Starting phenix.real_space_refine on Tue Mar 3 21:45:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x9y_33085/03_2026/7x9y_33085.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x9y_33085/03_2026/7x9y_33085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x9y_33085/03_2026/7x9y_33085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x9y_33085/03_2026/7x9y_33085.map" model { file = "/net/cci-nas-00/data/ceres_data/7x9y_33085/03_2026/7x9y_33085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x9y_33085/03_2026/7x9y_33085.cif" } resolution = 3.1 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5744 2.51 5 N 1523 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 8982 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2412 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain: "S" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1763 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Time building chain proxies: 2.22, per 1000 atoms: 0.25 Number of scatterers: 8982 At special positions: 0 Unit cell: (103.265, 130.44, 119.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1649 8.00 N 1523 7.00 C 5744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 260.9 milliseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 40.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 Processing helix chain 'A' and resid 51 through 438 removed outlier: 3.523A pdb=" N ILE A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 624 removed outlier: 4.263A pdb=" N ILE A 620 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N HIS A 621 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 639 removed outlier: 4.098A pdb=" N ASP A 639 " --> pdb=" O SER A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 639' Processing helix chain 'A' and resid 649 through 663 Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.991A pdb=" N LYS A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 703 through 718 removed outlier: 3.655A pdb=" N ALA A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 759 removed outlier: 3.672A pdb=" N PHE A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.627A pdb=" N CYS B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 removed outlier: 3.695A pdb=" N ILE B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'G' and resid 10 through 29 removed outlier: 3.944A pdb=" N ILE G 29 " --> pdb=" O MET G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 48 Processing helix chain 'G' and resid 49 through 52 removed outlier: 3.585A pdb=" N ASP G 52 " --> pdb=" O ALA G 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 49 through 52' Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.613A pdb=" N SER R 42 " --> pdb=" O PRO R 38 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU R 43 " --> pdb=" O PRO R 39 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 105 through 137 removed outlier: 3.637A pdb=" N TYR R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS R 114 " --> pdb=" O SER R 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.018A pdb=" N ARG R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 165 Processing helix chain 'R' and resid 165 through 170 Processing helix chain 'R' and resid 188 through 194 removed outlier: 3.508A pdb=" N VAL R 192 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR R 193 " --> pdb=" O ASP R 190 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER R 194 " --> pdb=" O THR R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 201 Processing helix chain 'R' and resid 201 through 206 removed outlier: 3.692A pdb=" N PHE R 206 " --> pdb=" O ARG R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 227 removed outlier: 3.892A pdb=" N GLY R 221 " --> pdb=" O ILE R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 264 removed outlier: 3.673A pdb=" N ALA R 237 " --> pdb=" O LYS R 233 " (cutoff:3.500A) Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 264 through 269 Processing helix chain 'R' and resid 272 through 292 Processing helix chain 'R' and resid 292 through 335 removed outlier: 3.590A pdb=" N MET R 296 " --> pdb=" O SER R 292 " (cutoff:3.500A) Proline residue: R 330 - end of helix Processing helix chain 'R' and resid 337 through 355 removed outlier: 3.746A pdb=" N ARG R 341 " --> pdb=" O GLY R 337 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.529A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 232 through 236 removed outlier: 3.831A pdb=" N VAL S 236 " --> pdb=" O ALA S 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 593 through 599 removed outlier: 6.985A pdb=" N LYS A 41 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE A 630 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU A 43 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N CYS A 632 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 45 " --> pdb=" O CYS A 632 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ALA A 634 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE A 629 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE A 675 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE A 631 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASN A 677 " --> pdb=" O PHE A 631 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 633 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 672 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N HIS A 730 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU A 674 " --> pdb=" O HIS A 730 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57 removed outlier: 6.441A pdb=" N THR B 53 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASN B 346 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 55 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 323 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 69 removed outlier: 3.749A pdb=" N ALA B 66 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 80 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 85 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 98 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 87 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 106 through 111 removed outlier: 6.928A pdb=" N GLY B 121 " --> pdb=" O MET B 107 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS B 109 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 119 " --> pdb=" O CYS B 109 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR B 111 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N TYR B 117 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE B 129 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 140 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 158 removed outlier: 3.706A pdb=" N GLN B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B 163 " --> pdb=" O TRP B 175 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS B 172 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR B 185 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 174 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 181 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 198 removed outlier: 6.865A pdb=" N GLY B 208 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 196 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL B 206 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 198 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU B 204 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 209 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 226 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 218 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS B 224 " --> pdb=" O ASP B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 235 through 240 removed outlier: 3.804A pdb=" N ALA B 237 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET B 268 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP B 260 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU B 266 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 279 through 284 removed outlier: 4.085A pdb=" N SER B 281 " --> pdb=" O GLY B 294 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 312 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.715A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.630A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 152 through 154 removed outlier: 3.552A pdb=" N VAL S 167 " --> pdb=" O ILE S 228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 158 through 160 removed outlier: 3.573A pdb=" N GLU S 258 " --> pdb=" O VAL S 159 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL S 238 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU S 186 " --> pdb=" O TYR S 202 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR S 202 " --> pdb=" O LEU S 186 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TRP S 188 " --> pdb=" O LEU S 200 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1482 1.32 - 1.45: 2551 1.45 - 1.57: 5050 1.57 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 9180 Sorted by residual: bond pdb=" CA LEU B 196 " pdb=" C LEU B 196 " ideal model delta sigma weight residual 1.524 1.455 0.069 1.23e-02 6.61e+03 3.13e+01 bond pdb=" CA LEU B 196 " pdb=" CB LEU B 196 " ideal model delta sigma weight residual 1.533 1.471 0.062 1.51e-02 4.39e+03 1.69e+01 bond pdb=" C SER B 197 " pdb=" O SER B 197 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.25e-02 6.40e+03 9.74e+00 bond pdb=" CA SER B 197 " pdb=" CB SER B 197 " ideal model delta sigma weight residual 1.533 1.478 0.056 1.89e-02 2.80e+03 8.64e+00 bond pdb=" N LEU B 196 " pdb=" CA LEU B 196 " ideal model delta sigma weight residual 1.455 1.425 0.030 1.25e-02 6.40e+03 5.69e+00 ... (remaining 9175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12321 1.94 - 3.89: 90 3.89 - 5.83: 14 5.83 - 7.78: 1 7.78 - 9.72: 3 Bond angle restraints: 12429 Sorted by residual: angle pdb=" N SER B 195 " pdb=" CA SER B 195 " pdb=" C SER B 195 " ideal model delta sigma weight residual 109.24 118.96 -9.72 1.67e+00 3.59e-01 3.39e+01 angle pdb=" C LEU B 196 " pdb=" CA LEU B 196 " pdb=" CB LEU B 196 " ideal model delta sigma weight residual 110.36 100.98 9.38 1.78e+00 3.16e-01 2.78e+01 angle pdb=" N VAL R 136 " pdb=" CA VAL R 136 " pdb=" C VAL R 136 " ideal model delta sigma weight residual 112.96 109.69 3.27 1.00e+00 1.00e+00 1.07e+01 angle pdb=" CA SER B 197 " pdb=" C SER B 197 " pdb=" N LEU B 198 " ideal model delta sigma weight residual 116.38 120.61 -4.23 1.35e+00 5.49e-01 9.82e+00 angle pdb=" C SER B 197 " pdb=" N LEU B 198 " pdb=" CA LEU B 198 " ideal model delta sigma weight residual 122.64 118.09 4.55 1.70e+00 3.46e-01 7.18e+00 ... (remaining 12424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 4939 16.62 - 33.25: 381 33.25 - 49.87: 76 49.87 - 66.50: 18 66.50 - 83.12: 4 Dihedral angle restraints: 5418 sinusoidal: 2113 harmonic: 3305 Sorted by residual: dihedral pdb=" C LEU B 196 " pdb=" N LEU B 196 " pdb=" CA LEU B 196 " pdb=" CB LEU B 196 " ideal model delta harmonic sigma weight residual -122.60 -109.01 -13.59 0 2.50e+00 1.60e-01 2.96e+01 dihedral pdb=" CA TYR S 202 " pdb=" C TYR S 202 " pdb=" N ARG S 203 " pdb=" CA ARG S 203 " ideal model delta harmonic sigma weight residual 180.00 162.22 17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG S 203 " pdb=" C ARG S 203 " pdb=" N MET S 204 " pdb=" CA MET S 204 " ideal model delta harmonic sigma weight residual 180.00 162.55 17.45 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 875 0.027 - 0.055: 347 0.055 - 0.082: 98 0.082 - 0.110: 54 0.110 - 0.137: 32 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA MET B 268 " pdb=" N MET B 268 " pdb=" C MET B 268 " pdb=" CB MET B 268 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA VAL S 2 " pdb=" N VAL S 2 " pdb=" C VAL S 2 " pdb=" CB VAL S 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1403 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 162 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO S 163 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO S 163 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 163 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 38 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO R 39 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 39 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 39 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 58 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO G 59 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 59 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 59 " -0.021 5.00e-02 4.00e+02 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 41 2.53 - 3.12: 6946 3.12 - 3.71: 13456 3.71 - 4.31: 18599 4.31 - 4.90: 32006 Nonbonded interactions: 71048 Sorted by model distance: nonbonded pdb=" O LYS S 43 " pdb=" OH TYR S 240 " model vdw 1.932 3.040 nonbonded pdb=" O SER R 231 " pdb=" NZ LYS R 234 " model vdw 2.124 3.120 nonbonded pdb=" OG SER R 79 " pdb=" OG SER R 119 " model vdw 2.147 3.040 nonbonded pdb=" OG SER B 285 " pdb=" OD2 ASP G 52 " model vdw 2.163 3.040 nonbonded pdb=" O THR S 63 " pdb=" NH2 ARG S 67 " model vdw 2.177 3.120 ... (remaining 71043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 : 0.003 0.069 9180 Z= 0.155 Angle : 0.487 9.721 12429 Z= 0.277 Chirality : 0.038 0.137 1406 Planarity : 0.003 0.054 1561 Dihedral : 12.624 83.122 3288 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.31 % Allowed : 0.31 % Favored : 99.39 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.33 % 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: 2.03 (0.27), residues: 1121 helix: 2.91 (0.28), residues: 374 sheet: 1.42 (0.32), residues: 277 loop : 0.01 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 87 TYR 0.012 0.001 TYR A 704 PHE 0.010 0.001 PHE R 340 TRP 0.009 0.001 TRP R 99 HIS 0.003 0.000 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9180) covalent geometry : angle 0.48715 (12429) hydrogen bonds : bond 0.17806 ( 426) hydrogen bonds : angle 6.21777 ( 1197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 324 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7715 (mttm) cc_final: 0.7492 (ttmm) REVERT: A 599 PHE cc_start: 0.8221 (t80) cc_final: 0.7978 (t80) REVERT: A 712 GLN cc_start: 0.7735 (tm130) cc_final: 0.7011 (tm-30) REVERT: A 714 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7372 (tp-100) REVERT: A 717 ASP cc_start: 0.7243 (m-30) cc_final: 0.6700 (m-30) REVERT: A 757 LYS cc_start: 0.8275 (mttp) cc_final: 0.7937 (mttp) REVERT: B 18 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8308 (mm-30) REVERT: B 52 ARG cc_start: 0.7119 (mpt90) cc_final: 0.6806 (mpt90) REVERT: B 124 ASP cc_start: 0.6833 (p0) cc_final: 0.6378 (p0) REVERT: B 143 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7613 (mmm-85) REVERT: B 154 CYS cc_start: 0.7211 (t) cc_final: 0.6865 (t) REVERT: B 234 ASP cc_start: 0.7114 (m-30) cc_final: 0.6653 (m-30) REVERT: B 297 ASP cc_start: 0.6717 (t0) cc_final: 0.6122 (t0) REVERT: B 331 MET cc_start: 0.7178 (tpp) cc_final: 0.6945 (tpp) REVERT: G 25 MET cc_start: 0.7534 (tpp) cc_final: 0.7062 (tpp) REVERT: R 70 ASN cc_start: 0.7397 (m110) cc_final: 0.7194 (m110) REVERT: R 84 LEU cc_start: 0.7609 (pp) cc_final: 0.7406 (pp) REVERT: R 152 ILE cc_start: 0.8093 (mt) cc_final: 0.7854 (mt) REVERT: R 203 MET cc_start: 0.4847 (mtp) cc_final: 0.4250 (mtp) REVERT: R 279 LEU cc_start: 0.8381 (tp) cc_final: 0.8162 (tp) REVERT: R 284 LEU cc_start: 0.7741 (mp) cc_final: 0.7398 (mp) REVERT: S 13 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8038 (mm-40) outliers start: 3 outliers final: 1 residues processed: 324 average time/residue: 0.1135 time to fit residues: 48.0376 Evaluate side-chains 310 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.0370 chunk 106 optimal weight: 6.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 HIS R 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.125965 restraints weight = 14007.579| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.72 r_work: 0.3578 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9180 Z= 0.135 Angle : 0.554 7.639 12429 Z= 0.292 Chirality : 0.043 0.196 1406 Planarity : 0.004 0.053 1561 Dihedral : 4.063 43.372 1238 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.53 % Allowed : 10.71 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.66 (0.26), residues: 1121 helix: 2.31 (0.27), residues: 392 sheet: 1.41 (0.31), residues: 285 loop : -0.19 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 225 TYR 0.013 0.001 TYR R 219 PHE 0.026 0.002 PHE R 348 TRP 0.021 0.002 TRP R 99 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9180) covalent geometry : angle 0.55379 (12429) hydrogen bonds : bond 0.04171 ( 426) hydrogen bonds : angle 4.61140 ( 1197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 303 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 597 PHE cc_start: 0.8221 (p90) cc_final: 0.7985 (p90) REVERT: A 599 PHE cc_start: 0.8304 (t80) cc_final: 0.8008 (t80) REVERT: A 714 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7900 (tp-100) REVERT: A 716 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 720 LYS cc_start: 0.8335 (mmtp) cc_final: 0.8133 (mmtm) REVERT: A 749 ASP cc_start: 0.8219 (t0) cc_final: 0.7861 (t0) REVERT: B 18 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8359 (mm-30) REVERT: B 25 ARG cc_start: 0.8710 (ttp80) cc_final: 0.8199 (ttp80) REVERT: B 52 ARG cc_start: 0.7988 (mpt90) cc_final: 0.7564 (mpt90) REVERT: B 124 ASP cc_start: 0.7377 (p0) cc_final: 0.6979 (p0) REVERT: B 126 ILE cc_start: 0.8153 (mm) cc_final: 0.7670 (mm) REVERT: B 154 CYS cc_start: 0.8266 (t) cc_final: 0.7970 (t) REVERT: B 218 ASP cc_start: 0.7301 (t0) cc_final: 0.7047 (t70) REVERT: B 234 ASP cc_start: 0.7552 (m-30) cc_final: 0.7113 (m-30) REVERT: B 260 ASP cc_start: 0.7320 (t70) cc_final: 0.7092 (t70) REVERT: B 304 ASP cc_start: 0.8003 (t0) cc_final: 0.7791 (t0) REVERT: B 318 ASP cc_start: 0.7662 (m-30) cc_final: 0.7449 (t0) REVERT: B 331 MET cc_start: 0.7902 (tpp) cc_final: 0.7552 (ttt) REVERT: G 25 MET cc_start: 0.7794 (tpp) cc_final: 0.7234 (tpp) REVERT: R 151 VAL cc_start: 0.8304 (t) cc_final: 0.8086 (m) REVERT: R 152 ILE cc_start: 0.8329 (mt) cc_final: 0.8067 (mt) REVERT: R 203 MET cc_start: 0.5122 (mtp) cc_final: 0.4514 (mtp) REVERT: R 245 MET cc_start: 0.8002 (ttp) cc_final: 0.7757 (ttp) REVERT: R 251 PHE cc_start: 0.7310 (m-10) cc_final: 0.7068 (m-10) REVERT: R 279 LEU cc_start: 0.8598 (tp) cc_final: 0.8377 (tp) REVERT: S 13 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8088 (mm-40) REVERT: S 240 TYR cc_start: 0.7944 (m-80) cc_final: 0.7105 (m-80) outliers start: 15 outliers final: 12 residues processed: 307 average time/residue: 0.1051 time to fit residues: 43.0575 Evaluate side-chains 301 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 289 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 113 TYR Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 216 SER Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 255 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 226 GLN S 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.142974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120306 restraints weight = 13912.642| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.66 r_work: 0.3482 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9180 Z= 0.213 Angle : 0.595 8.270 12429 Z= 0.313 Chirality : 0.045 0.272 1406 Planarity : 0.005 0.060 1561 Dihedral : 4.175 21.275 1236 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.27 % Allowed : 12.76 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.26), residues: 1121 helix: 1.94 (0.26), residues: 393 sheet: 1.32 (0.31), residues: 275 loop : -0.41 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 350 TYR 0.015 0.002 TYR B 111 PHE 0.022 0.002 PHE B 186 TRP 0.014 0.002 TRP B 88 HIS 0.008 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 9180) covalent geometry : angle 0.59521 (12429) hydrogen bonds : bond 0.04323 ( 426) hydrogen bonds : angle 4.52362 ( 1197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 315 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8304 (t80) cc_final: 0.7956 (t80) REVERT: A 684 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 705 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 716 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 720 LYS cc_start: 0.8476 (mmtp) cc_final: 0.8212 (mttp) REVERT: A 749 ASP cc_start: 0.8318 (t0) cc_final: 0.7869 (t0) REVERT: B 18 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8389 (mm-30) REVERT: B 19 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7700 (pp30) REVERT: B 48 ARG cc_start: 0.7783 (ttm-80) cc_final: 0.7347 (ttm-80) REVERT: B 52 ARG cc_start: 0.7977 (mpt90) cc_final: 0.7737 (mpt180) REVERT: B 82 ASP cc_start: 0.7659 (m-30) cc_final: 0.7448 (m-30) REVERT: B 84 LYS cc_start: 0.8336 (mtpp) cc_final: 0.8097 (mttp) REVERT: B 92 THR cc_start: 0.8579 (p) cc_final: 0.8019 (m) REVERT: B 124 ASP cc_start: 0.7474 (p0) cc_final: 0.7082 (p0) REVERT: B 126 ILE cc_start: 0.8230 (mm) cc_final: 0.7787 (mm) REVERT: B 234 ASP cc_start: 0.7568 (m-30) cc_final: 0.7053 (m-30) REVERT: B 235 ILE cc_start: 0.8039 (mm) cc_final: 0.7837 (mt) REVERT: B 260 ASP cc_start: 0.7471 (t70) cc_final: 0.7202 (t70) REVERT: B 285 SER cc_start: 0.7971 (t) cc_final: 0.7737 (t) REVERT: B 304 ASP cc_start: 0.8067 (t0) cc_final: 0.7700 (t0) REVERT: G 25 MET cc_start: 0.7818 (tpp) cc_final: 0.7266 (tpp) REVERT: R 151 VAL cc_start: 0.8318 (t) cc_final: 0.8106 (m) REVERT: R 152 ILE cc_start: 0.8375 (mt) cc_final: 0.8124 (mt) REVERT: R 203 MET cc_start: 0.5162 (mtp) cc_final: 0.4579 (mtp) REVERT: R 279 LEU cc_start: 0.8612 (tp) cc_final: 0.8371 (tp) REVERT: S 20 LEU cc_start: 0.8623 (mt) cc_final: 0.8388 (mt) REVERT: S 29 PHE cc_start: 0.8070 (t80) cc_final: 0.7574 (t80) REVERT: S 105 SER cc_start: 0.8358 (t) cc_final: 0.8156 (p) REVERT: S 240 TYR cc_start: 0.8142 (m-80) cc_final: 0.7272 (m-80) outliers start: 32 outliers final: 23 residues processed: 322 average time/residue: 0.0950 time to fit residues: 41.7711 Evaluate side-chains 327 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 303 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 90 TRP Chi-restraints excluded: chain R residue 113 TYR Chi-restraints excluded: chain R residue 239 ARG Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 216 SER Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 227 THR Chi-restraints excluded: chain S residue 255 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN R 278 HIS S 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.142830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120010 restraints weight = 14077.123| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.73 r_work: 0.3472 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9180 Z= 0.193 Angle : 0.589 8.215 12429 Z= 0.306 Chirality : 0.044 0.279 1406 Planarity : 0.005 0.061 1561 Dihedral : 4.238 21.321 1236 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.08 % Allowed : 15.51 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.24 (0.26), residues: 1121 helix: 2.01 (0.26), residues: 387 sheet: 1.08 (0.30), residues: 287 loop : -0.38 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 135 TYR 0.012 0.002 TYR S 50 PHE 0.037 0.002 PHE A 597 TRP 0.012 0.002 TRP B 345 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9180) covalent geometry : angle 0.58866 (12429) hydrogen bonds : bond 0.04039 ( 426) hydrogen bonds : angle 4.47338 ( 1197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 309 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8315 (t80) cc_final: 0.7920 (t80) REVERT: A 661 ILE cc_start: 0.8455 (pt) cc_final: 0.8231 (pt) REVERT: A 680 ASP cc_start: 0.8531 (p0) cc_final: 0.8276 (p0) REVERT: A 684 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 705 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 716 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7786 (mt-10) REVERT: A 717 ASP cc_start: 0.8155 (t0) cc_final: 0.7785 (t0) REVERT: A 720 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8218 (mttp) REVERT: A 749 ASP cc_start: 0.8319 (t0) cc_final: 0.7797 (t0) REVERT: B 18 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 19 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7723 (pp30) REVERT: B 48 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7279 (ttm-80) REVERT: B 52 ARG cc_start: 0.7990 (mpt90) cc_final: 0.7760 (mpt180) REVERT: B 84 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8048 (mttp) REVERT: B 92 THR cc_start: 0.8619 (p) cc_final: 0.7978 (m) REVERT: B 124 ASP cc_start: 0.7485 (p0) cc_final: 0.7083 (p0) REVERT: B 218 ASP cc_start: 0.7375 (t70) cc_final: 0.6842 (p0) REVERT: B 234 ASP cc_start: 0.7507 (m-30) cc_final: 0.7075 (m-30) REVERT: B 260 ASP cc_start: 0.7475 (t70) cc_final: 0.7212 (t70) REVERT: B 275 ILE cc_start: 0.8115 (mt) cc_final: 0.7791 (tp) REVERT: B 285 SER cc_start: 0.7951 (t) cc_final: 0.7717 (t) REVERT: B 304 ASP cc_start: 0.8082 (t0) cc_final: 0.7778 (t0) REVERT: G 25 MET cc_start: 0.7842 (tpp) cc_final: 0.7285 (tpp) REVERT: R 151 VAL cc_start: 0.8330 (t) cc_final: 0.8120 (m) REVERT: R 152 ILE cc_start: 0.8338 (mt) cc_final: 0.8088 (mt) REVERT: R 203 MET cc_start: 0.5072 (mtp) cc_final: 0.4517 (mtp) REVERT: R 219 TYR cc_start: 0.8322 (m-10) cc_final: 0.7997 (m-80) REVERT: R 279 LEU cc_start: 0.8567 (tp) cc_final: 0.8335 (tp) REVERT: S 20 LEU cc_start: 0.8673 (mt) cc_final: 0.8394 (mt) REVERT: S 87 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7109 (mtm-85) REVERT: S 105 SER cc_start: 0.8434 (t) cc_final: 0.8232 (p) REVERT: S 240 TYR cc_start: 0.8119 (m-80) cc_final: 0.7692 (m-80) REVERT: S 257 LEU cc_start: 0.7636 (mm) cc_final: 0.7431 (mt) outliers start: 40 outliers final: 29 residues processed: 322 average time/residue: 0.0997 time to fit residues: 43.3489 Evaluate side-chains 328 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 90 TRP Chi-restraints excluded: chain R residue 113 TYR Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 216 SER Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 225 THR Chi-restraints excluded: chain S residue 227 THR Chi-restraints excluded: chain S residue 255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.0770 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN S 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.144781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.122028 restraints weight = 13918.984| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.70 r_work: 0.3507 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9180 Z= 0.118 Angle : 0.552 7.684 12429 Z= 0.285 Chirality : 0.043 0.314 1406 Planarity : 0.004 0.057 1561 Dihedral : 4.134 21.658 1236 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.67 % Allowed : 17.35 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.36 (0.26), residues: 1121 helix: 2.15 (0.27), residues: 387 sheet: 1.06 (0.30), residues: 287 loop : -0.30 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 135 TYR 0.008 0.001 TYR S 94 PHE 0.040 0.001 PHE A 597 TRP 0.015 0.001 TRP R 252 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9180) covalent geometry : angle 0.55209 (12429) hydrogen bonds : bond 0.03571 ( 426) hydrogen bonds : angle 4.30647 ( 1197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 295 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8254 (t80) cc_final: 0.7858 (t80) REVERT: A 656 LYS cc_start: 0.8514 (tttm) cc_final: 0.8131 (ttmm) REVERT: A 661 ILE cc_start: 0.8457 (pt) cc_final: 0.8211 (pt) REVERT: A 680 ASP cc_start: 0.8499 (p0) cc_final: 0.8257 (p0) REVERT: A 684 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7839 (mm-30) REVERT: A 705 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 717 ASP cc_start: 0.8124 (t0) cc_final: 0.7727 (t0) REVERT: A 720 LYS cc_start: 0.8487 (mmtp) cc_final: 0.8186 (mttp) REVERT: A 749 ASP cc_start: 0.8350 (t0) cc_final: 0.7812 (t0) REVERT: B 18 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8422 (mm-30) REVERT: B 19 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7698 (pp30) REVERT: B 25 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8348 (ttp80) REVERT: B 48 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7264 (ttm-80) REVERT: B 52 ARG cc_start: 0.7957 (mpt90) cc_final: 0.7709 (mpt180) REVERT: B 84 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7892 (mttp) REVERT: B 92 THR cc_start: 0.8540 (p) cc_final: 0.7811 (m) REVERT: B 124 ASP cc_start: 0.7442 (p0) cc_final: 0.7010 (p0) REVERT: B 197 SER cc_start: 0.8141 (t) cc_final: 0.7478 (p) REVERT: B 218 ASP cc_start: 0.6949 (t70) cc_final: 0.6485 (p0) REVERT: B 234 ASP cc_start: 0.7413 (m-30) cc_final: 0.6920 (m-30) REVERT: B 260 ASP cc_start: 0.7504 (t70) cc_final: 0.7259 (t70) REVERT: B 275 ILE cc_start: 0.8177 (mt) cc_final: 0.7791 (tp) REVERT: B 285 SER cc_start: 0.7948 (t) cc_final: 0.7680 (t) REVERT: B 304 ASP cc_start: 0.8043 (t0) cc_final: 0.7724 (t70) REVERT: G 25 MET cc_start: 0.7848 (tpp) cc_final: 0.7291 (tpp) REVERT: G 41 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8557 (mp) REVERT: R 151 VAL cc_start: 0.8297 (t) cc_final: 0.8079 (m) REVERT: R 152 ILE cc_start: 0.8292 (mt) cc_final: 0.8036 (mt) REVERT: R 203 MET cc_start: 0.5093 (mtp) cc_final: 0.4545 (mtp) REVERT: R 219 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.8072 (m-10) REVERT: R 279 LEU cc_start: 0.8580 (tp) cc_final: 0.8319 (tp) REVERT: R 341 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7666 (mtp85) REVERT: S 20 LEU cc_start: 0.8644 (mt) cc_final: 0.8361 (mt) REVERT: S 224 PHE cc_start: 0.7647 (m-10) cc_final: 0.6995 (m-10) REVERT: S 240 TYR cc_start: 0.8090 (m-80) cc_final: 0.7621 (m-80) outliers start: 36 outliers final: 23 residues processed: 308 average time/residue: 0.0962 time to fit residues: 40.1861 Evaluate side-chains 311 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain R residue 90 TRP Chi-restraints excluded: chain R residue 113 TYR Chi-restraints excluded: chain R residue 219 TYR Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 216 SER Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 255 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.144239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121558 restraints weight = 13877.285| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.68 r_work: 0.3498 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9180 Z= 0.135 Angle : 0.565 7.734 12429 Z= 0.290 Chirality : 0.043 0.252 1406 Planarity : 0.004 0.059 1561 Dihedral : 4.128 20.109 1236 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.57 % Allowed : 18.67 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.35 (0.26), residues: 1121 helix: 2.16 (0.26), residues: 387 sheet: 1.04 (0.30), residues: 287 loop : -0.31 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 135 TYR 0.014 0.001 TYR R 93 PHE 0.031 0.002 PHE A 597 TRP 0.010 0.001 TRP B 345 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9180) covalent geometry : angle 0.56451 (12429) hydrogen bonds : bond 0.03609 ( 426) hydrogen bonds : angle 4.28493 ( 1197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8254 (t80) cc_final: 0.7819 (t80) REVERT: A 656 LYS cc_start: 0.8574 (tttm) cc_final: 0.8190 (ttmm) REVERT: A 661 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8174 (pt) REVERT: A 680 ASP cc_start: 0.8484 (p0) cc_final: 0.8237 (p0) REVERT: A 684 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 705 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7775 (mm-30) REVERT: A 716 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7852 (mt-10) REVERT: A 717 ASP cc_start: 0.8117 (t0) cc_final: 0.7751 (t0) REVERT: A 720 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8221 (mttp) REVERT: A 749 ASP cc_start: 0.8322 (t0) cc_final: 0.7797 (t0) REVERT: B 18 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8424 (mm-30) REVERT: B 19 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7694 (pp30) REVERT: B 25 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8353 (ttp80) REVERT: B 48 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7294 (ttm-80) REVERT: B 52 ARG cc_start: 0.7953 (mpt90) cc_final: 0.7687 (mpt180) REVERT: B 84 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7928 (mttp) REVERT: B 92 THR cc_start: 0.8566 (p) cc_final: 0.7804 (m) REVERT: B 111 TYR cc_start: 0.8267 (t80) cc_final: 0.7796 (t80) REVERT: B 124 ASP cc_start: 0.7464 (p0) cc_final: 0.7074 (p0) REVERT: B 126 ILE cc_start: 0.8246 (mm) cc_final: 0.7667 (mt) REVERT: B 197 SER cc_start: 0.8161 (t) cc_final: 0.7498 (p) REVERT: B 218 ASP cc_start: 0.6971 (t70) cc_final: 0.6516 (p0) REVERT: B 234 ASP cc_start: 0.7403 (m-30) cc_final: 0.6904 (m-30) REVERT: B 260 ASP cc_start: 0.7532 (t70) cc_final: 0.7291 (t70) REVERT: B 275 ILE cc_start: 0.8224 (mt) cc_final: 0.7804 (tp) REVERT: B 285 SER cc_start: 0.8031 (t) cc_final: 0.7765 (t) REVERT: B 304 ASP cc_start: 0.8029 (t0) cc_final: 0.7764 (t0) REVERT: G 25 MET cc_start: 0.7818 (tpp) cc_final: 0.7284 (tpp) REVERT: G 41 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8566 (mp) REVERT: R 151 VAL cc_start: 0.8308 (t) cc_final: 0.8095 (m) REVERT: R 152 ILE cc_start: 0.8324 (mt) cc_final: 0.8070 (mt) REVERT: R 203 MET cc_start: 0.5140 (mtp) cc_final: 0.4586 (mtp) REVERT: R 219 TYR cc_start: 0.8337 (m-10) cc_final: 0.8000 (m-80) REVERT: R 279 LEU cc_start: 0.8599 (tp) cc_final: 0.8343 (tp) REVERT: R 341 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7660 (mtp85) REVERT: S 20 LEU cc_start: 0.8670 (mt) cc_final: 0.8388 (mt) REVERT: S 25 SER cc_start: 0.8276 (p) cc_final: 0.8033 (p) REVERT: S 29 PHE cc_start: 0.8598 (t80) cc_final: 0.8299 (t80) REVERT: S 168 SER cc_start: 0.7938 (m) cc_final: 0.7661 (t) REVERT: S 240 TYR cc_start: 0.8122 (m-80) cc_final: 0.7566 (m-80) outliers start: 35 outliers final: 24 residues processed: 315 average time/residue: 0.0947 time to fit residues: 40.5324 Evaluate side-chains 321 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 292 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain R residue 113 TYR Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 216 SER Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 227 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 14 optimal weight: 0.0270 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 102 optimal weight: 0.0980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN S 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.145901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123154 restraints weight = 13926.662| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.70 r_work: 0.3521 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9180 Z= 0.111 Angle : 0.545 7.516 12429 Z= 0.280 Chirality : 0.042 0.222 1406 Planarity : 0.004 0.057 1561 Dihedral : 4.027 19.152 1236 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.37 % Allowed : 19.80 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.37 (0.26), residues: 1121 helix: 2.23 (0.26), residues: 387 sheet: 1.02 (0.30), residues: 288 loop : -0.32 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 38 TYR 0.012 0.001 TYR R 93 PHE 0.027 0.001 PHE A 597 TRP 0.012 0.001 TRP R 252 HIS 0.002 0.000 HIS R 114 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9180) covalent geometry : angle 0.54516 (12429) hydrogen bonds : bond 0.03393 ( 426) hydrogen bonds : angle 4.20597 ( 1197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 297 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6482 (tm-30) REVERT: A 599 PHE cc_start: 0.8243 (t80) cc_final: 0.7799 (t80) REVERT: A 618 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8796 (tppt) REVERT: A 656 LYS cc_start: 0.8557 (tttm) cc_final: 0.8170 (ttmm) REVERT: A 661 ILE cc_start: 0.8350 (pt) cc_final: 0.8081 (pt) REVERT: A 680 ASP cc_start: 0.8473 (p0) cc_final: 0.8229 (p0) REVERT: A 684 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7815 (mm-30) REVERT: A 705 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 716 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7816 (mt-10) REVERT: A 717 ASP cc_start: 0.8099 (t0) cc_final: 0.7747 (t0) REVERT: A 720 LYS cc_start: 0.8474 (mmtp) cc_final: 0.8197 (mttp) REVERT: A 749 ASP cc_start: 0.8285 (t0) cc_final: 0.7744 (t0) REVERT: B 18 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 19 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7673 (pp30) REVERT: B 25 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8352 (ttp80) REVERT: B 48 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7276 (ttm-80) REVERT: B 52 ARG cc_start: 0.7967 (mpt90) cc_final: 0.7705 (mpt180) REVERT: B 84 LYS cc_start: 0.8148 (mtpp) cc_final: 0.7923 (mttp) REVERT: B 92 THR cc_start: 0.8485 (p) cc_final: 0.7680 (m) REVERT: B 124 ASP cc_start: 0.7476 (p0) cc_final: 0.7085 (p0) REVERT: B 126 ILE cc_start: 0.8268 (mm) cc_final: 0.7693 (mt) REVERT: B 197 SER cc_start: 0.8114 (t) cc_final: 0.7487 (p) REVERT: B 218 ASP cc_start: 0.6884 (t70) cc_final: 0.6532 (p0) REVERT: B 234 ASP cc_start: 0.7395 (m-30) cc_final: 0.6828 (m-30) REVERT: B 260 ASP cc_start: 0.7498 (t70) cc_final: 0.7245 (t70) REVERT: B 285 SER cc_start: 0.7982 (t) cc_final: 0.7716 (t) REVERT: B 304 ASP cc_start: 0.7999 (t0) cc_final: 0.7732 (t0) REVERT: G 25 MET cc_start: 0.7808 (tpp) cc_final: 0.7272 (tpp) REVERT: G 41 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8578 (mp) REVERT: R 127 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7598 (mt) REVERT: R 151 VAL cc_start: 0.8299 (t) cc_final: 0.8088 (m) REVERT: R 152 ILE cc_start: 0.8318 (mt) cc_final: 0.8050 (mt) REVERT: R 203 MET cc_start: 0.5185 (mtp) cc_final: 0.4649 (mtp) REVERT: R 219 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: R 247 VAL cc_start: 0.7868 (t) cc_final: 0.6692 (m) REVERT: R 279 LEU cc_start: 0.8591 (tp) cc_final: 0.8335 (tp) REVERT: R 341 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7594 (mtp85) REVERT: S 18 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7973 (tpp80) REVERT: S 20 LEU cc_start: 0.8643 (mt) cc_final: 0.8325 (mt) REVERT: S 32 PHE cc_start: 0.8213 (m-80) cc_final: 0.7964 (m-80) REVERT: S 111 TRP cc_start: 0.8835 (m-10) cc_final: 0.8533 (m-10) REVERT: S 168 SER cc_start: 0.8026 (m) cc_final: 0.7738 (t) REVERT: S 240 TYR cc_start: 0.8111 (m-80) cc_final: 0.7323 (m-80) outliers start: 33 outliers final: 19 residues processed: 309 average time/residue: 0.0927 time to fit residues: 39.1118 Evaluate side-chains 315 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain R residue 90 TRP Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 219 TYR Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.144487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121796 restraints weight = 13965.969| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.69 r_work: 0.3500 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9180 Z= 0.127 Angle : 0.564 8.825 12429 Z= 0.288 Chirality : 0.043 0.217 1406 Planarity : 0.004 0.058 1561 Dihedral : 4.070 18.046 1236 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.76 % Allowed : 20.51 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.38 (0.26), residues: 1121 helix: 2.21 (0.26), residues: 387 sheet: 0.99 (0.30), residues: 293 loop : -0.28 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 135 TYR 0.017 0.001 TYR R 291 PHE 0.025 0.002 PHE A 597 TRP 0.009 0.001 TRP B 88 HIS 0.004 0.001 HIS R 293 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9180) covalent geometry : angle 0.56373 (12429) hydrogen bonds : bond 0.03500 ( 426) hydrogen bonds : angle 4.24216 ( 1197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8265 (t80) cc_final: 0.7829 (t80) REVERT: A 618 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8802 (tppt) REVERT: A 656 LYS cc_start: 0.8582 (tttm) cc_final: 0.8232 (ttmm) REVERT: A 661 ILE cc_start: 0.8339 (pt) cc_final: 0.8094 (pt) REVERT: A 680 ASP cc_start: 0.8484 (p0) cc_final: 0.8242 (p0) REVERT: A 684 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 705 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 716 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7852 (mt-10) REVERT: A 717 ASP cc_start: 0.8111 (t0) cc_final: 0.7751 (t0) REVERT: A 720 LYS cc_start: 0.8493 (mmtp) cc_final: 0.8273 (mttp) REVERT: A 749 ASP cc_start: 0.8321 (t0) cc_final: 0.7770 (t0) REVERT: B 18 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8409 (mm-30) REVERT: B 19 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7686 (pp30) REVERT: B 25 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8351 (ttp80) REVERT: B 48 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7296 (ttm-80) REVERT: B 52 ARG cc_start: 0.7943 (mpt90) cc_final: 0.7687 (mpt180) REVERT: B 84 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7893 (mttp) REVERT: B 92 THR cc_start: 0.8505 (p) cc_final: 0.7683 (m) REVERT: B 124 ASP cc_start: 0.7479 (p0) cc_final: 0.7083 (p0) REVERT: B 126 ILE cc_start: 0.8262 (mm) cc_final: 0.7695 (mt) REVERT: B 197 SER cc_start: 0.8172 (t) cc_final: 0.7537 (p) REVERT: B 218 ASP cc_start: 0.6974 (t70) cc_final: 0.6552 (p0) REVERT: B 234 ASP cc_start: 0.7381 (m-30) cc_final: 0.6789 (m-30) REVERT: B 260 ASP cc_start: 0.7509 (t70) cc_final: 0.7264 (t70) REVERT: B 285 SER cc_start: 0.7983 (t) cc_final: 0.7704 (t) REVERT: B 304 ASP cc_start: 0.7999 (t0) cc_final: 0.7695 (t0) REVERT: G 25 MET cc_start: 0.7814 (tpp) cc_final: 0.7279 (tpp) REVERT: G 41 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8584 (mp) REVERT: R 127 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7629 (mt) REVERT: R 151 VAL cc_start: 0.8293 (t) cc_final: 0.8076 (m) REVERT: R 152 ILE cc_start: 0.8304 (mt) cc_final: 0.8052 (mt) REVERT: R 203 MET cc_start: 0.5239 (mtp) cc_final: 0.4703 (mtp) REVERT: R 219 TYR cc_start: 0.8359 (m-10) cc_final: 0.8007 (m-80) REVERT: R 251 PHE cc_start: 0.7646 (m-10) cc_final: 0.7371 (m-10) REVERT: R 279 LEU cc_start: 0.8571 (tp) cc_final: 0.8331 (tp) REVERT: R 341 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7633 (mtp85) REVERT: S 20 LEU cc_start: 0.8668 (mt) cc_final: 0.8347 (mt) REVERT: S 29 PHE cc_start: 0.8614 (t80) cc_final: 0.7821 (t80) REVERT: S 34 MET cc_start: 0.8085 (mmt) cc_final: 0.7876 (mmm) REVERT: S 83 MET cc_start: 0.7739 (mmm) cc_final: 0.7533 (mmp) REVERT: S 111 TRP cc_start: 0.8824 (m-10) cc_final: 0.8505 (m-10) REVERT: S 240 TYR cc_start: 0.8204 (m-80) cc_final: 0.7419 (m-80) outliers start: 27 outliers final: 20 residues processed: 310 average time/residue: 0.0974 time to fit residues: 41.0396 Evaluate side-chains 320 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN S 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.143441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.120840 restraints weight = 13967.868| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.67 r_work: 0.3487 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9180 Z= 0.149 Angle : 0.587 12.640 12429 Z= 0.297 Chirality : 0.043 0.250 1406 Planarity : 0.004 0.059 1561 Dihedral : 4.142 17.634 1236 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.37 % Allowed : 20.92 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.34 (0.26), residues: 1121 helix: 2.19 (0.26), residues: 387 sheet: 0.96 (0.30), residues: 295 loop : -0.32 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 98 TYR 0.028 0.002 TYR A 704 PHE 0.045 0.002 PHE A 597 TRP 0.010 0.001 TRP B 345 HIS 0.004 0.001 HIS R 293 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9180) covalent geometry : angle 0.58707 (12429) hydrogen bonds : bond 0.03636 ( 426) hydrogen bonds : angle 4.29470 ( 1197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8298 (t80) cc_final: 0.7833 (t80) REVERT: A 656 LYS cc_start: 0.8623 (tttm) cc_final: 0.8297 (ttmm) REVERT: A 680 ASP cc_start: 0.8474 (p0) cc_final: 0.8219 (p0) REVERT: A 684 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 705 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 716 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7850 (mt-10) REVERT: A 717 ASP cc_start: 0.8116 (t0) cc_final: 0.7765 (t0) REVERT: A 720 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8272 (mttp) REVERT: A 749 ASP cc_start: 0.8309 (t0) cc_final: 0.7758 (t0) REVERT: B 18 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8411 (mm-30) REVERT: B 19 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7706 (pp30) REVERT: B 25 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8360 (ttp80) REVERT: B 48 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7277 (ttm-80) REVERT: B 52 ARG cc_start: 0.7926 (mpt90) cc_final: 0.7663 (mpt180) REVERT: B 84 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7918 (mttp) REVERT: B 92 THR cc_start: 0.8537 (p) cc_final: 0.7730 (m) REVERT: B 120 CYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7106 (p) REVERT: B 124 ASP cc_start: 0.7487 (p0) cc_final: 0.7089 (p0) REVERT: B 126 ILE cc_start: 0.8270 (mm) cc_final: 0.7708 (mt) REVERT: B 197 SER cc_start: 0.8205 (t) cc_final: 0.7559 (p) REVERT: B 218 ASP cc_start: 0.6928 (t70) cc_final: 0.6556 (p0) REVERT: B 220 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7717 (mtt180) REVERT: B 234 ASP cc_start: 0.7379 (m-30) cc_final: 0.6833 (m-30) REVERT: B 260 ASP cc_start: 0.7552 (t70) cc_final: 0.7225 (t70) REVERT: B 285 SER cc_start: 0.7968 (t) cc_final: 0.7725 (t) REVERT: B 304 ASP cc_start: 0.7999 (t0) cc_final: 0.7716 (t0) REVERT: G 25 MET cc_start: 0.7845 (tpp) cc_final: 0.7311 (tpp) REVERT: G 41 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8613 (mp) REVERT: R 127 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7788 (mt) REVERT: R 151 VAL cc_start: 0.8297 (t) cc_final: 0.8080 (m) REVERT: R 152 ILE cc_start: 0.8302 (mt) cc_final: 0.8069 (mt) REVERT: R 203 MET cc_start: 0.5305 (mtp) cc_final: 0.4773 (mtp) REVERT: R 219 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: R 341 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7707 (mtp85) REVERT: S 20 LEU cc_start: 0.8729 (mt) cc_final: 0.8454 (mt) REVERT: S 29 PHE cc_start: 0.8671 (t80) cc_final: 0.7930 (t80) REVERT: S 187 TYR cc_start: 0.8298 (m-10) cc_final: 0.8038 (m-10) REVERT: S 240 TYR cc_start: 0.8250 (m-80) cc_final: 0.7503 (m-80) outliers start: 33 outliers final: 23 residues processed: 312 average time/residue: 0.0958 time to fit residues: 40.5741 Evaluate side-chains 324 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 219 TYR Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 216 SER Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 227 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 0.0670 chunk 50 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.145383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.122669 restraints weight = 13975.295| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.71 r_work: 0.3517 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9180 Z= 0.116 Angle : 0.599 13.747 12429 Z= 0.299 Chirality : 0.043 0.246 1406 Planarity : 0.004 0.058 1561 Dihedral : 4.116 16.759 1236 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.06 % Allowed : 21.33 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.36 (0.26), residues: 1121 helix: 2.21 (0.27), residues: 387 sheet: 0.94 (0.30), residues: 297 loop : -0.29 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 135 TYR 0.028 0.001 TYR A 704 PHE 0.016 0.001 PHE A 742 TRP 0.013 0.001 TRP R 252 HIS 0.004 0.001 HIS R 293 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9180) covalent geometry : angle 0.59854 (12429) hydrogen bonds : bond 0.03460 ( 426) hydrogen bonds : angle 4.32122 ( 1197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 300 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8268 (t80) cc_final: 0.7762 (t80) REVERT: A 605 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7880 (mtmt) REVERT: A 618 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8786 (tppt) REVERT: A 656 LYS cc_start: 0.8507 (tttm) cc_final: 0.8182 (ttmm) REVERT: A 680 ASP cc_start: 0.8466 (p0) cc_final: 0.8193 (p0) REVERT: A 684 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7812 (mm-30) REVERT: A 705 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 716 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7800 (mt-10) REVERT: A 717 ASP cc_start: 0.8084 (t0) cc_final: 0.7735 (t0) REVERT: A 720 LYS cc_start: 0.8471 (mmtp) cc_final: 0.8243 (mttp) REVERT: A 749 ASP cc_start: 0.8322 (t0) cc_final: 0.7743 (t0) REVERT: B 18 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8418 (mm-30) REVERT: B 19 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7673 (pp30) REVERT: B 25 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8361 (ttp80) REVERT: B 48 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7247 (ttm-80) REVERT: B 52 ARG cc_start: 0.7920 (mpt90) cc_final: 0.7664 (mpt180) REVERT: B 84 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7881 (mttp) REVERT: B 92 THR cc_start: 0.8483 (p) cc_final: 0.7574 (m) REVERT: B 120 CYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7031 (p) REVERT: B 124 ASP cc_start: 0.7479 (p0) cc_final: 0.7075 (p0) REVERT: B 126 ILE cc_start: 0.8260 (mm) cc_final: 0.7725 (mt) REVERT: B 145 LEU cc_start: 0.8475 (mt) cc_final: 0.8248 (mp) REVERT: B 181 GLN cc_start: 0.7696 (tt0) cc_final: 0.7468 (tt0) REVERT: B 197 SER cc_start: 0.8137 (t) cc_final: 0.7516 (p) REVERT: B 218 ASP cc_start: 0.6936 (t70) cc_final: 0.6535 (p0) REVERT: B 220 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7636 (mtt180) REVERT: B 234 ASP cc_start: 0.7396 (m-30) cc_final: 0.6803 (m-30) REVERT: B 238 ILE cc_start: 0.8678 (mt) cc_final: 0.8373 (tp) REVERT: B 260 ASP cc_start: 0.7527 (t70) cc_final: 0.7190 (t70) REVERT: B 268 MET cc_start: 0.7727 (tpt) cc_final: 0.7511 (tpt) REVERT: B 304 ASP cc_start: 0.7966 (t0) cc_final: 0.7640 (t70) REVERT: G 25 MET cc_start: 0.7819 (tpp) cc_final: 0.7291 (tpp) REVERT: R 151 VAL cc_start: 0.8282 (t) cc_final: 0.8072 (m) REVERT: R 152 ILE cc_start: 0.8269 (mt) cc_final: 0.8029 (mt) REVERT: R 203 MET cc_start: 0.5273 (mtp) cc_final: 0.4771 (mtp) REVERT: R 219 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: R 279 LEU cc_start: 0.8567 (tp) cc_final: 0.8340 (tp) REVERT: R 341 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7637 (mtp85) REVERT: S 20 LEU cc_start: 0.8645 (mt) cc_final: 0.8364 (mt) REVERT: S 29 PHE cc_start: 0.8603 (t80) cc_final: 0.7921 (t80) REVERT: S 47 TRP cc_start: 0.7971 (t60) cc_final: 0.7333 (t60) REVERT: S 111 TRP cc_start: 0.8829 (m-10) cc_final: 0.8559 (m-10) REVERT: S 152 MET cc_start: 0.8456 (mmm) cc_final: 0.8060 (mmm) REVERT: S 240 TYR cc_start: 0.8259 (m-80) cc_final: 0.7551 (m-80) REVERT: S 241 CYS cc_start: 0.7995 (p) cc_final: 0.7724 (p) outliers start: 30 outliers final: 21 residues processed: 310 average time/residue: 0.1019 time to fit residues: 42.2302 Evaluate side-chains 321 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 294 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain R residue 219 TYR Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 216 SER Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 227 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.0470 chunk 106 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.145650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122938 restraints weight = 13751.921| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.68 r_work: 0.3522 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9180 Z= 0.118 Angle : 0.596 13.024 12429 Z= 0.299 Chirality : 0.042 0.231 1406 Planarity : 0.004 0.059 1561 Dihedral : 4.104 17.809 1236 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.76 % Allowed : 21.53 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.40 (0.26), residues: 1121 helix: 2.20 (0.27), residues: 387 sheet: 1.07 (0.30), residues: 288 loop : -0.28 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 14 TYR 0.029 0.001 TYR A 704 PHE 0.015 0.001 PHE A 742 TRP 0.012 0.001 TRP R 252 HIS 0.004 0.001 HIS R 293 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9180) covalent geometry : angle 0.59599 (12429) hydrogen bonds : bond 0.03456 ( 426) hydrogen bonds : angle 4.32223 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2195.67 seconds wall clock time: 38 minutes 20.52 seconds (2300.52 seconds total)