Starting phenix.real_space_refine on Tue Apr 29 19:42:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqt_38588/04_2025/8xqt_38588.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqt_38588/04_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_38588/04_2025/8xqt_38588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqt_38588/04_2025/8xqt_38588.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqt_38588/04_2025/8xqt_38588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqt_38588/04_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-5669/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: 5.62, per 1000 atoms: 0.63 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: 2.47 Conformation dependent library (CDL) restraints added in 977.8 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: 1.19 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: 2.65 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: 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: 1.230 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.810 Find NCS groups from input model: 0.140 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- 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 9087 Z= 0.140 Angle : 0.595 15.265 12303 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 Details of bonding type rmsd hydrogen bonds : bond 0.16409 ( 474) hydrogen bonds : angle 6.95143 ( 1362) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.36009 ( 4) covalent geometry : bond 0.00309 ( 9085) covalent geometry : angle 0.59495 (12299) *********************** 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 : 0.973 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: 1.1010 time to fit residues: 241.2653 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 : 0.907 ------------------------------------------------------------------------------- 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 9087 Z= 0.198 Angle : 0.583 8.587 12303 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 Details of bonding type rmsd hydrogen bonds : bond 0.04787 ( 474) hydrogen bonds : angle 5.35480 ( 1362) SS BOND : bond 0.00306 ( 2) SS BOND : angle 0.73621 ( 4) covalent geometry : bond 0.00439 ( 9085) covalent geometry : angle 0.58341 (12299) *********************** 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 : 1.007 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: 1.0001 time to fit residues: 261.9095 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 : 0.994 ------------------------------------------------------------------------------- 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 9087 Z= 0.169 Angle : 0.571 7.732 12303 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 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 474) hydrogen bonds : angle 5.11290 ( 1362) SS BOND : bond 0.00247 ( 2) SS BOND : angle 0.76792 ( 4) covalent geometry : bond 0.00376 ( 9085) covalent geometry : angle 0.57098 (12299) *********************** 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 : 1.296 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: 0.9810 time to fit residues: 256.1353 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 : 0.931 ------------------------------------------------------------------------------- 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 9087 Z= 0.153 Angle : 0.554 8.653 12303 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 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 474) hydrogen bonds : angle 4.99270 ( 1362) SS BOND : bond 0.00219 ( 2) SS BOND : angle 0.63009 ( 4) covalent geometry : bond 0.00338 ( 9085) covalent geometry : angle 0.55433 (12299) *********************** 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 : 0.909 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: 0.9577 time to fit residues: 260.2209 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 : 0.903 ------------------------------------------------------------------------------- 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 9087 Z= 0.139 Angle : 0.548 8.856 12303 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 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 474) hydrogen bonds : angle 4.87645 ( 1362) SS BOND : bond 0.00209 ( 2) SS BOND : angle 0.51824 ( 4) covalent geometry : bond 0.00306 ( 9085) covalent geometry : angle 0.54829 (12299) *********************** 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 : 1.043 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: 0.9626 time to fit residues: 250.3810 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 : 0.949 ------------------------------------------------------------------------------- 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 9087 Z= 0.229 Angle : 0.607 9.841 12303 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 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 474) hydrogen bonds : angle 4.94783 ( 1362) SS BOND : bond 0.00264 ( 2) SS BOND : angle 0.60989 ( 4) covalent geometry : bond 0.00513 ( 9085) covalent geometry : angle 0.60739 (12299) *********************** 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 : 1.018 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: 0.9737 time to fit residues: 256.9326 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 : 0.792 ------------------------------------------------------------------------------- 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 9087 Z= 0.159 Angle : 0.583 9.926 12303 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 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 474) hydrogen bonds : angle 4.86166 ( 1362) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.40831 ( 4) covalent geometry : bond 0.00356 ( 9085) covalent geometry : angle 0.58256 (12299) *********************** 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 : 0.751 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: 0.9426 time to fit residues: 244.8562 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 : 0.909 ------------------------------------------------------------------------------- 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: 0.6980 chunk 93 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3995 r_free = 0.3995 target = 0.150900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130584 restraints weight = 13618.365| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.07 r_work: 0.3617 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9087 Z= 0.171 Angle : 0.577 8.690 12303 Z= 0.301 Chirality : 0.041 0.177 1410 Planarity : 0.005 0.059 1525 Dihedral : 5.523 56.684 1334 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.62 % Allowed : 23.64 % Favored : 71.74 % 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: 0.24 (0.25), residues: 1107 helix: 1.80 (0.24), residues: 412 sheet: -0.85 (0.30), residues: 276 loop : -0.69 (0.31), residues: 419 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 0.023 0.002 TYR S 223 ARG 0.008 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 474) hydrogen bonds : angle 4.83439 ( 1362) SS BOND : bond 0.00260 ( 2) SS BOND : angle 0.40749 ( 4) covalent geometry : bond 0.00386 ( 9085) covalent geometry : angle 0.57689 (12299) *********************** 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 : 0.965 Fit side-chains REVERT: A 188 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6934 (m170) REVERT: A 245 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7152 (tm-30) REVERT: A 271 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7787 (ptpp) REVERT: A 315 ASP cc_start: 0.7408 (p0) cc_final: 0.7024 (p0) REVERT: B 52 ARG cc_start: 0.8139 (ptp90) cc_final: 0.7897 (ptp-170) REVERT: B 61 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7859 (ppp) REVERT: B 137 ARG cc_start: 0.7499 (tpp-160) cc_final: 0.7205 (tpp-160) REVERT: B 234 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8598 (m-80) REVERT: B 289 TYR cc_start: 0.8421 (m-80) cc_final: 0.7882 (m-80) REVERT: C 48 ASP cc_start: 0.7675 (t0) cc_final: 0.7451 (t0) REVERT: S 69 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7874 (t) REVERT: S 145 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7983 (mt) REVERT: S 216 TYR cc_start: 0.8336 (m-80) cc_final: 0.8006 (m-80) REVERT: R 81 MET cc_start: 0.5670 (OUTLIER) cc_final: 0.5347 (tmm) REVERT: R 197 MET cc_start: 0.7056 (ttm) cc_final: 0.6801 (ttm) outliers start: 45 outliers final: 29 residues processed: 234 average time/residue: 0.9691 time to fit residues: 245.3451 Evaluate side-chains 253 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 37 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3993 r_free = 0.3993 target = 0.150666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130241 restraints weight = 13415.455| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.05 r_work: 0.3619 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9087 Z= 0.188 Angle : 0.593 8.555 12303 Z= 0.311 Chirality : 0.042 0.178 1410 Planarity : 0.005 0.058 1525 Dihedral : 5.550 56.957 1334 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.32 % Allowed : 24.46 % Favored : 71.22 % 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: 0.17 (0.25), residues: 1107 helix: 1.72 (0.24), residues: 412 sheet: -0.87 (0.29), residues: 282 loop : -0.71 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 164 HIS 0.005 0.001 HIS A 188 PHE 0.031 0.002 PHE R 72 TYR 0.026 0.002 TYR S 223 ARG 0.008 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 474) hydrogen bonds : angle 4.87735 ( 1362) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.51900 ( 4) covalent geometry : bond 0.00425 ( 9085) covalent geometry : angle 0.59279 (12299) *********************** 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 258 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.886 Fit side-chains REVERT: A 25 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6765 (mp0) REVERT: A 188 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6921 (m170) REVERT: A 245 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 271 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7797 (ptpp) REVERT: A 315 ASP cc_start: 0.7400 (p0) cc_final: 0.7006 (p0) REVERT: B 52 ARG cc_start: 0.8107 (ptp90) cc_final: 0.7839 (ptp-170) REVERT: B 137 ARG cc_start: 0.7505 (tpp-160) cc_final: 0.7215 (tpp-160) REVERT: B 234 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: B 289 TYR cc_start: 0.8424 (m-80) cc_final: 0.7939 (m-80) REVERT: C 48 ASP cc_start: 0.7670 (t0) cc_final: 0.7449 (t0) REVERT: S 69 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7832 (t) REVERT: S 145 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7984 (mt) REVERT: S 172 SER cc_start: 0.8610 (m) cc_final: 0.8401 (t) REVERT: S 216 TYR cc_start: 0.8352 (m-80) cc_final: 0.7950 (m-80) REVERT: R 81 MET cc_start: 0.5611 (OUTLIER) cc_final: 0.5294 (tmm) REVERT: R 197 MET cc_start: 0.7179 (ttm) cc_final: 0.6968 (ttm) REVERT: R 205 MET cc_start: 0.7453 (mmp) cc_final: 0.7138 (mmm) outliers start: 42 outliers final: 29 residues processed: 234 average time/residue: 0.9397 time to fit residues: 238.7451 Evaluate side-chains 248 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 43 ILE 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 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 145 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 74 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.151130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.130766 restraints weight = 13364.731| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.05 r_work: 0.3613 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9087 Z= 0.196 Angle : 0.609 9.587 12303 Z= 0.319 Chirality : 0.042 0.184 1410 Planarity : 0.005 0.061 1525 Dihedral : 5.582 56.516 1334 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.32 % Allowed : 24.67 % Favored : 71.02 % 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: 0.11 (0.25), residues: 1107 helix: 1.64 (0.24), residues: 412 sheet: -0.86 (0.30), residues: 281 loop : -0.74 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 164 HIS 0.005 0.001 HIS A 188 PHE 0.036 0.002 PHE A 259 TYR 0.024 0.002 TYR S 223 ARG 0.008 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 474) hydrogen bonds : angle 4.90498 ( 1362) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.47110 ( 4) covalent geometry : bond 0.00445 ( 9085) covalent geometry : angle 0.60939 (12299) ********************** 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 260 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.873 Fit side-chains REVERT: A 25 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6768 (mp0) REVERT: A 188 HIS cc_start: 0.7218 (OUTLIER) cc_final: 0.6909 (m170) REVERT: A 245 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 271 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7804 (ptpp) REVERT: A 315 ASP cc_start: 0.7434 (p0) cc_final: 0.7038 (p0) REVERT: B 52 ARG cc_start: 0.8177 (ptp90) cc_final: 0.7931 (ptp-170) REVERT: B 61 MET cc_start: 0.8104 (tmm) cc_final: 0.7854 (ppp) REVERT: B 78 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7579 (mttp) REVERT: B 111 TYR cc_start: 0.8642 (m-80) cc_final: 0.8415 (m-80) REVERT: B 137 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.7231 (tpp-160) REVERT: B 234 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: B 289 TYR cc_start: 0.8418 (m-80) cc_final: 0.7943 (m-80) REVERT: C 48 ASP cc_start: 0.7682 (t0) cc_final: 0.7457 (t0) REVERT: S 69 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7835 (t) REVERT: S 145 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7975 (mt) REVERT: S 172 SER cc_start: 0.8618 (m) cc_final: 0.8409 (t) REVERT: S 216 TYR cc_start: 0.8387 (m-80) cc_final: 0.8007 (m-80) REVERT: R 81 MET cc_start: 0.5659 (OUTLIER) cc_final: 0.5347 (tmm) REVERT: R 197 MET cc_start: 0.7229 (ttm) cc_final: 0.7028 (ttm) REVERT: R 205 MET cc_start: 0.7487 (mmp) cc_final: 0.7272 (mmm) outliers start: 42 outliers final: 28 residues processed: 237 average time/residue: 0.8969 time to fit residues: 230.6822 Evaluate side-chains 255 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.151944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.131712 restraints weight = 13406.285| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.04 r_work: 0.3637 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9087 Z= 0.150 Angle : 0.588 9.062 12303 Z= 0.307 Chirality : 0.041 0.156 1410 Planarity : 0.004 0.062 1525 Dihedral : 5.479 55.682 1334 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.91 % Allowed : 25.08 % Favored : 71.02 % 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: 0.19 (0.25), residues: 1107 helix: 1.72 (0.25), residues: 413 sheet: -0.87 (0.30), residues: 275 loop : -0.68 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP S 164 HIS 0.005 0.001 HIS A 188 PHE 0.031 0.002 PHE R 72 TYR 0.027 0.001 TYR S 223 ARG 0.007 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 474) hydrogen bonds : angle 4.84179 ( 1362) SS BOND : bond 0.00217 ( 2) SS BOND : angle 0.46629 ( 4) covalent geometry : bond 0.00339 ( 9085) covalent geometry : angle 0.58821 (12299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7770.24 seconds wall clock time: 135 minutes 7.15 seconds (8107.15 seconds total)