 561 GLU cc_start: 0.8113 (mp0) cc_final: 0.7782 (mp0) REVERT: C 219 MET cc_start: 0.8518 (mtm) cc_final: 0.8178 (mtt) REVERT: C 384 LEU cc_start: 0.7715 (mt) cc_final: 0.7466 (mt) REVERT: C 548 ASP cc_start: 0.7268 (p0) cc_final: 0.7049 (t0) REVERT: C 561 GLU cc_start: 0.8118 (mp0) cc_final: 0.7790 (mp0) REVERT: D 75 MET cc_start: 0.7327 (mtt) cc_final: 0.6941 (mtp) REVERT: D 384 LEU cc_start: 0.7678 (mt) cc_final: 0.7412 (mt) REVERT: D 548 ASP cc_start: 0.7251 (p0) cc_final: 0.7004 (t0) REVERT: D 561 GLU cc_start: 0.8114 (mp0) cc_final: 0.7880 (mp0) outliers start: 32 outliers final: 30 residues processed: 234 average time/residue: 0.5487 time to fit residues: 144.9410 Evaluate side-chains 230 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 222 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 214 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105753 restraints weight = 18349.838| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.71 r_work: 0.3039 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18300 Z= 0.116 Angle : 0.505 7.697 24820 Z= 0.253 Chirality : 0.043 0.177 2752 Planarity : 0.004 0.036 3196 Dihedral : 4.669 43.128 2484 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.57 % Allowed : 15.09 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.18), residues: 2240 helix: 1.46 (0.17), residues: 1048 sheet: 0.01 (0.32), residues: 216 loop : 0.62 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.008 0.001 TYR C 347 PHE 0.020 0.001 PHE B 471 TRP 0.005 0.001 TRP C 558 HIS 0.002 0.000 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (18300) covalent geometry : angle 0.50523 / 0.25 (24820) hydrogen bonds : bond 0.03361 / 2.24 ( 796) hydrogen bonds : angle 4.28799 / 3.05 ( 2280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.605 Fit side-chains REVERT: A 75 MET cc_start: 0.7609 (mtt) cc_final: 0.7227 (mtp) REVERT: A 219 MET cc_start: 0.8612 (mtm) cc_final: 0.8333 (mtt) REVERT: A 384 LEU cc_start: 0.7892 (mt) cc_final: 0.7618 (mt) REVERT: A 561 GLU cc_start: 0.8410 (mp0) cc_final: 0.8191 (mp0) REVERT: B 75 MET cc_start: 0.7599 (mtt) cc_final: 0.7216 (mtp) REVERT: B 325 MET cc_start: 0.8126 (mtp) cc_final: 0.7856 (mtm) REVERT: B 384 LEU cc_start: 0.7891 (mt) cc_final: 0.7632 (mt) REVERT: B 561 GLU cc_start: 0.8319 (mp0) cc_final: 0.8050 (mp0) REVERT: C 219 MET cc_start: 0.8618 (mtm) cc_final: 0.8314 (mtt) REVERT: C 325 MET cc_start: 0.8130 (mtp) cc_final: 0.7861 (mtm) REVERT: C 347 TYR cc_start: 0.7668 (m-10) cc_final: 0.7266 (m-80) REVERT: C 384 LEU cc_start: 0.7919 (mt) cc_final: 0.7667 (mt) REVERT: C 561 GLU cc_start: 0.8316 (mp0) cc_final: 0.8042 (mp0) REVERT: D 75 MET cc_start: 0.7614 (mtt) cc_final: 0.7234 (mtp) REVERT: D 325 MET cc_start: 0.8121 (mtp) cc_final: 0.7851 (mtm) REVERT: D 384 LEU cc_start: 0.7880 (mt) cc_final: 0.7626 (mt) REVERT: D 561 GLU cc_start: 0.8408 (mp0) cc_final: 0.8184 (mp0) outliers start: 30 outliers final: 30 residues processed: 230 average time/residue: 0.5587 time to fit residues: 145.3784 Evaluate side-chains 229 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 204 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 GLN C 425 GLN D 425 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100378 restraints weight = 19287.245| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.92 r_work: 0.2955 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18300 Z= 0.228 Angle : 0.597 9.807 24820 Z= 0.299 Chirality : 0.048 0.214 2752 Planarity : 0.004 0.034 3196 Dihedral : 4.902 40.687 2484 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.62 % Allowed : 15.15 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2240 helix: 1.24 (0.16), residues: 1048 sheet: 0.37 (0.37), residues: 180 loop : 0.47 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 70 TYR 0.014 0.002 TYR C 97 PHE 0.030 0.002 PHE D 471 TRP 0.006 0.001 TRP C 558 HIS 0.004 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.23 (18300) covalent geometry : angle 0.59736 / 0.30 (24820) hydrogen bonds : bond 0.04231 / 2.80 ( 796) hydrogen bonds : angle 4.57310 / 3.26 ( 2280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5741.99 seconds wall clock time: 98 minutes 42.47 seconds (5922.47 seconds total)