Starting phenix.real_space_refine on Tue Mar 3 22:22:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6v_25729/03_2026/7t6v_25729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6v_25729/03_2026/7t6v_25729.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/7t6v_25729/03_2026/7t6v_25729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6v_25729/03_2026/7t6v_25729.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6v_25729/03_2026/7t6v_25729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6v_25729/03_2026/7t6v_25729.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.048 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 64 5.16 5 C 5734 2.51 5 N 1506 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8949 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2346 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.25 Number of scatterers: 8949 At special positions: 0 Unit cell: (106.029, 106.029, 132.804, 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 64 16.00 O 1645 8.00 N 1506 7.00 C 5734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.08 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 349.6 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 40.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'R' and resid 22 through 53 Proline residue: R 29 - end of helix Processing helix chain 'R' and resid 58 through 77 Processing helix chain 'R' and resid 77 through 87 removed outlier: 4.019A pdb=" N LEU R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.584A pdb=" N ASP R 106 " --> pdb=" O HIS R 102 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 157 removed outlier: 4.079A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 164 removed outlier: 3.590A pdb=" N PHE R 161 " --> pdb=" O THR R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 208 removed outlier: 3.535A pdb=" N THR R 196 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET R 197 " --> pdb=" O VAL R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 Processing helix chain 'R' and resid 237 through 267 removed outlier: 3.855A pdb=" N LEU R 243 " --> pdb=" O PRO R 239 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR R 244 " --> pdb=" O LEU R 240 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 275 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.647A pdb=" N ILE R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.755A pdb=" N LEU R 290 " --> pdb=" O PRO R 286 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 291 " --> pdb=" O THR R 287 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.898A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.551A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.005A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.001A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.538A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.978A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.541A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.720A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.561A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.099A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.546A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 165 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.698A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.850A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.925A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.748A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.825A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.770A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.677A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.442A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.972A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.345A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.882A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1578 1.32 - 1.45: 2386 1.45 - 1.57: 5081 1.57 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 9139 Sorted by residual: bond pdb=" CA SER R 84 " pdb=" CB SER R 84 " ideal model delta sigma weight residual 1.528 1.470 0.058 1.56e-02 4.11e+03 1.40e+01 bond pdb=" CA SER R 112 " pdb=" CB SER R 112 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.55e-02 4.16e+03 1.32e+01 bond pdb=" CA SER R 73 " pdb=" CB SER R 73 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.21e+01 bond pdb=" N ILE R 195 " pdb=" CA ILE R 195 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.20e+01 bond pdb=" CA SER R 211 " pdb=" CB SER R 211 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.58e-02 4.01e+03 1.19e+01 ... (remaining 9134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11575 2.39 - 4.77: 738 4.77 - 7.16: 52 7.16 - 9.55: 5 9.55 - 11.94: 3 Bond angle restraints: 12373 Sorted by residual: angle pdb=" C PRO R 92 " pdb=" CA PRO R 92 " pdb=" CB PRO R 92 " ideal model delta sigma weight residual 112.64 100.70 11.94 1.43e+00 4.89e-01 6.97e+01 angle pdb=" CA PHE B 235 " pdb=" CB PHE B 235 " pdb=" CG PHE B 235 " ideal model delta sigma weight residual 113.80 120.19 -6.39 1.00e+00 1.00e+00 4.08e+01 angle pdb=" C PHE R 161 " pdb=" CA PHE R 161 " pdb=" CB PHE R 161 " ideal model delta sigma weight residual 110.88 101.62 9.26 1.57e+00 4.06e-01 3.48e+01 angle pdb=" C LYS R 99 " pdb=" CA LYS R 99 " pdb=" CB LYS R 99 " ideal model delta sigma weight residual 110.85 120.76 -9.91 1.70e+00 3.46e-01 3.40e+01 angle pdb=" C TYR R 302 " pdb=" N VAL R 303 " pdb=" CA VAL R 303 " ideal model delta sigma weight residual 122.77 116.71 6.06 1.05e+00 9.07e-01 3.33e+01 ... (remaining 12368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 4918 16.49 - 32.99: 396 32.99 - 49.48: 67 49.48 - 65.97: 10 65.97 - 82.46: 8 Dihedral angle restraints: 5399 sinusoidal: 2108 harmonic: 3291 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -163.28 77.28 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 163.97 -70.97 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" C LYS R 99 " pdb=" N LYS R 99 " pdb=" CA LYS R 99 " pdb=" CB LYS R 99 " ideal model delta harmonic sigma weight residual -122.60 -138.12 15.52 0 2.50e+00 1.60e-01 3.86e+01 ... (remaining 5396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1078 0.102 - 0.205: 303 0.205 - 0.307: 26 0.307 - 0.409: 4 0.409 - 0.512: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA LYS R 99 " pdb=" N LYS R 99 " pdb=" C LYS R 99 " pdb=" CB LYS R 99 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA ASP R 106 " pdb=" N ASP R 106 " pdb=" C ASP R 106 " pdb=" CB ASP R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ASN R 135 " pdb=" N ASN R 135 " pdb=" C ASN R 135 " pdb=" CB ASN R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1409 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 205 " -0.020 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C ARG R 205 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG R 205 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE R 206 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 299 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C PRO R 299 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO R 299 " -0.023 2.00e-02 2.50e+03 pdb=" N MET R 300 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 183 " 0.027 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP R 183 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP R 183 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 183 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP R 183 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP R 183 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 183 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 183 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 183 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 183 " 0.000 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 85 2.62 - 3.19: 7877 3.19 - 3.76: 13170 3.76 - 4.33: 18862 4.33 - 4.90: 31124 Nonbonded interactions: 71118 Sorted by model distance: nonbonded pdb=" O ILE L 4 " pdb=" OXT ILE L 5 " model vdw 2.047 3.040 nonbonded pdb=" O THR A 262 " pdb=" NZ LYS A 317 " model vdw 2.268 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.319 3.120 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.325 3.040 ... (remaining 71113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.058 9141 Z= 0.766 Angle : 1.267 11.936 12377 Z= 0.934 Chirality : 0.089 0.512 1412 Planarity : 0.006 0.054 1553 Dihedral : 12.331 82.461 3271 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.24), residues: 1123 helix: 2.04 (0.24), residues: 402 sheet: 0.60 (0.30), residues: 278 loop : -0.19 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 54 TYR 0.022 0.002 TYR R 302 PHE 0.033 0.002 PHE B 235 TRP 0.033 0.003 TRP R 183 HIS 0.012 0.002 HIS R 136 Details of bonding type rmsd covalent geometry : bond 0.01068 ( 9139) covalent geometry : angle 1.26462 (12373) SS BOND : bond 0.03756 ( 2) SS BOND : angle 4.37559 ( 4) hydrogen bonds : bond 0.18948 ( 457) hydrogen bonds : angle 7.36262 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: R 77 THR cc_start: 0.8744 (t) cc_final: 0.8414 (p) REVERT: R 103 ILE cc_start: 0.8263 (mm) cc_final: 0.8023 (mt) REVERT: R 161 PHE cc_start: 0.8002 (m-80) cc_final: 0.7785 (m-80) REVERT: R 229 HIS cc_start: 0.7711 (t-90) cc_final: 0.7482 (t-170) REVERT: R 278 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8611 (mmmt) REVERT: R 281 ASP cc_start: 0.7515 (m-30) cc_final: 0.7149 (m-30) REVERT: A 209 LYS cc_start: 0.8085 (mttt) cc_final: 0.7885 (mttt) REVERT: A 271 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7851 (ttpp) REVERT: A 275 GLU cc_start: 0.8400 (tp30) cc_final: 0.8074 (tp30) REVERT: A 309 ASP cc_start: 0.8277 (t70) cc_final: 0.7985 (t70) REVERT: B 45 MET cc_start: 0.8520 (mtt) cc_final: 0.8295 (mtt) REVERT: B 215 GLU cc_start: 0.7986 (mp0) cc_final: 0.7173 (mp0) REVERT: B 233 CYS cc_start: 0.7807 (t) cc_final: 0.7568 (t) REVERT: B 258 ASP cc_start: 0.7777 (t0) cc_final: 0.7333 (t0) REVERT: B 259 GLN cc_start: 0.7507 (tt0) cc_final: 0.7294 (tt0) outliers start: 1 outliers final: 1 residues processed: 270 average time/residue: 0.1282 time to fit residues: 44.0303 Evaluate side-chains 239 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 119 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.105027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.090690 restraints weight = 14719.091| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.43 r_work: 0.3156 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9141 Z= 0.141 Angle : 0.584 9.361 12377 Z= 0.311 Chirality : 0.044 0.193 1412 Planarity : 0.005 0.047 1553 Dihedral : 4.687 53.136 1245 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.54 % Allowed : 10.36 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1123 helix: 2.04 (0.25), residues: 406 sheet: 0.60 (0.30), residues: 269 loop : -0.24 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 310 TYR 0.017 0.001 TYR R 175 PHE 0.024 0.002 PHE R 161 TRP 0.014 0.002 TRP R 95 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9139) covalent geometry : angle 0.58335 (12373) SS BOND : bond 0.01146 ( 2) SS BOND : angle 2.09754 ( 4) hydrogen bonds : bond 0.04426 ( 457) hydrogen bonds : angle 5.23929 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 261 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 ARG cc_start: 0.9132 (tpp80) cc_final: 0.8907 (tpp80) REVERT: R 83 VAL cc_start: 0.8666 (t) cc_final: 0.8460 (m) REVERT: R 91 TRP cc_start: 0.8974 (t-100) cc_final: 0.8560 (t-100) REVERT: R 106 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8125 (t0) REVERT: R 189 GLU cc_start: 0.8547 (tm-30) cc_final: 0.7995 (tm-30) REVERT: R 197 MET cc_start: 0.7288 (tmm) cc_final: 0.7079 (tmm) REVERT: R 241 ARG cc_start: 0.7106 (tmt170) cc_final: 0.6876 (ttp-170) REVERT: A 8 GLU cc_start: 0.7486 (tt0) cc_final: 0.7284 (tt0) REVERT: A 197 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8093 (mtpp) REVERT: A 209 LYS cc_start: 0.8665 (mttt) cc_final: 0.8460 (mttt) REVERT: A 275 GLU cc_start: 0.8599 (tp30) cc_final: 0.8339 (tp30) REVERT: A 298 GLU cc_start: 0.7225 (tt0) cc_final: 0.6984 (tt0) REVERT: A 309 ASP cc_start: 0.8435 (t70) cc_final: 0.8033 (t70) REVERT: B 212 ASP cc_start: 0.8447 (t0) cc_final: 0.7603 (t0) REVERT: B 215 GLU cc_start: 0.8621 (mp0) cc_final: 0.7981 (mp0) REVERT: B 233 CYS cc_start: 0.8742 (t) cc_final: 0.8457 (t) REVERT: B 258 ASP cc_start: 0.8236 (t0) cc_final: 0.7841 (t0) REVERT: B 294 CYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7910 (t) outliers start: 15 outliers final: 7 residues processed: 267 average time/residue: 0.1224 time to fit residues: 42.1028 Evaluate side-chains 250 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 241 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 ILE Chi-restraints excluded: chain R residue 106 ASP Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 106 optimal weight: 0.0050 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.091448 restraints weight = 14537.673| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.41 r_work: 0.3170 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9141 Z= 0.112 Angle : 0.531 10.089 12377 Z= 0.276 Chirality : 0.041 0.180 1412 Planarity : 0.004 0.042 1553 Dihedral : 4.488 59.379 1243 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.05 % Allowed : 13.74 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1123 helix: 2.03 (0.26), residues: 407 sheet: 0.53 (0.30), residues: 266 loop : -0.20 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 46 TYR 0.021 0.001 TYR A 296 PHE 0.022 0.001 PHE R 180 TRP 0.011 0.001 TRP R 95 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9139) covalent geometry : angle 0.52959 (12373) SS BOND : bond 0.00690 ( 2) SS BOND : angle 1.92599 ( 4) hydrogen bonds : bond 0.03767 ( 457) hydrogen bonds : angle 4.80982 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 258 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 87 MET cc_start: 0.8677 (mtt) cc_final: 0.8359 (mtm) REVERT: R 91 TRP cc_start: 0.8895 (t-100) cc_final: 0.8590 (t-100) REVERT: R 189 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7988 (tm-30) REVERT: R 231 LYS cc_start: 0.8864 (mttm) cc_final: 0.8573 (ttmm) REVERT: R 241 ARG cc_start: 0.7023 (tmt170) cc_final: 0.6756 (ttp-170) REVERT: R 310 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8338 (mtm110) REVERT: A 189 PHE cc_start: 0.8717 (p90) cc_final: 0.8304 (p90) REVERT: A 197 LYS cc_start: 0.8366 (mmmt) cc_final: 0.8142 (mtpp) REVERT: A 210 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8407 (mmtt) REVERT: A 275 GLU cc_start: 0.8657 (tp30) cc_final: 0.8318 (tp30) REVERT: A 298 GLU cc_start: 0.7237 (tt0) cc_final: 0.6967 (tt0) REVERT: A 309 ASP cc_start: 0.8363 (t70) cc_final: 0.7836 (t70) REVERT: B 191 SER cc_start: 0.8787 (t) cc_final: 0.8456 (t) REVERT: B 212 ASP cc_start: 0.8408 (t0) cc_final: 0.7475 (t0) REVERT: B 215 GLU cc_start: 0.8601 (mp0) cc_final: 0.7890 (mp0) REVERT: B 233 CYS cc_start: 0.8724 (t) cc_final: 0.8377 (t) REVERT: B 258 ASP cc_start: 0.8244 (t0) cc_final: 0.7814 (t0) REVERT: B 294 CYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7962 (t) REVERT: E 76 LYS cc_start: 0.9128 (mtpt) cc_final: 0.8879 (mtpt) REVERT: E 132 THR cc_start: 0.8420 (m) cc_final: 0.8112 (t) REVERT: E 179 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7311 (mtt180) REVERT: E 218 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.8045 (ttm) outliers start: 20 outliers final: 13 residues processed: 267 average time/residue: 0.1265 time to fit residues: 43.1446 Evaluate side-chains 266 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 218 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 0.0370 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.091316 restraints weight = 14743.711| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.45 r_work: 0.3168 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9141 Z= 0.111 Angle : 0.529 8.995 12377 Z= 0.272 Chirality : 0.041 0.175 1412 Planarity : 0.004 0.040 1553 Dihedral : 4.299 53.561 1243 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.44 % Allowed : 16.21 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.25), residues: 1123 helix: 2.02 (0.26), residues: 409 sheet: 0.51 (0.30), residues: 266 loop : -0.17 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 46 TYR 0.020 0.001 TYR A 296 PHE 0.019 0.001 PHE R 161 TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9139) covalent geometry : angle 0.52879 (12373) SS BOND : bond 0.00411 ( 2) SS BOND : angle 1.52515 ( 4) hydrogen bonds : bond 0.03541 ( 457) hydrogen bonds : angle 4.59810 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 259 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8470 (m) REVERT: R 87 MET cc_start: 0.8680 (mtt) cc_final: 0.8364 (mtm) REVERT: R 189 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8011 (tm-30) REVERT: R 241 ARG cc_start: 0.6964 (tmt170) cc_final: 0.6672 (ttp-170) REVERT: R 292 PHE cc_start: 0.8502 (m-10) cc_final: 0.8272 (m-10) REVERT: R 310 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8294 (mtm110) REVERT: A 189 PHE cc_start: 0.8649 (p90) cc_final: 0.8290 (p90) REVERT: A 197 LYS cc_start: 0.8358 (mmmt) cc_final: 0.8117 (mtpp) REVERT: A 232 LEU cc_start: 0.8791 (mt) cc_final: 0.8567 (mp) REVERT: A 275 GLU cc_start: 0.8649 (tp30) cc_final: 0.8307 (tp30) REVERT: A 298 GLU cc_start: 0.7341 (tt0) cc_final: 0.7057 (tt0) REVERT: A 309 ASP cc_start: 0.8404 (t70) cc_final: 0.7935 (t70) REVERT: B 13 GLN cc_start: 0.8606 (tt0) cc_final: 0.8348 (tm-30) REVERT: B 191 SER cc_start: 0.8804 (t) cc_final: 0.8459 (t) REVERT: B 212 ASP cc_start: 0.8440 (t0) cc_final: 0.7465 (t0) REVERT: B 215 GLU cc_start: 0.8639 (mp0) cc_final: 0.7894 (mp0) REVERT: B 233 CYS cc_start: 0.8704 (t) cc_final: 0.8367 (t) REVERT: B 258 ASP cc_start: 0.8284 (t0) cc_final: 0.7850 (t0) REVERT: B 259 GLN cc_start: 0.8132 (tt0) cc_final: 0.7912 (mt0) REVERT: B 294 CYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7890 (t) REVERT: E 132 THR cc_start: 0.8421 (m) cc_final: 0.8079 (t) REVERT: E 218 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8140 (ttm) REVERT: E 234 GLU cc_start: 0.7797 (pm20) cc_final: 0.6720 (pm20) outliers start: 14 outliers final: 8 residues processed: 265 average time/residue: 0.1198 time to fit residues: 40.9587 Evaluate side-chains 259 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 248 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 218 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 103 optimal weight: 0.0000 chunk 102 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.105940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.091626 restraints weight = 14705.009| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.45 r_work: 0.3171 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9141 Z= 0.110 Angle : 0.526 8.349 12377 Z= 0.270 Chirality : 0.041 0.185 1412 Planarity : 0.004 0.043 1553 Dihedral : 4.118 42.484 1243 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.64 % Allowed : 16.41 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1123 helix: 2.09 (0.26), residues: 409 sheet: 0.50 (0.30), residues: 275 loop : -0.15 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 46 TYR 0.020 0.001 TYR A 296 PHE 0.021 0.001 PHE R 161 TRP 0.009 0.001 TRP R 91 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9139) covalent geometry : angle 0.52509 (12373) SS BOND : bond 0.00453 ( 2) SS BOND : angle 1.51078 ( 4) hydrogen bonds : bond 0.03431 ( 457) hydrogen bonds : angle 4.49335 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8441 (m) REVERT: R 87 MET cc_start: 0.8681 (mtt) cc_final: 0.8364 (mtm) REVERT: R 189 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7982 (tm-30) REVERT: R 231 LYS cc_start: 0.8812 (mttm) cc_final: 0.8547 (ttmm) REVERT: R 252 ILE cc_start: 0.8769 (mm) cc_final: 0.8546 (mt) REVERT: R 292 PHE cc_start: 0.8508 (m-10) cc_final: 0.8281 (m-10) REVERT: R 310 ARG cc_start: 0.8790 (mtm-85) cc_final: 0.8300 (mtm110) REVERT: A 189 PHE cc_start: 0.8620 (p90) cc_final: 0.8225 (p90) REVERT: A 197 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8134 (mtpp) REVERT: A 257 LYS cc_start: 0.8995 (pttp) cc_final: 0.8607 (pttp) REVERT: A 271 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7958 (mtpp) REVERT: A 275 GLU cc_start: 0.8629 (tp30) cc_final: 0.8287 (tp30) REVERT: A 298 GLU cc_start: 0.7348 (tt0) cc_final: 0.7055 (tt0) REVERT: A 309 ASP cc_start: 0.8440 (t70) cc_final: 0.7986 (t70) REVERT: B 13 GLN cc_start: 0.8597 (tt0) cc_final: 0.8343 (tm-30) REVERT: B 212 ASP cc_start: 0.8453 (t0) cc_final: 0.7625 (t0) REVERT: B 215 GLU cc_start: 0.8693 (mp0) cc_final: 0.8072 (mp0) REVERT: B 233 CYS cc_start: 0.8698 (t) cc_final: 0.8389 (t) REVERT: B 254 ASP cc_start: 0.8067 (t0) cc_final: 0.7613 (t0) REVERT: B 258 ASP cc_start: 0.8389 (t0) cc_final: 0.8040 (t0) REVERT: B 294 CYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7933 (t) REVERT: B 336 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8393 (mp) REVERT: E 76 LYS cc_start: 0.9098 (mtpt) cc_final: 0.8887 (mtpt) REVERT: E 132 THR cc_start: 0.8420 (m) cc_final: 0.8073 (t) REVERT: E 219 GLN cc_start: 0.9061 (pp30) cc_final: 0.8355 (pp30) REVERT: E 234 GLU cc_start: 0.7818 (pm20) cc_final: 0.6764 (pm20) outliers start: 16 outliers final: 12 residues processed: 268 average time/residue: 0.1233 time to fit residues: 42.5178 Evaluate side-chains 273 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 258 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 276 LYS Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 75 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** 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 = 0.3501 r_free = 0.3501 target = 0.105506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.091105 restraints weight = 14737.086| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.45 r_work: 0.3163 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9141 Z= 0.117 Angle : 0.533 8.611 12377 Z= 0.274 Chirality : 0.041 0.189 1412 Planarity : 0.004 0.047 1553 Dihedral : 4.095 36.088 1243 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.05 % Allowed : 16.72 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1123 helix: 2.07 (0.26), residues: 410 sheet: 0.47 (0.29), residues: 287 loop : -0.13 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 46 TYR 0.020 0.001 TYR A 296 PHE 0.026 0.001 PHE R 163 TRP 0.016 0.001 TRP R 91 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9139) covalent geometry : angle 0.53274 (12373) SS BOND : bond 0.00493 ( 2) SS BOND : angle 1.62483 ( 4) hydrogen bonds : bond 0.03473 ( 457) hydrogen bonds : angle 4.45375 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8461 (m) REVERT: R 87 MET cc_start: 0.8700 (mtt) cc_final: 0.8401 (mtm) REVERT: R 189 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7976 (tm-30) REVERT: R 203 ILE cc_start: 0.8800 (tt) cc_final: 0.8405 (mm) REVERT: R 235 LYS cc_start: 0.8588 (pttp) cc_final: 0.8228 (pttp) REVERT: R 252 ILE cc_start: 0.8748 (mm) cc_final: 0.8520 (mt) REVERT: R 292 PHE cc_start: 0.8534 (m-10) cc_final: 0.8301 (m-10) REVERT: R 310 ARG cc_start: 0.8825 (mtm-85) cc_final: 0.8514 (mtm-85) REVERT: A 8 GLU cc_start: 0.7510 (tt0) cc_final: 0.7307 (tt0) REVERT: A 189 PHE cc_start: 0.8584 (p90) cc_final: 0.8231 (p90) REVERT: A 197 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8133 (mtpp) REVERT: A 232 LEU cc_start: 0.8776 (mt) cc_final: 0.8571 (mp) REVERT: A 257 LYS cc_start: 0.8970 (pttp) cc_final: 0.8576 (pttp) REVERT: A 271 LYS cc_start: 0.8257 (ttpp) cc_final: 0.8008 (mtpp) REVERT: A 275 GLU cc_start: 0.8629 (tp30) cc_final: 0.8297 (tp30) REVERT: A 298 GLU cc_start: 0.7350 (tt0) cc_final: 0.7049 (tt0) REVERT: A 309 ASP cc_start: 0.8437 (t70) cc_final: 0.7990 (t70) REVERT: B 13 GLN cc_start: 0.8590 (tt0) cc_final: 0.8380 (tm-30) REVERT: B 212 ASP cc_start: 0.8447 (t0) cc_final: 0.7647 (t0) REVERT: B 215 GLU cc_start: 0.8696 (mp0) cc_final: 0.8082 (mp0) REVERT: B 233 CYS cc_start: 0.8695 (t) cc_final: 0.8382 (t) REVERT: B 254 ASP cc_start: 0.8209 (t0) cc_final: 0.7726 (t0) REVERT: B 258 ASP cc_start: 0.8298 (t0) cc_final: 0.7980 (t0) REVERT: B 259 GLN cc_start: 0.8290 (tt0) cc_final: 0.7993 (mt0) REVERT: B 294 CYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7906 (t) REVERT: B 336 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8384 (mp) REVERT: E 76 LYS cc_start: 0.9101 (mtpt) cc_final: 0.8876 (mtpt) REVERT: E 128 MET cc_start: 0.9172 (mmm) cc_final: 0.8183 (mmm) REVERT: E 132 THR cc_start: 0.8419 (m) cc_final: 0.8080 (t) REVERT: E 218 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.8012 (ttm) REVERT: E 219 GLN cc_start: 0.9074 (pp30) cc_final: 0.8295 (pp30) REVERT: E 234 GLU cc_start: 0.7866 (pm20) cc_final: 0.6824 (pm20) outliers start: 20 outliers final: 13 residues processed: 275 average time/residue: 0.1225 time to fit residues: 43.5829 Evaluate side-chains 268 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** 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 = 0.3431 r_free = 0.3431 target = 0.100954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.086632 restraints weight = 14832.764| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.45 r_work: 0.3085 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9141 Z= 0.231 Angle : 0.617 8.645 12377 Z= 0.321 Chirality : 0.045 0.201 1412 Planarity : 0.004 0.055 1553 Dihedral : 4.499 30.850 1243 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.56 % Allowed : 17.03 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1123 helix: 1.79 (0.26), residues: 410 sheet: 0.30 (0.30), residues: 287 loop : -0.23 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 46 TYR 0.021 0.002 TYR A 296 PHE 0.017 0.002 PHE R 180 TRP 0.017 0.002 TRP R 91 HIS 0.006 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 9139) covalent geometry : angle 0.61534 (12373) SS BOND : bond 0.00748 ( 2) SS BOND : angle 2.31781 ( 4) hydrogen bonds : bond 0.04296 ( 457) hydrogen bonds : angle 4.71873 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 ARG cc_start: 0.8286 (mmm160) cc_final: 0.8013 (mmm-85) REVERT: R 83 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8483 (m) REVERT: R 91 TRP cc_start: 0.9197 (t-100) cc_final: 0.8793 (t-100) REVERT: R 170 PRO cc_start: 0.8000 (Cg_endo) cc_final: 0.7796 (Cg_exo) REVERT: R 189 GLU cc_start: 0.8519 (tm-30) cc_final: 0.7944 (tm-30) REVERT: R 203 ILE cc_start: 0.8828 (tt) cc_final: 0.8610 (mm) REVERT: R 231 LYS cc_start: 0.8919 (mttm) cc_final: 0.8437 (ttmm) REVERT: R 235 LYS cc_start: 0.8588 (pttp) cc_final: 0.8220 (pttp) REVERT: R 310 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.8514 (mtm-85) REVERT: A 197 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7991 (mttm) REVERT: A 275 GLU cc_start: 0.8624 (tp30) cc_final: 0.8288 (tp30) REVERT: A 298 GLU cc_start: 0.7431 (tt0) cc_final: 0.7101 (tt0) REVERT: A 309 ASP cc_start: 0.8526 (t70) cc_final: 0.8124 (t0) REVERT: A 312 LYS cc_start: 0.8849 (mmpt) cc_final: 0.8644 (mmtp) REVERT: B 10 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8141 (tm-30) REVERT: B 13 GLN cc_start: 0.8634 (tt0) cc_final: 0.8381 (tm-30) REVERT: B 23 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8313 (tmmt) REVERT: B 195 ASP cc_start: 0.8381 (p0) cc_final: 0.8162 (p0) REVERT: B 212 ASP cc_start: 0.8607 (t0) cc_final: 0.7930 (t0) REVERT: B 215 GLU cc_start: 0.8776 (mp0) cc_final: 0.7981 (mp0) REVERT: B 233 CYS cc_start: 0.8821 (t) cc_final: 0.8567 (t) REVERT: B 254 ASP cc_start: 0.8188 (t0) cc_final: 0.7730 (t0) REVERT: B 258 ASP cc_start: 0.8200 (t0) cc_final: 0.7825 (t0) REVERT: B 289 TYR cc_start: 0.8822 (m-80) cc_final: 0.8386 (m-80) REVERT: B 336 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8373 (mp) REVERT: E 219 GLN cc_start: 0.9091 (pp30) cc_final: 0.8347 (pp30) REVERT: E 234 GLU cc_start: 0.7758 (pm20) cc_final: 0.6651 (pm20) outliers start: 25 outliers final: 17 residues processed: 269 average time/residue: 0.1170 time to fit residues: 40.5464 Evaluate side-chains 265 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** 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 = 0.3472 r_free = 0.3472 target = 0.103607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.089295 restraints weight = 14676.907| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.43 r_work: 0.3133 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9141 Z= 0.134 Angle : 0.566 8.823 12377 Z= 0.292 Chirality : 0.042 0.208 1412 Planarity : 0.004 0.053 1553 Dihedral : 4.329 33.135 1243 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.85 % Allowed : 18.77 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1123 helix: 1.85 (0.26), residues: 410 sheet: 0.26 (0.30), residues: 282 loop : -0.16 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 46 TYR 0.014 0.001 TYR E 102 PHE 0.021 0.001 PHE A 189 TRP 0.009 0.001 TRP R 91 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9139) covalent geometry : angle 0.56510 (12373) SS BOND : bond 0.00568 ( 2) SS BOND : angle 1.81544 ( 4) hydrogen bonds : bond 0.03688 ( 457) hydrogen bonds : angle 4.58598 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 246 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 ARG cc_start: 0.8266 (mmm160) cc_final: 0.7987 (mmm-85) REVERT: R 83 VAL cc_start: 0.8758 (p) cc_final: 0.8499 (m) REVERT: R 87 MET cc_start: 0.8762 (mtt) cc_final: 0.8481 (mtm) REVERT: R 91 TRP cc_start: 0.9107 (t-100) cc_final: 0.8740 (t-100) REVERT: R 189 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7910 (tm-30) REVERT: R 203 ILE cc_start: 0.8829 (tt) cc_final: 0.8565 (mm) REVERT: R 214 MET cc_start: 0.8013 (tpp) cc_final: 0.7805 (tpt) REVERT: R 231 LYS cc_start: 0.8820 (mttm) cc_final: 0.8390 (ttmm) REVERT: R 235 LYS cc_start: 0.8532 (pttp) cc_final: 0.8172 (pttp) REVERT: R 310 ARG cc_start: 0.8812 (mtm-85) cc_final: 0.8509 (mtm-85) REVERT: A 197 LYS cc_start: 0.8409 (mmmt) cc_final: 0.8024 (mttm) REVERT: A 232 LEU cc_start: 0.8859 (mt) cc_final: 0.8631 (mp) REVERT: A 275 GLU cc_start: 0.8601 (tp30) cc_final: 0.8289 (tp30) REVERT: A 298 GLU cc_start: 0.7365 (tt0) cc_final: 0.7070 (tt0) REVERT: A 309 ASP cc_start: 0.8438 (t70) cc_final: 0.8026 (t0) REVERT: B 13 GLN cc_start: 0.8599 (tt0) cc_final: 0.8089 (tm-30) REVERT: B 23 LYS cc_start: 0.8585 (ttpp) cc_final: 0.8300 (tmmt) REVERT: B 212 ASP cc_start: 0.8524 (t0) cc_final: 0.7853 (t0) REVERT: B 215 GLU cc_start: 0.8710 (mp0) cc_final: 0.7923 (mp0) REVERT: B 233 CYS cc_start: 0.8723 (t) cc_final: 0.8426 (t) REVERT: B 254 ASP cc_start: 0.8203 (t0) cc_final: 0.7722 (t0) REVERT: B 258 ASP cc_start: 0.8094 (t0) cc_final: 0.7683 (t0) REVERT: B 259 GLN cc_start: 0.8458 (tt0) cc_final: 0.8197 (mt0) REVERT: B 336 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8384 (mp) REVERT: E 132 THR cc_start: 0.8388 (m) cc_final: 0.8068 (t) REVERT: E 219 GLN cc_start: 0.9063 (pp30) cc_final: 0.8393 (pp30) REVERT: E 234 GLU cc_start: 0.7699 (pm20) cc_final: 0.6589 (pm20) outliers start: 18 outliers final: 14 residues processed: 257 average time/residue: 0.1162 time to fit residues: 38.4459 Evaluate side-chains 256 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.0170 chunk 73 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 52 optimal weight: 0.0570 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 0.0000 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.3340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 258 GLN ** B 259 GLN ** 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 = 0.3514 r_free = 0.3514 target = 0.106488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.092091 restraints weight = 14606.004| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.44 r_work: 0.3180 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9141 Z= 0.108 Angle : 0.559 12.366 12377 Z= 0.283 Chirality : 0.041 0.199 1412 Planarity : 0.004 0.058 1553 Dihedral : 4.118 32.701 1243 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.44 % Allowed : 19.28 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1123 helix: 2.11 (0.26), residues: 407 sheet: 0.25 (0.30), residues: 278 loop : -0.15 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 46 TYR 0.018 0.001 TYR A 296 PHE 0.024 0.001 PHE A 189 TRP 0.011 0.001 TRP R 95 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9139) covalent geometry : angle 0.55846 (12373) SS BOND : bond 0.00370 ( 2) SS BOND : angle 1.39704 ( 4) hydrogen bonds : bond 0.03278 ( 457) hydrogen bonds : angle 4.43479 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 VAL cc_start: 0.8822 (t) cc_final: 0.8620 (p) REVERT: R 57 ARG cc_start: 0.9022 (tpp80) cc_final: 0.8730 (tpp80) REVERT: R 83 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8420 (m) REVERT: R 87 MET cc_start: 0.8656 (mtt) cc_final: 0.8379 (mtm) REVERT: R 91 TRP cc_start: 0.9027 (t-100) cc_final: 0.8718 (t-100) REVERT: R 189 GLU cc_start: 0.8536 (tm-30) cc_final: 0.7932 (tm-30) REVERT: R 203 ILE cc_start: 0.8803 (tt) cc_final: 0.8537 (mm) REVERT: R 231 LYS cc_start: 0.8757 (mttm) cc_final: 0.8410 (ttmm) REVERT: R 235 LYS cc_start: 0.8624 (pttp) cc_final: 0.8260 (pttp) REVERT: R 252 ILE cc_start: 0.8736 (mm) cc_final: 0.8497 (mt) REVERT: R 292 PHE cc_start: 0.8467 (m-10) cc_final: 0.8256 (m-10) REVERT: R 310 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8521 (mtm-85) REVERT: A 232 LEU cc_start: 0.8815 (mt) cc_final: 0.8593 (mp) REVERT: A 275 GLU cc_start: 0.8599 (tp30) cc_final: 0.8241 (tp30) REVERT: A 298 GLU cc_start: 0.7335 (tt0) cc_final: 0.7046 (tt0) REVERT: A 310 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8775 (mm) REVERT: B 10 GLU cc_start: 0.8565 (tp30) cc_final: 0.8345 (tp30) REVERT: B 13 GLN cc_start: 0.8510 (tt0) cc_final: 0.8258 (tm-30) REVERT: B 23 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8306 (tmmt) REVERT: B 189 SER cc_start: 0.8390 (p) cc_final: 0.8050 (t) REVERT: B 212 ASP cc_start: 0.8459 (t0) cc_final: 0.7730 (t0) REVERT: B 215 GLU cc_start: 0.8681 (mp0) cc_final: 0.8038 (mp0) REVERT: B 233 CYS cc_start: 0.8698 (t) cc_final: 0.8388 (t) REVERT: B 254 ASP cc_start: 0.8219 (t0) cc_final: 0.7756 (t0) REVERT: B 258 ASP cc_start: 0.8040 (t0) cc_final: 0.7635 (t0) REVERT: E 132 THR cc_start: 0.8321 (m) cc_final: 0.8038 (t) REVERT: E 219 GLN cc_start: 0.9030 (pp30) cc_final: 0.8518 (pp30) REVERT: E 234 GLU cc_start: 0.7822 (pm20) cc_final: 0.6825 (pm20) outliers start: 14 outliers final: 7 residues processed: 250 average time/residue: 0.1160 time to fit residues: 37.4861 Evaluate side-chains 247 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 238 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 259 GLN ** 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 = 0.3497 r_free = 0.3497 target = 0.105274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.090854 restraints weight = 14641.748| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.44 r_work: 0.3159 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9141 Z= 0.127 Angle : 0.587 10.558 12377 Z= 0.298 Chirality : 0.042 0.193 1412 Planarity : 0.004 0.043 1553 Dihedral : 4.186 32.657 1243 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.33 % Allowed : 20.21 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.25), residues: 1123 helix: 2.07 (0.26), residues: 413 sheet: 0.32 (0.30), residues: 279 loop : -0.12 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 27 TYR 0.017 0.001 TYR A 296 PHE 0.028 0.002 PHE E 227 TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9139) covalent geometry : angle 0.58597 (12373) SS BOND : bond 0.00399 ( 2) SS BOND : angle 1.59393 ( 4) hydrogen bonds : bond 0.03557 ( 457) hydrogen bonds : angle 4.47470 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 247 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 VAL cc_start: 0.8827 (t) cc_final: 0.8627 (p) REVERT: R 54 ARG cc_start: 0.8421 (mmm160) cc_final: 0.7615 (mmm-85) REVERT: R 57 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8725 (tpp80) REVERT: R 83 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8430 (m) REVERT: R 87 MET cc_start: 0.8670 (mtt) cc_final: 0.8409 (mtm) REVERT: R 91 TRP cc_start: 0.9050 (t-100) cc_final: 0.8745 (t-100) REVERT: R 189 GLU cc_start: 0.8536 (tm-30) cc_final: 0.7928 (tm-30) REVERT: R 203 ILE cc_start: 0.8819 (tt) cc_final: 0.8572 (mm) REVERT: R 231 LYS cc_start: 0.8780 (mttm) cc_final: 0.8418 (ttmm) REVERT: R 235 LYS cc_start: 0.8580 (pttp) cc_final: 0.8225 (pttp) REVERT: R 274 TYR cc_start: 0.8567 (m-80) cc_final: 0.8287 (m-10) REVERT: R 292 PHE cc_start: 0.8536 (m-10) cc_final: 0.8307 (m-10) REVERT: R 304 PHE cc_start: 0.8568 (m-10) cc_final: 0.8352 (m-10) REVERT: R 310 ARG cc_start: 0.8839 (mtm-85) cc_final: 0.8529 (mtm-85) REVERT: A 232 LEU cc_start: 0.8809 (mt) cc_final: 0.8597 (mp) REVERT: A 298 GLU cc_start: 0.7366 (tt0) cc_final: 0.7065 (tt0) REVERT: A 310 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8812 (mm) REVERT: B 10 GLU cc_start: 0.8560 (tp30) cc_final: 0.8325 (tp30) REVERT: B 13 GLN cc_start: 0.8475 (tt0) cc_final: 0.8182 (tm-30) REVERT: B 23 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8342 (tmmt) REVERT: B 189 SER cc_start: 0.8308 (p) cc_final: 0.7971 (t) REVERT: B 212 ASP cc_start: 0.8506 (t0) cc_final: 0.7919 (t0) REVERT: B 215 GLU cc_start: 0.8674 (mp0) cc_final: 0.8062 (mp0) REVERT: B 233 CYS cc_start: 0.8668 (t) cc_final: 0.8347 (t) REVERT: B 254 ASP cc_start: 0.8192 (t0) cc_final: 0.7753 (t0) REVERT: B 258 ASP cc_start: 0.8079 (t0) cc_final: 0.7658 (t0) REVERT: B 259 GLN cc_start: 0.8441 (tt0) cc_final: 0.8131 (mt0) REVERT: E 132 THR cc_start: 0.8336 (m) cc_final: 0.8108 (t) REVERT: E 219 GLN cc_start: 0.8977 (pp30) cc_final: 0.8444 (pp30) REVERT: E 234 GLU cc_start: 0.7862 (pm20) cc_final: 0.6768 (pm20) outliers start: 13 outliers final: 10 residues processed: 256 average time/residue: 0.1114 time to fit residues: 37.0110 Evaluate side-chains 254 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** 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 = 0.3491 r_free = 0.3491 target = 0.104917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090550 restraints weight = 14536.104| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.42 r_work: 0.3153 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9141 Z= 0.133 Angle : 0.591 10.803 12377 Z= 0.301 Chirality : 0.042 0.191 1412 Planarity : 0.004 0.061 1553 Dihedral : 4.212 32.657 1243 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.33 % Allowed : 20.41 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.25), residues: 1123 helix: 2.06 (0.26), residues: 413 sheet: 0.33 (0.30), residues: 280 loop : -0.11 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 46 TYR 0.017 0.001 TYR A 296 PHE 0.037 0.002 PHE R 161 TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9139) covalent geometry : angle 0.58998 (12373) SS BOND : bond 0.00575 ( 2) SS BOND : angle 1.68135 ( 4) hydrogen bonds : bond 0.03588 ( 457) hydrogen bonds : angle 4.49150 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2399.46 seconds wall clock time: 41 minutes 41.30 seconds (2501.30 seconds total)