Starting phenix.real_space_refine on Thu Jan 16 02:27:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqn_38582/01_2025/8xqn_38582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqn_38582/01_2025/8xqn_38582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqn_38582/01_2025/8xqn_38582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqn_38582/01_2025/8xqn_38582.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqn_38582/01_2025/8xqn_38582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqn_38582/01_2025/8xqn_38582.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 59 5.16 5 C 5747 2.51 5 N 1512 2.21 5 O 1658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8976 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1813 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2298 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 3, 'TRANS': 280} Chain breaks: 2 Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'CLR': 1, 'GOQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.34, per 1000 atoms: 0.59 Number of scatterers: 8976 At special positions: 0 Unit cell: (91.52, 120.64, 125.84, 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 59 16.00 O 1658 8.00 N 1512 7.00 C 5747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 977.0 milliseconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 41.3% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.501A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.572A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.331A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.697A 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 241 through 255 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.672A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.805A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 37 Processing helix chain 'R' and resid 42 through 72 Processing helix chain 'R' and resid 73 through 78 Processing helix chain 'R' and resid 79 through 112 Processing helix chain 'R' and resid 116 through 125 removed outlier: 3.733A pdb=" N ARG R 125 " --> pdb=" O TYR R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 137 removed outlier: 3.509A pdb=" N LEU R 131 " --> pdb=" O LYS R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 160 Processing helix chain 'R' and resid 173 through 216 Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 222 through 226 Processing helix chain 'R' and resid 227 through 253 removed outlier: 3.845A pdb=" N LYS R 231 " --> pdb=" O HIS R 227 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 259 removed outlier: 3.535A pdb=" N GLU R 259 " --> pdb=" O ARG R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 284 removed outlier: 4.166A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 4.168A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS R 278 " --> pdb=" O SER R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.766A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.010A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.100A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.088A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.433A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.662A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.653A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.413A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.644A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.354A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2851 1.34 - 1.46: 1947 1.46 - 1.58: 4281 1.58 - 1.70: 0 1.70 - 1.81: 87 Bond restraints: 9166 Sorted by residual: bond pdb=" C5 GOQ R 501 " pdb=" C6 GOQ R 501 " ideal model delta sigma weight residual 1.454 1.416 0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C8 GOQ R 501 " pdb=" C9 GOQ R 501 " ideal model delta sigma weight residual 1.350 1.386 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C10 GOQ R 501 " pdb=" C9 GOQ R 501 " ideal model delta sigma weight residual 1.423 1.393 0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C LEU B 146 " pdb=" N SER B 147 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.40e-02 5.10e+03 1.87e+00 bond pdb=" O GOQ R 501 " pdb=" C1 GOQ R 501 " ideal model delta sigma weight residual 1.340 1.367 -0.027 2.00e-02 2.50e+03 1.85e+00 ... (remaining 9161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 12234 2.21 - 4.41: 138 4.41 - 6.62: 23 6.62 - 8.83: 7 8.83 - 11.03: 3 Bond angle restraints: 12405 Sorted by residual: angle pdb=" C ASP A 328 " pdb=" CA ASP A 328 " pdb=" CB ASP A 328 " ideal model delta sigma weight residual 115.79 109.88 5.91 1.19e+00 7.06e-01 2.47e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.20e+01 angle pdb=" CB MET S 180 " pdb=" CG MET S 180 " pdb=" SD MET S 180 " ideal model delta sigma weight residual 112.70 122.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CB MET R 268 " pdb=" CG MET R 268 " pdb=" SD MET R 268 " ideal model delta sigma weight residual 112.70 122.25 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CA LEU R 13 " pdb=" CB LEU R 13 " pdb=" CG LEU R 13 " ideal model delta sigma weight residual 116.30 127.33 -11.03 3.50e+00 8.16e-02 9.94e+00 ... (remaining 12400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4732 17.51 - 35.02: 562 35.02 - 52.53: 137 52.53 - 70.04: 24 70.04 - 87.55: 4 Dihedral angle restraints: 5459 sinusoidal: 2173 harmonic: 3286 Sorted by residual: dihedral pdb=" CA TYR A 296 " pdb=" C TYR A 296 " pdb=" N GLU A 297 " pdb=" CA GLU A 297 " ideal model delta harmonic sigma weight residual -180.00 -157.95 -22.05 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP B 333 " pdb=" CB ASP B 333 " pdb=" CG ASP B 333 " pdb=" OD1 ASP B 333 " ideal model delta sinusoidal sigma weight residual -30.00 -86.86 56.86 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1128 0.049 - 0.098: 227 0.098 - 0.147: 52 0.147 - 0.197: 2 0.197 - 0.246: 4 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CB ILE R 19 " pdb=" CA ILE R 19 " pdb=" CG1 ILE R 19 " pdb=" CG2 ILE R 19 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB ILE R 179 " pdb=" CA ILE R 179 " pdb=" CG1 ILE R 179 " pdb=" CG2 ILE R 179 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASP B 258 " pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CB ASP B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1410 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO S 14 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 79 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C GLU R 79 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU R 79 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS R 80 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET S 180 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C MET S 180 " 0.040 2.00e-02 2.50e+03 pdb=" O MET S 180 " -0.015 2.00e-02 2.50e+03 pdb=" N SER S 181 " -0.014 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 132 2.64 - 3.20: 8374 3.20 - 3.77: 14536 3.77 - 4.33: 19962 4.33 - 4.90: 32958 Nonbonded interactions: 75962 Sorted by model distance: nonbonded pdb=" NZ LYS A 210 " pdb=" OD2 ASP B 228 " model vdw 2.075 3.120 nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.102 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.121 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.181 3.040 ... (remaining 75957 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: 0.870 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 : 0.004 0.045 9166 Z= 0.272 Angle : 0.621 11.034 12405 Z= 0.313 Chirality : 0.043 0.246 1413 Planarity : 0.004 0.066 1542 Dihedral : 15.732 87.549 3327 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 29.26 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1117 helix: 2.12 (0.25), residues: 418 sheet: 0.21 (0.32), residues: 290 loop : -0.43 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 98 HIS 0.004 0.001 HIS R 208 PHE 0.032 0.002 PHE R 76 TYR 0.030 0.001 TYR S 223 ARG 0.007 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7892 (m-30) cc_final: 0.7530 (m-30) REVERT: B 97 SER cc_start: 0.8688 (t) cc_final: 0.8284 (p) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2302 time to fit residues: 76.8312 Evaluate side-chains 239 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.138172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117889 restraints weight = 13598.225| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.20 r_work: 0.3427 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9166 Z= 0.255 Angle : 0.588 8.111 12405 Z= 0.310 Chirality : 0.043 0.235 1413 Planarity : 0.004 0.062 1542 Dihedral : 5.131 51.164 1288 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.49 % Allowed : 24.26 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1117 helix: 2.17 (0.25), residues: 423 sheet: -0.10 (0.31), residues: 290 loop : -0.45 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.018 0.002 PHE R 82 TYR 0.030 0.002 TYR S 223 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 1.020 Fit side-chains REVERT: A 251 ASP cc_start: 0.8286 (m-30) cc_final: 0.7802 (m-30) REVERT: A 310 LEU cc_start: 0.8222 (tp) cc_final: 0.7853 (tt) REVERT: B 6 GLN cc_start: 0.8316 (pm20) cc_final: 0.8102 (pm20) REVERT: B 75 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: B 97 SER cc_start: 0.8732 (t) cc_final: 0.8377 (p) REVERT: B 200 VAL cc_start: 0.8762 (m) cc_final: 0.8522 (p) REVERT: B 274 THR cc_start: 0.8218 (p) cc_final: 0.8003 (p) REVERT: C 42 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7853 (tm-30) REVERT: S 46 GLU cc_start: 0.8334 (tt0) cc_final: 0.8100 (tt0) REVERT: S 223 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.7121 (t80) outliers start: 44 outliers final: 30 residues processed: 266 average time/residue: 0.2473 time to fit residues: 88.0940 Evaluate side-chains 281 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 267 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118290 restraints weight = 13661.841| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.20 r_work: 0.3434 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9166 Z= 0.217 Angle : 0.544 6.847 12405 Z= 0.287 Chirality : 0.042 0.226 1413 Planarity : 0.004 0.058 1542 Dihedral : 4.948 50.102 1288 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.99 % Allowed : 23.55 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1117 helix: 2.25 (0.24), residues: 423 sheet: -0.12 (0.31), residues: 287 loop : -0.53 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS B 311 PHE 0.017 0.001 PHE R 82 TYR 0.031 0.001 TYR S 223 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 268 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.8221 (mtm-85) REVERT: A 349 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7776 (mtpp) REVERT: B 97 SER cc_start: 0.8745 (t) cc_final: 0.8402 (p) REVERT: B 200 VAL cc_start: 0.8785 (m) cc_final: 0.8531 (p) REVERT: B 230 ASN cc_start: 0.8052 (m-40) cc_final: 0.7823 (m-40) REVERT: B 274 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7983 (p) REVERT: B 283 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7655 (mmm-85) REVERT: C 42 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7842 (tm-30) REVERT: S 46 GLU cc_start: 0.8307 (tt0) cc_final: 0.8000 (tt0) REVERT: S 63 THR cc_start: 0.8482 (p) cc_final: 0.8241 (t) REVERT: S 223 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.7101 (t80) REVERT: R 245 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6966 (mm) outliers start: 49 outliers final: 36 residues processed: 286 average time/residue: 0.2385 time to fit residues: 91.0100 Evaluate side-chains 301 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 265 SER Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.139059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118501 restraints weight = 13505.748| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.22 r_work: 0.3398 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9166 Z= 0.366 Angle : 0.603 7.542 12405 Z= 0.317 Chirality : 0.044 0.266 1413 Planarity : 0.004 0.061 1542 Dihedral : 5.175 51.615 1288 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.81 % Allowed : 25.38 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1117 helix: 2.06 (0.24), residues: 422 sheet: -0.21 (0.31), residues: 289 loop : -0.62 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.007 0.001 HIS B 311 PHE 0.016 0.002 PHE R 82 TYR 0.031 0.002 TYR S 223 ARG 0.003 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 192 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7441 (mptm) REVERT: A 243 MET cc_start: 0.7889 (tpp) cc_final: 0.6973 (tpp) REVERT: A 313 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8143 (mtm-85) REVERT: A 349 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7834 (mtpp) REVERT: B 97 SER cc_start: 0.8740 (t) cc_final: 0.8403 (p) REVERT: B 150 ARG cc_start: 0.8437 (mmt-90) cc_final: 0.8181 (mmt-90) REVERT: B 195 ASP cc_start: 0.7876 (p0) cc_final: 0.7606 (t70) REVERT: B 200 VAL cc_start: 0.8773 (m) cc_final: 0.8516 (p) REVERT: B 230 ASN cc_start: 0.8119 (m-40) cc_final: 0.7899 (m-40) REVERT: B 245 SER cc_start: 0.7700 (m) cc_final: 0.7248 (t) REVERT: B 253 PHE cc_start: 0.8157 (m-80) cc_final: 0.7804 (m-80) REVERT: B 274 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.8074 (p) REVERT: B 283 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7658 (mmm-85) REVERT: B 314 ARG cc_start: 0.8499 (ttm170) cc_final: 0.8054 (mtp180) REVERT: S 46 GLU cc_start: 0.8354 (tt0) cc_final: 0.8072 (tt0) REVERT: S 87 ARG cc_start: 0.8048 (ptp-110) cc_final: 0.7776 (ptp90) REVERT: S 223 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7253 (t80) REVERT: R 98 TRP cc_start: 0.8627 (m100) cc_final: 0.7930 (m100) REVERT: R 212 MET cc_start: 0.7484 (mmm) cc_final: 0.6796 (mmm) outliers start: 57 outliers final: 43 residues processed: 279 average time/residue: 0.2580 time to fit residues: 93.7775 Evaluate side-chains 304 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 86 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 52 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120695 restraints weight = 13519.397| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.21 r_work: 0.3437 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9166 Z= 0.192 Angle : 0.563 7.730 12405 Z= 0.293 Chirality : 0.042 0.221 1413 Planarity : 0.004 0.055 1542 Dihedral : 4.960 48.947 1288 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.30 % Allowed : 25.59 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1117 helix: 2.31 (0.24), residues: 421 sheet: -0.21 (0.30), residues: 292 loop : -0.61 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 98 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE R 76 TYR 0.030 0.001 TYR S 223 ARG 0.007 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 1.005 Fit side-chains REVERT: A 243 MET cc_start: 0.7997 (tpp) cc_final: 0.7069 (tpp) REVERT: A 349 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7768 (mtpp) REVERT: B 97 SER cc_start: 0.8726 (t) cc_final: 0.8394 (p) REVERT: B 200 VAL cc_start: 0.8777 (m) cc_final: 0.8486 (p) REVERT: B 230 ASN cc_start: 0.7980 (m-40) cc_final: 0.7724 (m-40) REVERT: B 234 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8683 (m-80) REVERT: B 245 SER cc_start: 0.7574 (m) cc_final: 0.7164 (t) REVERT: C 42 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7830 (tm-30) REVERT: C 47 GLU cc_start: 0.7886 (mp0) cc_final: 0.7360 (mp0) REVERT: S 46 GLU cc_start: 0.8332 (tt0) cc_final: 0.8061 (tt0) REVERT: S 116 THR cc_start: 0.8801 (t) cc_final: 0.8481 (m) REVERT: S 223 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.7073 (t80) REVERT: R 212 MET cc_start: 0.7398 (mmm) cc_final: 0.6931 (mmm) REVERT: R 245 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6970 (mm) outliers start: 52 outliers final: 36 residues processed: 292 average time/residue: 0.2529 time to fit residues: 96.9558 Evaluate side-chains 304 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 265 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.139624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120177 restraints weight = 13587.302| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.17 r_work: 0.3428 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9166 Z= 0.250 Angle : 0.581 8.981 12405 Z= 0.301 Chirality : 0.043 0.230 1413 Planarity : 0.004 0.060 1542 Dihedral : 5.001 49.434 1288 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.20 % Allowed : 26.40 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1117 helix: 2.27 (0.25), residues: 423 sheet: -0.21 (0.31), residues: 289 loop : -0.62 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.005 0.001 HIS B 311 PHE 0.015 0.001 PHE R 82 TYR 0.030 0.002 TYR S 223 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 0.965 Fit side-chains REVERT: A 243 MET cc_start: 0.8020 (tpp) cc_final: 0.7111 (tpp) REVERT: A 349 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7796 (mtpp) REVERT: B 75 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: B 78 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7960 (mptp) REVERT: B 97 SER cc_start: 0.8729 (t) cc_final: 0.8385 (p) REVERT: B 200 VAL cc_start: 0.8765 (m) cc_final: 0.8481 (p) REVERT: B 230 ASN cc_start: 0.8005 (m-40) cc_final: 0.7743 (m-40) REVERT: B 234 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: B 245 SER cc_start: 0.7590 (m) cc_final: 0.7190 (t) REVERT: B 283 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7595 (mmm-85) REVERT: C 42 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7833 (tm-30) REVERT: S 116 THR cc_start: 0.8768 (t) cc_final: 0.8450 (m) REVERT: S 223 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.7130 (t80) REVERT: R 212 MET cc_start: 0.7396 (mmm) cc_final: 0.6956 (mmm) REVERT: R 245 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6999 (mm) outliers start: 51 outliers final: 39 residues processed: 288 average time/residue: 0.2487 time to fit residues: 94.0189 Evaluate side-chains 309 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 265 SER Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120141 restraints weight = 13723.221| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.19 r_work: 0.3426 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9166 Z= 0.247 Angle : 0.584 9.734 12405 Z= 0.302 Chirality : 0.043 0.234 1413 Planarity : 0.003 0.057 1542 Dihedral : 4.991 49.135 1288 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.71 % Allowed : 25.69 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1117 helix: 2.29 (0.24), residues: 422 sheet: -0.21 (0.31), residues: 289 loop : -0.66 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.017 0.001 PHE R 82 TYR 0.031 0.002 TYR S 223 ARG 0.006 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8038 (tpp) cc_final: 0.7122 (tpp) REVERT: A 261 ASP cc_start: 0.7644 (p0) cc_final: 0.7413 (p0) REVERT: A 349 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7764 (mtpp) REVERT: B 78 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7955 (mptp) REVERT: B 97 SER cc_start: 0.8753 (t) cc_final: 0.8420 (p) REVERT: B 170 ASP cc_start: 0.8225 (t70) cc_final: 0.7983 (t70) REVERT: B 197 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7802 (mmm-85) REVERT: B 200 VAL cc_start: 0.8768 (m) cc_final: 0.8488 (p) REVERT: B 230 ASN cc_start: 0.7999 (m-40) cc_final: 0.7747 (m-40) REVERT: B 234 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8680 (m-80) REVERT: B 245 SER cc_start: 0.7604 (m) cc_final: 0.7195 (t) REVERT: B 283 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7595 (mmm-85) REVERT: S 68 PHE cc_start: 0.7791 (m-10) cc_final: 0.7441 (m-10) REVERT: S 116 THR cc_start: 0.8785 (t) cc_final: 0.8469 (m) REVERT: S 223 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.7131 (t80) REVERT: R 212 MET cc_start: 0.7389 (mmm) cc_final: 0.6976 (mmm) REVERT: R 245 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7020 (mm) outliers start: 56 outliers final: 44 residues processed: 283 average time/residue: 0.2583 time to fit residues: 95.7401 Evaluate side-chains 312 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 265 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 86 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120866 restraints weight = 13843.988| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.20 r_work: 0.3435 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9166 Z= 0.198 Angle : 0.574 10.654 12405 Z= 0.295 Chirality : 0.042 0.225 1413 Planarity : 0.003 0.059 1542 Dihedral : 4.915 46.497 1288 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.30 % Allowed : 26.40 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1117 helix: 2.38 (0.25), residues: 422 sheet: -0.21 (0.30), residues: 289 loop : -0.64 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 98 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE R 247 TYR 0.030 0.001 TYR S 223 ARG 0.003 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 0.983 Fit side-chains REVERT: A 243 MET cc_start: 0.8065 (tpp) cc_final: 0.7213 (tpp) REVERT: A 261 ASP cc_start: 0.7612 (p0) cc_final: 0.7366 (p0) REVERT: A 349 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7777 (mtpp) REVERT: B 78 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7873 (mptp) REVERT: B 97 SER cc_start: 0.8751 (t) cc_final: 0.8427 (p) REVERT: B 197 ARG cc_start: 0.7955 (mmm-85) cc_final: 0.7723 (mmm-85) REVERT: B 200 VAL cc_start: 0.8772 (m) cc_final: 0.8493 (p) REVERT: B 230 ASN cc_start: 0.7932 (m-40) cc_final: 0.7316 (m-40) REVERT: B 234 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8682 (m-80) REVERT: B 245 SER cc_start: 0.7568 (m) cc_final: 0.7157 (t) REVERT: B 246 ASP cc_start: 0.8037 (m-30) cc_final: 0.7359 (m-30) REVERT: B 283 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7571 (mmm-85) REVERT: B 314 ARG cc_start: 0.8430 (ttm170) cc_final: 0.7996 (mtp180) REVERT: S 68 PHE cc_start: 0.7866 (m-10) cc_final: 0.7441 (m-10) REVERT: S 116 THR cc_start: 0.8759 (t) cc_final: 0.8440 (m) REVERT: S 163 TYR cc_start: 0.8364 (m-80) cc_final: 0.8060 (m-80) REVERT: S 223 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.7094 (t80) REVERT: R 212 MET cc_start: 0.7395 (mmm) cc_final: 0.6997 (mmm) REVERT: R 245 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6974 (mm) outliers start: 52 outliers final: 40 residues processed: 293 average time/residue: 0.2527 time to fit residues: 96.8895 Evaluate side-chains 312 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 265 SER Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 18 optimal weight: 0.0570 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120471 restraints weight = 13645.669| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.18 r_work: 0.3418 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9166 Z= 0.251 Angle : 0.593 8.468 12405 Z= 0.307 Chirality : 0.043 0.231 1413 Planarity : 0.004 0.059 1542 Dihedral : 4.989 46.681 1288 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.59 % Allowed : 27.22 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1117 helix: 2.33 (0.25), residues: 422 sheet: -0.22 (0.30), residues: 289 loop : -0.66 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.017 0.002 PHE R 247 TYR 0.032 0.002 TYR S 223 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 1.049 Fit side-chains REVERT: A 243 MET cc_start: 0.8032 (tpp) cc_final: 0.7147 (tpp) REVERT: A 349 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7800 (mtpp) REVERT: B 97 SER cc_start: 0.8775 (t) cc_final: 0.8453 (p) REVERT: B 197 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7751 (mmm-85) REVERT: B 200 VAL cc_start: 0.8789 (m) cc_final: 0.8508 (p) REVERT: B 230 ASN cc_start: 0.7978 (m-40) cc_final: 0.7396 (m-40) REVERT: B 234 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8683 (m-80) REVERT: B 245 SER cc_start: 0.7587 (m) cc_final: 0.7174 (t) REVERT: B 246 ASP cc_start: 0.8050 (m-30) cc_final: 0.7439 (m-30) REVERT: B 283 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7624 (mmm-85) REVERT: S 68 PHE cc_start: 0.7694 (m-10) cc_final: 0.7208 (m-10) REVERT: S 83 MET cc_start: 0.7745 (mtm) cc_final: 0.7149 (mtm) REVERT: S 116 THR cc_start: 0.8767 (t) cc_final: 0.8449 (m) REVERT: S 163 TYR cc_start: 0.8366 (m-80) cc_final: 0.8030 (m-80) REVERT: S 223 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.7176 (t80) REVERT: R 212 MET cc_start: 0.7432 (mmm) cc_final: 0.7015 (mmm) REVERT: R 245 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6997 (mm) outliers start: 45 outliers final: 37 residues processed: 285 average time/residue: 0.2581 time to fit residues: 96.2737 Evaluate side-chains 306 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.0070 chunk 25 optimal weight: 0.0670 chunk 86 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.141735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122261 restraints weight = 13763.826| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.19 r_work: 0.3454 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9166 Z= 0.171 Angle : 0.583 11.031 12405 Z= 0.298 Chirality : 0.042 0.239 1413 Planarity : 0.003 0.058 1542 Dihedral : 4.823 44.222 1288 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.87 % Allowed : 27.62 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1117 helix: 2.46 (0.25), residues: 422 sheet: -0.28 (0.30), residues: 297 loop : -0.59 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 98 HIS 0.003 0.001 HIS B 311 PHE 0.016 0.001 PHE R 247 TYR 0.030 0.002 TYR S 223 ARG 0.004 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 0.999 Fit side-chains REVERT: A 243 MET cc_start: 0.8056 (tpp) cc_final: 0.7172 (tpp) REVERT: A 349 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7754 (mtpp) REVERT: B 97 SER cc_start: 0.8773 (t) cc_final: 0.8445 (p) REVERT: B 200 VAL cc_start: 0.8790 (m) cc_final: 0.8505 (p) REVERT: B 230 ASN cc_start: 0.7916 (m-40) cc_final: 0.7276 (m-40) REVERT: B 234 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8691 (m-80) REVERT: B 245 SER cc_start: 0.7588 (m) cc_final: 0.7141 (t) REVERT: B 246 ASP cc_start: 0.8010 (m-30) cc_final: 0.7320 (m-30) REVERT: B 249 THR cc_start: 0.8155 (p) cc_final: 0.7837 (t) REVERT: B 314 ARG cc_start: 0.8347 (ttm170) cc_final: 0.8010 (mtp180) REVERT: S 116 THR cc_start: 0.8741 (t) cc_final: 0.8419 (m) REVERT: S 163 TYR cc_start: 0.8368 (m-80) cc_final: 0.8066 (m-80) REVERT: S 223 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6937 (t80) REVERT: R 212 MET cc_start: 0.7387 (mmm) cc_final: 0.7025 (mmm) REVERT: R 245 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6896 (mm) outliers start: 38 outliers final: 32 residues processed: 289 average time/residue: 0.2579 time to fit residues: 98.0666 Evaluate side-chains 299 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120612 restraints weight = 13778.010| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.19 r_work: 0.3431 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9166 Z= 0.254 Angle : 0.600 9.732 12405 Z= 0.310 Chirality : 0.043 0.233 1413 Planarity : 0.004 0.060 1542 Dihedral : 5.008 45.825 1288 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.57 % Allowed : 28.34 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1117 helix: 2.39 (0.25), residues: 422 sheet: -0.25 (0.30), residues: 291 loop : -0.62 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 332 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.002 PHE R 82 TYR 0.031 0.002 TYR B 59 ARG 0.005 0.000 ARG S 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5480.40 seconds wall clock time: 98 minutes 5.38 seconds (5885.38 seconds total)