Starting phenix.real_space_refine on Tue Aug 6 02:15:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsu_43506/08_2024/8vsu_43506.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsu_43506/08_2024/8vsu_43506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsu_43506/08_2024/8vsu_43506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsu_43506/08_2024/8vsu_43506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsu_43506/08_2024/8vsu_43506.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsu_43506/08_2024/8vsu_43506.cif" } resolution = 2.86 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= 0.102 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 41 5.16 5 C 4859 2.51 5 N 1301 2.21 5 O 1391 1.98 5 H 7646 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15240 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 9, 'TRANS': 318} Chain: "C" Number of atoms: 4900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4900 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 21, 'TRANS': 285} Chain: "B" Number of atoms: 4855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4855 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain breaks: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.28, per 1000 atoms: 0.48 Number of scatterers: 15240 At special positions: 0 Unit cell: (87.675, 88.51, 106.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 2 15.00 O 1391 8.00 N 1301 7.00 C 4859 6.00 H 7646 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 12.69 Conformation dependent library (CDL) restraints added in 1.6 seconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 58.7% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 11 through 27 Processing helix chain 'A' and resid 32 through 56 removed outlier: 3.654A pdb=" N ALA A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.744A pdb=" N LYS A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 104 " --> pdb=" O GLN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.798A pdb=" N PHE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.672A pdb=" N TYR A 167 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.646A pdb=" N ASP A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 206 through 219 removed outlier: 3.612A pdb=" N SER A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS A 216 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 239 removed outlier: 3.629A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.505A pdb=" N LEU A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 284 removed outlier: 3.546A pdb=" N VAL A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 282 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 298 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.886A pdb=" N ASN A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.532A pdb=" N ARG C 86 " --> pdb=" O LYS C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 86' Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 149 through 170 removed outlier: 3.575A pdb=" N GLY C 155 " --> pdb=" O CYS C 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 194 through 198 removed outlier: 4.308A pdb=" N VAL C 197 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 233 through 251 removed outlier: 3.585A pdb=" N ASP C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 279 through 289 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 125 removed outlier: 3.859A pdb=" N GLU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 168 through 189 removed outlier: 3.602A pdb=" N TYR B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.748A pdb=" N LEU B 241 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Proline residue: B 242 - end of helix Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 258 through 275 removed outlier: 4.281A pdb=" N ILE B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 349 through 359 Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 375 through 382 removed outlier: 6.085A pdb=" N PHE B 378 " --> pdb=" O ASN B 375 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 381 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 394 Proline residue: B 391 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 46 removed outlier: 4.987A pdb=" N GLU C 65 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU C 54 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 63 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS C 62 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS C 124 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR C 118 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR C 126 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL C 116 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 128 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.781A pdb=" N CYS C 134 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 172 through 173 Processing sheet with id=AA4, first strand: chain 'C' and resid 209 through 210 Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 78 removed outlier: 6.809A pdb=" N LEU B 87 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL B 74 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL B 85 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLY B 76 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N MET B 83 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 135 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SER B 148 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR B 133 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AA7, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AA8, first strand: chain 'B' and resid 221 through 222 363 hydrogen bonds defined for protein. 1032 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: 5.23 Time building geometry restraints manager: 13.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.74 - 0.96: 22 0.96 - 1.17: 7608 1.17 - 1.39: 2601 1.39 - 1.60: 5111 1.60 - 1.82: 67 Bond restraints: 15409 Sorted by residual: bond pdb=" N LYS B 91 " pdb=" H LYS B 91 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD2 TYR A 325 " pdb=" HD2 TYR A 325 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NH1 ARG A 113 " pdb="HH11 ARG A 113 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE1 TYR B 152 " pdb=" HE1 TYR B 152 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE1 HIS C 313 " pdb=" HE1 HIS C 313 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 15404 not shown) Histogram of bond angle deviations from ideal: 95.61 - 103.44: 114 103.44 - 111.28: 16274 111.28 - 119.12: 5775 119.12 - 126.95: 5671 126.95 - 134.79: 98 Bond angle restraints: 27932 Sorted by residual: angle pdb=" CA ASP B 301 " pdb=" CB ASP B 301 " pdb=" CG ASP B 301 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" CA PHE C 298 " pdb=" CB PHE C 298 " pdb=" CG PHE C 298 " ideal model delta sigma weight residual 113.80 118.88 -5.08 1.00e+00 1.00e+00 2.58e+01 angle pdb=" O1B ADP B2001 " pdb=" PB ADP B2001 " pdb=" O2B ADP B2001 " ideal model delta sigma weight residual 119.90 105.13 14.77 3.00e+00 1.11e-01 2.42e+01 angle pdb=" CA PHE B 279 " pdb=" CB PHE B 279 " pdb=" CG PHE B 279 " ideal model delta sigma weight residual 113.80 118.48 -4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" CA PHE C 148 " pdb=" CB PHE C 148 " pdb=" CG PHE C 148 " ideal model delta sigma weight residual 113.80 118.43 -4.63 1.00e+00 1.00e+00 2.14e+01 ... (remaining 27927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 6808 21.69 - 43.37: 232 43.37 - 65.06: 164 65.06 - 86.74: 22 86.74 - 108.43: 2 Dihedral angle restraints: 7228 sinusoidal: 3975 harmonic: 3253 Sorted by residual: dihedral pdb=" CA GLY C 288 " pdb=" C GLY C 288 " pdb=" N MET C 289 " pdb=" CA MET C 289 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 48.43 -108.43 1 2.00e+01 2.50e-03 3.16e+01 dihedral pdb=" CA GLN B 358 " pdb=" C GLN B 358 " pdb=" N CYS B 359 " pdb=" CA CYS B 359 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 7225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 661 0.067 - 0.133: 363 0.133 - 0.200: 115 0.200 - 0.267: 19 0.267 - 0.334: 6 Chirality restraints: 1164 Sorted by residual: chirality pdb=" C2' ADP B2001 " pdb=" C1' ADP B2001 " pdb=" C3' ADP B2001 " pdb=" O2' ADP B2001 " both_signs ideal model delta sigma weight residual False -2.51 -2.84 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA SER C 193 " pdb=" N SER C 193 " pdb=" C SER C 193 " pdb=" CB SER C 193 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA SER B 195 " pdb=" N SER B 195 " pdb=" C SER B 195 " pdb=" CB SER B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1161 not shown) Planarity restraints: 2229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 207 " 0.139 2.00e-02 2.50e+03 5.75e-02 9.92e+01 pdb=" CG TYR A 207 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 207 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR A 207 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 207 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 207 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 207 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 207 " 0.103 2.00e-02 2.50e+03 pdb=" HD1 TYR A 207 " -0.049 2.00e-02 2.50e+03 pdb=" HD2 TYR A 207 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 TYR A 207 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR A 207 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 243 " 0.106 2.00e-02 2.50e+03 4.81e-02 9.25e+01 pdb=" CG TRP B 243 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 243 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 243 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 243 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP B 243 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 243 " -0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 243 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 243 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 243 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 TRP B 243 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP B 243 " -0.075 2.00e-02 2.50e+03 pdb=" HE3 TRP B 243 " -0.090 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 243 " 0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 243 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 243 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 227 " 0.198 9.50e-02 1.11e+02 8.72e-02 7.75e+01 pdb=" NE ARG A 227 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 227 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 227 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 227 " 0.015 2.00e-02 2.50e+03 pdb="HH11 ARG A 227 " -0.117 2.00e-02 2.50e+03 pdb="HH12 ARG A 227 " 0.095 2.00e-02 2.50e+03 pdb="HH21 ARG A 227 " -0.018 2.00e-02 2.50e+03 pdb="HH22 ARG A 227 " -0.062 2.00e-02 2.50e+03 ... (remaining 2226 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 778 2.18 - 2.79: 26413 2.79 - 3.39: 41785 3.39 - 4.00: 55814 4.00 - 4.60: 81224 Nonbonded interactions: 206014 Sorted by model distance: nonbonded pdb=" OD2 ASP C 208 " pdb=" HG SER C 232 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP B 301 " pdb=" HG SER B 303 " model vdw 1.597 2.450 nonbonded pdb=" OD1 ASP C 207 " pdb=" HG1 THR C 209 " model vdw 1.609 2.450 nonbonded pdb=" OE1 GLU C 65 " pdb=" HG1 THR C 336 " model vdw 1.614 2.450 nonbonded pdb=" HH TYR A 223 " pdb=" OE1 GLU B 105 " model vdw 1.618 2.450 ... (remaining 206009 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: 1.070 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: 0.240 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 51.060 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.013 0.141 7763 Z= 0.813 Angle : 1.761 14.765 10493 Z= 1.194 Chirality : 0.086 0.334 1164 Planarity : 0.013 0.117 1339 Dihedral : 12.495 108.425 2943 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.12 % Allowed : 0.60 % Favored : 99.28 % 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: -1.20 (0.25), residues: 933 helix: -1.20 (0.20), residues: 478 sheet: -0.48 (0.52), residues: 87 loop : 0.04 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.013 TRP B 243 HIS 0.010 0.002 HIS B 200 PHE 0.052 0.010 PHE A 188 TYR 0.119 0.016 TYR A 207 ARG 0.010 0.001 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8469 (mttt) cc_final: 0.8250 (mtmt) REVERT: C 104 ARG cc_start: 0.7980 (ptt90) cc_final: 0.7401 (mmt90) REVERT: B 287 MET cc_start: 0.8750 (tmm) cc_final: 0.8542 (tmm) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 3.0009 time to fit residues: 510.2157 Evaluate side-chains 117 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 329 GLN C 220 GLN B 227 GLN B 286 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7763 Z= 0.213 Angle : 0.605 6.623 10493 Z= 0.325 Chirality : 0.042 0.146 1164 Planarity : 0.005 0.045 1339 Dihedral : 7.027 120.454 1030 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.91 % Allowed : 6.09 % Favored : 92.00 % 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: 0.47 (0.27), residues: 933 helix: 0.64 (0.24), residues: 479 sheet: -0.17 (0.55), residues: 75 loop : 0.20 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 308 HIS 0.007 0.001 HIS A 276 PHE 0.024 0.002 PHE A 188 TYR 0.011 0.001 TYR C 246 ARG 0.004 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6681 (pp20) REVERT: A 257 LYS cc_start: 0.8290 (mttt) cc_final: 0.8005 (mtmt) REVERT: B 247 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: B 287 MET cc_start: 0.8733 (tmm) cc_final: 0.8445 (tmm) outliers start: 16 outliers final: 6 residues processed: 125 average time/residue: 2.9212 time to fit residues: 383.8602 Evaluate side-chains 108 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 247 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 289 GLN C 220 GLN B 225 GLN B 227 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7763 Z= 0.152 Angle : 0.516 5.810 10493 Z= 0.266 Chirality : 0.039 0.149 1164 Planarity : 0.004 0.045 1339 Dihedral : 6.252 120.117 1030 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.31 % Allowed : 8.00 % Favored : 90.69 % 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 (0.27), residues: 933 helix: 1.46 (0.25), residues: 477 sheet: -0.25 (0.58), residues: 75 loop : 0.06 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 239 HIS 0.012 0.001 HIS B 162 PHE 0.016 0.001 PHE A 188 TYR 0.010 0.001 TYR C 246 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8277 (mttt) cc_final: 0.7996 (mtmt) REVERT: C 162 ASP cc_start: 0.7541 (m-30) cc_final: 0.7253 (m-30) REVERT: C 336 THR cc_start: 0.7240 (OUTLIER) cc_final: 0.6956 (t) REVERT: B 81 ASP cc_start: 0.7722 (t0) cc_final: 0.7231 (t0) REVERT: B 287 MET cc_start: 0.8672 (tmm) cc_final: 0.8424 (tmm) outliers start: 11 outliers final: 3 residues processed: 107 average time/residue: 2.7849 time to fit residues: 314.8369 Evaluate side-chains 100 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain B residue 206 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 289 GLN C 345 HIS ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7763 Z= 0.240 Angle : 0.532 6.016 10493 Z= 0.277 Chirality : 0.040 0.152 1164 Planarity : 0.004 0.048 1339 Dihedral : 6.064 106.303 1030 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.43 % Allowed : 8.11 % Favored : 90.45 % 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: 1.08 (0.27), residues: 933 helix: 1.51 (0.24), residues: 482 sheet: -0.36 (0.59), residues: 75 loop : 0.02 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 239 HIS 0.006 0.001 HIS B 193 PHE 0.024 0.001 PHE A 188 TYR 0.011 0.001 TYR C 246 ARG 0.002 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7658 (tp) REVERT: A 215 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6765 (pp20) REVERT: A 257 LYS cc_start: 0.8275 (mttt) cc_final: 0.7985 (mtmt) REVERT: C 45 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8600 (mp) REVERT: B 81 ASP cc_start: 0.7763 (t0) cc_final: 0.7191 (t0) REVERT: B 287 MET cc_start: 0.8678 (tmm) cc_final: 0.8453 (tmm) outliers start: 12 outliers final: 4 residues processed: 105 average time/residue: 2.8524 time to fit residues: 315.7687 Evaluate side-chains 101 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain B residue 206 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7763 Z= 0.234 Angle : 0.524 6.149 10493 Z= 0.270 Chirality : 0.040 0.149 1164 Planarity : 0.004 0.047 1339 Dihedral : 5.893 100.608 1030 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.31 % Allowed : 8.59 % Favored : 90.10 % 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: 1.14 (0.28), residues: 933 helix: 1.62 (0.25), residues: 484 sheet: -0.33 (0.60), residues: 75 loop : -0.06 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 239 HIS 0.005 0.001 HIS B 193 PHE 0.020 0.001 PHE A 188 TYR 0.011 0.001 TYR C 246 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: A 141 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7687 (tp) REVERT: A 215 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6812 (pp20) REVERT: A 257 LYS cc_start: 0.8272 (mttt) cc_final: 0.7993 (mtmt) REVERT: B 81 ASP cc_start: 0.7783 (t0) cc_final: 0.7293 (t0) REVERT: B 287 MET cc_start: 0.8666 (tmm) cc_final: 0.8446 (tmm) REVERT: B 380 LYS cc_start: 0.8054 (mttm) cc_final: 0.7705 (mtmp) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 2.8292 time to fit residues: 304.7697 Evaluate side-chains 104 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain B residue 206 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7763 Z= 0.158 Angle : 0.493 5.992 10493 Z= 0.253 Chirality : 0.039 0.145 1164 Planarity : 0.004 0.044 1339 Dihedral : 5.689 97.769 1030 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.84 % Allowed : 10.74 % Favored : 88.42 % 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: 1.35 (0.28), residues: 933 helix: 1.85 (0.25), residues: 484 sheet: -0.29 (0.61), residues: 75 loop : -0.05 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 239 HIS 0.004 0.001 HIS B 162 PHE 0.016 0.001 PHE A 188 TYR 0.008 0.001 TYR C 246 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7656 (tp) REVERT: A 257 LYS cc_start: 0.8251 (mttt) cc_final: 0.7973 (mtmt) REVERT: A 289 GLN cc_start: 0.7983 (tp40) cc_final: 0.7441 (tp-100) REVERT: B 81 ASP cc_start: 0.7739 (t0) cc_final: 0.7217 (t0) REVERT: B 287 MET cc_start: 0.8638 (tmm) cc_final: 0.8419 (tmm) REVERT: B 380 LYS cc_start: 0.8009 (mttm) cc_final: 0.7653 (mtmp) outliers start: 7 outliers final: 3 residues processed: 101 average time/residue: 2.7574 time to fit residues: 294.2694 Evaluate side-chains 97 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain B residue 206 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7763 Z= 0.140 Angle : 0.483 6.137 10493 Z= 0.244 Chirality : 0.039 0.146 1164 Planarity : 0.004 0.045 1339 Dihedral : 5.449 91.939 1030 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.84 % Allowed : 10.86 % Favored : 88.31 % 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: 1.64 (0.28), residues: 933 helix: 2.17 (0.25), residues: 478 sheet: -0.27 (0.61), residues: 75 loop : 0.03 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 239 HIS 0.004 0.001 HIS B 162 PHE 0.013 0.001 PHE A 188 TYR 0.007 0.001 TYR C 166 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7672 (tp) REVERT: A 257 LYS cc_start: 0.8242 (mttt) cc_final: 0.7960 (mtmt) REVERT: B 287 MET cc_start: 0.8616 (tmm) cc_final: 0.8399 (tmm) REVERT: B 380 LYS cc_start: 0.7979 (mttm) cc_final: 0.7623 (mtmp) outliers start: 7 outliers final: 1 residues processed: 103 average time/residue: 2.6904 time to fit residues: 293.3048 Evaluate side-chains 99 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 332 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7763 Z= 0.138 Angle : 0.482 6.276 10493 Z= 0.243 Chirality : 0.038 0.146 1164 Planarity : 0.004 0.041 1339 Dihedral : 5.300 82.898 1030 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.48 % Allowed : 11.81 % Favored : 87.71 % 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: 1.75 (0.28), residues: 933 helix: 2.30 (0.25), residues: 479 sheet: -0.49 (0.55), residues: 85 loop : 0.12 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 239 HIS 0.003 0.001 HIS B 162 PHE 0.014 0.001 PHE A 188 TYR 0.007 0.001 TYR C 166 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8225 (mttt) cc_final: 0.7968 (mtmt) REVERT: B 380 LYS cc_start: 0.7950 (mttm) cc_final: 0.7585 (mtmp) outliers start: 4 outliers final: 1 residues processed: 103 average time/residue: 2.6647 time to fit residues: 290.3020 Evaluate side-chains 97 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7763 Z= 0.155 Angle : 0.484 6.442 10493 Z= 0.244 Chirality : 0.039 0.145 1164 Planarity : 0.004 0.042 1339 Dihedral : 5.270 76.324 1030 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.84 % Allowed : 11.81 % Favored : 87.35 % 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: 1.74 (0.28), residues: 933 helix: 2.29 (0.25), residues: 479 sheet: -0.48 (0.56), residues: 85 loop : 0.11 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 239 HIS 0.006 0.001 HIS B 162 PHE 0.015 0.001 PHE A 188 TYR 0.008 0.001 TYR C 246 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8236 (mttt) cc_final: 0.7985 (mtmt) REVERT: B 380 LYS cc_start: 0.7957 (mttm) cc_final: 0.7596 (mtmp) outliers start: 7 outliers final: 3 residues processed: 103 average time/residue: 2.7246 time to fit residues: 297.5014 Evaluate side-chains 100 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain C residue 232 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7763 Z= 0.206 Angle : 0.507 6.739 10493 Z= 0.257 Chirality : 0.039 0.142 1164 Planarity : 0.004 0.050 1339 Dihedral : 5.156 68.111 1030 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.84 % Allowed : 11.81 % Favored : 87.35 % 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: 1.64 (0.28), residues: 933 helix: 2.23 (0.25), residues: 478 sheet: -0.50 (0.56), residues: 85 loop : 0.03 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 239 HIS 0.006 0.001 HIS B 162 PHE 0.020 0.001 PHE A 188 TYR 0.010 0.001 TYR C 246 ARG 0.008 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6842 (pp20) REVERT: A 257 LYS cc_start: 0.8233 (mttt) cc_final: 0.7975 (mtmt) REVERT: B 380 LYS cc_start: 0.7977 (mttm) cc_final: 0.7613 (mtmp) outliers start: 7 outliers final: 4 residues processed: 101 average time/residue: 2.7260 time to fit residues: 291.1496 Evaluate side-chains 99 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 206 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100277 restraints weight = 26403.273| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.14 r_work: 0.2887 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 7763 Z= 0.268 Angle : 0.889 59.198 10493 Z= 0.541 Chirality : 0.040 0.143 1164 Planarity : 0.004 0.044 1339 Dihedral : 5.147 68.044 1030 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.84 % Allowed : 12.05 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.28), residues: 933 helix: 2.21 (0.25), residues: 478 sheet: -0.50 (0.56), residues: 85 loop : 0.01 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 239 HIS 0.005 0.001 HIS B 162 PHE 0.020 0.001 PHE A 188 TYR 0.010 0.001 TYR C 246 ARG 0.006 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6273.27 seconds wall clock time: 108 minutes 56.31 seconds (6536.31 seconds total)