Starting phenix.real_space_refine on Thu Feb 13 09:33:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x9y_33085/02_2025/7x9y_33085.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x9y_33085/02_2025/7x9y_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_33085/02_2025/7x9y_33085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x9y_33085/02_2025/7x9y_33085.map" model { file = "/net/cci-nas-00/data/ceres_data/7x9y_33085/02_2025/7x9y_33085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x9y_33085/02_2025/7x9y_33085.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.05, per 1000 atoms: 0.56 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.88 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: 2.72 Time building geometry restraints manager: 2.78 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.770 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- 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= 0.173 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (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 TRP 0.009 0.001 TRP R 99 HIS 0.003 0.000 HIS B 231 PHE 0.010 0.001 PHE R 340 TYR 0.012 0.001 TYR A 704 ARG 0.009 0.001 ARG S 87 *********************** 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 : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7716 (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: 0.6379 (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: 0.2651 time to fit residues: 111.8173 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 : 0.935 ------------------------------------------------------------------------------- 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 92 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.148465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.125981 restraints weight = 13900.152| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.71 r_work: 0.3577 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1610 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= 0.187 Angle : 0.552 7.420 12429 Z= 0.291 Chirality : 0.043 0.197 1406 Planarity : 0.004 0.053 1561 Dihedral : 4.085 43.204 1238 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.63 % Allowed : 10.51 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1121 helix: 2.28 (0.27), residues: 392 sheet: 1.40 (0.31), residues: 285 loop : -0.19 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 99 HIS 0.003 0.001 HIS B 97 PHE 0.026 0.002 PHE R 348 TYR 0.013 0.002 TYR R 219 ARG 0.004 0.000 ARG A 38 *********************** 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 320 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 304 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 597 PHE cc_start: 0.8225 (p90) cc_final: 0.7985 (p90) REVERT: A 599 PHE cc_start: 0.8291 (t80) cc_final: 0.7994 (t80) REVERT: A 631 PHE cc_start: 0.8097 (t80) cc_final: 0.7890 (t80) REVERT: A 705 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 714 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7912 (tp-100) REVERT: A 716 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 720 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8135 (mmtm) REVERT: A 749 ASP cc_start: 0.8231 (t0) cc_final: 0.7857 (t0) REVERT: B 18 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8368 (mm-30) REVERT: B 19 GLN cc_start: 0.8238 (pp30) cc_final: 0.7738 (pp30) REVERT: B 25 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8201 (ttp80) REVERT: B 52 ARG cc_start: 0.7988 (mpt90) cc_final: 0.7564 (mpt90) REVERT: B 82 ASP cc_start: 0.7647 (m-30) cc_final: 0.7390 (m-30) REVERT: B 124 ASP cc_start: 0.7373 (p0) cc_final: 0.6979 (p0) REVERT: B 126 ILE cc_start: 0.8147 (mm) cc_final: 0.7668 (mm) REVERT: B 154 CYS cc_start: 0.8253 (t) cc_final: 0.7952 (t) REVERT: B 218 ASP cc_start: 0.7232 (t0) cc_final: 0.6982 (t70) REVERT: B 234 ASP cc_start: 0.7543 (m-30) cc_final: 0.7104 (m-30) REVERT: B 260 ASP cc_start: 0.7321 (t70) cc_final: 0.7093 (t70) REVERT: B 304 ASP cc_start: 0.8000 (t0) cc_final: 0.7779 (t0) REVERT: B 318 ASP cc_start: 0.7662 (m-30) cc_final: 0.7449 (t0) REVERT: B 331 MET cc_start: 0.7908 (tpp) cc_final: 0.7566 (ttt) REVERT: G 25 MET cc_start: 0.7807 (tpp) cc_final: 0.7235 (tpp) REVERT: R 151 VAL cc_start: 0.8304 (t) cc_final: 0.8087 (m) REVERT: R 152 ILE cc_start: 0.8335 (mt) cc_final: 0.8059 (mt) REVERT: R 203 MET cc_start: 0.5118 (mtp) cc_final: 0.4509 (mtp) REVERT: R 245 MET cc_start: 0.8003 (ttp) cc_final: 0.7763 (ttp) REVERT: R 251 PHE cc_start: 0.7303 (m-10) cc_final: 0.7069 (m-10) REVERT: R 279 LEU cc_start: 0.8595 (tp) cc_final: 0.8373 (tp) REVERT: S 13 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8089 (mm-40) REVERT: S 168 SER cc_start: 0.7897 (m) cc_final: 0.7620 (t) REVERT: S 240 TYR cc_start: 0.7931 (m-80) cc_final: 0.7051 (m-80) outliers start: 16 outliers final: 12 residues processed: 308 average time/residue: 0.2423 time to fit residues: 98.4361 Evaluate side-chains 300 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 288 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 LEU 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 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 78 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 9 optimal weight: 0.1980 chunk 21 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 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 = 0.3935 r_free = 0.3935 target = 0.144132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121440 restraints weight = 14008.213| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.69 r_work: 0.3503 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9180 Z= 0.260 Angle : 0.573 7.662 12429 Z= 0.300 Chirality : 0.044 0.190 1406 Planarity : 0.005 0.059 1561 Dihedral : 4.068 20.302 1236 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.16 % Allowed : 12.35 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1121 helix: 2.04 (0.27), residues: 392 sheet: 1.32 (0.31), residues: 275 loop : -0.37 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 345 HIS 0.006 0.001 HIS S 35 PHE 0.019 0.002 PHE R 348 TYR 0.014 0.002 TYR B 111 ARG 0.007 0.000 ARG S 67 *********************** 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 349 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 318 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8288 (t80) cc_final: 0.7935 (t80) REVERT: A 680 ASP cc_start: 0.8548 (p0) cc_final: 0.8241 (p0) REVERT: A 684 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 705 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 716 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 720 LYS cc_start: 0.8462 (mmtp) cc_final: 0.8171 (mttp) REVERT: A 749 ASP cc_start: 0.8323 (t0) cc_final: 0.7861 (t0) REVERT: B 18 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8379 (mm-30) REVERT: B 19 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7676 (pp30) REVERT: B 25 ARG cc_start: 0.8722 (ttp80) cc_final: 0.8517 (ttp80) REVERT: B 52 ARG cc_start: 0.7994 (mpt90) cc_final: 0.7749 (mpt180) REVERT: B 82 ASP cc_start: 0.7705 (m-30) cc_final: 0.7485 (m-30) REVERT: B 84 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7976 (mttp) REVERT: B 92 THR cc_start: 0.8582 (p) cc_final: 0.7877 (m) REVERT: B 124 ASP cc_start: 0.7474 (p0) cc_final: 0.7068 (p0) REVERT: B 126 ILE cc_start: 0.8233 (mm) cc_final: 0.7787 (mm) REVERT: B 234 ASP cc_start: 0.7554 (m-30) cc_final: 0.7012 (m-30) REVERT: B 235 ILE cc_start: 0.8073 (mm) cc_final: 0.7872 (mt) REVERT: B 260 ASP cc_start: 0.7465 (t70) cc_final: 0.7202 (t70) REVERT: B 285 SER cc_start: 0.7950 (t) cc_final: 0.7723 (t) REVERT: B 304 ASP cc_start: 0.8057 (t0) cc_final: 0.7724 (t0) REVERT: B 331 MET cc_start: 0.8039 (tpp) cc_final: 0.7830 (ttt) REVERT: G 25 MET cc_start: 0.7828 (tpp) cc_final: 0.7277 (tpp) REVERT: R 151 VAL cc_start: 0.8318 (t) cc_final: 0.8110 (m) REVERT: R 152 ILE cc_start: 0.8356 (mt) cc_final: 0.8107 (mt) REVERT: R 203 MET cc_start: 0.5178 (mtp) cc_final: 0.4600 (mtp) REVERT: R 279 LEU cc_start: 0.8601 (tp) cc_final: 0.8358 (tp) REVERT: S 20 LEU cc_start: 0.8594 (mt) cc_final: 0.8337 (mt) REVERT: S 29 PHE cc_start: 0.8065 (t80) cc_final: 0.7578 (t80) REVERT: S 240 TYR cc_start: 0.8051 (m-80) cc_final: 0.7139 (m-80) REVERT: S 243 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8436 (pp30) outliers start: 31 outliers final: 24 residues processed: 326 average time/residue: 0.2139 time to fit residues: 94.5679 Evaluate side-chains 325 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 299 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 136 VAL Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 63 THR 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 243 GLN 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 11 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.142654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120096 restraints weight = 14046.075| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.68 r_work: 0.3479 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9180 Z= 0.288 Angle : 0.586 7.949 12429 Z= 0.306 Chirality : 0.045 0.336 1406 Planarity : 0.005 0.062 1561 Dihedral : 4.205 21.096 1236 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.57 % Allowed : 16.22 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1121 helix: 2.05 (0.26), residues: 387 sheet: 1.17 (0.30), residues: 277 loop : -0.40 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 88 HIS 0.007 0.001 HIS S 35 PHE 0.040 0.002 PHE A 597 TYR 0.013 0.002 TYR B 111 ARG 0.006 0.000 ARG B 135 *********************** 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 346 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 311 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8313 (t80) cc_final: 0.7918 (t80) REVERT: A 651 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7954 (ttp) REVERT: A 680 ASP cc_start: 0.8530 (p0) cc_final: 0.8260 (p0) REVERT: A 684 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 705 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7839 (mm-30) REVERT: A 716 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 717 ASP cc_start: 0.8152 (t0) cc_final: 0.7764 (t0) REVERT: A 749 ASP cc_start: 0.8312 (t0) cc_final: 0.7795 (t0) REVERT: B 18 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8421 (mm-30) REVERT: B 19 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7700 (pp30) REVERT: B 25 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8519 (ttp80) REVERT: B 48 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7310 (ttm-80) REVERT: B 52 ARG cc_start: 0.7964 (mpt90) cc_final: 0.7740 (mpt180) REVERT: B 82 ASP cc_start: 0.7714 (m-30) cc_final: 0.7512 (m-30) REVERT: B 84 LYS cc_start: 0.8377 (mtpp) cc_final: 0.8065 (mttp) REVERT: B 92 THR cc_start: 0.8628 (p) cc_final: 0.7909 (m) REVERT: B 124 ASP cc_start: 0.7484 (p0) cc_final: 0.7075 (p0) REVERT: B 218 ASP cc_start: 0.7285 (t70) cc_final: 0.6727 (p0) REVERT: B 234 ASP cc_start: 0.7506 (m-30) cc_final: 0.7085 (m-30) REVERT: B 260 ASP cc_start: 0.7464 (t70) cc_final: 0.7216 (t70) REVERT: B 275 ILE cc_start: 0.8129 (mt) cc_final: 0.7823 (tp) REVERT: B 285 SER cc_start: 0.7945 (t) cc_final: 0.7703 (t) REVERT: B 304 ASP cc_start: 0.8077 (t0) cc_final: 0.7755 (t0) REVERT: B 331 MET cc_start: 0.8026 (tpp) cc_final: 0.7799 (mtp) REVERT: G 25 MET cc_start: 0.7831 (tpp) cc_final: 0.7280 (tpp) REVERT: R 151 VAL cc_start: 0.8324 (t) cc_final: 0.8111 (m) REVERT: R 152 ILE cc_start: 0.8323 (mt) cc_final: 0.8074 (mt) REVERT: R 203 MET cc_start: 0.5151 (mtp) cc_final: 0.4565 (mtp) REVERT: R 219 TYR cc_start: 0.8281 (m-10) cc_final: 0.7928 (m-80) REVERT: R 279 LEU cc_start: 0.8597 (tp) cc_final: 0.8356 (tp) REVERT: S 20 LEU cc_start: 0.8669 (mt) cc_final: 0.8404 (mt) REVERT: S 29 PHE cc_start: 0.8254 (t80) cc_final: 0.7629 (t80) REVERT: S 240 TYR cc_start: 0.8113 (m-80) cc_final: 0.7680 (m-80) REVERT: S 242 MET cc_start: 0.7426 (ttm) cc_final: 0.7099 (ttm) REVERT: S 243 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8309 (pp30) outliers start: 35 outliers final: 25 residues processed: 320 average time/residue: 0.2420 time to fit residues: 102.7244 Evaluate side-chains 325 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 651 MET 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 204 LEU 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 113 TYR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 263 SER 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 227 THR Chi-restraints excluded: chain S residue 243 GLN 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 42 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 182 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.144374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121823 restraints weight = 13947.084| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.68 r_work: 0.3507 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2840 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= 0.184 Angle : 0.551 7.558 12429 Z= 0.284 Chirality : 0.043 0.305 1406 Planarity : 0.004 0.058 1561 Dihedral : 4.095 21.781 1236 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.47 % Allowed : 17.35 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1121 helix: 2.22 (0.27), residues: 386 sheet: 1.14 (0.30), residues: 283 loop : -0.31 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 252 HIS 0.003 0.001 HIS B 60 PHE 0.027 0.001 PHE A 597 TYR 0.011 0.001 TYR R 72 ARG 0.006 0.000 ARG B 135 *********************** 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 327 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 293 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8278 (t80) cc_final: 0.7899 (t80) REVERT: A 651 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7932 (ttp) REVERT: A 656 LYS cc_start: 0.8486 (tttm) cc_final: 0.8121 (ttmm) REVERT: A 680 ASP cc_start: 0.8500 (p0) cc_final: 0.8263 (p0) REVERT: A 684 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 717 ASP cc_start: 0.8111 (t0) cc_final: 0.7716 (t0) REVERT: A 720 LYS cc_start: 0.8431 (mmtp) cc_final: 0.8181 (mttp) REVERT: A 749 ASP cc_start: 0.8355 (t0) cc_final: 0.7807 (t0) REVERT: B 18 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8432 (mm-30) REVERT: B 19 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7677 (pp30) REVERT: B 25 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8498 (ttp80) REVERT: B 48 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7258 (ttm-80) REVERT: B 52 ARG cc_start: 0.7926 (mpt90) cc_final: 0.7689 (mpt180) REVERT: B 82 ASP cc_start: 0.7698 (m-30) cc_final: 0.7494 (m-30) REVERT: B 84 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7991 (mttp) REVERT: B 92 THR cc_start: 0.8560 (p) cc_final: 0.7785 (m) REVERT: B 124 ASP cc_start: 0.7454 (p0) cc_final: 0.7038 (p0) REVERT: B 197 SER cc_start: 0.8268 (t) cc_final: 0.7553 (p) REVERT: B 218 ASP cc_start: 0.6945 (t70) cc_final: 0.6492 (p0) REVERT: B 234 ASP cc_start: 0.7449 (m-30) cc_final: 0.6964 (m-30) REVERT: B 260 ASP cc_start: 0.7486 (t70) cc_final: 0.7253 (t70) REVERT: B 275 ILE cc_start: 0.8201 (mt) cc_final: 0.7829 (tp) REVERT: B 285 SER cc_start: 0.8046 (t) cc_final: 0.7799 (t) REVERT: B 304 ASP cc_start: 0.8034 (t0) cc_final: 0.7718 (t70) REVERT: G 25 MET cc_start: 0.7829 (tpp) cc_final: 0.7282 (tpp) REVERT: G 41 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8563 (mp) REVERT: R 68 MET cc_start: 0.7901 (ttt) cc_final: 0.7655 (ttt) REVERT: R 151 VAL cc_start: 0.8310 (t) cc_final: 0.8095 (m) REVERT: R 152 ILE cc_start: 0.8328 (mt) cc_final: 0.8073 (mt) REVERT: R 203 MET cc_start: 0.5134 (mtp) cc_final: 0.4576 (mtp) REVERT: R 219 TYR cc_start: 0.8321 (m-10) cc_final: 0.7996 (m-80) REVERT: R 247 VAL cc_start: 0.7927 (t) cc_final: 0.6768 (m) REVERT: R 279 LEU cc_start: 0.8577 (tp) cc_final: 0.8328 (tp) REVERT: R 341 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7663 (mtp85) REVERT: S 20 LEU cc_start: 0.8640 (mt) cc_final: 0.8375 (mt) REVERT: S 224 PHE cc_start: 0.7678 (m-10) cc_final: 0.7000 (m-10) REVERT: S 240 TYR cc_start: 0.8099 (m-80) cc_final: 0.7660 (m-80) REVERT: S 243 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8330 (pp30) outliers start: 34 outliers final: 25 residues processed: 307 average time/residue: 0.2371 time to fit residues: 97.5511 Evaluate side-chains 314 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 284 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 651 MET 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 87 ILE Chi-restraints excluded: chain B residue 120 CYS 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 81 LEU Chi-restraints excluded: chain R residue 113 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 222 THR Chi-restraints excluded: chain S residue 243 GLN 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 67 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121260 restraints weight = 13769.367| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.68 r_work: 0.3499 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9180 Z= 0.194 Angle : 0.551 7.511 12429 Z= 0.285 Chirality : 0.042 0.234 1406 Planarity : 0.004 0.059 1561 Dihedral : 4.072 20.116 1236 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.88 % Allowed : 18.16 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1121 helix: 2.22 (0.27), residues: 387 sheet: 1.11 (0.30), residues: 287 loop : -0.30 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 252 HIS 0.003 0.001 HIS S 244 PHE 0.041 0.002 PHE A 597 TYR 0.014 0.001 TYR R 93 ARG 0.007 0.000 ARG B 135 *********************** 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 333 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8267 (t80) cc_final: 0.7876 (t80) REVERT: A 651 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7929 (ttp) REVERT: A 656 LYS cc_start: 0.8523 (tttm) cc_final: 0.8148 (ttmm) REVERT: A 680 ASP cc_start: 0.8499 (p0) cc_final: 0.8241 (p0) REVERT: A 684 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 716 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7867 (mt-10) REVERT: A 717 ASP cc_start: 0.8126 (t0) cc_final: 0.7759 (t0) REVERT: A 720 LYS cc_start: 0.8461 (mmtp) cc_final: 0.8205 (mttp) REVERT: A 749 ASP cc_start: 0.8353 (t0) cc_final: 0.7810 (t0) REVERT: B 18 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8440 (mm-30) REVERT: B 19 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7667 (pp30) REVERT: B 25 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8483 (ttp80) REVERT: B 48 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7264 (ttm-80) REVERT: B 52 ARG cc_start: 0.7955 (mpt90) cc_final: 0.7691 (mpt180) REVERT: B 82 ASP cc_start: 0.7696 (m-30) cc_final: 0.7485 (m-30) REVERT: B 84 LYS cc_start: 0.8227 (mtpp) cc_final: 0.8000 (mttp) REVERT: B 92 THR cc_start: 0.8556 (p) cc_final: 0.7764 (m) REVERT: B 124 ASP cc_start: 0.7465 (p0) cc_final: 0.7050 (p0) REVERT: B 197 SER cc_start: 0.8276 (t) cc_final: 0.7573 (p) REVERT: B 218 ASP cc_start: 0.6947 (t70) cc_final: 0.6492 (p0) REVERT: B 234 ASP cc_start: 0.7437 (m-30) cc_final: 0.6913 (m-30) REVERT: B 245 ASN cc_start: 0.7955 (p0) cc_final: 0.7693 (p0) REVERT: B 260 ASP cc_start: 0.7508 (t70) cc_final: 0.7262 (t70) REVERT: B 275 ILE cc_start: 0.8224 (mt) cc_final: 0.7802 (tp) REVERT: B 285 SER cc_start: 0.8026 (t) cc_final: 0.7760 (t) REVERT: B 304 ASP cc_start: 0.8031 (t0) cc_final: 0.7761 (t0) REVERT: G 25 MET cc_start: 0.7835 (tpp) cc_final: 0.7295 (tpp) REVERT: G 41 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8556 (mp) REVERT: R 68 MET cc_start: 0.7886 (ttt) cc_final: 0.7631 (ttt) REVERT: R 151 VAL cc_start: 0.8301 (t) cc_final: 0.8084 (m) REVERT: R 152 ILE cc_start: 0.8317 (mt) cc_final: 0.8064 (mt) REVERT: R 203 MET cc_start: 0.5164 (mtp) cc_final: 0.4607 (mtp) REVERT: R 219 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: R 279 LEU cc_start: 0.8592 (tp) cc_final: 0.8334 (tp) REVERT: R 341 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7651 (mtp85) REVERT: S 20 LEU cc_start: 0.8660 (mt) cc_final: 0.8317 (mt) REVERT: S 50 TYR cc_start: 0.8198 (t80) cc_final: 0.7908 (t80) REVERT: S 168 SER cc_start: 0.7960 (m) cc_final: 0.7668 (t) REVERT: S 240 TYR cc_start: 0.8111 (m-80) cc_final: 0.7394 (m-80) outliers start: 38 outliers final: 28 residues processed: 310 average time/residue: 0.2389 time to fit residues: 99.3985 Evaluate side-chains 320 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 651 MET 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 87 ILE 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 81 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 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 227 THR Chi-restraints excluded: chain S residue 255 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 182 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.144177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.121512 restraints weight = 13982.127| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.68 r_work: 0.3494 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3164 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= 0.196 Angle : 0.559 7.512 12429 Z= 0.288 Chirality : 0.043 0.235 1406 Planarity : 0.004 0.059 1561 Dihedral : 4.125 19.958 1236 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.18 % Allowed : 18.47 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1121 helix: 2.21 (0.27), residues: 387 sheet: 1.07 (0.30), residues: 287 loop : -0.32 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 252 HIS 0.003 0.001 HIS S 35 PHE 0.036 0.002 PHE A 597 TYR 0.019 0.001 TYR R 113 ARG 0.007 0.000 ARG B 135 *********************** 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 342 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8273 (t80) cc_final: 0.7837 (t80) REVERT: A 651 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7946 (ttp) REVERT: A 680 ASP cc_start: 0.8476 (p0) cc_final: 0.8245 (p0) REVERT: A 684 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7856 (mm-30) REVERT: A 716 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7869 (mt-10) REVERT: A 717 ASP cc_start: 0.8111 (t0) cc_final: 0.7735 (t0) REVERT: A 738 LYS cc_start: 0.8373 (ptpp) cc_final: 0.8060 (ptpp) REVERT: A 749 ASP cc_start: 0.8302 (t0) cc_final: 0.7763 (t0) REVERT: B 18 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8443 (mm-30) REVERT: B 19 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7678 (pp30) REVERT: B 25 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8503 (ttp80) REVERT: B 48 ARG cc_start: 0.7739 (ttm-80) cc_final: 0.7272 (ttm-80) REVERT: B 52 ARG cc_start: 0.7940 (mpt90) cc_final: 0.7686 (mpt180) REVERT: B 82 ASP cc_start: 0.7691 (m-30) cc_final: 0.7490 (m-30) REVERT: B 84 LYS cc_start: 0.8255 (mtpp) cc_final: 0.8031 (mttp) REVERT: B 92 THR cc_start: 0.8551 (p) cc_final: 0.7741 (m) REVERT: B 124 ASP cc_start: 0.7462 (p0) cc_final: 0.7046 (p0) REVERT: B 197 SER cc_start: 0.8292 (t) cc_final: 0.7657 (p) REVERT: B 218 ASP cc_start: 0.6939 (t70) cc_final: 0.6520 (p0) REVERT: B 234 ASP cc_start: 0.7427 (m-30) cc_final: 0.6936 (m-30) REVERT: B 257 ARG cc_start: 0.8536 (mtt180) cc_final: 0.8323 (mtp180) REVERT: B 260 ASP cc_start: 0.7501 (t70) cc_final: 0.7102 (t70) REVERT: B 285 SER cc_start: 0.7998 (t) cc_final: 0.7727 (t) REVERT: B 304 ASP cc_start: 0.8014 (t0) cc_final: 0.7777 (t0) REVERT: G 25 MET cc_start: 0.7814 (tpp) cc_final: 0.7272 (tpp) REVERT: G 41 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8566 (mp) REVERT: R 68 MET cc_start: 0.7869 (ttt) cc_final: 0.7629 (ttt) REVERT: R 127 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7656 (mt) REVERT: R 151 VAL cc_start: 0.8294 (t) cc_final: 0.8075 (m) REVERT: R 152 ILE cc_start: 0.8344 (mt) cc_final: 0.8082 (mt) REVERT: R 203 MET cc_start: 0.5255 (mtp) cc_final: 0.4698 (mtp) REVERT: R 212 LEU cc_start: 0.8294 (mt) cc_final: 0.8052 (mt) REVERT: R 219 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: R 279 LEU cc_start: 0.8602 (tp) cc_final: 0.8346 (tp) REVERT: R 341 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7684 (mtp85) REVERT: S 20 LEU cc_start: 0.8682 (mt) cc_final: 0.8356 (mt) REVERT: S 29 PHE cc_start: 0.8567 (t80) cc_final: 0.7682 (t80) REVERT: S 78 THR cc_start: 0.7482 (p) cc_final: 0.7063 (p) REVERT: S 240 TYR cc_start: 0.8141 (m-80) cc_final: 0.7381 (m-80) REVERT: S 243 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8395 (pp30) REVERT: S 245 LEU cc_start: 0.8593 (tp) cc_final: 0.8302 (tp) outliers start: 41 outliers final: 28 residues processed: 315 average time/residue: 0.2347 time to fit residues: 98.7442 Evaluate side-chains 325 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 290 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 651 MET 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 87 ILE Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 182 GLN 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 G residue 56 THR 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 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 227 THR Chi-restraints excluded: chain S residue 243 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.0770 chunk 36 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 chunk 31 optimal weight: 0.0010 chunk 109 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 59 optimal weight: 0.0570 chunk 66 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN ** R 70 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 = 0.3945 r_free = 0.3945 target = 0.145089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.122535 restraints weight = 14108.717| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.70 r_work: 0.3519 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9180 Z= 0.153 Angle : 0.550 8.447 12429 Z= 0.283 Chirality : 0.042 0.223 1406 Planarity : 0.004 0.057 1561 Dihedral : 4.041 18.795 1236 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.78 % Allowed : 19.18 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1121 helix: 2.24 (0.27), residues: 387 sheet: 1.10 (0.30), residues: 282 loop : -0.34 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 252 HIS 0.004 0.000 HIS A 730 PHE 0.032 0.001 PHE A 597 TYR 0.026 0.001 TYR R 113 ARG 0.005 0.000 ARG S 87 *********************** 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 344 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8247 (t80) cc_final: 0.7803 (t80) REVERT: A 607 PHE cc_start: 0.8010 (m-80) cc_final: 0.7802 (m-10) REVERT: A 651 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7899 (ttp) REVERT: A 680 ASP cc_start: 0.8479 (p0) cc_final: 0.8233 (p0) REVERT: A 684 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 716 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7847 (mt-10) REVERT: A 717 ASP cc_start: 0.8077 (t0) cc_final: 0.7707 (t0) REVERT: A 738 LYS cc_start: 0.8366 (ptpp) cc_final: 0.8044 (ptpp) REVERT: A 749 ASP cc_start: 0.8301 (t0) cc_final: 0.7720 (t0) REVERT: B 18 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8428 (mm-30) REVERT: B 19 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7648 (pp30) REVERT: B 25 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8489 (ttp80) REVERT: B 48 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7234 (ttm-80) REVERT: B 52 ARG cc_start: 0.7941 (mpt90) cc_final: 0.7685 (mpt180) REVERT: B 84 LYS cc_start: 0.8148 (mtpp) cc_final: 0.7920 (mttp) REVERT: B 92 THR cc_start: 0.8524 (p) cc_final: 0.7628 (m) REVERT: B 124 ASP cc_start: 0.7468 (p0) cc_final: 0.7078 (p0) REVERT: B 126 ILE cc_start: 0.8274 (mm) cc_final: 0.7692 (mt) REVERT: B 197 SER cc_start: 0.8176 (t) cc_final: 0.7514 (p) REVERT: B 198 LEU cc_start: 0.8074 (mp) cc_final: 0.7868 (mt) REVERT: B 218 ASP cc_start: 0.6867 (t70) cc_final: 0.6537 (p0) REVERT: B 234 ASP cc_start: 0.7447 (m-30) cc_final: 0.6929 (m-30) REVERT: B 238 ILE cc_start: 0.8645 (mm) cc_final: 0.8311 (tp) REVERT: B 257 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8157 (mtp180) REVERT: B 260 ASP cc_start: 0.7473 (t70) cc_final: 0.7232 (t70) REVERT: B 285 SER cc_start: 0.7958 (t) cc_final: 0.7702 (t) REVERT: B 304 ASP cc_start: 0.8007 (t0) cc_final: 0.7681 (t70) REVERT: G 25 MET cc_start: 0.7776 (tpp) cc_final: 0.7245 (tpp) REVERT: G 41 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8600 (mp) REVERT: R 68 MET cc_start: 0.7850 (ttt) cc_final: 0.7593 (ttt) REVERT: R 151 VAL cc_start: 0.8277 (t) cc_final: 0.8058 (m) REVERT: R 152 ILE cc_start: 0.8314 (mt) cc_final: 0.8041 (mt) REVERT: R 203 MET cc_start: 0.5239 (mtp) cc_final: 0.4704 (mtp) REVERT: R 219 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: R 279 LEU cc_start: 0.8593 (tp) cc_final: 0.8336 (tp) REVERT: R 341 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7622 (mtp85) REVERT: S 20 LEU cc_start: 0.8647 (mt) cc_final: 0.8360 (mt) REVERT: S 29 PHE cc_start: 0.8551 (t80) cc_final: 0.7725 (t80) REVERT: S 50 TYR cc_start: 0.8206 (t80) cc_final: 0.7886 (t80) REVERT: S 83 MET cc_start: 0.7863 (mmm) cc_final: 0.7645 (mmp) REVERT: S 93 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7548 (tpp) REVERT: S 111 TRP cc_start: 0.8814 (m-10) cc_final: 0.8519 (m-10) REVERT: S 240 TYR cc_start: 0.8109 (m-80) cc_final: 0.7317 (m-80) REVERT: S 245 LEU cc_start: 0.8582 (tp) cc_final: 0.8250 (tp) outliers start: 37 outliers final: 24 residues processed: 317 average time/residue: 0.2537 time to fit residues: 108.3845 Evaluate side-chains 334 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 651 MET 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 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 90 TRP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 182 GLN B 226 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.141555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.118731 restraints weight = 13879.568| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.66 r_work: 0.3463 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9180 Z= 0.317 Angle : 0.607 8.029 12429 Z= 0.316 Chirality : 0.045 0.261 1406 Planarity : 0.005 0.061 1561 Dihedral : 4.331 20.160 1236 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.57 % Allowed : 19.08 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1121 helix: 2.06 (0.27), residues: 387 sheet: 0.91 (0.30), residues: 288 loop : -0.39 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 111 HIS 0.008 0.001 HIS A 730 PHE 0.033 0.002 PHE A 597 TYR 0.023 0.002 TYR R 291 ARG 0.006 0.000 ARG S 67 *********************** 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 355 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 320 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8323 (t80) cc_final: 0.7863 (t80) REVERT: A 651 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8050 (ttp) REVERT: A 680 ASP cc_start: 0.8494 (p0) cc_final: 0.8269 (p0) REVERT: A 684 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 716 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 717 ASP cc_start: 0.8145 (t0) cc_final: 0.7787 (t0) REVERT: A 738 LYS cc_start: 0.8417 (ptpp) cc_final: 0.8118 (ptpp) REVERT: A 739 ASN cc_start: 0.8316 (m110) cc_final: 0.8089 (m110) REVERT: A 749 ASP cc_start: 0.8331 (t0) cc_final: 0.7786 (t0) REVERT: B 19 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7710 (pp30) REVERT: B 25 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8478 (ttp80) REVERT: B 48 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7240 (ttm-80) REVERT: B 52 ARG cc_start: 0.7983 (mpt90) cc_final: 0.7700 (mpt180) REVERT: B 84 LYS cc_start: 0.8275 (mtpp) cc_final: 0.7998 (mttp) REVERT: B 92 THR cc_start: 0.8622 (p) cc_final: 0.7861 (m) REVERT: B 120 CYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7185 (p) REVERT: B 124 ASP cc_start: 0.7484 (p0) cc_final: 0.7083 (p0) REVERT: B 197 SER cc_start: 0.8377 (t) cc_final: 0.7575 (p) REVERT: B 218 ASP cc_start: 0.7029 (t70) cc_final: 0.6552 (p0) REVERT: B 234 ASP cc_start: 0.7412 (m-30) cc_final: 0.6893 (m-30) REVERT: B 238 ILE cc_start: 0.8569 (mm) cc_final: 0.8249 (tp) REVERT: B 260 ASP cc_start: 0.7551 (t70) cc_final: 0.7225 (t70) REVERT: B 285 SER cc_start: 0.8018 (t) cc_final: 0.7750 (t) REVERT: B 304 ASP cc_start: 0.8013 (t0) cc_final: 0.7769 (t0) REVERT: G 25 MET cc_start: 0.7817 (tpp) cc_final: 0.7287 (tpp) REVERT: G 41 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8606 (mp) REVERT: R 68 MET cc_start: 0.7897 (ttt) cc_final: 0.7585 (ttt) REVERT: R 151 VAL cc_start: 0.8298 (t) cc_final: 0.8080 (m) REVERT: R 152 ILE cc_start: 0.8333 (mt) cc_final: 0.8089 (mt) REVERT: R 203 MET cc_start: 0.5315 (mtp) cc_final: 0.4760 (mtp) REVERT: R 219 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: R 341 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7780 (mtp85) REVERT: S 20 LEU cc_start: 0.8789 (mt) cc_final: 0.8470 (mt) REVERT: S 29 PHE cc_start: 0.8647 (t80) cc_final: 0.7852 (t80) REVERT: S 87 ARG cc_start: 0.8178 (mpp80) cc_final: 0.7960 (mpp80) REVERT: S 240 TYR cc_start: 0.8226 (m-80) cc_final: 0.7531 (m-80) REVERT: S 242 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6756 (tpp) outliers start: 35 outliers final: 23 residues processed: 330 average time/residue: 0.2309 time to fit residues: 102.3474 Evaluate side-chains 340 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 310 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 651 MET Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN 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 G residue 41 LEU Chi-restraints excluded: chain R residue 71 ILE 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 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 Chi-restraints excluded: chain S residue 242 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 52 optimal weight: 0.0050 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN B 42 ASN B 182 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.143563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.120706 restraints weight = 14015.503| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.69 r_work: 0.3497 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3514 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= 0.198 Angle : 0.603 12.934 12429 Z= 0.305 Chirality : 0.044 0.415 1406 Planarity : 0.004 0.059 1561 Dihedral : 4.255 19.622 1236 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.16 % Allowed : 20.92 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1121 helix: 2.17 (0.27), residues: 388 sheet: 0.93 (0.30), residues: 284 loop : -0.36 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 252 HIS 0.003 0.001 HIS A 730 PHE 0.048 0.002 PHE A 597 TYR 0.017 0.001 TYR R 93 ARG 0.007 0.000 ARG B 135 ********************** 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 356 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 325 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8292 (t80) cc_final: 0.7786 (t80) REVERT: A 607 PHE cc_start: 0.8038 (m-80) cc_final: 0.7811 (m-10) REVERT: A 680 ASP cc_start: 0.8477 (p0) cc_final: 0.8231 (p0) REVERT: A 684 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7832 (mm-30) REVERT: A 716 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7843 (mt-10) REVERT: A 717 ASP cc_start: 0.8114 (t0) cc_final: 0.7756 (t0) REVERT: A 738 LYS cc_start: 0.8455 (ptpp) cc_final: 0.8124 (ptpp) REVERT: A 749 ASP cc_start: 0.8356 (t0) cc_final: 0.7778 (t0) REVERT: B 18 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8441 (mm-30) REVERT: B 19 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7679 (pp30) REVERT: B 25 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8484 (ttp80) REVERT: B 48 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7258 (ttm-80) REVERT: B 52 ARG cc_start: 0.7925 (mpt90) cc_final: 0.7646 (mpt180) REVERT: B 84 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7894 (mttp) REVERT: B 92 THR cc_start: 0.8519 (p) cc_final: 0.7698 (m) REVERT: B 120 CYS cc_start: 0.7375 (OUTLIER) cc_final: 0.7060 (p) REVERT: B 124 ASP cc_start: 0.7457 (p0) cc_final: 0.7077 (p0) REVERT: B 126 ILE cc_start: 0.8268 (mm) cc_final: 0.7687 (mt) REVERT: B 197 SER cc_start: 0.8247 (t) cc_final: 0.7513 (p) REVERT: B 218 ASP cc_start: 0.6939 (t70) cc_final: 0.6561 (p0) REVERT: B 234 ASP cc_start: 0.7456 (m-30) cc_final: 0.6931 (m-30) REVERT: B 238 ILE cc_start: 0.8530 (mm) cc_final: 0.8235 (tp) REVERT: B 260 ASP cc_start: 0.7503 (t70) cc_final: 0.7173 (t70) REVERT: B 285 SER cc_start: 0.8000 (t) cc_final: 0.7724 (t) REVERT: B 304 ASP cc_start: 0.8009 (t0) cc_final: 0.7722 (t0) REVERT: G 25 MET cc_start: 0.7814 (tpp) cc_final: 0.7281 (tpp) REVERT: R 68 MET cc_start: 0.7862 (ttt) cc_final: 0.7537 (ttt) REVERT: R 149 PHE cc_start: 0.8395 (t80) cc_final: 0.8114 (t80) REVERT: R 151 VAL cc_start: 0.8273 (t) cc_final: 0.8065 (m) REVERT: R 152 ILE cc_start: 0.8263 (mt) cc_final: 0.8026 (mt) REVERT: R 203 MET cc_start: 0.5279 (mtp) cc_final: 0.4768 (mtp) REVERT: R 219 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: R 279 LEU cc_start: 0.8583 (tp) cc_final: 0.8348 (tp) REVERT: R 341 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7688 (mtp85) REVERT: S 20 LEU cc_start: 0.8672 (mt) cc_final: 0.8368 (mt) REVERT: S 29 PHE cc_start: 0.8593 (t80) cc_final: 0.7831 (t80) REVERT: S 47 TRP cc_start: 0.7929 (t60) cc_final: 0.7299 (t60) REVERT: S 50 TYR cc_start: 0.8200 (t80) cc_final: 0.7816 (t80) REVERT: S 78 THR cc_start: 0.7449 (p) cc_final: 0.7043 (p) REVERT: S 111 TRP cc_start: 0.8827 (m-10) cc_final: 0.8364 (m-10) REVERT: S 187 TYR cc_start: 0.7914 (m-10) cc_final: 0.7450 (m-10) REVERT: S 224 PHE cc_start: 0.7460 (m-10) cc_final: 0.6802 (m-10) REVERT: S 240 TYR cc_start: 0.8207 (m-80) cc_final: 0.7546 (m-80) outliers start: 31 outliers final: 22 residues processed: 333 average time/residue: 0.2291 time to fit residues: 102.7136 Evaluate side-chains 346 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 320 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 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 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 68 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 89 optimal weight: 0.0040 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.144869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122275 restraints weight = 13947.719| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.68 r_work: 0.3510 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3570 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= 0.186 Angle : 0.587 13.923 12429 Z= 0.296 Chirality : 0.043 0.306 1406 Planarity : 0.004 0.059 1561 Dihedral : 4.214 18.944 1236 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.06 % Allowed : 22.04 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1121 helix: 2.22 (0.27), residues: 388 sheet: 0.82 (0.30), residues: 286 loop : -0.31 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 252 HIS 0.003 0.001 HIS A 730 PHE 0.046 0.002 PHE A 597 TYR 0.025 0.001 TYR S 187 ARG 0.007 0.000 ARG B 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.02 seconds wall clock time: 84 minutes 30.49 seconds (5070.49 seconds total)