Starting phenix.real_space_refine on Thu Mar 13 15:31:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kfy_37208/03_2025/8kfy_37208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kfy_37208/03_2025/8kfy_37208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kfy_37208/03_2025/8kfy_37208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kfy_37208/03_2025/8kfy_37208.map" model { file = "/net/cci-nas-00/data/ceres_data/8kfy_37208/03_2025/8kfy_37208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kfy_37208/03_2025/8kfy_37208.cif" } resolution = 3.06 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5754 2.51 5 N 1505 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8992 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2342 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 5, 'TRANS': 282} 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'OXF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.12, per 1000 atoms: 0.68 Number of scatterers: 8992 At special positions: 0 Unit cell: (94.64, 120.64, 128.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1667 8.00 N 1505 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.0 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 39.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.137A 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 228 through 231 removed outlier: 3.524A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.145A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.790A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.702A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.600A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.621A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'R' and resid 31 through 62 Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.831A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 191 through 205 removed outlier: 3.799A pdb=" N LYS R 195 " --> pdb=" O THR R 191 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN R 199 " --> pdb=" O LYS R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 removed outlier: 3.637A pdb=" N ILE R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 266 Proline residue: R 253 - end of helix Processing helix chain 'R' and resid 271 through 290 Processing helix chain 'R' and resid 291 through 301 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.887A 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 208 through 212 removed outlier: 4.003A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.266A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.813A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.962A 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: 4.093A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.194A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.810A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.534A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.865A 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: 6.405A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 177 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.616A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.528A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.650A 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) 473 hydrogen bonds defined for protein. 1353 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: 2.80 Time building geometry restraints manager: 2.41 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: 2856 1.34 - 1.46: 2115 1.46 - 1.58: 4116 1.58 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 9182 Sorted by residual: bond pdb=" CA TYR S 161 " pdb=" CB TYR S 161 " ideal model delta sigma weight residual 1.525 1.497 0.028 1.47e-02 4.63e+03 3.61e+00 bond pdb=" C12 OXF R 601 " pdb=" O3 OXF R 601 " ideal model delta sigma weight residual 1.363 1.391 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" SD MET R 105 " pdb=" CE MET R 105 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.72e+00 bond pdb=" C MET R 105 " pdb=" O MET R 105 " ideal model delta sigma weight residual 1.237 1.224 0.012 1.17e-02 7.31e+03 1.12e+00 bond pdb=" CG LEU R 278 " pdb=" CD2 LEU R 278 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 ... (remaining 9177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 12284 2.01 - 4.03: 126 4.03 - 6.04: 12 6.04 - 8.05: 2 8.05 - 10.06: 1 Bond angle restraints: 12425 Sorted by residual: angle pdb=" CB MET R 105 " pdb=" CG MET R 105 " pdb=" SD MET R 105 " ideal model delta sigma weight residual 112.70 122.76 -10.06 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 127.67 -6.13 1.91e+00 2.74e-01 1.03e+01 angle pdb=" N THR S 198 " pdb=" CA THR S 198 " pdb=" C THR S 198 " ideal model delta sigma weight residual 113.43 109.56 3.87 1.26e+00 6.30e-01 9.45e+00 angle pdb=" CG ARG B 19 " pdb=" CD ARG B 19 " pdb=" NE ARG B 19 " ideal model delta sigma weight residual 112.00 118.59 -6.59 2.20e+00 2.07e-01 8.98e+00 angle pdb=" C PHE R 290 " pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta sigma weight residual 121.18 115.92 5.26 1.98e+00 2.55e-01 7.05e+00 ... (remaining 12420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4723 17.68 - 35.37: 561 35.37 - 53.05: 143 53.05 - 70.73: 16 70.73 - 88.42: 4 Dihedral angle restraints: 5447 sinusoidal: 2133 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE R 290 " pdb=" C PHE R 290 " pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta harmonic sigma weight residual 180.00 148.76 31.24 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLN S 130 " pdb=" C GLN S 130 " pdb=" N ALA S 131 " pdb=" CA ALA S 131 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 969 0.036 - 0.071: 318 0.071 - 0.107: 102 0.107 - 0.142: 20 0.142 - 0.178: 5 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA PHE R 290 " pdb=" N PHE R 290 " pdb=" C PHE R 290 " pdb=" CB PHE R 290 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB VAL R 109 " pdb=" CA VAL R 109 " pdb=" CG1 VAL R 109 " pdb=" CG2 VAL R 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB THR R 291 " pdb=" CA THR R 291 " pdb=" OG1 THR R 291 " pdb=" CG2 THR R 291 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1411 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 236 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO S 224 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET R 105 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C MET R 105 " -0.035 2.00e-02 2.50e+03 pdb=" O MET R 105 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS R 106 " 0.012 2.00e-02 2.50e+03 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 251 2.70 - 3.25: 8859 3.25 - 3.80: 14802 3.80 - 4.35: 19109 4.35 - 4.90: 32205 Nonbonded interactions: 75226 Sorted by model distance: nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.155 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.187 3.040 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.249 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.269 3.040 ... (remaining 75221 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: 1.220 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.840 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 0.034 9182 Z= 0.226 Angle : 0.537 10.063 12425 Z= 0.300 Chirality : 0.041 0.178 1414 Planarity : 0.004 0.058 1556 Dihedral : 15.791 88.418 3300 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.20 % Allowed : 25.61 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1125 helix: 2.52 (0.26), residues: 398 sheet: 0.62 (0.30), residues: 288 loop : -0.42 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.003 0.001 HIS R 292 PHE 0.021 0.001 PHE R 84 TYR 0.014 0.001 TYR B 85 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7448 (mpp) cc_final: 0.7088 (mmm) REVERT: A 349 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7578 (mtmm) REVERT: B 19 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7122 (mtm-85) REVERT: R 46 PHE cc_start: 0.8327 (t80) cc_final: 0.8052 (t80) REVERT: R 202 MET cc_start: 0.7523 (mmm) cc_final: 0.7200 (mtp) REVERT: S 154 LEU cc_start: 0.8196 (tp) cc_final: 0.7943 (tp) outliers start: 2 outliers final: 1 residues processed: 227 average time/residue: 0.2672 time to fit residues: 78.5677 Evaluate side-chains 223 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS S 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112960 restraints weight = 13625.030| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.21 r_work: 0.3313 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9182 Z= 0.215 Angle : 0.517 8.057 12425 Z= 0.285 Chirality : 0.042 0.194 1414 Planarity : 0.004 0.060 1556 Dihedral : 4.748 50.754 1252 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.95 % Allowed : 21.05 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1125 helix: 2.69 (0.25), residues: 403 sheet: 0.63 (0.30), residues: 285 loop : -0.33 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS S 155 PHE 0.021 0.001 PHE R 214 TYR 0.016 0.001 TYR S 178 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7229 (mpp) cc_final: 0.6976 (mmm) REVERT: A 184 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 245 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 279 LYS cc_start: 0.8544 (mttt) cc_final: 0.8328 (mptt) REVERT: A 298 GLU cc_start: 0.7137 (tp30) cc_final: 0.6681 (tp30) REVERT: A 328 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: B 19 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7341 (mtm-85) REVERT: B 212 ASP cc_start: 0.7889 (t0) cc_final: 0.7566 (t0) REVERT: B 263 THR cc_start: 0.8249 (p) cc_final: 0.7891 (m) REVERT: B 335 PHE cc_start: 0.8471 (m-80) cc_final: 0.8026 (m-80) REVERT: R 46 PHE cc_start: 0.8264 (t80) cc_final: 0.8029 (t80) REVERT: R 124 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7886 (mm) REVERT: R 202 MET cc_start: 0.7801 (mmm) cc_final: 0.7550 (mtp) REVERT: R 215 MET cc_start: 0.7909 (mmm) cc_final: 0.7382 (mpp) REVERT: R 257 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8072 (p) REVERT: S 34 MET cc_start: 0.8196 (mmm) cc_final: 0.7977 (mmm) REVERT: S 154 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7762 (tp) REVERT: S 160 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8382 (m) outliers start: 39 outliers final: 23 residues processed: 241 average time/residue: 0.2468 time to fit residues: 79.9933 Evaluate side-chains 240 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 0.0060 chunk 43 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 0.0770 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 142 HIS R 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114073 restraints weight = 13782.330| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.19 r_work: 0.3326 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9182 Z= 0.159 Angle : 0.478 7.457 12425 Z= 0.262 Chirality : 0.040 0.190 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.636 52.449 1252 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.05 % Allowed : 21.76 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1125 helix: 2.75 (0.25), residues: 406 sheet: 0.63 (0.30), residues: 281 loop : -0.28 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS A 213 PHE 0.017 0.001 PHE R 214 TYR 0.023 0.001 TYR S 223 ARG 0.002 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7117 (mpp) cc_final: 0.6770 (mmm) REVERT: A 279 LYS cc_start: 0.8496 (mttt) cc_final: 0.8279 (mptt) REVERT: A 298 GLU cc_start: 0.7189 (tp30) cc_final: 0.6797 (tp30) REVERT: A 317 LYS cc_start: 0.8272 (ptpp) cc_final: 0.7535 (ptpp) REVERT: A 345 LYS cc_start: 0.8315 (ttpt) cc_final: 0.7824 (mptt) REVERT: B 19 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7323 (mtm-85) REVERT: B 134 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7943 (ttp80) REVERT: B 137 ARG cc_start: 0.8445 (tpp80) cc_final: 0.8200 (tpp80) REVERT: B 197 ARG cc_start: 0.7385 (mpt-90) cc_final: 0.6984 (mpt-90) REVERT: B 212 ASP cc_start: 0.7880 (t0) cc_final: 0.7555 (t0) REVERT: B 335 PHE cc_start: 0.8397 (m-80) cc_final: 0.7921 (m-80) REVERT: R 46 PHE cc_start: 0.8306 (t80) cc_final: 0.8056 (t80) REVERT: R 72 VAL cc_start: 0.8078 (t) cc_final: 0.7762 (p) REVERT: R 250 PHE cc_start: 0.7364 (m-10) cc_final: 0.7074 (m-10) REVERT: R 257 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8085 (p) REVERT: S 148 ARG cc_start: 0.7572 (ttm110) cc_final: 0.7263 (ttm170) REVERT: S 154 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7770 (tp) outliers start: 40 outliers final: 25 residues processed: 246 average time/residue: 0.2529 time to fit residues: 82.6758 Evaluate side-chains 251 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 142 HIS B 268 ASN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.131675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111759 restraints weight = 13657.579| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.16 r_work: 0.3300 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9182 Z= 0.254 Angle : 0.511 7.137 12425 Z= 0.280 Chirality : 0.042 0.205 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.725 52.145 1252 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.86 % Allowed : 21.46 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1125 helix: 2.63 (0.25), residues: 405 sheet: 0.47 (0.30), residues: 284 loop : -0.21 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.023 0.002 PHE R 214 TYR 0.021 0.002 TYR S 223 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 233 time to evaluate : 1.751 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7179 (mpp) cc_final: 0.6851 (mmm) REVERT: A 279 LYS cc_start: 0.8518 (mttt) cc_final: 0.8294 (mptt) REVERT: A 298 GLU cc_start: 0.7212 (tp30) cc_final: 0.6805 (tp30) REVERT: A 345 LYS cc_start: 0.8334 (ttpt) cc_final: 0.7848 (mptt) REVERT: B 19 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: B 134 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7907 (ttp80) REVERT: B 178 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8420 (p) REVERT: B 197 ARG cc_start: 0.7417 (mpt-90) cc_final: 0.7007 (mpt-90) REVERT: B 212 ASP cc_start: 0.7999 (t0) cc_final: 0.7775 (m-30) REVERT: B 263 THR cc_start: 0.8263 (p) cc_final: 0.7905 (m) REVERT: B 283 ARG cc_start: 0.8379 (tpt-90) cc_final: 0.8030 (tpt170) REVERT: B 335 PHE cc_start: 0.8439 (m-80) cc_final: 0.8030 (m-80) REVERT: R 46 PHE cc_start: 0.8339 (t80) cc_final: 0.8088 (t80) REVERT: R 191 THR cc_start: 0.3794 (OUTLIER) cc_final: 0.3571 (m) REVERT: R 250 PHE cc_start: 0.7311 (m-10) cc_final: 0.7095 (m-10) REVERT: R 257 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8082 (p) REVERT: R 278 LEU cc_start: 0.8114 (mm) cc_final: 0.7835 (mt) REVERT: S 148 ARG cc_start: 0.7620 (ttm110) cc_final: 0.7314 (ttm170) REVERT: S 154 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7867 (tp) REVERT: S 180 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7680 (ttm) REVERT: S 185 SER cc_start: 0.8508 (m) cc_final: 0.8233 (p) outliers start: 48 outliers final: 34 residues processed: 254 average time/residue: 0.2968 time to fit residues: 99.7553 Evaluate side-chains 262 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 106 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 119 ASN B 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.132531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112503 restraints weight = 13675.351| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.17 r_work: 0.3314 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.180 Angle : 0.483 6.712 12425 Z= 0.265 Chirality : 0.040 0.191 1414 Planarity : 0.004 0.056 1556 Dihedral : 4.630 53.157 1252 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.66 % Allowed : 22.17 % 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: 1.52 (0.25), residues: 1125 helix: 2.73 (0.25), residues: 405 sheet: 0.49 (0.30), residues: 281 loop : -0.26 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.002 0.001 HIS A 213 PHE 0.018 0.001 PHE R 214 TYR 0.019 0.001 TYR S 223 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7210 (mpp) cc_final: 0.6995 (mmt) REVERT: A 298 GLU cc_start: 0.7205 (tp30) cc_final: 0.6838 (tp30) REVERT: A 345 LYS cc_start: 0.8324 (ttpt) cc_final: 0.7849 (mptt) REVERT: B 19 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7325 (mtm-85) REVERT: B 134 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7919 (ttp80) REVERT: B 150 ARG cc_start: 0.8037 (mmt-90) cc_final: 0.7725 (mpt180) REVERT: B 178 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8388 (p) REVERT: B 197 ARG cc_start: 0.7463 (mpt-90) cc_final: 0.6974 (mpt-90) REVERT: B 212 ASP cc_start: 0.7992 (t0) cc_final: 0.7631 (t0) REVERT: B 263 THR cc_start: 0.8220 (p) cc_final: 0.7951 (m) REVERT: B 283 ARG cc_start: 0.8350 (tpt-90) cc_final: 0.8064 (tpt170) REVERT: B 301 LYS cc_start: 0.8393 (mtpt) cc_final: 0.8110 (mtpp) REVERT: B 335 PHE cc_start: 0.8384 (m-80) cc_final: 0.7956 (m-80) REVERT: R 46 PHE cc_start: 0.8390 (t80) cc_final: 0.8120 (t80) REVERT: R 72 VAL cc_start: 0.8118 (t) cc_final: 0.7759 (p) REVERT: R 257 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8067 (p) REVERT: R 278 LEU cc_start: 0.8154 (mm) cc_final: 0.7767 (mt) REVERT: S 78 THR cc_start: 0.8255 (t) cc_final: 0.7986 (p) REVERT: S 148 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7274 (ttm170) REVERT: S 154 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7801 (tp) REVERT: S 185 SER cc_start: 0.8500 (m) cc_final: 0.8220 (p) outliers start: 46 outliers final: 34 residues processed: 243 average time/residue: 0.2767 time to fit residues: 89.0163 Evaluate side-chains 259 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112783 restraints weight = 13715.315| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.17 r_work: 0.3304 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9182 Z= 0.226 Angle : 0.494 6.593 12425 Z= 0.271 Chirality : 0.041 0.195 1414 Planarity : 0.004 0.054 1556 Dihedral : 4.647 53.171 1252 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.35 % Allowed : 22.87 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1125 helix: 2.70 (0.25), residues: 405 sheet: 0.41 (0.30), residues: 281 loop : -0.26 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.002 0.001 HIS B 91 PHE 0.021 0.001 PHE R 214 TYR 0.023 0.002 TYR S 223 ARG 0.002 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7219 (mpp) cc_final: 0.6888 (mmm) REVERT: A 298 GLU cc_start: 0.7221 (tp30) cc_final: 0.6804 (tp30) REVERT: A 317 LYS cc_start: 0.8328 (ptpp) cc_final: 0.7920 (ptpt) REVERT: A 345 LYS cc_start: 0.8325 (ttpt) cc_final: 0.7843 (mptt) REVERT: B 19 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7318 (mtm-85) REVERT: B 134 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7904 (ttp80) REVERT: B 137 ARG cc_start: 0.8442 (tpp80) cc_final: 0.7642 (tpp80) REVERT: B 150 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7776 (mpt180) REVERT: B 197 ARG cc_start: 0.7447 (mpt-90) cc_final: 0.6985 (mpt-90) REVERT: B 212 ASP cc_start: 0.8010 (t0) cc_final: 0.7623 (t0) REVERT: B 263 THR cc_start: 0.8269 (p) cc_final: 0.7965 (m) REVERT: B 283 ARG cc_start: 0.8361 (tpt-90) cc_final: 0.8010 (tpt170) REVERT: B 301 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8153 (mtpp) REVERT: B 335 PHE cc_start: 0.8380 (m-80) cc_final: 0.7942 (m-80) REVERT: R 46 PHE cc_start: 0.8398 (t80) cc_final: 0.8129 (t80) REVERT: R 72 VAL cc_start: 0.8109 (t) cc_final: 0.7739 (p) REVERT: R 191 THR cc_start: 0.3855 (OUTLIER) cc_final: 0.3587 (m) REVERT: R 257 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8055 (p) REVERT: R 278 LEU cc_start: 0.8181 (mm) cc_final: 0.7776 (mt) REVERT: S 78 THR cc_start: 0.8272 (t) cc_final: 0.8007 (p) REVERT: S 148 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7318 (ttm170) REVERT: S 154 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7789 (tp) REVERT: S 185 SER cc_start: 0.8506 (m) cc_final: 0.8226 (p) outliers start: 43 outliers final: 34 residues processed: 243 average time/residue: 0.2788 time to fit residues: 88.8596 Evaluate side-chains 257 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111432 restraints weight = 13681.760| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.17 r_work: 0.3294 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9182 Z= 0.260 Angle : 0.511 6.800 12425 Z= 0.280 Chirality : 0.042 0.203 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.703 52.687 1252 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.55 % Allowed : 22.37 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1125 helix: 2.67 (0.25), residues: 405 sheet: 0.30 (0.30), residues: 283 loop : -0.22 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 47 HIS 0.004 0.001 HIS B 142 PHE 0.023 0.002 PHE R 214 TYR 0.022 0.002 TYR S 223 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7309 (mpp) cc_final: 0.6988 (mmt) REVERT: A 262 THR cc_start: 0.8306 (m) cc_final: 0.8048 (m) REVERT: A 298 GLU cc_start: 0.7243 (tp30) cc_final: 0.6826 (tp30) REVERT: A 317 LYS cc_start: 0.8363 (ptpp) cc_final: 0.7949 (ptpt) REVERT: A 345 LYS cc_start: 0.8326 (ttpt) cc_final: 0.7837 (mptt) REVERT: B 19 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7335 (mtm-85) REVERT: B 134 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7896 (ttp80) REVERT: B 137 ARG cc_start: 0.8461 (tpp80) cc_final: 0.7812 (tpp80) REVERT: B 150 ARG cc_start: 0.8076 (mmt-90) cc_final: 0.7771 (mpt180) REVERT: B 197 ARG cc_start: 0.7433 (mpt-90) cc_final: 0.6952 (mpt-90) REVERT: B 263 THR cc_start: 0.8289 (p) cc_final: 0.7941 (m) REVERT: B 335 PHE cc_start: 0.8416 (m-80) cc_final: 0.7989 (m-80) REVERT: R 46 PHE cc_start: 0.8419 (t80) cc_final: 0.8143 (t80) REVERT: R 191 THR cc_start: 0.3633 (OUTLIER) cc_final: 0.3302 (m) REVERT: R 257 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8055 (p) REVERT: R 278 LEU cc_start: 0.8216 (mm) cc_final: 0.7792 (mt) REVERT: S 78 THR cc_start: 0.8271 (t) cc_final: 0.8035 (p) REVERT: S 148 ARG cc_start: 0.7590 (ttm110) cc_final: 0.7296 (ttm170) REVERT: S 185 SER cc_start: 0.8492 (m) cc_final: 0.8199 (p) outliers start: 45 outliers final: 37 residues processed: 243 average time/residue: 0.2476 time to fit residues: 79.2959 Evaluate side-chains 269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111442 restraints weight = 13930.199| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.21 r_work: 0.3297 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9182 Z= 0.212 Angle : 0.507 6.279 12425 Z= 0.274 Chirality : 0.041 0.198 1414 Planarity : 0.004 0.054 1556 Dihedral : 4.670 52.766 1252 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.15 % Allowed : 23.28 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1125 helix: 2.69 (0.25), residues: 405 sheet: 0.24 (0.30), residues: 283 loop : -0.21 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.020 0.001 PHE R 214 TYR 0.021 0.002 TYR S 223 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7327 (mpp) cc_final: 0.7115 (mmt) REVERT: A 298 GLU cc_start: 0.7269 (tp30) cc_final: 0.6843 (tp30) REVERT: A 317 LYS cc_start: 0.8358 (ptpp) cc_final: 0.7681 (ptpp) REVERT: A 345 LYS cc_start: 0.8325 (ttpt) cc_final: 0.7819 (mptt) REVERT: B 19 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7430 (mtm-85) REVERT: B 134 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7887 (ttp80) REVERT: B 137 ARG cc_start: 0.8426 (tpp80) cc_final: 0.7825 (tpp80) REVERT: B 175 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7873 (mm-40) REVERT: B 197 ARG cc_start: 0.7453 (mpt-90) cc_final: 0.6978 (mpt-90) REVERT: B 263 THR cc_start: 0.8293 (p) cc_final: 0.7928 (m) REVERT: B 301 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8133 (mtpp) REVERT: B 335 PHE cc_start: 0.8410 (m-80) cc_final: 0.7994 (m-80) REVERT: R 46 PHE cc_start: 0.8403 (t80) cc_final: 0.8123 (t80) REVERT: R 57 ILE cc_start: 0.8025 (mt) cc_final: 0.7746 (mm) REVERT: R 72 VAL cc_start: 0.8139 (t) cc_final: 0.7767 (p) REVERT: R 257 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8061 (p) REVERT: R 278 LEU cc_start: 0.8174 (mm) cc_final: 0.7741 (mt) REVERT: S 29 PHE cc_start: 0.8478 (t80) cc_final: 0.7788 (t80) REVERT: S 78 THR cc_start: 0.8255 (t) cc_final: 0.8044 (p) REVERT: S 148 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7262 (ttm170) REVERT: S 185 SER cc_start: 0.8494 (m) cc_final: 0.8195 (p) outliers start: 41 outliers final: 30 residues processed: 242 average time/residue: 0.2632 time to fit residues: 83.9476 Evaluate side-chains 254 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 0.0570 chunk 78 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.132847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112956 restraints weight = 13735.254| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.18 r_work: 0.3313 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.172 Angle : 0.489 6.850 12425 Z= 0.265 Chirality : 0.040 0.200 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.604 53.914 1252 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.74 % Allowed : 23.79 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.26), residues: 1125 helix: 2.76 (0.25), residues: 405 sheet: 0.29 (0.29), residues: 288 loop : -0.22 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS B 183 PHE 0.021 0.001 PHE R 117 TYR 0.022 0.001 TYR S 223 ARG 0.003 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7332 (mpp) cc_final: 0.7012 (mmt) REVERT: A 262 THR cc_start: 0.8288 (m) cc_final: 0.8032 (m) REVERT: A 298 GLU cc_start: 0.7252 (tp30) cc_final: 0.6869 (tp30) REVERT: A 317 LYS cc_start: 0.8355 (ptpp) cc_final: 0.7988 (ptpt) REVERT: A 345 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7823 (mptt) REVERT: B 19 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7443 (mtm-85) REVERT: B 134 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7906 (ttp80) REVERT: B 137 ARG cc_start: 0.8427 (tpp80) cc_final: 0.7872 (tpp80) REVERT: B 197 ARG cc_start: 0.7422 (mpt-90) cc_final: 0.6938 (mpt-90) REVERT: B 263 THR cc_start: 0.8264 (p) cc_final: 0.7909 (m) REVERT: B 301 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8130 (mtpp) REVERT: B 335 PHE cc_start: 0.8368 (m-80) cc_final: 0.7961 (m-80) REVERT: R 46 PHE cc_start: 0.8408 (t80) cc_final: 0.8098 (t80) REVERT: R 57 ILE cc_start: 0.8096 (mt) cc_final: 0.7787 (mm) REVERT: R 72 VAL cc_start: 0.8117 (t) cc_final: 0.7809 (p) REVERT: R 103 THR cc_start: 0.8104 (p) cc_final: 0.7723 (t) REVERT: R 183 CYS cc_start: 0.6397 (OUTLIER) cc_final: 0.6071 (t) REVERT: R 257 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8077 (p) REVERT: R 278 LEU cc_start: 0.8158 (mm) cc_final: 0.7720 (mt) REVERT: S 29 PHE cc_start: 0.8473 (t80) cc_final: 0.7771 (t80) REVERT: S 34 MET cc_start: 0.8153 (mmm) cc_final: 0.7941 (mmm) REVERT: S 78 THR cc_start: 0.8248 (t) cc_final: 0.8040 (p) REVERT: S 148 ARG cc_start: 0.7545 (ttm110) cc_final: 0.7251 (ttm170) REVERT: S 154 LEU cc_start: 0.7973 (tp) cc_final: 0.7726 (tp) REVERT: S 185 SER cc_start: 0.8490 (m) cc_final: 0.8197 (p) outliers start: 37 outliers final: 33 residues processed: 253 average time/residue: 0.2468 time to fit residues: 82.4387 Evaluate side-chains 269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.132641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112719 restraints weight = 13812.276| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.18 r_work: 0.3309 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9182 Z= 0.196 Angle : 0.501 6.635 12425 Z= 0.272 Chirality : 0.041 0.201 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.593 53.806 1252 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.95 % Allowed : 24.19 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1125 helix: 2.76 (0.25), residues: 405 sheet: 0.26 (0.30), residues: 289 loop : -0.24 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS A 213 PHE 0.023 0.001 PHE R 117 TYR 0.024 0.002 TYR S 223 ARG 0.002 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7365 (mpp) cc_final: 0.7047 (mmt) REVERT: A 298 GLU cc_start: 0.7255 (tp30) cc_final: 0.6882 (tp30) REVERT: A 317 LYS cc_start: 0.8371 (ptpp) cc_final: 0.7726 (ptpp) REVERT: A 345 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7828 (mptt) REVERT: B 19 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7448 (mtm-85) REVERT: B 134 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7901 (ttp80) REVERT: B 137 ARG cc_start: 0.8436 (tpp80) cc_final: 0.7880 (tpp80) REVERT: B 197 ARG cc_start: 0.7450 (mpt-90) cc_final: 0.6945 (mpt-90) REVERT: B 301 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8132 (mtpp) REVERT: B 335 PHE cc_start: 0.8373 (m-80) cc_final: 0.7961 (m-80) REVERT: R 72 VAL cc_start: 0.8123 (t) cc_final: 0.7812 (p) REVERT: R 103 THR cc_start: 0.8093 (p) cc_final: 0.7745 (t) REVERT: R 257 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8068 (p) REVERT: R 278 LEU cc_start: 0.8133 (mm) cc_final: 0.7694 (mt) REVERT: S 29 PHE cc_start: 0.8472 (t80) cc_final: 0.7825 (t80) REVERT: S 78 THR cc_start: 0.8258 (t) cc_final: 0.8050 (p) REVERT: S 148 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7363 (ttm170) REVERT: S 154 LEU cc_start: 0.8007 (tp) cc_final: 0.7716 (tp) REVERT: S 185 SER cc_start: 0.8496 (m) cc_final: 0.8208 (p) outliers start: 39 outliers final: 34 residues processed: 252 average time/residue: 0.2701 time to fit residues: 89.9477 Evaluate side-chains 270 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 195 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 73 optimal weight: 0.0270 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112704 restraints weight = 13747.559| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.18 r_work: 0.3314 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.185 Angle : 0.502 6.025 12425 Z= 0.271 Chirality : 0.041 0.204 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.574 54.003 1252 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.25 % Allowed : 24.09 % Favored : 71.66 % 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: 1.46 (0.26), residues: 1125 helix: 2.76 (0.25), residues: 405 sheet: 0.28 (0.30), residues: 288 loop : -0.26 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS A 213 PHE 0.026 0.001 PHE R 117 TYR 0.021 0.002 TYR S 223 ARG 0.005 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5572.14 seconds wall clock time: 98 minutes 19.22 seconds (5899.22 seconds total)