Starting phenix.real_space_refine on Thu Mar 13 12:21:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqt_38588/03_2025/8xqt_38588.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqt_38588/03_2025/8xqt_38588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqt_38588/03_2025/8xqt_38588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqt_38588/03_2025/8xqt_38588.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqt_38588/03_2025/8xqt_38588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqt_38588/03_2025/8xqt_38588.cif" } resolution = 2.94 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= 0.021 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 5707 2.51 5 N 1494 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8897 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: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2216 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 3, 'TRANS': 270} Chain breaks: 2 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.26, per 1000 atoms: 0.59 Number of scatterers: 8897 At special positions: 0 Unit cell: (90.48, 119.6, 122.72, 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 1637 8.00 N 1494 7.00 C 5707 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: 2.13 Conformation dependent library (CDL) restraints added in 962.2 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 41.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.657A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.809A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.859A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 352 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 53 through 56 removed outlier: 4.288A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.846A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.615A 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 72 through 77 removed outlier: 3.561A pdb=" N PHE R 76 " --> pdb=" O PHE R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 112 Processing helix chain 'R' and resid 116 through 125 removed outlier: 3.731A pdb=" N LEU R 120 " --> pdb=" O ASN R 116 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR R 121 " --> pdb=" O SER R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 157 Processing helix chain 'R' and resid 173 through 216 removed outlier: 4.067A pdb=" N ILE R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 229 through 252 removed outlier: 3.534A pdb=" N ILE R 234 " --> pdb=" O VAL R 230 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU R 239 " --> pdb=" O THR R 235 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE R 249 " --> pdb=" O LEU R 245 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER R 250 " --> pdb=" O SER R 246 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRP R 252 " --> pdb=" O PHE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 284 removed outlier: 3.831A pdb=" N ILE R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.966A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.954A 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 188 through 190 removed outlier: 3.591A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.619A 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 52 removed outlier: 6.422A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.236A 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: 3.730A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.179A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.192A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.996A 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: 3.545A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.698A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.494A 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: 6.252A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.241A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 17 through 23 Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.545A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.756A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1362 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: 2.62 Time building geometry restraints manager: 2.48 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: 2822 1.34 - 1.46: 1932 1.46 - 1.58: 4244 1.58 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 9085 Sorted by residual: bond pdb=" CB MET R 212 " pdb=" CG MET R 212 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.84e+00 bond pdb=" CB GLU A 245 " pdb=" CG GLU A 245 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" C TYR A 287 " pdb=" O TYR A 287 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.75e+00 bond pdb=" CB GLN B 44 " pdb=" CG GLN B 44 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" C3 CLR R 501 " pdb=" O1 CLR R 501 " ideal model delta sigma weight residual 1.413 1.433 -0.020 2.00e-02 2.50e+03 9.78e-01 ... (remaining 9080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 12238 3.05 - 6.11: 50 6.11 - 9.16: 10 9.16 - 12.21: 0 12.21 - 15.27: 1 Bond angle restraints: 12299 Sorted by residual: angle pdb=" CB MET R 212 " pdb=" CG MET R 212 " pdb=" SD MET R 212 " ideal model delta sigma weight residual 112.70 97.43 15.27 3.00e+00 1.11e-01 2.59e+01 angle pdb=" N THR B 196 " pdb=" CA THR B 196 " pdb=" CB THR B 196 " ideal model delta sigma weight residual 114.17 109.27 4.90 1.14e+00 7.69e-01 1.85e+01 angle pdb=" CA GLU A 245 " pdb=" CB GLU A 245 " pdb=" CG GLU A 245 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" C LYS R 211 " pdb=" N MET R 212 " pdb=" CA MET R 212 " ideal model delta sigma weight residual 122.38 116.07 6.31 1.81e+00 3.05e-01 1.22e+01 angle pdb=" CA GLN B 44 " pdb=" CB GLN B 44 " pdb=" CG GLN B 44 " ideal model delta sigma weight residual 114.10 120.91 -6.81 2.00e+00 2.50e-01 1.16e+01 ... (remaining 12294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4823 17.73 - 35.47: 484 35.47 - 53.20: 128 53.20 - 70.93: 24 70.93 - 88.66: 6 Dihedral angle restraints: 5465 sinusoidal: 2210 harmonic: 3255 Sorted by residual: dihedral pdb=" CA GLU S 222 " pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta harmonic sigma weight residual 180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA MET R 212 " pdb=" C MET R 212 " pdb=" N GLN R 213 " pdb=" CA GLN R 213 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1036 0.040 - 0.081: 290 0.081 - 0.121: 74 0.121 - 0.161: 6 0.161 - 0.202: 4 Chirality restraints: 1410 Sorted by residual: chirality pdb=" C9 CLR R 502 " pdb=" C10 CLR R 502 " pdb=" C11 CLR R 502 " pdb=" C8 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.45 -2.25 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA MET R 212 " pdb=" N MET R 212 " pdb=" C MET R 212 " pdb=" CB MET R 212 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA ASP A 341 " pdb=" N ASP A 341 " pdb=" C ASP A 341 " pdb=" CB ASP A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 1407 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO S 224 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 259 " 0.011 2.00e-02 2.50e+03 1.36e-02 3.24e+00 pdb=" CG PHE A 259 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 259 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 259 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 259 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 259 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 259 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 223 " 0.019 2.00e-02 2.50e+03 1.18e-02 2.77e+00 pdb=" CG TYR S 223 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR S 223 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR S 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 223 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR S 223 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR S 223 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 223 " 0.006 2.00e-02 2.50e+03 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 345 2.71 - 3.26: 9147 3.26 - 3.81: 15297 3.81 - 4.35: 18945 4.35 - 4.90: 31925 Nonbonded interactions: 75659 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.168 3.040 nonbonded pdb=" OG SER R 250 " pdb=" O SER R 254 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR B 289 " pdb=" NE1 TRP B 297 " model vdw 2.222 3.120 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.223 3.040 nonbonded pdb=" O THR R 86 " pdb=" OG1 THR R 90 " model vdw 2.249 3.040 ... (remaining 75654 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: 1.170 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.200 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9085 Z= 0.203 Angle : 0.595 15.265 12299 Z= 0.311 Chirality : 0.040 0.202 1410 Planarity : 0.004 0.054 1525 Dihedral : 15.339 88.665 3353 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.21 % Allowed : 24.46 % Favored : 75.33 % 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: 0.33 (0.25), residues: 1107 helix: 1.64 (0.25), residues: 417 sheet: -0.55 (0.33), residues: 253 loop : -0.62 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 98 HIS 0.004 0.001 HIS R 94 PHE 0.031 0.002 PHE A 259 TYR 0.027 0.001 TYR S 223 ARG 0.011 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 LYS cc_start: 0.7935 (mttm) cc_final: 0.7700 (mttm) REVERT: B 10 GLU cc_start: 0.7620 (tp30) cc_final: 0.7246 (tp30) REVERT: S 38 ARG cc_start: 0.8272 (ptt-90) cc_final: 0.7972 (ptt180) REVERT: S 69 THR cc_start: 0.8065 (p) cc_final: 0.7819 (t) REVERT: S 119 VAL cc_start: 0.8430 (t) cc_final: 0.8102 (m) outliers start: 2 outliers final: 2 residues processed: 204 average time/residue: 1.0965 time to fit residues: 240.0217 Evaluate side-chains 190 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 87 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 239 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.150107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.130260 restraints weight = 13143.165| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.99 r_work: 0.3616 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9085 Z= 0.289 Angle : 0.583 8.587 12299 Z= 0.309 Chirality : 0.042 0.222 1410 Planarity : 0.004 0.058 1525 Dihedral : 6.042 57.140 1340 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.55 % Allowed : 19.63 % Favored : 74.82 % 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: 0.36 (0.25), residues: 1107 helix: 1.78 (0.25), residues: 413 sheet: -0.62 (0.30), residues: 265 loop : -0.65 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS B 311 PHE 0.025 0.002 PHE R 82 TYR 0.022 0.002 TYR S 223 ARG 0.006 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 0.967 Fit side-chains REVERT: A 245 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7177 (tm-30) REVERT: A 271 LYS cc_start: 0.7999 (ptpp) cc_final: 0.7763 (ptpp) REVERT: A 315 ASP cc_start: 0.7420 (p0) cc_final: 0.7136 (p0) REVERT: B 137 ARG cc_start: 0.7631 (tpp-160) cc_final: 0.7251 (tpp80) REVERT: B 219 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7856 (mpt90) REVERT: C 48 ASP cc_start: 0.7660 (t0) cc_final: 0.7407 (t0) REVERT: S 67 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7900 (mtp180) REVERT: S 218 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7968 (ttp) REVERT: R 81 MET cc_start: 0.5539 (OUTLIER) cc_final: 0.5264 (tmm) outliers start: 54 outliers final: 26 residues processed: 241 average time/residue: 1.0070 time to fit residues: 264.0241 Evaluate side-chains 233 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 119 ASN B 230 ASN B 239 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.150515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130436 restraints weight = 13244.033| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.01 r_work: 0.3620 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9085 Z= 0.246 Angle : 0.571 7.732 12299 Z= 0.299 Chirality : 0.042 0.215 1410 Planarity : 0.004 0.056 1525 Dihedral : 5.688 56.989 1334 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.24 % Allowed : 21.27 % Favored : 73.48 % 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: 0.29 (0.25), residues: 1107 helix: 1.79 (0.25), residues: 414 sheet: -0.79 (0.29), residues: 274 loop : -0.64 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.027 0.002 PHE R 82 TYR 0.021 0.002 TYR S 223 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.972 Fit side-chains REVERT: A 245 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7045 (tm-30) REVERT: A 271 LYS cc_start: 0.8026 (ptpp) cc_final: 0.7768 (ptpp) REVERT: A 315 ASP cc_start: 0.7426 (p0) cc_final: 0.7127 (p0) REVERT: B 227 SER cc_start: 0.8806 (m) cc_final: 0.8577 (t) REVERT: B 234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: B 276 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7940 (p) REVERT: C 48 ASP cc_start: 0.7654 (t0) cc_final: 0.7441 (t0) REVERT: S 216 TYR cc_start: 0.8203 (m-80) cc_final: 0.7908 (m-80) REVERT: R 81 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.5194 (tmm) outliers start: 51 outliers final: 25 residues processed: 241 average time/residue: 0.9678 time to fit residues: 252.0811 Evaluate side-chains 235 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 45 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 230 ASN B 239 ASN B 340 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.151527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131190 restraints weight = 13107.210| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.00 r_work: 0.3628 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9085 Z= 0.222 Angle : 0.554 8.653 12299 Z= 0.290 Chirality : 0.041 0.207 1410 Planarity : 0.004 0.058 1525 Dihedral : 5.571 56.839 1334 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.76 % Allowed : 21.07 % Favored : 73.18 % 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: 0.32 (0.25), residues: 1107 helix: 1.84 (0.25), residues: 415 sheet: -0.83 (0.29), residues: 275 loop : -0.62 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 151 PHE 0.027 0.002 PHE R 82 TYR 0.022 0.001 TYR S 223 ARG 0.006 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.832 Fit side-chains REVERT: A 245 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6999 (tm-30) REVERT: A 271 LYS cc_start: 0.8059 (ptpp) cc_final: 0.7770 (ptpp) REVERT: A 315 ASP cc_start: 0.7417 (p0) cc_final: 0.7103 (p0) REVERT: B 101 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8147 (mtp) REVERT: B 137 ARG cc_start: 0.7579 (tpp-160) cc_final: 0.7349 (tpp-160) REVERT: B 227 SER cc_start: 0.8797 (m) cc_final: 0.8558 (t) REVERT: B 234 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: C 48 ASP cc_start: 0.7684 (t0) cc_final: 0.7455 (t0) REVERT: S 216 TYR cc_start: 0.8227 (m-80) cc_final: 0.7873 (m-80) REVERT: R 81 MET cc_start: 0.5488 (OUTLIER) cc_final: 0.5135 (tmm) REVERT: R 126 VAL cc_start: 0.4957 (OUTLIER) cc_final: 0.4730 (t) outliers start: 56 outliers final: 30 residues processed: 251 average time/residue: 0.9541 time to fit residues: 258.7037 Evaluate side-chains 248 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.151919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.131729 restraints weight = 13347.757| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.02 r_work: 0.3637 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9085 Z= 0.203 Angle : 0.548 8.856 12299 Z= 0.286 Chirality : 0.040 0.202 1410 Planarity : 0.004 0.057 1525 Dihedral : 5.453 56.208 1334 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.93 % Allowed : 22.30 % Favored : 72.76 % 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: 0.37 (0.25), residues: 1107 helix: 1.92 (0.25), residues: 415 sheet: -0.83 (0.29), residues: 275 loop : -0.62 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 188 PHE 0.035 0.002 PHE R 72 TYR 0.021 0.001 TYR S 223 ARG 0.006 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.910 Fit side-chains REVERT: A 245 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7105 (tm-30) REVERT: A 271 LYS cc_start: 0.8070 (ptpp) cc_final: 0.7788 (ptpp) REVERT: A 315 ASP cc_start: 0.7436 (p0) cc_final: 0.7059 (p0) REVERT: B 10 GLU cc_start: 0.7819 (tp30) cc_final: 0.7391 (tp30) REVERT: B 101 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8100 (mtp) REVERT: B 137 ARG cc_start: 0.7490 (tpp-160) cc_final: 0.7277 (tpp-160) REVERT: B 234 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: C 48 ASP cc_start: 0.7629 (t0) cc_final: 0.7413 (t0) REVERT: S 69 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7837 (t) REVERT: S 216 TYR cc_start: 0.8214 (m-80) cc_final: 0.7926 (m-80) REVERT: R 6 LYS cc_start: 0.7634 (mmmm) cc_final: 0.7211 (mmmm) REVERT: R 81 MET cc_start: 0.5657 (OUTLIER) cc_final: 0.5321 (tmm) outliers start: 48 outliers final: 25 residues processed: 240 average time/residue: 0.9809 time to fit residues: 254.7734 Evaluate side-chains 232 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 97 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 119 ASN B 230 ASN B 239 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.149578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129293 restraints weight = 13317.951| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.03 r_work: 0.3610 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9085 Z= 0.340 Angle : 0.607 9.841 12299 Z= 0.318 Chirality : 0.043 0.218 1410 Planarity : 0.005 0.058 1525 Dihedral : 5.648 57.115 1334 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.86 % Allowed : 21.48 % Favored : 72.66 % 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: 0.16 (0.25), residues: 1107 helix: 1.69 (0.24), residues: 415 sheet: -0.86 (0.30), residues: 275 loop : -0.72 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 164 HIS 0.005 0.002 HIS A 188 PHE 0.029 0.002 PHE R 72 TYR 0.023 0.002 TYR S 223 ARG 0.008 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 0.960 Fit side-chains REVERT: A 188 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.6919 (m170) REVERT: A 245 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7090 (tm-30) REVERT: A 271 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7785 (ptpp) REVERT: A 315 ASP cc_start: 0.7420 (p0) cc_final: 0.7042 (p0) REVERT: A 341 ASP cc_start: 0.7581 (m-30) cc_final: 0.7291 (m-30) REVERT: B 234 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8625 (m-80) REVERT: C 48 ASP cc_start: 0.7685 (t0) cc_final: 0.7470 (t0) REVERT: S 69 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7888 (t) REVERT: S 216 TYR cc_start: 0.8346 (m-80) cc_final: 0.7947 (m-80) REVERT: R 6 LYS cc_start: 0.7578 (mmmm) cc_final: 0.7094 (mmmt) REVERT: R 81 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.5233 (tmm) outliers start: 57 outliers final: 30 residues processed: 243 average time/residue: 0.9487 time to fit residues: 249.7749 Evaluate side-chains 252 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 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 230 ASN B 239 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.151174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130872 restraints weight = 13424.162| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.04 r_work: 0.3629 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9085 Z= 0.235 Angle : 0.583 9.926 12299 Z= 0.302 Chirality : 0.041 0.202 1410 Planarity : 0.004 0.057 1525 Dihedral : 5.535 57.193 1334 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.83 % Allowed : 23.12 % Favored : 72.05 % 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: 0.23 (0.25), residues: 1107 helix: 1.79 (0.24), residues: 415 sheet: -0.83 (0.30), residues: 275 loop : -0.74 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 188 PHE 0.029 0.002 PHE R 72 TYR 0.021 0.001 TYR S 223 ARG 0.007 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 188 HIS cc_start: 0.7267 (OUTLIER) cc_final: 0.6902 (m170) REVERT: A 245 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7114 (tm-30) REVERT: A 271 LYS cc_start: 0.8075 (ptpp) cc_final: 0.7780 (ptpp) REVERT: A 315 ASP cc_start: 0.7388 (p0) cc_final: 0.7002 (p0) REVERT: A 341 ASP cc_start: 0.7613 (m-30) cc_final: 0.7255 (m-30) REVERT: B 52 ARG cc_start: 0.8119 (ptp90) cc_final: 0.7857 (ptp-170) REVERT: B 137 ARG cc_start: 0.7489 (tpp-160) cc_final: 0.7182 (tpp-160) REVERT: B 159 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.8021 (p) REVERT: B 234 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: B 289 TYR cc_start: 0.8448 (m-80) cc_final: 0.7925 (m-80) REVERT: C 48 ASP cc_start: 0.7657 (t0) cc_final: 0.7442 (t0) REVERT: S 69 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7881 (t) REVERT: S 216 TYR cc_start: 0.8297 (m-80) cc_final: 0.7977 (m-80) REVERT: R 6 LYS cc_start: 0.7658 (mmmm) cc_final: 0.7196 (mmmt) REVERT: R 81 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.5323 (tmm) outliers start: 47 outliers final: 29 residues processed: 240 average time/residue: 1.0314 time to fit residues: 267.9251 Evaluate side-chains 252 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.150718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130407 restraints weight = 13616.855| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.07 r_work: 0.3617 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9085 Z= 0.258 Angle : 0.579 8.697 12299 Z= 0.302 Chirality : 0.041 0.181 1410 Planarity : 0.005 0.059 1525 Dihedral : 5.533 56.747 1334 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.62 % Allowed : 23.54 % Favored : 71.84 % 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: 0.24 (0.25), residues: 1107 helix: 1.79 (0.24), residues: 412 sheet: -0.82 (0.30), residues: 273 loop : -0.71 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 164 HIS 0.005 0.001 HIS A 188 PHE 0.029 0.002 PHE R 72 TYR 0.024 0.002 TYR S 223 ARG 0.008 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 0.874 Fit side-chains REVERT: A 188 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6932 (m170) REVERT: A 245 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 271 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7794 (ptpp) REVERT: A 315 ASP cc_start: 0.7402 (p0) cc_final: 0.7019 (p0) REVERT: B 52 ARG cc_start: 0.8141 (ptp90) cc_final: 0.7894 (ptp-170) REVERT: B 61 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7856 (ppp) REVERT: B 137 ARG cc_start: 0.7499 (tpp-160) cc_final: 0.7203 (tpp-160) REVERT: B 234 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8598 (m-80) REVERT: B 289 TYR cc_start: 0.8427 (m-80) cc_final: 0.7952 (m-80) REVERT: C 48 ASP cc_start: 0.7661 (t0) cc_final: 0.7437 (t0) REVERT: S 69 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7875 (t) REVERT: S 145 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7982 (mt) REVERT: S 216 TYR cc_start: 0.8337 (m-80) cc_final: 0.8003 (m-80) REVERT: R 81 MET cc_start: 0.5672 (OUTLIER) cc_final: 0.5353 (tmm) REVERT: R 197 MET cc_start: 0.7068 (ttm) cc_final: 0.6809 (ttm) outliers start: 45 outliers final: 28 residues processed: 233 average time/residue: 0.9166 time to fit residues: 231.1015 Evaluate side-chains 251 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.0570 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 65 optimal weight: 0.0000 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.151937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.131678 restraints weight = 13442.405| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.05 r_work: 0.3637 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9085 Z= 0.214 Angle : 0.574 9.368 12299 Z= 0.300 Chirality : 0.041 0.169 1410 Planarity : 0.004 0.058 1525 Dihedral : 5.442 56.424 1334 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.91 % Allowed : 24.97 % Favored : 71.12 % 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: 0.25 (0.25), residues: 1107 helix: 1.79 (0.25), residues: 416 sheet: -0.86 (0.30), residues: 275 loop : -0.68 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 164 HIS 0.005 0.001 HIS A 188 PHE 0.031 0.002 PHE R 72 TYR 0.024 0.001 TYR S 223 ARG 0.007 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.979 Fit side-chains REVERT: A 25 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6724 (mp0) REVERT: A 188 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6898 (m170) REVERT: A 245 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 271 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7796 (ptpp) REVERT: A 315 ASP cc_start: 0.7370 (p0) cc_final: 0.6982 (p0) REVERT: B 48 ARG cc_start: 0.8008 (mmt-90) cc_final: 0.7792 (mmt-90) REVERT: B 52 ARG cc_start: 0.8082 (ptp90) cc_final: 0.7821 (ptp-170) REVERT: B 61 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7818 (ppp) REVERT: B 65 THR cc_start: 0.8044 (m) cc_final: 0.7774 (p) REVERT: B 137 ARG cc_start: 0.7465 (tpp-160) cc_final: 0.7177 (tpp-160) REVERT: B 234 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8567 (m-80) REVERT: B 289 TYR cc_start: 0.8390 (m-80) cc_final: 0.7819 (m-80) REVERT: C 48 ASP cc_start: 0.7650 (t0) cc_final: 0.7423 (t0) REVERT: S 69 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7808 (t) REVERT: S 145 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7980 (mt) REVERT: S 216 TYR cc_start: 0.8304 (m-80) cc_final: 0.7908 (m-80) REVERT: R 81 MET cc_start: 0.5677 (OUTLIER) cc_final: 0.5348 (tmm) outliers start: 38 outliers final: 25 residues processed: 243 average time/residue: 0.9407 time to fit residues: 247.9792 Evaluate side-chains 258 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 237 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.150682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130368 restraints weight = 13433.169| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.05 r_work: 0.3604 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9085 Z= 0.339 Angle : 0.645 13.493 12299 Z= 0.334 Chirality : 0.043 0.164 1410 Planarity : 0.005 0.060 1525 Dihedral : 5.617 55.863 1334 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.21 % Allowed : 24.46 % Favored : 71.33 % 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: 0.06 (0.25), residues: 1107 helix: 1.56 (0.24), residues: 412 sheet: -0.88 (0.29), residues: 282 loop : -0.75 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 164 HIS 0.005 0.002 HIS A 213 PHE 0.032 0.002 PHE R 72 TYR 0.030 0.002 TYR S 223 ARG 0.007 0.001 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.988 Fit side-chains REVERT: A 25 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6736 (mp0) REVERT: A 188 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6902 (m170) REVERT: A 245 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 271 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7820 (ptpp) REVERT: A 315 ASP cc_start: 0.7449 (p0) cc_final: 0.7054 (p0) REVERT: B 52 ARG cc_start: 0.8162 (ptp90) cc_final: 0.7924 (ptp-170) REVERT: B 61 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7831 (ppp) REVERT: B 78 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7558 (mttp) REVERT: B 111 TYR cc_start: 0.8648 (m-80) cc_final: 0.8402 (m-80) REVERT: B 137 ARG cc_start: 0.7553 (tpp-160) cc_final: 0.7243 (tpp-160) REVERT: B 234 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8621 (m-80) REVERT: B 289 TYR cc_start: 0.8428 (m-80) cc_final: 0.7934 (m-80) REVERT: C 48 ASP cc_start: 0.7712 (t0) cc_final: 0.7491 (t0) REVERT: S 69 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7830 (t) REVERT: S 145 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7982 (mt) REVERT: R 81 MET cc_start: 0.5660 (OUTLIER) cc_final: 0.5347 (tmm) outliers start: 41 outliers final: 26 residues processed: 231 average time/residue: 0.9921 time to fit residues: 247.9515 Evaluate side-chains 242 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 239 ASN S 77 ASN ** R 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.150821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130633 restraints weight = 13385.699| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.03 r_work: 0.3621 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9085 Z= 0.273 Angle : 0.609 9.917 12299 Z= 0.319 Chirality : 0.042 0.174 1410 Planarity : 0.005 0.062 1525 Dihedral : 5.581 55.899 1334 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.60 % Allowed : 25.59 % Favored : 70.81 % 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: 0.01 (0.25), residues: 1107 helix: 1.53 (0.25), residues: 412 sheet: -0.93 (0.29), residues: 281 loop : -0.76 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 164 HIS 0.005 0.001 HIS A 213 PHE 0.035 0.002 PHE A 259 TYR 0.027 0.002 TYR S 223 ARG 0.007 0.001 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7338.22 seconds wall clock time: 127 minutes 30.72 seconds (7650.72 seconds total)