Starting phenix.real_space_refine on Thu Mar 5 01:24:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xde_33145/03_2026/7xde_33145.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xde_33145/03_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_33145/03_2026/7xde_33145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xde_33145/03_2026/7xde_33145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xde_33145/03_2026/7xde_33145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xde_33145/03_2026/7xde_33145.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.37, per 1000 atoms: 0.24 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: 1.58 Conformation dependent library (CDL) restraints added in 786.9 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: 0.63 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: 3.86 Time building geometry restraints manager: 2.16 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: 10066 17.01 - 34.01: 932 34.01 - 51.02: 190 51.02 - 68.03: 20 68.03 - 85.03: 20 Dihedral angle restraints: 11228 sinusoidal: 4712 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 11225 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.530 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:10.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 13.604 85.035 7052 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 covalent geometry : bond 0.01122 (18300) covalent geometry : angle 0.82374 (24820) hydrogen bonds : bond 0.16754 ( 796) hydrogen bonds : angle 7.26325 ( 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 : 0.553 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: 0.7088 time to fit residues: 197.0151 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 : 0.667 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3580 r_free = 0.3580 target = 0.138795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101498 restraints weight = 19019.669| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.91 r_work: 0.2987 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18300 Z= 0.155 Angle : 0.572 7.198 24820 Z= 0.292 Chirality : 0.045 0.181 2752 Planarity : 0.004 0.032 3196 Dihedral : 7.705 86.596 2684 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 0.83 (0.36), residues: 208 loop : 0.61 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 70 TYR 0.013 0.001 TYR B 222 PHE 0.023 0.002 PHE B 471 TRP 0.005 0.001 TRP D 558 HIS 0.004 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00373 (18300) covalent geometry : angle 0.57241 (24820) hydrogen bonds : bond 0.04568 ( 796) hydrogen bonds : angle 5.01732 ( 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 236 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.730 Fit side-chains REVERT: A 70 ARG cc_start: 0.7579 (ptm-80) cc_final: 0.7273 (ppt170) REVERT: A 219 MET cc_start: 0.8451 (mtm) cc_final: 0.8213 (mtt) REVERT: A 222 TYR cc_start: 0.8777 (m-80) cc_final: 0.8434 (m-80) REVERT: A 239 MET cc_start: 0.8536 (mmm) cc_final: 0.8225 (mmm) REVERT: A 384 LEU cc_start: 0.7473 (mt) cc_final: 0.7212 (mt) REVERT: A 559 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7740 (mpp-170) REVERT: A 561 GLU cc_start: 0.8314 (mp0) cc_final: 0.8032 (mp0) REVERT: B 70 ARG cc_start: 0.7586 (ptm-80) cc_final: 0.7271 (ppt170) REVERT: B 222 TYR cc_start: 0.8788 (m-80) cc_final: 0.8435 (m-80) REVERT: B 239 MET cc_start: 0.8538 (mmm) cc_final: 0.8229 (mmm) REVERT: B 384 LEU cc_start: 0.7450 (mt) cc_final: 0.7196 (mt) REVERT: B 551 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7743 (ttpp) REVERT: B 561 GLU cc_start: 0.8223 (mp0) cc_final: 0.7994 (mp0) REVERT: C 70 ARG cc_start: 0.7573 (ptm-80) cc_final: 0.7266 (ppt170) REVERT: C 219 MET cc_start: 0.8470 (mtm) cc_final: 0.8233 (mtt) REVERT: C 222 TYR cc_start: 0.8769 (m-80) cc_final: 0.8423 (m-80) REVERT: C 239 MET cc_start: 0.8551 (mmm) cc_final: 0.8244 (mmm) REVERT: C 384 LEU cc_start: 0.7483 (mt) cc_final: 0.7221 (mt) REVERT: C 551 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7756 (ttpp) REVERT: C 561 GLU cc_start: 0.8239 (mp0) cc_final: 0.8004 (mp0) REVERT: D 70 ARG cc_start: 0.7574 (ptm-80) cc_final: 0.7272 (ppt170) REVERT: D 239 MET cc_start: 0.8525 (mmm) cc_final: 0.8212 (mmm) REVERT: D 384 LEU cc_start: 0.7485 (mt) cc_final: 0.7226 (mt) REVERT: D 551 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7755 (ttpp) REVERT: D 559 ARG cc_start: 0.7930 (mmt-90) cc_final: 0.7724 (mpp-170) REVERT: D 561 GLU cc_start: 0.8305 (mp0) cc_final: 0.8021 (mp0) outliers start: 24 outliers final: 8 residues processed: 224 average time/residue: 0.7632 time to fit residues: 187.5773 Evaluate side-chains 210 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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: 0.9990 chunk 207 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 196 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.140378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104003 restraints weight = 19124.982| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.83 r_work: 0.3004 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18300 Z= 0.127 Angle : 0.517 7.220 24820 Z= 0.262 Chirality : 0.043 0.181 2752 Planarity : 0.004 0.030 3196 Dihedral : 7.305 81.369 2684 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.68 % Allowed : 12.16 % Favored : 86.16 % 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: 1.22 (0.18), residues: 2240 helix: 1.14 (0.17), residues: 1048 sheet: 0.77 (0.36), residues: 208 loop : 0.66 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 70 TYR 0.016 0.001 TYR D 222 PHE 0.022 0.002 PHE B 471 TRP 0.005 0.001 TRP B 558 HIS 0.003 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00306 (18300) covalent geometry : angle 0.51692 (24820) hydrogen bonds : bond 0.03921 ( 796) hydrogen bonds : angle 4.62079 ( 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 239 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.679 Fit side-chains REVERT: A 219 MET cc_start: 0.8440 (mtm) cc_final: 0.8082 (mtt) REVERT: A 384 LEU cc_start: 0.7529 (mt) cc_final: 0.7272 (mt) REVERT: A 559 ARG cc_start: 0.7767 (mmt-90) cc_final: 0.7486 (mpp-170) REVERT: A 561 GLU cc_start: 0.8139 (mp0) cc_final: 0.7804 (mp0) REVERT: B 384 LEU cc_start: 0.7455 (mt) cc_final: 0.7184 (mt) REVERT: B 561 GLU cc_start: 0.8054 (mp0) cc_final: 0.7742 (mp0) REVERT: C 70 ARG cc_start: 0.7447 (ptm-80) cc_final: 0.7194 (ppt170) REVERT: C 219 MET cc_start: 0.8422 (mtm) cc_final: 0.8122 (mtt) REVERT: C 384 LEU cc_start: 0.7532 (mt) cc_final: 0.7276 (mt) REVERT: C 561 GLU cc_start: 0.8096 (mp0) cc_final: 0.7783 (mp0) REVERT: D 70 ARG cc_start: 0.7446 (ptm-80) cc_final: 0.7192 (ppt170) REVERT: D 222 TYR cc_start: 0.8589 (m-80) cc_final: 0.8336 (m-80) REVERT: D 384 LEU cc_start: 0.7516 (mt) cc_final: 0.7259 (mt) REVERT: D 559 ARG cc_start: 0.7755 (mmt-90) cc_final: 0.7466 (mpp-170) REVERT: D 561 GLU cc_start: 0.8135 (mp0) cc_final: 0.7796 (mp0) outliers start: 32 outliers final: 12 residues processed: 223 average time/residue: 0.7372 time to fit residues: 181.8359 Evaluate side-chains 205 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 90 GLU 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 90 GLU 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: 3.9990 chunk 16 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.101016 restraints weight = 19025.989| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.83 r_work: 0.2978 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18300 Z= 0.207 Angle : 0.573 6.722 24820 Z= 0.291 Chirality : 0.047 0.213 2752 Planarity : 0.004 0.032 3196 Dihedral : 7.445 80.031 2684 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.94 % Allowed : 12.26 % Favored : 85.80 % 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: 1.06 (0.18), residues: 2240 helix: 1.04 (0.16), residues: 1048 sheet: 0.61 (0.36), residues: 208 loop : 0.54 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 70 TYR 0.020 0.002 TYR A 222 PHE 0.030 0.002 PHE D 471 TRP 0.006 0.001 TRP A 558 HIS 0.005 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00521 (18300) covalent geometry : angle 0.57284 (24820) hydrogen bonds : bond 0.04389 ( 796) hydrogen bonds : angle 4.70036 ( 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 224 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.592 Fit side-chains REVERT: A 219 MET cc_start: 0.8456 (mtm) cc_final: 0.8152 (mtt) REVERT: A 239 MET cc_start: 0.8557 (mmm) cc_final: 0.8293 (mmm) REVERT: A 384 LEU cc_start: 0.7588 (mt) cc_final: 0.7319 (mt) REVERT: A 559 ARG cc_start: 0.7851 (mmt-90) cc_final: 0.7592 (mpp-170) REVERT: A 561 GLU cc_start: 0.8142 (mp0) cc_final: 0.7851 (mp0) REVERT: B 75 MET cc_start: 0.7579 (mtt) cc_final: 0.6967 (mtp) REVERT: B 239 MET cc_start: 0.8560 (mmm) cc_final: 0.8293 (mmm) REVERT: B 384 LEU cc_start: 0.7446 (mt) cc_final: 0.7191 (mt) REVERT: B 561 GLU cc_start: 0.8072 (mp0) cc_final: 0.7797 (mp0) REVERT: C 70 ARG cc_start: 0.7368 (ptm-80) cc_final: 0.7154 (ppt170) REVERT: C 219 MET cc_start: 0.8470 (mtm) cc_final: 0.8167 (mtt) REVERT: C 239 MET cc_start: 0.8575 (mmm) cc_final: 0.8305 (mmm) REVERT: C 384 LEU cc_start: 0.7579 (mt) cc_final: 0.7312 (mt) REVERT: C 561 GLU cc_start: 0.8090 (mp0) cc_final: 0.7815 (mp0) REVERT: D 70 ARG cc_start: 0.7398 (ptm-80) cc_final: 0.7191 (ppt170) REVERT: D 239 MET cc_start: 0.8551 (mmm) cc_final: 0.8282 (mmm) REVERT: D 384 LEU cc_start: 0.7567 (mt) cc_final: 0.7301 (mt) REVERT: D 559 ARG cc_start: 0.7854 (mmt-90) cc_final: 0.7590 (mpp-170) REVERT: D 561 GLU cc_start: 0.8134 (mp0) cc_final: 0.7847 (mp0) outliers start: 37 outliers final: 28 residues processed: 208 average time/residue: 0.6591 time to fit residues: 152.5221 Evaluate side-chains 208 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 196 ASP 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 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 196 ASP 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 196 ASP 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: 2.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100992 restraints weight = 18953.117| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.92 r_work: 0.2930 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 : 0.004 0.048 18300 Z= 0.180 Angle : 0.546 6.937 24820 Z= 0.277 Chirality : 0.045 0.201 2752 Planarity : 0.004 0.030 3196 Dihedral : 7.226 80.329 2684 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.30 % Allowed : 11.95 % Favored : 84.75 % 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: 1.07 (0.18), residues: 2240 helix: 1.11 (0.16), residues: 1048 sheet: 0.53 (0.35), residues: 208 loop : 0.48 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 70 TYR 0.017 0.001 TYR D 222 PHE 0.026 0.002 PHE C 471 TRP 0.007 0.001 TRP A 558 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00450 (18300) covalent geometry : angle 0.54613 (24820) hydrogen bonds : bond 0.04100 ( 796) hydrogen bonds : angle 4.62683 ( 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 252 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 0.661 Fit side-chains REVERT: A 219 MET cc_start: 0.8506 (mtm) cc_final: 0.8170 (mtt) REVERT: A 239 MET cc_start: 0.8608 (mmm) cc_final: 0.8323 (mmm) REVERT: A 384 LEU cc_start: 0.7712 (mt) cc_final: 0.7444 (mt) REVERT: A 559 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7606 (mpp-170) REVERT: A 561 GLU cc_start: 0.8180 (mp0) cc_final: 0.7869 (mp0) REVERT: B 75 MET cc_start: 0.7602 (mtt) cc_final: 0.7037 (mtp) REVERT: B 239 MET cc_start: 0.8603 (mmm) cc_final: 0.8315 (mmm) REVERT: B 384 LEU cc_start: 0.7505 (mt) cc_final: 0.7237 (mt) REVERT: B 561 GLU cc_start: 0.8167 (mp0) cc_final: 0.7856 (mp0) REVERT: C 219 MET cc_start: 0.8503 (mtm) cc_final: 0.8196 (mtt) REVERT: C 239 MET cc_start: 0.8623 (mmm) cc_final: 0.8331 (mmm) REVERT: C 384 LEU cc_start: 0.7720 (mt) cc_final: 0.7454 (mt) REVERT: C 561 GLU cc_start: 0.8185 (mp0) cc_final: 0.7872 (mp0) REVERT: D 239 MET cc_start: 0.8601 (mmm) cc_final: 0.8311 (mmm) REVERT: D 384 LEU cc_start: 0.7700 (mt) cc_final: 0.7435 (mt) REVERT: D 559 ARG cc_start: 0.7896 (mmt-90) cc_final: 0.7612 (mpp-170) REVERT: D 561 GLU cc_start: 0.8182 (mp0) cc_final: 0.7869 (mp0) outliers start: 63 outliers final: 32 residues processed: 232 average time/residue: 0.6464 time to fit residues: 167.1129 Evaluate side-chains 222 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 196 ASP 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 196 ASP 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 196 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 4.9990 chunk 131 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 208 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 105 optimal weight: 0.0470 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104402 restraints weight = 18774.948| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.91 r_work: 0.2921 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18300 Z= 0.107 Angle : 0.489 7.365 24820 Z= 0.249 Chirality : 0.042 0.179 2752 Planarity : 0.004 0.031 3196 Dihedral : 6.844 78.850 2684 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.47 % Allowed : 13.63 % Favored : 84.91 % 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: 1.33 (0.17), residues: 1048 sheet: 0.61 (0.34), residues: 212 loop : 0.59 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.013 0.001 TYR D 222 PHE 0.020 0.001 PHE D 471 TRP 0.005 0.001 TRP A 558 HIS 0.002 0.000 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00250 (18300) covalent geometry : angle 0.48915 (24820) hydrogen bonds : bond 0.03379 ( 796) hydrogen bonds : angle 4.37980 ( 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 238 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.677 Fit side-chains REVERT: A 219 MET cc_start: 0.8517 (mtm) cc_final: 0.8172 (mtt) REVERT: A 384 LEU cc_start: 0.7625 (mt) cc_final: 0.7369 (mt) REVERT: A 548 ASP cc_start: 0.7275 (p0) cc_final: 0.7073 (t0) REVERT: A 551 LYS cc_start: 0.7723 (ttpp) cc_final: 0.7456 (tttm) REVERT: A 559 ARG cc_start: 0.7785 (mmt-90) cc_final: 0.7470 (mpp-170) REVERT: A 561 GLU cc_start: 0.8090 (mp0) cc_final: 0.7802 (mp0) REVERT: B 75 MET cc_start: 0.7468 (mtt) cc_final: 0.6859 (mtp) REVERT: B 219 MET cc_start: 0.8853 (mtt) cc_final: 0.8536 (mtt) REVERT: B 384 LEU cc_start: 0.7579 (mt) cc_final: 0.7328 (mt) REVERT: B 548 ASP cc_start: 0.7300 (p0) cc_final: 0.6955 (t0) REVERT: B 561 GLU cc_start: 0.8121 (mp0) cc_final: 0.7830 (mp0) REVERT: C 219 MET cc_start: 0.8528 (mtm) cc_final: 0.8213 (mtt) REVERT: C 384 LEU cc_start: 0.7639 (mt) cc_final: 0.7383 (mt) REVERT: C 548 ASP cc_start: 0.7299 (p0) cc_final: 0.6962 (t0) REVERT: C 561 GLU cc_start: 0.8120 (mp0) cc_final: 0.7828 (mp0) REVERT: D 222 TYR cc_start: 0.8562 (m-80) cc_final: 0.8332 (m-80) REVERT: D 384 LEU cc_start: 0.7634 (mt) cc_final: 0.7378 (mt) REVERT: D 548 ASP cc_start: 0.7304 (p0) cc_final: 0.6963 (t0) REVERT: D 559 ARG cc_start: 0.7800 (mmt-90) cc_final: 0.7488 (mpp-170) REVERT: D 561 GLU cc_start: 0.8091 (mp0) cc_final: 0.7803 (mp0) outliers start: 28 outliers final: 20 residues processed: 230 average time/residue: 0.6765 time to fit residues: 172.1686 Evaluate side-chains 211 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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 160 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 131 LYS 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 D residue 21 ILE Chi-restraints excluded: chain D residue 131 LYS 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: 5.9990 chunk 64 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 67 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102675 restraints weight = 18975.071| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.93 r_work: 0.2976 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18300 Z= 0.149 Angle : 0.518 6.864 24820 Z= 0.262 Chirality : 0.044 0.198 2752 Planarity : 0.004 0.030 3196 Dihedral : 6.894 76.552 2684 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.57 % Allowed : 14.05 % 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: 1.32 (0.18), residues: 2240 helix: 1.32 (0.17), residues: 1048 sheet: 0.95 (0.36), residues: 200 loop : 0.55 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 129 TYR 0.018 0.001 TYR B 222 PHE 0.025 0.002 PHE B 471 TRP 0.005 0.001 TRP B 558 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00368 (18300) covalent geometry : angle 0.51799 (24820) hydrogen bonds : bond 0.03715 ( 796) hydrogen bonds : angle 4.42470 ( 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 232 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.628 Fit side-chains REVERT: A 219 MET cc_start: 0.8567 (mtm) cc_final: 0.8227 (mtt) REVERT: A 325 MET cc_start: 0.7775 (mtp) cc_final: 0.7522 (mtm) REVERT: A 384 LEU cc_start: 0.7706 (mt) cc_final: 0.7450 (mt) REVERT: A 548 ASP cc_start: 0.7398 (p0) cc_final: 0.7126 (t0) REVERT: A 551 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7597 (tttm) REVERT: A 559 ARG cc_start: 0.7892 (mmt-90) cc_final: 0.7591 (mpp-170) REVERT: A 561 GLU cc_start: 0.8196 (mp0) cc_final: 0.7893 (mp0) REVERT: B 75 MET cc_start: 0.7571 (mtt) cc_final: 0.6956 (mtp) REVERT: B 219 MET cc_start: 0.8894 (mtt) cc_final: 0.8562 (mtt) REVERT: B 325 MET cc_start: 0.7776 (mtp) cc_final: 0.7526 (mtm) REVERT: B 384 LEU cc_start: 0.7728 (mt) cc_final: 0.7456 (mt) REVERT: B 548 ASP cc_start: 0.7403 (p0) cc_final: 0.7037 (t0) REVERT: B 561 GLU cc_start: 0.8134 (mp0) cc_final: 0.7817 (mp0) REVERT: C 219 MET cc_start: 0.8531 (mtm) cc_final: 0.8200 (mtt) REVERT: C 325 MET cc_start: 0.7780 (mtp) cc_final: 0.7531 (mtm) REVERT: C 384 LEU cc_start: 0.7726 (mt) cc_final: 0.7460 (mt) REVERT: C 548 ASP cc_start: 0.7395 (p0) cc_final: 0.7028 (t0) REVERT: C 561 GLU cc_start: 0.8178 (mp0) cc_final: 0.7863 (mp0) REVERT: D 325 MET cc_start: 0.7781 (mtp) cc_final: 0.7531 (mtm) REVERT: D 384 LEU cc_start: 0.7730 (mt) cc_final: 0.7472 (mt) REVERT: D 548 ASP cc_start: 0.7376 (p0) cc_final: 0.7010 (t0) REVERT: D 559 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7600 (mpp-170) REVERT: D 561 GLU cc_start: 0.8192 (mp0) cc_final: 0.7888 (mp0) outliers start: 30 outliers final: 19 residues processed: 224 average time/residue: 0.5832 time to fit residues: 146.3565 Evaluate side-chains 212 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 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 160 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 131 LYS 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 D residue 21 ILE 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: 0.9990 chunk 13 optimal weight: 0.9990 chunk 173 optimal weight: 0.0870 chunk 113 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 124 optimal weight: 0.0070 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 HIS D 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.106033 restraints weight = 18826.807| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.91 r_work: 0.3014 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18300 Z= 0.100 Angle : 0.480 7.134 24820 Z= 0.242 Chirality : 0.041 0.171 2752 Planarity : 0.003 0.031 3196 Dihedral : 6.696 74.879 2684 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.62 % Allowed : 14.52 % Favored : 83.86 % 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: 1.43 (0.18), residues: 2240 helix: 1.45 (0.17), residues: 1048 sheet: 0.52 (0.32), residues: 236 loop : 0.67 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 245 TYR 0.012 0.001 TYR D 222 PHE 0.018 0.001 PHE B 471 TRP 0.005 0.001 TRP A 558 HIS 0.001 0.000 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00232 (18300) covalent geometry : angle 0.48009 (24820) hydrogen bonds : bond 0.03183 ( 796) hydrogen bonds : angle 4.25112 ( 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 257 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.729 Fit side-chains REVERT: A 219 MET cc_start: 0.8588 (mtm) cc_final: 0.8208 (mtt) REVERT: A 222 TYR cc_start: 0.8633 (m-80) cc_final: 0.8406 (m-80) REVERT: A 239 MET cc_start: 0.8499 (mmm) cc_final: 0.8228 (mmm) REVERT: A 384 LEU cc_start: 0.7672 (mt) cc_final: 0.7412 (mt) REVERT: A 551 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7580 (tttm) REVERT: A 561 GLU cc_start: 0.8133 (mp0) cc_final: 0.7904 (mp0) REVERT: B 75 MET cc_start: 0.7488 (mtt) cc_final: 0.6877 (mtp) REVERT: B 222 TYR cc_start: 0.8627 (m-80) cc_final: 0.8384 (m-80) REVERT: B 384 LEU cc_start: 0.7655 (mt) cc_final: 0.7373 (mt) REVERT: B 561 GLU cc_start: 0.8076 (mp0) cc_final: 0.7741 (mp0) REVERT: C 219 MET cc_start: 0.8512 (mtm) cc_final: 0.8195 (mtt) REVERT: C 222 TYR cc_start: 0.8631 (m-80) cc_final: 0.8393 (m-80) REVERT: C 239 MET cc_start: 0.8523 (mmm) cc_final: 0.8235 (mmm) REVERT: C 384 LEU cc_start: 0.7673 (mt) cc_final: 0.7411 (mt) REVERT: C 561 GLU cc_start: 0.8106 (mp0) cc_final: 0.7771 (mp0) REVERT: D 222 TYR cc_start: 0.8493 (m-80) cc_final: 0.8239 (m-80) REVERT: D 239 MET cc_start: 0.8519 (mmm) cc_final: 0.8234 (mmm) REVERT: D 384 LEU cc_start: 0.7669 (mt) cc_final: 0.7407 (mt) REVERT: D 561 GLU cc_start: 0.8129 (mp0) cc_final: 0.7899 (mp0) outliers start: 31 outliers final: 24 residues processed: 253 average time/residue: 0.5729 time to fit residues: 163.3705 Evaluate side-chains 231 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 429 THR Chi-restraints excluded: chain B residue 441 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 210 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102010 restraints weight = 18957.984| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.92 r_work: 0.2954 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1694 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= 0.177 Angle : 0.543 6.795 24820 Z= 0.274 Chirality : 0.045 0.199 2752 Planarity : 0.004 0.037 3196 Dihedral : 6.882 78.755 2684 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.73 % Allowed : 15.41 % Favored : 82.86 % 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: 1.27 (0.18), residues: 2240 helix: 1.36 (0.17), residues: 1048 sheet: 0.22 (0.35), residues: 192 loop : 0.58 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 559 TYR 0.020 0.002 TYR D 222 PHE 0.026 0.002 PHE B 471 TRP 0.005 0.001 TRP C 558 HIS 0.002 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00443 (18300) covalent geometry : angle 0.54311 (24820) hydrogen bonds : bond 0.03839 ( 796) hydrogen bonds : angle 4.43941 ( 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 235 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.743 Fit side-chains REVERT: A 219 MET cc_start: 0.8581 (mtm) cc_final: 0.8214 (mtt) REVERT: A 325 MET cc_start: 0.7759 (mtp) cc_final: 0.7523 (mtm) REVERT: A 384 LEU cc_start: 0.7679 (mt) cc_final: 0.7457 (mt) REVERT: A 464 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: A 561 GLU cc_start: 0.8165 (mp0) cc_final: 0.7903 (mp0) REVERT: B 75 MET cc_start: 0.7496 (mtt) cc_final: 0.6916 (mtp) REVERT: B 325 MET cc_start: 0.7772 (mtp) cc_final: 0.7528 (mtm) REVERT: B 384 LEU cc_start: 0.7677 (mt) cc_final: 0.7424 (mt) REVERT: B 464 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: B 561 GLU cc_start: 0.8121 (mp0) cc_final: 0.7797 (mp0) REVERT: C 219 MET cc_start: 0.8518 (mtm) cc_final: 0.8162 (mtt) REVERT: C 325 MET cc_start: 0.7778 (mtp) cc_final: 0.7541 (mtm) REVERT: C 384 LEU cc_start: 0.7693 (mt) cc_final: 0.7469 (mt) REVERT: C 464 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: C 561 GLU cc_start: 0.8146 (mp0) cc_final: 0.7810 (mp0) REVERT: D 325 MET cc_start: 0.7770 (mtp) cc_final: 0.7534 (mtm) REVERT: D 384 LEU cc_start: 0.7689 (mt) cc_final: 0.7468 (mt) REVERT: D 464 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: D 561 GLU cc_start: 0.8157 (mp0) cc_final: 0.7893 (mp0) outliers start: 33 outliers final: 27 residues processed: 231 average time/residue: 0.6121 time to fit residues: 158.7181 Evaluate side-chains 231 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 464 GLN 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 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 464 GLN 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 464 GLN 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 464 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 222 optimal weight: 0.0270 chunk 99 optimal weight: 0.0570 chunk 184 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 169 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107109 restraints weight = 18788.085| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.90 r_work: 0.3020 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18300 Z= 0.097 Angle : 0.485 7.167 24820 Z= 0.243 Chirality : 0.041 0.160 2752 Planarity : 0.004 0.035 3196 Dihedral : 6.562 77.188 2684 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.47 % Allowed : 15.57 % Favored : 82.97 % 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: 1.39 (0.18), residues: 2240 helix: 1.49 (0.17), residues: 1048 sheet: 0.11 (0.32), residues: 216 loop : 0.67 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 559 TYR 0.010 0.001 TYR D 222 PHE 0.014 0.001 PHE A 471 TRP 0.006 0.001 TRP A 558 HIS 0.001 0.000 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00226 (18300) covalent geometry : angle 0.48484 (24820) hydrogen bonds : bond 0.03022 ( 796) hydrogen bonds : angle 4.19938 ( 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 245 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.758 Fit side-chains REVERT: A 219 MET cc_start: 0.8478 (mtm) cc_final: 0.8132 (mtt) REVERT: A 222 TYR cc_start: 0.8536 (m-80) cc_final: 0.8267 (m-80) REVERT: A 347 TYR cc_start: 0.7661 (m-10) cc_final: 0.7259 (m-80) REVERT: A 384 LEU cc_start: 0.7561 (mt) cc_final: 0.7322 (mt) REVERT: A 464 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: A 561 GLU cc_start: 0.8069 (mp0) cc_final: 0.7827 (mp0) REVERT: B 75 MET cc_start: 0.7327 (mtt) cc_final: 0.6837 (mtp) REVERT: B 219 MET cc_start: 0.8827 (mtt) cc_final: 0.8497 (mtt) REVERT: B 222 TYR cc_start: 0.8539 (m-80) cc_final: 0.8236 (m-80) REVERT: B 347 TYR cc_start: 0.7665 (m-10) cc_final: 0.7263 (m-80) REVERT: B 384 LEU cc_start: 0.7520 (mt) cc_final: 0.7301 (mt) REVERT: B 464 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: B 561 GLU cc_start: 0.7956 (mp0) cc_final: 0.7522 (mp0) REVERT: C 219 MET cc_start: 0.8443 (mtm) cc_final: 0.8076 (mtt) REVERT: C 222 TYR cc_start: 0.8547 (m-80) cc_final: 0.8276 (m-80) REVERT: C 347 TYR cc_start: 0.7666 (m-10) cc_final: 0.7267 (m-80) REVERT: C 384 LEU cc_start: 0.7579 (mt) cc_final: 0.7336 (mt) REVERT: C 464 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: C 561 GLU cc_start: 0.7977 (mp0) cc_final: 0.7545 (mp0) REVERT: D 219 MET cc_start: 0.8807 (mtt) cc_final: 0.8488 (mtt) REVERT: D 222 TYR cc_start: 0.8453 (m-80) cc_final: 0.8199 (m-80) REVERT: D 347 TYR cc_start: 0.7663 (m-10) cc_final: 0.7263 (m-80) REVERT: D 384 LEU cc_start: 0.7572 (mt) cc_final: 0.7334 (mt) REVERT: D 464 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: D 561 GLU cc_start: 0.8038 (mp0) cc_final: 0.7798 (mp0) outliers start: 28 outliers final: 24 residues processed: 241 average time/residue: 0.6148 time to fit residues: 166.6007 Evaluate side-chains 233 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 464 GLN 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 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 464 GLN 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 464 GLN 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 464 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 137 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN D 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.140046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102790 restraints weight = 19026.402| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.92 r_work: 0.2974 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18300 Z= 0.162 Angle : 0.541 7.867 24820 Z= 0.271 Chirality : 0.045 0.198 2752 Planarity : 0.004 0.039 3196 Dihedral : 6.754 82.166 2684 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.62 % Allowed : 15.57 % Favored : 82.81 % 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: 1.32 (0.18), residues: 2240 helix: 1.40 (0.17), residues: 1072 sheet: -0.02 (0.32), residues: 216 loop : 0.67 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 559 TYR 0.017 0.001 TYR D 222 PHE 0.025 0.002 PHE C 471 TRP 0.005 0.001 TRP C 558 HIS 0.002 0.001 HIS D 260 Details of bonding type rmsd covalent geometry : bond 0.00404 (18300) covalent geometry : angle 0.54065 (24820) hydrogen bonds : bond 0.03691 ( 796) hydrogen bonds : angle 4.38442 ( 2280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5767.32 seconds wall clock time: 99 minutes 11.92 seconds (5951.92 seconds total)