Starting phenix.real_space_refine on Sat Dec 28 15:06:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwh_37888/12_2024/8wwh_37888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwh_37888/12_2024/8wwh_37888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwh_37888/12_2024/8wwh_37888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwh_37888/12_2024/8wwh_37888.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwh_37888/12_2024/8wwh_37888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwh_37888/12_2024/8wwh_37888.cif" } resolution = 2.84 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= 0.002 sd= 0.072 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 64 5.16 5 C 5618 2.51 5 N 1491 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8821 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2235 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 5.07, per 1000 atoms: 0.57 Number of scatterers: 8821 At special positions: 0 Unit cell: (88.81, 116.63, 123.05, 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 64 16.00 O 1648 8.00 N 1491 7.00 C 5618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " 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: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 38.8% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.503A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.101A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.002A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.607A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.295A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.599A 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 3 through 25 removed outlier: 3.509A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.542A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 138 Proline residue: R 113 - end of helix Processing helix chain 'R' and resid 145 through 164 Processing helix chain 'R' and resid 165 through 170 Processing helix chain 'R' and resid 180 through 216 removed outlier: 4.004A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU R 187 " --> pdb=" O THR R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.581A pdb=" N THR R 221 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 removed outlier: 3.517A pdb=" N TRP R 248 " --> pdb=" O ILE R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.637A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 303 Processing helix chain 'R' and resid 313 through 351 Proline residue: R 340 - end of helix removed outlier: 3.901A pdb=" N LEU R 349 " --> pdb=" O GLN R 345 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.229A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.242A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.593A 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: 5.767A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.593A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.973A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.233A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.629A 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: 6.921A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.482A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.885A 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: 3.686A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.809A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.257A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.170A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 253 through 255 removed outlier: 3.651A pdb=" N GLY R 262 " --> pdb=" O ILE R 254 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1299 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: 3.65 Time building geometry restraints manager: 2.99 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: 2844 1.34 - 1.46: 2035 1.46 - 1.58: 4038 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 9010 Sorted by residual: bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.66e-01 bond pdb=" CG LEU B 318 " pdb=" CD2 LEU B 318 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.84e-01 bond pdb=" CB ASP A 20 " pdb=" CG ASP A 20 " ideal model delta sigma weight residual 1.516 1.497 0.019 2.50e-02 1.60e+03 5.73e-01 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.11e-01 bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.14e-01 ... (remaining 9005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 11872 1.02 - 2.03: 292 2.03 - 3.05: 52 3.05 - 4.07: 7 4.07 - 5.09: 10 Bond angle restraints: 12233 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.42e+00 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 110.80 114.53 -3.73 2.13e+00 2.20e-01 3.06e+00 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 108.96 106.52 2.44 1.49e+00 4.50e-01 2.67e+00 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 121.39 -5.09 3.50e+00 8.16e-02 2.11e+00 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 123.93 126.11 -2.18 1.54e+00 4.22e-01 2.01e+00 ... (remaining 12228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 4984 11.72 - 23.44: 267 23.44 - 35.17: 58 35.17 - 46.89: 18 46.89 - 58.61: 4 Dihedral angle restraints: 5331 sinusoidal: 2014 harmonic: 3317 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 835 0.028 - 0.056: 359 0.056 - 0.084: 112 0.084 - 0.112: 80 0.112 - 0.140: 20 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1403 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO B 236 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO E 107 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS R 216 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO R 217 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO R 217 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 217 " -0.014 5.00e-02 4.00e+02 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 221 2.70 - 3.25: 8621 3.25 - 3.80: 14364 3.80 - 4.35: 19363 4.35 - 4.90: 32441 Nonbonded interactions: 75010 Sorted by model distance: nonbonded pdb=" O SER R 243 " pdb=" OH TYR R 280 " model vdw 2.156 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.253 3.040 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.263 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.273 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.285 3.040 ... (remaining 75005 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.410 Find NCS groups from input model: 0.110 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 0.036 9010 Z= 0.197 Angle : 0.421 5.087 12233 Z= 0.222 Chirality : 0.041 0.140 1406 Planarity : 0.003 0.046 1547 Dihedral : 8.125 58.611 3182 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.63 % Allowed : 2.42 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.92 (0.25), residues: 1129 helix: 1.05 (0.26), residues: 399 sheet: 0.78 (0.29), residues: 283 loop : 0.26 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE A 196 TYR 0.009 0.001 TYR R 280 ARG 0.002 0.000 ARG R 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 0.974 Fit side-chains REVERT: A 29 LYS cc_start: 0.8323 (tttt) cc_final: 0.7971 (ttmm) REVERT: A 186 GLU cc_start: 0.8163 (tt0) cc_final: 0.7792 (tt0) REVERT: A 197 LYS cc_start: 0.8119 (mttt) cc_final: 0.7898 (mtpt) REVERT: A 208 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7756 (ttp80) REVERT: A 209 LYS cc_start: 0.8466 (pttt) cc_final: 0.8244 (ptmt) REVERT: A 251 ASP cc_start: 0.8280 (t70) cc_final: 0.8066 (t0) REVERT: A 309 ASP cc_start: 0.7741 (t70) cc_final: 0.7482 (t0) REVERT: A 330 LYS cc_start: 0.7586 (mttt) cc_final: 0.7027 (mtpt) REVERT: B 46 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7400 (mmt-90) REVERT: B 129 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7531 (mmt180) REVERT: C 21 MET cc_start: 0.8460 (mmm) cc_final: 0.7499 (ttt) REVERT: E 43 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8116 (mptp) REVERT: R 148 ASP cc_start: 0.7806 (m-30) cc_final: 0.7534 (m-30) REVERT: R 165 MET cc_start: 0.8601 (ttm) cc_final: 0.7922 (tmm) REVERT: R 191 MET cc_start: 0.7631 (tpt) cc_final: 0.7377 (ttt) REVERT: R 211 TYR cc_start: 0.8489 (t80) cc_final: 0.8183 (t80) REVERT: R 274 LEU cc_start: 0.7266 (tp) cc_final: 0.7020 (tp) REVERT: R 313 GLN cc_start: 0.7252 (tt0) cc_final: 0.6860 (mt0) outliers start: 6 outliers final: 2 residues processed: 189 average time/residue: 1.4459 time to fit residues: 289.1644 Evaluate side-chains 137 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 280 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 255 ASN A 269 ASN A 322 HIS B 91 HIS R 127 ASN R 196 GLN R 281 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9010 Z= 0.177 Angle : 0.510 9.498 12233 Z= 0.276 Chirality : 0.042 0.152 1406 Planarity : 0.004 0.058 1547 Dihedral : 4.324 56.090 1236 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.73 % Allowed : 9.24 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.57 (0.25), residues: 1129 helix: 2.05 (0.26), residues: 403 sheet: 0.86 (0.30), residues: 278 loop : 0.33 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.018 0.001 PHE R 116 TYR 0.015 0.001 TYR E 190 ARG 0.007 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.912 Fit side-chains REVERT: A 29 LYS cc_start: 0.8352 (tttt) cc_final: 0.7961 (ttmm) REVERT: A 186 GLU cc_start: 0.8203 (tt0) cc_final: 0.7823 (tt0) REVERT: A 208 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7740 (ttp80) REVERT: A 209 LYS cc_start: 0.8480 (pttt) cc_final: 0.8265 (ptmt) REVERT: A 229 ASP cc_start: 0.6380 (m-30) cc_final: 0.6178 (m-30) REVERT: A 309 ASP cc_start: 0.7758 (t70) cc_final: 0.7493 (t0) REVERT: A 330 LYS cc_start: 0.7663 (mttt) cc_final: 0.7054 (mtpt) REVERT: B 19 ARG cc_start: 0.6622 (ttp80) cc_final: 0.6232 (ttm110) REVERT: B 46 ARG cc_start: 0.7888 (mtp-110) cc_final: 0.7404 (mmt-90) REVERT: B 129 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7657 (mmt180) REVERT: C 21 MET cc_start: 0.8474 (mmm) cc_final: 0.7847 (ttt) REVERT: E 43 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8113 (mptp) REVERT: E 77 ASN cc_start: 0.8569 (m-40) cc_final: 0.8337 (m-40) REVERT: E 223 ASP cc_start: 0.7678 (m-30) cc_final: 0.7462 (m-30) REVERT: R 165 MET cc_start: 0.8522 (ttm) cc_final: 0.7855 (tmm) REVERT: R 173 MET cc_start: 0.6821 (tmm) cc_final: 0.6233 (tpt) REVERT: R 313 GLN cc_start: 0.7259 (tt0) cc_final: 0.6901 (mt0) outliers start: 26 outliers final: 12 residues processed: 165 average time/residue: 1.4988 time to fit residues: 262.3583 Evaluate side-chains 148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 245 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 269 ASN R 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 9010 Z= 0.440 Angle : 0.603 9.119 12233 Z= 0.322 Chirality : 0.047 0.163 1406 Planarity : 0.005 0.054 1547 Dihedral : 4.471 39.281 1232 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.26 % Allowed : 12.18 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.40 (0.25), residues: 1129 helix: 2.00 (0.26), residues: 403 sheet: 0.61 (0.30), residues: 286 loop : 0.25 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.006 0.002 HIS B 142 PHE 0.017 0.002 PHE A 196 TYR 0.015 0.002 TYR R 280 ARG 0.010 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.030 Fit side-chains REVERT: A 29 LYS cc_start: 0.8550 (tttt) cc_final: 0.8187 (ttmm) REVERT: A 53 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7446 (mtp) REVERT: A 186 GLU cc_start: 0.8298 (tt0) cc_final: 0.7843 (tt0) REVERT: A 207 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: A 208 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7803 (ttp80) REVERT: A 209 LYS cc_start: 0.8501 (pttt) cc_final: 0.8254 (ptmt) REVERT: A 309 ASP cc_start: 0.7800 (t70) cc_final: 0.7541 (t0) REVERT: A 330 LYS cc_start: 0.7742 (mttt) cc_final: 0.7144 (mtpt) REVERT: B 17 GLN cc_start: 0.7228 (tm-30) cc_final: 0.7005 (tm-30) REVERT: B 19 ARG cc_start: 0.6751 (ttp80) cc_final: 0.6387 (ttm110) REVERT: B 46 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7432 (mmt-90) REVERT: B 129 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7737 (mmt180) REVERT: B 226 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: C 21 MET cc_start: 0.8514 (mmm) cc_final: 0.7771 (ttt) REVERT: E 43 LYS cc_start: 0.8586 (mmtm) cc_final: 0.8274 (mptp) REVERT: E 93 MET cc_start: 0.8419 (tpp) cc_final: 0.8206 (tpp) REVERT: E 145 SER cc_start: 0.8330 (m) cc_final: 0.7955 (p) REVERT: E 160 ARG cc_start: 0.7196 (ttp-110) cc_final: 0.6922 (ttp-110) REVERT: E 223 ASP cc_start: 0.8033 (m-30) cc_final: 0.7689 (m-30) REVERT: E 230 MET cc_start: 0.9130 (ttp) cc_final: 0.8797 (ttp) REVERT: R 173 MET cc_start: 0.6973 (tmm) cc_final: 0.5843 (tpt) REVERT: R 279 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7697 (mp) REVERT: R 283 PHE cc_start: 0.7341 (t80) cc_final: 0.7119 (m-10) REVERT: R 303 ARG cc_start: 0.6938 (mmm160) cc_final: 0.6696 (mmm-85) REVERT: R 313 GLN cc_start: 0.7430 (tt0) cc_final: 0.6994 (mt0) REVERT: R 387 PHE cc_start: 0.7703 (t80) cc_final: 0.7484 (t80) outliers start: 31 outliers final: 15 residues processed: 157 average time/residue: 1.4606 time to fit residues: 242.9042 Evaluate side-chains 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 347 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.0570 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 255 ASN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9010 Z= 0.141 Angle : 0.484 11.351 12233 Z= 0.254 Chirality : 0.041 0.145 1406 Planarity : 0.003 0.055 1547 Dihedral : 4.040 36.309 1232 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.79 % Allowed : 14.08 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.66 (0.25), residues: 1129 helix: 2.35 (0.26), residues: 403 sheet: 0.60 (0.30), residues: 281 loop : 0.38 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.010 0.001 PHE B 199 TYR 0.017 0.001 TYR R 280 ARG 0.006 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8253 (tttt) cc_final: 0.7819 (ttmm) REVERT: A 186 GLU cc_start: 0.8218 (tt0) cc_final: 0.7578 (tt0) REVERT: A 197 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8233 (mtpp) REVERT: A 208 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7717 (ttp80) REVERT: A 209 LYS cc_start: 0.8447 (pttt) cc_final: 0.8222 (ptmt) REVERT: A 330 LYS cc_start: 0.7722 (mttt) cc_final: 0.7108 (mtpt) REVERT: B 17 GLN cc_start: 0.7283 (tm-30) cc_final: 0.7001 (tm-30) REVERT: B 19 ARG cc_start: 0.6740 (ttp80) cc_final: 0.6418 (ttm110) REVERT: B 46 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7388 (mmt-90) REVERT: B 129 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7765 (mmt180) REVERT: C 21 MET cc_start: 0.8487 (mmm) cc_final: 0.7748 (ttt) REVERT: E 43 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8304 (mptm) REVERT: E 145 SER cc_start: 0.8207 (m) cc_final: 0.7882 (p) REVERT: E 223 ASP cc_start: 0.7914 (m-30) cc_final: 0.7448 (m-30) REVERT: E 230 MET cc_start: 0.9089 (ttp) cc_final: 0.8771 (ttp) REVERT: R 173 MET cc_start: 0.6723 (tmm) cc_final: 0.6179 (tpt) REVERT: R 250 TYR cc_start: 0.8034 (m-10) cc_final: 0.7239 (m-10) REVERT: R 278 THR cc_start: 0.8368 (m) cc_final: 0.8140 (p) REVERT: R 279 LEU cc_start: 0.7915 (mt) cc_final: 0.7710 (mp) REVERT: R 283 PHE cc_start: 0.7415 (t80) cc_final: 0.7210 (m-10) REVERT: R 313 GLN cc_start: 0.7166 (tt0) cc_final: 0.6852 (mt0) REVERT: R 387 PHE cc_start: 0.7720 (t80) cc_final: 0.7511 (t80) outliers start: 17 outliers final: 7 residues processed: 167 average time/residue: 1.3474 time to fit residues: 238.6650 Evaluate side-chains 151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 204 GLN A 269 ASN B 268 ASN R 179 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9010 Z= 0.341 Angle : 0.558 8.161 12233 Z= 0.294 Chirality : 0.045 0.153 1406 Planarity : 0.004 0.051 1547 Dihedral : 4.361 42.005 1232 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.05 % Allowed : 14.39 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.44 (0.25), residues: 1129 helix: 2.21 (0.26), residues: 403 sheet: 0.45 (0.30), residues: 274 loop : 0.23 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.002 PHE A 196 TYR 0.011 0.002 TYR B 59 ARG 0.012 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.975 Fit side-chains REVERT: A 29 LYS cc_start: 0.8331 (tttt) cc_final: 0.7910 (ttmm) REVERT: A 186 GLU cc_start: 0.8325 (tt0) cc_final: 0.7704 (tt0) REVERT: A 197 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8206 (mtpp) REVERT: A 208 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7760 (ttp80) REVERT: A 209 LYS cc_start: 0.8470 (pttt) cc_final: 0.8239 (ptmt) REVERT: A 309 ASP cc_start: 0.7759 (t70) cc_final: 0.7489 (t0) REVERT: A 330 LYS cc_start: 0.7741 (mttt) cc_final: 0.7133 (mtpt) REVERT: B 19 ARG cc_start: 0.6765 (ttp80) cc_final: 0.6402 (ttm110) REVERT: B 46 ARG cc_start: 0.7931 (mtp-110) cc_final: 0.7427 (mmt-90) REVERT: B 129 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7644 (mmt180) REVERT: B 226 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: C 21 MET cc_start: 0.8521 (mmm) cc_final: 0.7767 (ttt) REVERT: E 43 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8325 (mptm) REVERT: E 145 SER cc_start: 0.8203 (m) cc_final: 0.7865 (p) REVERT: E 160 ARG cc_start: 0.7145 (ttp-110) cc_final: 0.6832 (ttp-110) REVERT: E 230 MET cc_start: 0.9120 (ttp) cc_final: 0.8758 (ttp) REVERT: R 165 MET cc_start: 0.8034 (tmm) cc_final: 0.7779 (tmm) REVERT: R 173 MET cc_start: 0.6992 (tmm) cc_final: 0.6164 (tpt) REVERT: R 250 TYR cc_start: 0.8105 (m-10) cc_final: 0.7265 (m-10) REVERT: R 278 THR cc_start: 0.8367 (m) cc_final: 0.8122 (p) REVERT: R 283 PHE cc_start: 0.7379 (t80) cc_final: 0.7174 (m-10) REVERT: R 313 GLN cc_start: 0.7279 (tt0) cc_final: 0.6861 (mt0) REVERT: R 366 ILE cc_start: 0.7783 (mt) cc_final: 0.7537 (mp) REVERT: R 387 PHE cc_start: 0.7762 (t80) cc_final: 0.7560 (t80) outliers start: 29 outliers final: 12 residues processed: 164 average time/residue: 1.4449 time to fit residues: 250.4855 Evaluate side-chains 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 204 GLN A 255 ASN A 269 ASN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9010 Z= 0.289 Angle : 0.544 11.716 12233 Z= 0.283 Chirality : 0.044 0.150 1406 Planarity : 0.004 0.051 1547 Dihedral : 4.372 44.529 1232 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.84 % Allowed : 15.76 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1129 helix: 2.26 (0.26), residues: 403 sheet: 0.39 (0.30), residues: 272 loop : 0.18 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.002 PHE A 196 TYR 0.015 0.002 TYR R 280 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.058 Fit side-chains REVERT: A 29 LYS cc_start: 0.8252 (tttt) cc_final: 0.7811 (ttmm) REVERT: A 186 GLU cc_start: 0.8244 (tt0) cc_final: 0.7617 (tt0) REVERT: A 197 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8261 (mtpp) REVERT: A 208 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7776 (ttp80) REVERT: A 209 LYS cc_start: 0.8420 (pttt) cc_final: 0.8218 (ptmt) REVERT: A 330 LYS cc_start: 0.7756 (mttt) cc_final: 0.7133 (mtpt) REVERT: B 19 ARG cc_start: 0.6750 (ttp80) cc_final: 0.6330 (ttp80) REVERT: B 46 ARG cc_start: 0.7882 (mtp-110) cc_final: 0.7397 (mmt-90) REVERT: B 129 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7656 (mmt180) REVERT: B 226 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: C 21 MET cc_start: 0.8524 (mmm) cc_final: 0.7769 (ttt) REVERT: E 43 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8311 (mptm) REVERT: E 145 SER cc_start: 0.8178 (m) cc_final: 0.7846 (p) REVERT: E 230 MET cc_start: 0.9116 (ttp) cc_final: 0.8761 (ttp) REVERT: R 165 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7855 (tmm) REVERT: R 173 MET cc_start: 0.6765 (tmm) cc_final: 0.6237 (tpt) REVERT: R 250 TYR cc_start: 0.8124 (m-10) cc_final: 0.7351 (m-10) REVERT: R 278 THR cc_start: 0.8347 (m) cc_final: 0.8057 (p) REVERT: R 283 PHE cc_start: 0.7369 (t80) cc_final: 0.7137 (m-10) REVERT: R 299 ARG cc_start: 0.7578 (mtp85) cc_final: 0.7162 (mmm-85) REVERT: R 303 ARG cc_start: 0.7218 (mmm160) cc_final: 0.6800 (mmm-85) REVERT: R 313 GLN cc_start: 0.7322 (tt0) cc_final: 0.6883 (mt0) REVERT: R 319 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.6272 (ttp-170) REVERT: R 345 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6593 (mp10) REVERT: R 366 ILE cc_start: 0.7661 (mt) cc_final: 0.7444 (mp) outliers start: 27 outliers final: 13 residues processed: 167 average time/residue: 1.4875 time to fit residues: 262.4711 Evaluate side-chains 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 319 ARG Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 269 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9010 Z= 0.160 Angle : 0.484 7.613 12233 Z= 0.254 Chirality : 0.041 0.139 1406 Planarity : 0.004 0.055 1547 Dihedral : 4.088 41.689 1232 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.31 % Allowed : 16.07 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1129 helix: 2.48 (0.26), residues: 403 sheet: 0.56 (0.30), residues: 270 loop : 0.21 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.012 0.001 PHE R 161 TYR 0.015 0.001 TYR E 190 ARG 0.012 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.999 Fit side-chains REVERT: A 29 LYS cc_start: 0.8169 (tttt) cc_final: 0.7733 (ttmm) REVERT: A 186 GLU cc_start: 0.8202 (tt0) cc_final: 0.7561 (tt0) REVERT: A 197 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: A 208 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7748 (ttp80) REVERT: A 209 LYS cc_start: 0.8393 (pttt) cc_final: 0.8189 (ptmt) REVERT: A 330 LYS cc_start: 0.7768 (mttt) cc_final: 0.7189 (mtpt) REVERT: B 19 ARG cc_start: 0.6735 (ttp80) cc_final: 0.6324 (ttp80) REVERT: B 46 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.7384 (mmt-90) REVERT: B 129 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7660 (mmt180) REVERT: C 21 MET cc_start: 0.8500 (mmm) cc_final: 0.7768 (ttt) REVERT: E 43 LYS cc_start: 0.8528 (mmtm) cc_final: 0.8268 (mptm) REVERT: E 145 SER cc_start: 0.8169 (m) cc_final: 0.7853 (p) REVERT: E 160 ARG cc_start: 0.7063 (ttp-110) cc_final: 0.6735 (ttp-110) REVERT: R 165 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7811 (tmm) REVERT: R 173 MET cc_start: 0.6869 (tmm) cc_final: 0.6141 (tpt) REVERT: R 250 TYR cc_start: 0.8102 (m-10) cc_final: 0.7331 (m-10) REVERT: R 278 THR cc_start: 0.8312 (m) cc_final: 0.8073 (p) REVERT: R 299 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7073 (mmm-85) REVERT: R 303 ARG cc_start: 0.7165 (mmm160) cc_final: 0.6724 (mmm-85) outliers start: 22 outliers final: 13 residues processed: 171 average time/residue: 1.4305 time to fit residues: 258.3371 Evaluate side-chains 165 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 255 ASN A 269 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9010 Z= 0.175 Angle : 0.507 12.324 12233 Z= 0.261 Chirality : 0.042 0.176 1406 Planarity : 0.003 0.050 1547 Dihedral : 4.066 40.076 1232 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.00 % Allowed : 17.33 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.63 (0.25), residues: 1129 helix: 2.50 (0.26), residues: 403 sheet: 0.45 (0.30), residues: 277 loop : 0.26 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 188 PHE 0.012 0.001 PHE R 161 TYR 0.013 0.001 TYR E 190 ARG 0.011 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.952 Fit side-chains REVERT: A 29 LYS cc_start: 0.8157 (tttt) cc_final: 0.7728 (ttmm) REVERT: A 186 GLU cc_start: 0.8202 (tt0) cc_final: 0.7562 (tt0) REVERT: A 197 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8132 (mtpp) REVERT: A 208 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7727 (ttp80) REVERT: A 209 LYS cc_start: 0.8393 (pttt) cc_final: 0.8188 (ptmt) REVERT: A 330 LYS cc_start: 0.7743 (mttt) cc_final: 0.7126 (mtpt) REVERT: B 19 ARG cc_start: 0.6718 (ttp80) cc_final: 0.6300 (ttp80) REVERT: B 46 ARG cc_start: 0.7921 (mtp-110) cc_final: 0.7370 (mmt-90) REVERT: B 129 ARG cc_start: 0.8047 (mtp180) cc_final: 0.7676 (mmt180) REVERT: B 134 ARG cc_start: 0.8362 (ptm-80) cc_final: 0.8117 (ptt-90) REVERT: C 21 MET cc_start: 0.8523 (mmm) cc_final: 0.7837 (ttt) REVERT: E 43 LYS cc_start: 0.8532 (mmtm) cc_final: 0.8270 (mptm) REVERT: E 145 SER cc_start: 0.8184 (m) cc_final: 0.7856 (p) REVERT: E 160 ARG cc_start: 0.7106 (ttp-110) cc_final: 0.6777 (ttp-110) REVERT: E 230 MET cc_start: 0.9112 (ttp) cc_final: 0.8763 (ttp) REVERT: R 165 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7808 (tmm) REVERT: R 173 MET cc_start: 0.6644 (tmm) cc_final: 0.6389 (tpt) REVERT: R 250 TYR cc_start: 0.8163 (m-10) cc_final: 0.7435 (m-10) REVERT: R 278 THR cc_start: 0.8302 (m) cc_final: 0.8071 (p) REVERT: R 299 ARG cc_start: 0.7500 (mtp85) cc_final: 0.7050 (mmm-85) REVERT: R 303 ARG cc_start: 0.7212 (mmm160) cc_final: 0.6795 (mmm-85) REVERT: R 366 ILE cc_start: 0.7609 (mt) cc_final: 0.7399 (mp) outliers start: 19 outliers final: 13 residues processed: 158 average time/residue: 1.5568 time to fit residues: 259.1148 Evaluate side-chains 166 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 204 GLN A 269 ASN A 346 ASN B 268 ASN E 82 GLN E 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9010 Z= 0.140 Angle : 0.467 7.263 12233 Z= 0.246 Chirality : 0.041 0.168 1406 Planarity : 0.003 0.049 1547 Dihedral : 3.925 36.060 1232 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.21 % Allowed : 17.33 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.72 (0.25), residues: 1129 helix: 2.61 (0.26), residues: 403 sheet: 0.46 (0.30), residues: 277 loop : 0.32 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.012 0.001 PHE R 161 TYR 0.013 0.001 TYR E 190 ARG 0.010 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.053 Fit side-chains REVERT: A 29 LYS cc_start: 0.8041 (tttt) cc_final: 0.7485 (tppp) REVERT: A 186 GLU cc_start: 0.8177 (tt0) cc_final: 0.7690 (tt0) REVERT: A 197 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8077 (mtpp) REVERT: A 209 LYS cc_start: 0.8374 (pttt) cc_final: 0.8174 (ptmt) REVERT: A 251 ASP cc_start: 0.7997 (t0) cc_final: 0.7688 (t0) REVERT: A 255 ASN cc_start: 0.8480 (m-40) cc_final: 0.8186 (m110) REVERT: A 306 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7291 (mm-40) REVERT: A 310 LEU cc_start: 0.8846 (mt) cc_final: 0.8445 (mt) REVERT: A 330 LYS cc_start: 0.7667 (mttt) cc_final: 0.7044 (mtpt) REVERT: B 19 ARG cc_start: 0.6709 (ttp80) cc_final: 0.6369 (ttp80) REVERT: B 46 ARG cc_start: 0.7919 (mtp-110) cc_final: 0.7448 (mmt-90) REVERT: B 129 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7693 (mmt180) REVERT: B 134 ARG cc_start: 0.8354 (ptm-80) cc_final: 0.8125 (ptt-90) REVERT: B 220 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8690 (mt0) REVERT: C 21 MET cc_start: 0.8469 (mmm) cc_final: 0.7746 (ttt) REVERT: E 43 LYS cc_start: 0.8522 (mmtm) cc_final: 0.8252 (mptm) REVERT: E 93 MET cc_start: 0.8112 (tpp) cc_final: 0.7868 (tpp) REVERT: E 160 ARG cc_start: 0.7116 (ttp-110) cc_final: 0.6827 (ttm110) REVERT: R 165 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7802 (tmm) REVERT: R 173 MET cc_start: 0.6855 (tmm) cc_final: 0.6206 (tpt) REVERT: R 250 TYR cc_start: 0.8195 (m-10) cc_final: 0.7358 (m-10) REVERT: R 278 THR cc_start: 0.8277 (m) cc_final: 0.8030 (p) REVERT: R 299 ARG cc_start: 0.7567 (mtp85) cc_final: 0.7202 (mmm-85) outliers start: 21 outliers final: 14 residues processed: 164 average time/residue: 1.4649 time to fit residues: 253.6861 Evaluate side-chains 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 204 GLN A 269 ASN A 346 ASN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9010 Z= 0.164 Angle : 0.500 12.740 12233 Z= 0.256 Chirality : 0.042 0.164 1406 Planarity : 0.003 0.048 1547 Dihedral : 3.932 35.100 1232 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.10 % Allowed : 17.65 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.72 (0.25), residues: 1129 helix: 2.59 (0.26), residues: 402 sheet: 0.49 (0.30), residues: 277 loop : 0.31 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE R 161 TYR 0.014 0.001 TYR E 190 ARG 0.010 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.025 Fit side-chains REVERT: A 29 LYS cc_start: 0.8047 (tttt) cc_final: 0.7484 (tppp) REVERT: A 186 GLU cc_start: 0.8202 (tt0) cc_final: 0.7708 (tt0) REVERT: A 197 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8073 (mtpp) REVERT: A 209 LYS cc_start: 0.8380 (pttt) cc_final: 0.8169 (ptmt) REVERT: A 306 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7378 (mm-40) REVERT: A 315 ASP cc_start: 0.7827 (p0) cc_final: 0.7473 (p0) REVERT: A 330 LYS cc_start: 0.7664 (mttt) cc_final: 0.7042 (mtpt) REVERT: B 19 ARG cc_start: 0.6707 (ttp80) cc_final: 0.6367 (ttp80) REVERT: B 32 GLN cc_start: 0.8159 (mt0) cc_final: 0.7955 (mt0) REVERT: B 44 GLN cc_start: 0.8160 (mt0) cc_final: 0.7885 (tt0) REVERT: B 46 ARG cc_start: 0.7964 (mtp-110) cc_final: 0.7473 (mmt-90) REVERT: B 129 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7723 (mmt180) REVERT: B 134 ARG cc_start: 0.8325 (ptm-80) cc_final: 0.8124 (ptt-90) REVERT: B 220 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8590 (mt0) REVERT: C 21 MET cc_start: 0.8474 (mmm) cc_final: 0.7745 (ttt) REVERT: E 43 LYS cc_start: 0.8531 (mmtm) cc_final: 0.8259 (mptm) REVERT: E 160 ARG cc_start: 0.7100 (ttp-110) cc_final: 0.6825 (ttm110) REVERT: R 173 MET cc_start: 0.6691 (tmm) cc_final: 0.6445 (tpt) REVERT: R 250 TYR cc_start: 0.8199 (m-10) cc_final: 0.7453 (m-10) REVERT: R 278 THR cc_start: 0.8308 (m) cc_final: 0.8048 (p) REVERT: R 299 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7127 (mmm-85) REVERT: R 303 ARG cc_start: 0.7368 (mmm160) cc_final: 0.6818 (mmm-85) outliers start: 20 outliers final: 14 residues processed: 156 average time/residue: 1.5487 time to fit residues: 254.5344 Evaluate side-chains 163 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 78 optimal weight: 0.0020 chunk 5 optimal weight: 3.9990 overall best weight: 0.5950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 269 ASN A 346 ASN B 268 ASN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119852 restraints weight = 10070.329| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.04 r_work: 0.3252 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9010 Z= 0.145 Angle : 0.481 7.951 12233 Z= 0.250 Chirality : 0.041 0.155 1406 Planarity : 0.004 0.048 1547 Dihedral : 3.884 33.193 1232 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.10 % Allowed : 17.23 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.69 (0.25), residues: 1129 helix: 2.53 (0.26), residues: 405 sheet: 0.51 (0.30), residues: 275 loop : 0.30 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.015 0.001 PHE R 161 TYR 0.014 0.001 TYR E 190 ARG 0.009 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.37 seconds wall clock time: 75 minutes 16.30 seconds (4516.30 seconds total)