Starting phenix.real_space_refine on Sat Dec 28 19:35:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kfy_37208/12_2024/8kfy_37208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kfy_37208/12_2024/8kfy_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_37208/12_2024/8kfy_37208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kfy_37208/12_2024/8kfy_37208.map" model { file = "/net/cci-nas-00/data/ceres_data/8kfy_37208/12_2024/8kfy_37208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kfy_37208/12_2024/8kfy_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.41, per 1000 atoms: 0.60 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 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: 1.13 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: 2.88 Time building geometry restraints manager: 2.57 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: 0.010 Normalize map: mean=0, sd=1: 1.040 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.080 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.680 ------------------------------------------------------------------------------- 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 : 0.890 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: 0.2709 time to fit residues: 79.3097 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 : 1.037 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 1.054 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7456 (mpp) cc_final: 0.7205 (mmm) REVERT: A 184 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 298 GLU cc_start: 0.6696 (tp30) cc_final: 0.6317 (tp30) REVERT: B 19 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.7024 (mtm-85) REVERT: B 212 ASP cc_start: 0.7591 (t0) cc_final: 0.7292 (t0) REVERT: B 263 THR cc_start: 0.8193 (p) cc_final: 0.7864 (m) REVERT: B 335 PHE cc_start: 0.8492 (m-80) cc_final: 0.8032 (m-80) REVERT: R 46 PHE cc_start: 0.8356 (t80) cc_final: 0.8116 (t80) REVERT: R 124 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8249 (mm) REVERT: R 202 MET cc_start: 0.7633 (mmm) cc_final: 0.7329 (mtp) REVERT: R 215 MET cc_start: 0.8031 (mmm) cc_final: 0.7563 (mpp) REVERT: R 250 PHE cc_start: 0.7131 (m-10) cc_final: 0.6927 (m-10) REVERT: R 257 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8180 (p) REVERT: S 154 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7821 (tp) REVERT: S 160 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8328 (m) outliers start: 39 outliers final: 23 residues processed: 241 average time/residue: 0.2400 time to fit residues: 77.1489 Evaluate side-chains 239 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 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 56 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 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 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9182 Z= 0.254 Angle : 0.511 7.463 12425 Z= 0.281 Chirality : 0.042 0.210 1414 Planarity : 0.004 0.056 1556 Dihedral : 4.784 51.355 1252 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.25 % Allowed : 21.56 % 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: 1.45 (0.25), residues: 1125 helix: 2.60 (0.25), residues: 405 sheet: 0.56 (0.30), residues: 280 loop : -0.31 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 47 HIS 0.003 0.001 HIS B 142 PHE 0.023 0.001 PHE R 214 TYR 0.025 0.002 TYR S 223 ARG 0.003 0.000 ARG A 15 *********************** 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 260 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7376 (mpp) cc_final: 0.7058 (mmm) REVERT: A 298 GLU cc_start: 0.6800 (tp30) cc_final: 0.6469 (tp30) REVERT: A 317 LYS cc_start: 0.8466 (ptpp) cc_final: 0.7832 (ptpp) REVERT: A 345 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7873 (mptt) REVERT: B 19 ARG cc_start: 0.7304 (mtm-85) cc_final: 0.7034 (mtm-85) REVERT: B 134 ARG cc_start: 0.7877 (ttp80) cc_final: 0.7574 (ttp80) REVERT: B 178 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8326 (p) REVERT: B 197 ARG cc_start: 0.6977 (mpt-90) cc_final: 0.6582 (mpt-90) REVERT: B 301 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7910 (mtpp) REVERT: B 335 PHE cc_start: 0.8476 (m-80) cc_final: 0.8030 (m-80) REVERT: R 46 PHE cc_start: 0.8403 (t80) cc_final: 0.8152 (t80) REVERT: R 124 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8257 (mm) REVERT: R 250 PHE cc_start: 0.7039 (m-10) cc_final: 0.6789 (m-10) REVERT: R 257 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8175 (p) REVERT: S 148 ARG cc_start: 0.7173 (ttm110) cc_final: 0.6884 (ttm170) REVERT: S 154 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7866 (tp) REVERT: S 185 SER cc_start: 0.8385 (m) cc_final: 0.8120 (p) outliers start: 42 outliers final: 30 residues processed: 241 average time/residue: 0.2389 time to fit residues: 77.1016 Evaluate side-chains 248 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 271 LYS 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 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 301 LYS 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 124 ILE Chi-restraints excluded: chain R residue 151 THR 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 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 75 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.0050 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 268 ASN R 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 9182 Z= 0.498 Angle : 0.605 7.630 12425 Z= 0.332 Chirality : 0.047 0.241 1414 Planarity : 0.005 0.061 1556 Dihedral : 5.076 49.760 1252 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.96 % Allowed : 21.56 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1125 helix: 2.24 (0.25), residues: 405 sheet: 0.25 (0.30), residues: 283 loop : -0.42 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP S 47 HIS 0.005 0.001 HIS B 311 PHE 0.032 0.002 PHE R 214 TYR 0.026 0.002 TYR S 223 ARG 0.005 0.001 ARG A 15 *********************** 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 272 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7539 (mpp) cc_final: 0.7249 (mmm) REVERT: A 298 GLU cc_start: 0.6694 (tp30) cc_final: 0.6351 (tp30) REVERT: B 16 ASN cc_start: 0.8418 (m-40) cc_final: 0.7839 (m-40) REVERT: B 19 ARG cc_start: 0.7337 (mtm-85) cc_final: 0.6959 (mtm-85) REVERT: B 178 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8393 (p) REVERT: B 197 ARG cc_start: 0.7009 (mpt-90) cc_final: 0.6600 (mpt-90) REVERT: B 251 ARG cc_start: 0.8667 (mtt90) cc_final: 0.8360 (mtt90) REVERT: B 263 THR cc_start: 0.8310 (p) cc_final: 0.7862 (m) REVERT: B 301 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7937 (mtpp) REVERT: B 335 PHE cc_start: 0.8546 (m-80) cc_final: 0.8111 (m-80) REVERT: R 46 PHE cc_start: 0.8434 (t80) cc_final: 0.8208 (t80) REVERT: R 124 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8206 (mm) REVERT: R 208 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7923 (mt) REVERT: R 250 PHE cc_start: 0.7189 (m-10) cc_final: 0.6941 (m-10) REVERT: R 257 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8180 (p) REVERT: R 278 LEU cc_start: 0.8278 (mm) cc_final: 0.8026 (mt) REVERT: S 148 ARG cc_start: 0.7245 (ttm110) cc_final: 0.6939 (ttm170) REVERT: S 160 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8524 (m) REVERT: S 185 SER cc_start: 0.8412 (m) cc_final: 0.8104 (p) outliers start: 49 outliers final: 28 residues processed: 247 average time/residue: 0.2501 time to fit residues: 80.9832 Evaluate side-chains 250 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 271 LYS 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 270 ILE Chi-restraints excluded: chain B residue 301 LYS 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 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 208 LEU 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 135 VAL 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 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 0.0030 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1651 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= 0.212 Angle : 0.514 6.611 12425 Z= 0.281 Chirality : 0.041 0.195 1414 Planarity : 0.004 0.059 1556 Dihedral : 4.594 28.217 1250 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.55 % Allowed : 21.66 % Favored : 73.79 % 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: 1.18 (0.25), residues: 1125 helix: 2.47 (0.25), residues: 405 sheet: 0.28 (0.31), residues: 273 loop : -0.44 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.021 0.001 PHE R 214 TYR 0.020 0.002 TYR S 223 ARG 0.005 0.000 ARG B 134 *********************** 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: 45 poor density : 222 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7520 (mpp) cc_final: 0.7225 (mmm) REVERT: A 298 GLU cc_start: 0.6790 (tp30) cc_final: 0.6411 (tp30) REVERT: A 345 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7888 (mptt) REVERT: B 19 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6961 (mtm-85) REVERT: B 134 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7583 (ttp80) REVERT: B 178 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8347 (p) REVERT: B 197 ARG cc_start: 0.7020 (mpt-90) cc_final: 0.6552 (mpt-90) REVERT: B 263 THR cc_start: 0.8299 (p) cc_final: 0.7926 (m) REVERT: B 335 PHE cc_start: 0.8469 (m-80) cc_final: 0.8077 (m-80) REVERT: R 46 PHE cc_start: 0.8461 (t80) cc_final: 0.8204 (t80) REVERT: R 124 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8158 (mm) REVERT: R 208 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7914 (mt) REVERT: R 250 PHE cc_start: 0.7067 (m-10) cc_final: 0.6838 (m-10) REVERT: R 257 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8174 (p) REVERT: R 278 LEU cc_start: 0.8188 (mm) cc_final: 0.7906 (mt) REVERT: S 78 THR cc_start: 0.8248 (t) cc_final: 0.7992 (p) REVERT: S 148 ARG cc_start: 0.7142 (ttm110) cc_final: 0.6865 (ttm170) REVERT: S 160 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8470 (m) REVERT: S 185 SER cc_start: 0.8378 (m) cc_final: 0.8070 (p) outliers start: 45 outliers final: 31 residues processed: 240 average time/residue: 0.2523 time to fit residues: 79.3044 Evaluate side-chains 258 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 178 THR 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 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 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 208 LEU 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 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9182 Z= 0.220 Angle : 0.505 7.310 12425 Z= 0.275 Chirality : 0.041 0.197 1414 Planarity : 0.004 0.057 1556 Dihedral : 4.497 27.825 1250 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.16 % Allowed : 21.05 % Favored : 73.79 % 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: 1.23 (0.25), residues: 1125 helix: 2.52 (0.25), residues: 405 sheet: 0.29 (0.31), residues: 273 loop : -0.41 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.021 0.001 PHE R 214 TYR 0.021 0.002 TYR S 223 ARG 0.005 0.000 ARG A 32 *********************** 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 279 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7523 (mpp) cc_final: 0.7209 (mmm) REVERT: A 298 GLU cc_start: 0.6807 (tp30) cc_final: 0.6434 (tp30) REVERT: A 345 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7897 (mptt) REVERT: B 19 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.6969 (mtm-85) REVERT: B 134 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7602 (ttp80) REVERT: B 137 ARG cc_start: 0.8312 (tpp80) cc_final: 0.7516 (tpp80) REVERT: B 150 ARG cc_start: 0.8073 (mmt-90) cc_final: 0.7778 (mpt180) REVERT: B 170 ASP cc_start: 0.7764 (p0) cc_final: 0.7561 (p0) REVERT: B 197 ARG cc_start: 0.7024 (mpt-90) cc_final: 0.6542 (mpt-90) REVERT: B 335 PHE cc_start: 0.8456 (m-80) cc_final: 0.8071 (m-80) REVERT: R 46 PHE cc_start: 0.8465 (t80) cc_final: 0.8189 (t80) REVERT: R 124 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8158 (mm) REVERT: R 208 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7908 (mt) REVERT: R 250 PHE cc_start: 0.7054 (m-10) cc_final: 0.6821 (m-10) REVERT: R 257 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8169 (p) REVERT: R 278 LEU cc_start: 0.8179 (mm) cc_final: 0.7865 (mt) REVERT: S 29 PHE cc_start: 0.8432 (t80) cc_final: 0.7744 (t80) REVERT: S 148 ARG cc_start: 0.7147 (ttm110) cc_final: 0.6874 (ttm170) REVERT: S 185 SER cc_start: 0.8371 (m) cc_final: 0.8063 (p) outliers start: 51 outliers final: 38 residues processed: 249 average time/residue: 0.2793 time to fit residues: 92.0744 Evaluate side-chains 261 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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 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 108 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 163 MET 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 208 LEU 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 R residue 308 LYS 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 180 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1850 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= 0.190 Angle : 0.495 6.398 12425 Z= 0.270 Chirality : 0.041 0.204 1414 Planarity : 0.004 0.056 1556 Dihedral : 4.414 27.823 1250 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.35 % Allowed : 22.47 % 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: 1.28 (0.25), residues: 1125 helix: 2.60 (0.25), residues: 405 sheet: 0.26 (0.31), residues: 274 loop : -0.38 (0.29), residues: 446 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 0.019 0.001 PHE R 214 TYR 0.024 0.001 TYR S 223 ARG 0.005 0.000 ARG B 49 *********************** 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 269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7482 (mpp) cc_final: 0.7134 (mmm) REVERT: A 298 GLU cc_start: 0.6802 (tp30) cc_final: 0.6456 (tp30) REVERT: A 345 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7897 (mptt) REVERT: B 19 ARG cc_start: 0.7372 (mtm-85) cc_final: 0.7053 (mtm-85) REVERT: B 134 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7596 (ttp80) REVERT: B 137 ARG cc_start: 0.8282 (tpp80) cc_final: 0.7600 (tpp80) REVERT: B 150 ARG cc_start: 0.8057 (mmt-90) cc_final: 0.7779 (mpt180) REVERT: B 170 ASP cc_start: 0.7687 (p0) cc_final: 0.7474 (p0) REVERT: B 197 ARG cc_start: 0.6992 (mpt-90) cc_final: 0.6563 (mpt-90) REVERT: B 263 THR cc_start: 0.8202 (p) cc_final: 0.7931 (m) REVERT: B 335 PHE cc_start: 0.8437 (m-80) cc_final: 0.8064 (m-80) REVERT: R 46 PHE cc_start: 0.8385 (t80) cc_final: 0.8125 (t80) REVERT: R 57 ILE cc_start: 0.8160 (mt) cc_final: 0.7888 (mm) REVERT: R 124 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8145 (mm) REVERT: R 250 PHE cc_start: 0.7048 (m-10) cc_final: 0.6825 (m-10) REVERT: R 257 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8183 (p) REVERT: R 278 LEU cc_start: 0.8150 (mm) cc_final: 0.7759 (mt) REVERT: S 29 PHE cc_start: 0.8437 (t80) cc_final: 0.7727 (t80) REVERT: S 78 THR cc_start: 0.8252 (t) cc_final: 0.8022 (p) REVERT: S 148 ARG cc_start: 0.7138 (ttm110) cc_final: 0.6872 (ttm170) REVERT: S 185 SER cc_start: 0.8363 (m) cc_final: 0.8056 (p) outliers start: 43 outliers final: 35 residues processed: 241 average time/residue: 0.2567 time to fit residues: 81.4252 Evaluate side-chains 258 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 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 110 SER Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 163 MET 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 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain R residue 308 LYS 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 180 MET 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 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 0.0470 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1932 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= 0.201 Angle : 0.491 6.115 12425 Z= 0.269 Chirality : 0.041 0.205 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.387 27.737 1250 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.86 % Allowed : 22.06 % 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: 1.31 (0.25), residues: 1125 helix: 2.66 (0.25), residues: 405 sheet: 0.27 (0.31), residues: 280 loop : -0.41 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 213 PHE 0.020 0.001 PHE R 214 TYR 0.022 0.002 TYR S 223 ARG 0.006 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: 48 poor density : 218 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7499 (mpp) cc_final: 0.7142 (mmt) REVERT: A 298 GLU cc_start: 0.6816 (tp30) cc_final: 0.6518 (tp30) REVERT: A 345 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7900 (mptt) REVERT: B 19 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.7094 (mtm-85) REVERT: B 134 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7588 (ttp80) REVERT: B 137 ARG cc_start: 0.8269 (tpp80) cc_final: 0.7668 (tpp80) REVERT: B 150 ARG cc_start: 0.8087 (mmt-90) cc_final: 0.7790 (mpt180) REVERT: B 170 ASP cc_start: 0.7655 (p0) cc_final: 0.7427 (p0) REVERT: B 197 ARG cc_start: 0.7028 (mpt-90) cc_final: 0.6548 (mpt-90) REVERT: B 263 THR cc_start: 0.8231 (p) cc_final: 0.7951 (m) REVERT: B 301 LYS cc_start: 0.8306 (mtpt) cc_final: 0.8025 (mtpp) REVERT: B 335 PHE cc_start: 0.8426 (m-80) cc_final: 0.8052 (m-80) REVERT: R 46 PHE cc_start: 0.8395 (t80) cc_final: 0.8120 (t80) REVERT: R 124 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8142 (mm) REVERT: R 257 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8126 (p) REVERT: R 278 LEU cc_start: 0.8160 (mm) cc_final: 0.7756 (mt) REVERT: S 29 PHE cc_start: 0.8439 (t80) cc_final: 0.7715 (t80) REVERT: S 78 THR cc_start: 0.8246 (t) cc_final: 0.8020 (p) REVERT: S 148 ARG cc_start: 0.7147 (ttm110) cc_final: 0.6875 (ttm170) REVERT: S 185 SER cc_start: 0.8366 (m) cc_final: 0.8062 (p) outliers start: 48 outliers final: 38 residues processed: 236 average time/residue: 0.2674 time to fit residues: 82.5099 Evaluate side-chains 257 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 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 110 SER Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 163 MET 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 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 2 VAL 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 180 MET Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0040 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9182 Z= 0.163 Angle : 0.478 5.865 12425 Z= 0.261 Chirality : 0.040 0.200 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.312 27.499 1250 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.35 % Allowed : 22.77 % Favored : 72.87 % 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: 1.38 (0.26), residues: 1125 helix: 2.74 (0.25), residues: 405 sheet: 0.28 (0.31), residues: 280 loop : -0.37 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS R 292 PHE 0.020 0.001 PHE R 117 TYR 0.023 0.001 TYR S 223 ARG 0.005 0.000 ARG A 32 *********************** 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 280 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7473 (mpp) cc_final: 0.7138 (mmt) REVERT: A 298 GLU cc_start: 0.6815 (tp30) cc_final: 0.6552 (tp30) REVERT: A 345 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7896 (mptt) REVERT: B 19 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.7099 (mtm-85) REVERT: B 134 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7577 (ttp80) REVERT: B 137 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7662 (tpp80) REVERT: B 170 ASP cc_start: 0.7618 (p0) cc_final: 0.7360 (p0) REVERT: B 197 ARG cc_start: 0.7027 (mpt-90) cc_final: 0.6527 (mpt-90) REVERT: B 263 THR cc_start: 0.8206 (p) cc_final: 0.7903 (m) REVERT: B 301 LYS cc_start: 0.8313 (mtpt) cc_final: 0.8025 (mtpp) REVERT: B 335 PHE cc_start: 0.8371 (m-80) cc_final: 0.7994 (m-80) REVERT: R 46 PHE cc_start: 0.8405 (t80) cc_final: 0.8117 (t80) REVERT: R 57 ILE cc_start: 0.8180 (mt) cc_final: 0.7782 (mm) REVERT: R 72 VAL cc_start: 0.8177 (t) cc_final: 0.7974 (p) REVERT: R 103 THR cc_start: 0.8131 (p) cc_final: 0.7771 (t) REVERT: R 183 CYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5793 (t) REVERT: R 250 PHE cc_start: 0.6893 (m-10) cc_final: 0.6681 (m-10) REVERT: R 257 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8086 (p) REVERT: R 278 LEU cc_start: 0.8141 (mm) cc_final: 0.7733 (mt) REVERT: S 29 PHE cc_start: 0.8438 (t80) cc_final: 0.7766 (t80) REVERT: S 78 THR cc_start: 0.8253 (t) cc_final: 0.8013 (p) REVERT: S 148 ARG cc_start: 0.7211 (ttm110) cc_final: 0.6934 (ttm170) REVERT: S 160 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8639 (m) REVERT: S 182 ASN cc_start: 0.8573 (m110) cc_final: 0.8342 (m-40) REVERT: S 185 SER cc_start: 0.8361 (m) cc_final: 0.8066 (p) outliers start: 43 outliers final: 33 residues processed: 253 average time/residue: 0.2556 time to fit residues: 85.0209 Evaluate side-chains 269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 52 GLN Chi-restraints excluded: chain A residue 186 GLU 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 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 153 ASP 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 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 85 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 149 MET 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 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 2 VAL 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 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2056 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= 0.220 Angle : 0.504 6.200 12425 Z= 0.276 Chirality : 0.041 0.207 1414 Planarity : 0.004 0.055 1556 Dihedral : 4.354 27.464 1250 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.85 % Allowed : 23.99 % Favored : 72.17 % 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: 1.31 (0.26), residues: 1125 helix: 2.65 (0.25), residues: 405 sheet: 0.25 (0.31), residues: 280 loop : -0.39 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 47 HIS 0.003 0.001 HIS A 213 PHE 0.023 0.001 PHE R 117 TYR 0.025 0.002 TYR S 223 ARG 0.005 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 266 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7505 (mpp) cc_final: 0.7141 (mmt) REVERT: A 298 GLU cc_start: 0.6672 (tp30) cc_final: 0.6405 (tp30) REVERT: A 317 LYS cc_start: 0.8535 (ptpp) cc_final: 0.8060 (ptpp) REVERT: A 345 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7893 (mptt) REVERT: B 19 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.7109 (mtm-85) REVERT: B 134 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7574 (ttp80) REVERT: B 137 ARG cc_start: 0.8264 (tpp80) cc_final: 0.7664 (tpp80) REVERT: B 170 ASP cc_start: 0.7584 (p0) cc_final: 0.7354 (p0) REVERT: B 197 ARG cc_start: 0.7022 (mpt-90) cc_final: 0.6501 (mpt-90) REVERT: B 263 THR cc_start: 0.8233 (p) cc_final: 0.7959 (m) REVERT: B 301 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8042 (mtpp) REVERT: B 335 PHE cc_start: 0.8411 (m-80) cc_final: 0.8037 (m-80) REVERT: R 46 PHE cc_start: 0.8430 (t80) cc_final: 0.8129 (t80) REVERT: R 72 VAL cc_start: 0.8193 (t) cc_final: 0.7948 (p) REVERT: R 257 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8124 (p) REVERT: R 278 LEU cc_start: 0.8197 (mm) cc_final: 0.7783 (mt) REVERT: S 29 PHE cc_start: 0.8444 (t80) cc_final: 0.7730 (t80) REVERT: S 78 THR cc_start: 0.8248 (t) cc_final: 0.8017 (p) REVERT: S 148 ARG cc_start: 0.7248 (ttm110) cc_final: 0.6973 (ttm170) REVERT: S 160 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8640 (m) REVERT: S 182 ASN cc_start: 0.8546 (m110) cc_final: 0.8319 (m-40) REVERT: S 185 SER cc_start: 0.8374 (m) cc_final: 0.8066 (p) outliers start: 38 outliers final: 34 residues processed: 242 average time/residue: 0.2608 time to fit residues: 82.5947 Evaluate side-chains 263 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 245 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 248 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 153 ASP 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 B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE 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 149 MET 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 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 2 VAL 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 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111603 restraints weight = 13726.580| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.12 r_work: 0.3291 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2110 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= 0.247 Angle : 0.520 7.603 12425 Z= 0.283 Chirality : 0.042 0.217 1414 Planarity : 0.004 0.056 1556 Dihedral : 4.403 27.416 1250 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.45 % Allowed : 23.58 % Favored : 71.96 % 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: 1.23 (0.26), residues: 1125 helix: 2.57 (0.25), residues: 405 sheet: 0.23 (0.30), residues: 280 loop : -0.42 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 47 HIS 0.003 0.001 HIS A 213 PHE 0.023 0.002 PHE R 117 TYR 0.016 0.002 TYR S 223 ARG 0.004 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.97 seconds wall clock time: 47 minutes 41.64 seconds (2861.64 seconds total)