Starting phenix.real_space_refine on Wed Jan 15 19:16:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwh_37888/01_2025/8wwh_37888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwh_37888/01_2025/8wwh_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_37888/01_2025/8wwh_37888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwh_37888/01_2025/8wwh_37888.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwh_37888/01_2025/8wwh_37888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwh_37888/01_2025/8wwh_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-5571/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: 3.83, per 1000 atoms: 0.43 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: 2.15 Conformation dependent library (CDL) restraints added in 1.0 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: 0.95 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: 2.77 Time building geometry restraints manager: 2.47 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: 3.100 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: 0.000 Extract box with map and model: 4.310 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 18.590 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.180 ------------------------------------------------------------------------------- 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 : 0.943 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: 1.3946 time to fit residues: 279.4958 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 : 0.987 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.170241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117759 restraints weight = 9967.998| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.98 r_work: 0.3202 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 1.099 Fit side-chains REVERT: A 29 LYS cc_start: 0.8556 (tttt) cc_final: 0.8105 (ttmm) REVERT: A 186 GLU cc_start: 0.8353 (tt0) cc_final: 0.7933 (tt0) REVERT: A 208 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7706 (ttp80) REVERT: A 209 LYS cc_start: 0.8560 (pttt) cc_final: 0.8278 (ptmt) REVERT: A 309 ASP cc_start: 0.7952 (t70) cc_final: 0.7662 (t0) REVERT: A 330 LYS cc_start: 0.7721 (mttt) cc_final: 0.7128 (mtpt) REVERT: B 19 ARG cc_start: 0.6989 (ttp80) cc_final: 0.6561 (ttm110) REVERT: B 46 ARG cc_start: 0.8116 (mtp-110) cc_final: 0.7486 (mmt-90) REVERT: B 129 ARG cc_start: 0.8312 (mtp180) cc_final: 0.7767 (mmt180) REVERT: B 226 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8169 (mp0) REVERT: C 21 MET cc_start: 0.8697 (mmm) cc_final: 0.7942 (ttt) REVERT: C 46 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8006 (pttp) REVERT: E 43 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8267 (mptp) REVERT: E 77 ASN cc_start: 0.8528 (m-40) cc_final: 0.8280 (m-40) REVERT: E 223 ASP cc_start: 0.7772 (m-30) cc_final: 0.7560 (m-30) REVERT: R 165 MET cc_start: 0.8581 (ttm) cc_final: 0.7976 (tmm) REVERT: R 173 MET cc_start: 0.6951 (tmm) cc_final: 0.6353 (tpt) REVERT: R 313 GLN cc_start: 0.7327 (tt0) cc_final: 0.6930 (mt0) outliers start: 26 outliers final: 12 residues processed: 165 average time/residue: 1.4043 time to fit residues: 246.0736 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 : 1.219 ------------------------------------------------------------------------------- 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 10 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118463 restraints weight = 10176.323| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.07 r_work: 0.3240 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9010 Z= 0.182 Angle : 0.491 9.410 12233 Z= 0.261 Chirality : 0.042 0.147 1406 Planarity : 0.004 0.054 1547 Dihedral : 3.951 29.792 1232 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.63 % Allowed : 12.08 % Favored : 85.29 % 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: 1.71 (0.25), residues: 1129 helix: 2.32 (0.26), residues: 403 sheet: 0.71 (0.30), residues: 290 loop : 0.40 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE A 196 TYR 0.021 0.001 TYR R 280 ARG 0.009 0.000 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 181 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8401 (tttt) cc_final: 0.7869 (ttmm) REVERT: A 186 GLU cc_start: 0.8324 (tt0) cc_final: 0.7760 (tt0) REVERT: A 208 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7523 (ttp80) REVERT: A 209 LYS cc_start: 0.8493 (pttt) cc_final: 0.8153 (ptmt) REVERT: A 251 ASP cc_start: 0.8014 (t70) cc_final: 0.7693 (t0) REVERT: A 309 ASP cc_start: 0.7920 (t70) cc_final: 0.7621 (t0) REVERT: A 330 LYS cc_start: 0.7614 (mttt) cc_final: 0.6992 (mtpt) REVERT: B 17 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 19 ARG cc_start: 0.7043 (ttp80) cc_final: 0.6659 (ttm110) REVERT: B 46 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7269 (mmt-90) REVERT: B 129 ARG cc_start: 0.8284 (mtp180) cc_final: 0.7686 (mmt180) REVERT: B 226 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8081 (mp0) REVERT: C 21 MET cc_start: 0.8761 (mmm) cc_final: 0.7928 (ttt) REVERT: C 46 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7936 (pttp) REVERT: E 77 ASN cc_start: 0.8456 (m-40) cc_final: 0.8201 (m-40) REVERT: E 145 SER cc_start: 0.8271 (m) cc_final: 0.7928 (p) REVERT: E 223 ASP cc_start: 0.7906 (m-30) cc_final: 0.7446 (m-30) REVERT: R 165 MET cc_start: 0.8663 (ttm) cc_final: 0.7991 (tmm) REVERT: R 173 MET cc_start: 0.7042 (tmm) cc_final: 0.6655 (tmm) REVERT: R 283 PHE cc_start: 0.7413 (t80) cc_final: 0.7161 (m-10) REVERT: R 313 GLN cc_start: 0.7137 (tt0) cc_final: 0.6801 (mt0) REVERT: R 387 PHE cc_start: 0.7784 (t80) cc_final: 0.7557 (t80) outliers start: 25 outliers final: 10 residues processed: 166 average time/residue: 1.3116 time to fit residues: 231.6028 Evaluate side-chains 150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER 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 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 99 optimal weight: 40.0000 chunk 107 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 B 268 ASN E 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119069 restraints weight = 10148.798| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.06 r_work: 0.3253 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2231 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= 0.158 Angle : 0.484 10.941 12233 Z= 0.253 Chirality : 0.041 0.144 1406 Planarity : 0.003 0.048 1547 Dihedral : 3.884 29.518 1232 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.00 % Allowed : 13.45 % 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: 1.77 (0.25), residues: 1129 helix: 2.42 (0.26), residues: 405 sheet: 0.73 (0.30), residues: 283 loop : 0.39 (0.30), residues: 441 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 0.009 0.001 PHE R 161 TYR 0.014 0.001 TYR R 280 ARG 0.009 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 169 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.945 Fit side-chains REVERT: A 29 LYS cc_start: 0.8200 (tttt) cc_final: 0.7690 (ttmm) REVERT: A 186 GLU cc_start: 0.8355 (tt0) cc_final: 0.7620 (tt0) REVERT: A 197 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8091 (mtpp) REVERT: A 208 ARG cc_start: 0.7902 (ttm-80) cc_final: 0.7450 (ttp80) REVERT: A 209 LYS cc_start: 0.8420 (pttt) cc_final: 0.8099 (ptmt) REVERT: A 330 LYS cc_start: 0.7579 (mttt) cc_final: 0.6939 (mtpt) REVERT: B 19 ARG cc_start: 0.6994 (ttp80) cc_final: 0.6625 (ttm110) REVERT: B 46 ARG cc_start: 0.8023 (mtp-110) cc_final: 0.7256 (mmt-90) REVERT: B 129 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7699 (mmt180) REVERT: B 226 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8087 (mp0) REVERT: C 21 MET cc_start: 0.8738 (mmm) cc_final: 0.7894 (ttt) REVERT: C 46 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7966 (pttp) REVERT: E 43 LYS cc_start: 0.8068 (mptm) cc_final: 0.7760 (mptt) REVERT: E 77 ASN cc_start: 0.8498 (m-40) cc_final: 0.8243 (m-40) REVERT: E 82 GLN cc_start: 0.8486 (tp40) cc_final: 0.8281 (tp-100) REVERT: E 93 MET cc_start: 0.8210 (tpp) cc_final: 0.7992 (tpp) REVERT: E 145 SER cc_start: 0.8231 (m) cc_final: 0.7880 (p) REVERT: E 160 ARG cc_start: 0.7061 (ttp-110) cc_final: 0.6693 (ttp-110) REVERT: E 223 ASP cc_start: 0.7680 (m-30) cc_final: 0.7363 (m-30) REVERT: R 165 MET cc_start: 0.8589 (ttm) cc_final: 0.8003 (tmm) REVERT: R 173 MET cc_start: 0.6933 (tmm) cc_final: 0.6272 (tpt) REVERT: R 250 TYR cc_start: 0.8193 (m-10) cc_final: 0.7420 (m-10) REVERT: R 279 LEU cc_start: 0.7994 (mp) cc_final: 0.7764 (mt) REVERT: R 283 PHE cc_start: 0.7469 (t80) cc_final: 0.7214 (m-10) REVERT: R 313 GLN cc_start: 0.7066 (tt0) cc_final: 0.6769 (mt0) REVERT: R 387 PHE cc_start: 0.7764 (t80) cc_final: 0.7495 (t80) outliers start: 19 outliers final: 10 residues processed: 158 average time/residue: 1.3901 time to fit residues: 232.6505 Evaluate side-chains 156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER 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 154 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 184 MET 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 18 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.117197 restraints weight = 10069.177| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.04 r_work: 0.3206 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9010 Z= 0.225 Angle : 0.502 7.961 12233 Z= 0.264 Chirality : 0.042 0.144 1406 Planarity : 0.004 0.048 1547 Dihedral : 4.030 33.386 1232 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.31 % Allowed : 13.87 % Favored : 83.82 % 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: 1.67 (0.25), residues: 1129 helix: 2.39 (0.26), residues: 405 sheet: 0.63 (0.30), residues: 275 loop : 0.32 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 PHE 0.013 0.001 PHE A 196 TYR 0.012 0.001 TYR R 280 ARG 0.007 0.000 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: 22 poor density : 158 time to evaluate : 0.967 Fit side-chains REVERT: A 29 LYS cc_start: 0.8224 (tttt) cc_final: 0.7737 (ttmm) REVERT: A 186 GLU cc_start: 0.8380 (tt0) cc_final: 0.7641 (tt0) REVERT: A 197 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8080 (mtpp) REVERT: A 208 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7517 (ttp80) REVERT: A 209 LYS cc_start: 0.8436 (pttt) cc_final: 0.8120 (ptmt) REVERT: A 251 ASP cc_start: 0.8022 (t70) cc_final: 0.7775 (t0) REVERT: A 255 ASN cc_start: 0.8466 (m-40) cc_final: 0.8261 (m110) REVERT: A 330 LYS cc_start: 0.7678 (mttt) cc_final: 0.7054 (mtpt) REVERT: B 19 ARG cc_start: 0.7037 (ttp80) cc_final: 0.6596 (ttp80) REVERT: B 46 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7301 (mmt-90) REVERT: B 129 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7735 (mmt180) REVERT: B 226 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8138 (mp0) REVERT: C 21 MET cc_start: 0.8744 (mmm) cc_final: 0.7840 (ttt) REVERT: C 46 LYS cc_start: 0.8248 (mmtt) cc_final: 0.8006 (pttp) REVERT: E 43 LYS cc_start: 0.8199 (mptm) cc_final: 0.7866 (mptt) REVERT: E 77 ASN cc_start: 0.8559 (m-40) cc_final: 0.8317 (m-40) REVERT: E 145 SER cc_start: 0.8236 (m) cc_final: 0.7887 (p) REVERT: E 223 ASP cc_start: 0.7950 (m-30) cc_final: 0.7683 (m-30) REVERT: E 230 MET cc_start: 0.9126 (ttp) cc_final: 0.8768 (ttp) REVERT: R 165 MET cc_start: 0.8496 (ttm) cc_final: 0.7839 (tmm) REVERT: R 173 MET cc_start: 0.7123 (tmm) cc_final: 0.6021 (tpt) REVERT: R 250 TYR cc_start: 0.8182 (m-10) cc_final: 0.7343 (m-10) REVERT: R 387 PHE cc_start: 0.7824 (t80) cc_final: 0.7617 (t80) outliers start: 22 outliers final: 11 residues processed: 168 average time/residue: 1.3809 time to fit residues: 245.7238 Evaluate side-chains 157 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 350 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 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 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 3 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.170423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118651 restraints weight = 10113.947| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.04 r_work: 0.3227 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9010 Z= 0.172 Angle : 0.490 11.491 12233 Z= 0.255 Chirality : 0.042 0.140 1406 Planarity : 0.004 0.047 1547 Dihedral : 3.968 33.505 1232 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 14.92 % Favored : 82.35 % 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: 1.71 (0.25), residues: 1129 helix: 2.50 (0.26), residues: 405 sheet: 0.55 (0.30), residues: 277 loop : 0.35 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 PHE 0.010 0.001 PHE A 196 TYR 0.013 0.001 TYR R 380 ARG 0.011 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 178 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.007 Fit side-chains REVERT: A 29 LYS cc_start: 0.8154 (tttt) cc_final: 0.7664 (ttmm) REVERT: A 186 GLU cc_start: 0.8367 (tt0) cc_final: 0.7590 (tt0) REVERT: A 197 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8021 (mtpp) REVERT: A 208 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7500 (ttp80) REVERT: A 209 LYS cc_start: 0.8404 (pttt) cc_final: 0.8082 (ptmt) REVERT: A 251 ASP cc_start: 0.8046 (t70) cc_final: 0.7759 (t0) REVERT: A 255 ASN cc_start: 0.8448 (m-40) cc_final: 0.8207 (m110) REVERT: A 306 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7412 (mm-40) REVERT: A 330 LYS cc_start: 0.7658 (mttt) cc_final: 0.7055 (mtpt) REVERT: B 19 ARG cc_start: 0.7005 (ttp80) cc_final: 0.6571 (ttp80) REVERT: B 46 ARG cc_start: 0.8085 (mtp-110) cc_final: 0.7310 (mmt-90) REVERT: B 129 ARG cc_start: 0.8303 (mtp180) cc_final: 0.7732 (mmt180) REVERT: B 226 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8109 (mp0) REVERT: C 21 MET cc_start: 0.8747 (mmm) cc_final: 0.7837 (ttt) REVERT: C 46 LYS cc_start: 0.8221 (mmtt) cc_final: 0.8011 (pttp) REVERT: E 43 LYS cc_start: 0.8178 (mptm) cc_final: 0.7839 (mptt) REVERT: E 77 ASN cc_start: 0.8555 (m-40) cc_final: 0.8323 (m-40) REVERT: E 93 MET cc_start: 0.8250 (tpp) cc_final: 0.8031 (tpp) REVERT: E 160 ARG cc_start: 0.7080 (ttp-110) cc_final: 0.6736 (ttp-110) REVERT: E 223 ASP cc_start: 0.7941 (m-30) cc_final: 0.7714 (m-30) REVERT: E 230 MET cc_start: 0.9123 (ttp) cc_final: 0.8759 (ttp) REVERT: R 165 MET cc_start: 0.8456 (ttm) cc_final: 0.8036 (tmm) REVERT: R 173 MET cc_start: 0.6856 (tmm) cc_final: 0.6301 (tpt) REVERT: R 250 TYR cc_start: 0.8202 (m-10) cc_final: 0.7334 (m-10) outliers start: 26 outliers final: 14 residues processed: 163 average time/residue: 1.4920 time to fit residues: 256.9536 Evaluate side-chains 159 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 206 SER 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 155 VAL Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain R residue 206 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 318 LEU 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 106 optimal weight: 5.9990 chunk 60 optimal weight: 0.0270 chunk 9 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 40.0000 chunk 57 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- 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 269 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.168754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116498 restraints weight = 10201.081| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.04 r_work: 0.3195 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9010 Z= 0.258 Angle : 0.513 8.462 12233 Z= 0.270 Chirality : 0.043 0.144 1406 Planarity : 0.004 0.048 1547 Dihedral : 4.153 38.048 1232 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.52 % Allowed : 15.02 % Favored : 82.46 % 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: 1.63 (0.25), residues: 1129 helix: 2.43 (0.26), residues: 405 sheet: 0.51 (0.30), residues: 270 loop : 0.30 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 PHE 0.014 0.001 PHE A 196 TYR 0.016 0.001 TYR R 380 ARG 0.009 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 170 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.971 Fit side-chains REVERT: A 29 LYS cc_start: 0.8231 (tttt) cc_final: 0.7721 (ttmm) REVERT: A 186 GLU cc_start: 0.8360 (tt0) cc_final: 0.7616 (tt0) REVERT: A 197 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7980 (mtpp) REVERT: A 208 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7520 (ttp80) REVERT: A 209 LYS cc_start: 0.8447 (pttt) cc_final: 0.8118 (ptmt) REVERT: A 306 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7391 (mm-40) REVERT: A 330 LYS cc_start: 0.7692 (mttt) cc_final: 0.7079 (mtpt) REVERT: B 19 ARG cc_start: 0.7022 (ttp80) cc_final: 0.6587 (ttp80) REVERT: B 46 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.7313 (mmt-90) REVERT: B 129 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7725 (mmt180) REVERT: B 226 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8090 (mp0) REVERT: C 21 MET cc_start: 0.8763 (mmm) cc_final: 0.7858 (ttt) REVERT: E 43 LYS cc_start: 0.8194 (mptm) cc_final: 0.7860 (mptt) REVERT: E 77 ASN cc_start: 0.8602 (m-40) cc_final: 0.8333 (m-40) REVERT: E 89 GLU cc_start: 0.7834 (mp0) cc_final: 0.7397 (mm-30) REVERT: E 145 SER cc_start: 0.8223 (m) cc_final: 0.7884 (p) REVERT: E 160 ARG cc_start: 0.7111 (ttp-110) cc_final: 0.6795 (ttp-110) REVERT: E 223 ASP cc_start: 0.7985 (m-30) cc_final: 0.7721 (m-30) REVERT: E 230 MET cc_start: 0.9142 (ttp) cc_final: 0.8786 (ttp) REVERT: R 165 MET cc_start: 0.8504 (ttm) cc_final: 0.7856 (tmm) REVERT: R 173 MET cc_start: 0.7025 (tmm) cc_final: 0.6267 (tpt) REVERT: R 250 TYR cc_start: 0.8210 (m-10) cc_final: 0.7339 (m-10) REVERT: R 303 ARG cc_start: 0.7335 (mmm160) cc_final: 0.6858 (mmm-85) REVERT: R 387 PHE cc_start: 0.7805 (t80) cc_final: 0.7601 (t80) outliers start: 24 outliers final: 16 residues processed: 157 average time/residue: 1.4920 time to fit residues: 247.5536 Evaluate side-chains 163 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 17 SER 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 206 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 318 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 75 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 44 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.168795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116445 restraints weight = 10247.361| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.06 r_work: 0.3199 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9010 Z= 0.237 Angle : 0.515 12.552 12233 Z= 0.268 Chirality : 0.043 0.144 1406 Planarity : 0.004 0.048 1547 Dihedral : 4.192 40.361 1232 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.21 % Allowed : 15.97 % Favored : 81.83 % 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: 2.46 (0.26), residues: 403 sheet: 0.49 (0.30), residues: 275 loop : 0.27 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 PHE 0.013 0.001 PHE A 196 TYR 0.016 0.001 TYR R 280 ARG 0.008 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 171 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.078 Fit side-chains REVERT: A 29 LYS cc_start: 0.8175 (tttt) cc_final: 0.7665 (ttmm) REVERT: A 186 GLU cc_start: 0.8377 (tt0) cc_final: 0.7659 (tt0) REVERT: A 197 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7979 (mtpp) REVERT: A 208 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7498 (ttp80) REVERT: A 209 LYS cc_start: 0.8437 (pttt) cc_final: 0.8100 (ptmt) REVERT: A 251 ASP cc_start: 0.7955 (t70) cc_final: 0.7672 (t0) REVERT: A 255 ASN cc_start: 0.8381 (m-40) cc_final: 0.8124 (m110) REVERT: A 306 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7348 (mm-40) REVERT: A 330 LYS cc_start: 0.7691 (mttt) cc_final: 0.7063 (mtpt) REVERT: B 19 ARG cc_start: 0.6995 (ttp80) cc_final: 0.6554 (ttp80) REVERT: B 46 ARG cc_start: 0.8139 (mtp-110) cc_final: 0.7284 (mmt-90) REVERT: B 129 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7697 (mmt180) REVERT: B 226 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8098 (mp0) REVERT: C 21 MET cc_start: 0.8765 (mmm) cc_final: 0.7891 (ttt) REVERT: E 43 LYS cc_start: 0.8223 (mptm) cc_final: 0.7887 (mptt) REVERT: E 77 ASN cc_start: 0.8576 (m-40) cc_final: 0.8316 (m-40) REVERT: E 89 GLU cc_start: 0.7830 (mp0) cc_final: 0.7383 (mm-30) REVERT: E 145 SER cc_start: 0.8188 (m) cc_final: 0.7843 (p) REVERT: E 223 ASP cc_start: 0.7968 (m-30) cc_final: 0.7671 (m-30) REVERT: R 165 MET cc_start: 0.8506 (ttm) cc_final: 0.8045 (tmm) REVERT: R 173 MET cc_start: 0.6919 (tmm) cc_final: 0.6302 (tpt) REVERT: R 250 TYR cc_start: 0.8174 (m-10) cc_final: 0.7300 (m-10) REVERT: R 387 PHE cc_start: 0.7750 (t80) cc_final: 0.7533 (t80) outliers start: 21 outliers final: 16 residues processed: 160 average time/residue: 1.4750 time to fit residues: 249.3267 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 : 0.948 ------------------------------------------------------------------------------- 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 11 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 113 GLN 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 206 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 318 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 41 optimal weight: 0.0050 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116872 restraints weight = 10188.163| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.06 r_work: 0.3206 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9010 Z= 0.213 Angle : 0.502 8.146 12233 Z= 0.263 Chirality : 0.043 0.174 1406 Planarity : 0.004 0.057 1547 Dihedral : 4.162 41.204 1232 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.21 % Allowed : 16.39 % 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: 1.61 (0.25), residues: 1129 helix: 2.47 (0.26), residues: 405 sheet: 0.45 (0.30), residues: 275 loop : 0.25 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 PHE 0.012 0.001 PHE A 196 TYR 0.014 0.001 TYR R 380 ARG 0.015 0.001 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 170 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.020 Fit side-chains REVERT: A 29 LYS cc_start: 0.8151 (tttt) cc_final: 0.7646 (ttmm) REVERT: A 186 GLU cc_start: 0.8432 (tt0) cc_final: 0.7703 (tt0) REVERT: A 197 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7902 (mtpp) REVERT: A 208 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7488 (ttp80) REVERT: A 209 LYS cc_start: 0.8385 (pttt) cc_final: 0.8075 (ptmt) REVERT: A 255 ASN cc_start: 0.8381 (m-40) cc_final: 0.8055 (m110) REVERT: A 306 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7442 (mm-40) REVERT: A 330 LYS cc_start: 0.7626 (mttt) cc_final: 0.6981 (mtpt) REVERT: B 19 ARG cc_start: 0.6981 (ttp80) cc_final: 0.6536 (ttp80) REVERT: B 32 GLN cc_start: 0.8270 (mt0) cc_final: 0.8066 (mt0) REVERT: B 46 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7279 (mmt-90) REVERT: B 129 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7619 (mmt180) REVERT: B 134 ARG cc_start: 0.8464 (ptm-80) cc_final: 0.8195 (ptt-90) REVERT: B 226 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8089 (mp0) REVERT: C 21 MET cc_start: 0.8775 (mmm) cc_final: 0.7893 (ttt) REVERT: E 43 LYS cc_start: 0.8229 (mptm) cc_final: 0.7863 (mptt) REVERT: E 77 ASN cc_start: 0.8546 (m-40) cc_final: 0.8304 (m-40) REVERT: E 89 GLU cc_start: 0.7824 (mp0) cc_final: 0.7369 (mm-30) REVERT: E 145 SER cc_start: 0.8188 (m) cc_final: 0.7847 (p) REVERT: E 160 ARG cc_start: 0.7030 (ttp-110) cc_final: 0.6666 (ttp-110) REVERT: E 223 ASP cc_start: 0.7961 (m-30) cc_final: 0.7727 (m-30) REVERT: E 230 MET cc_start: 0.9124 (ttp) cc_final: 0.8773 (ttp) REVERT: R 165 MET cc_start: 0.8497 (ttm) cc_final: 0.8041 (tmm) REVERT: R 173 MET cc_start: 0.7041 (tmm) cc_final: 0.6334 (tpt) REVERT: R 250 TYR cc_start: 0.8150 (m-10) cc_final: 0.7359 (m-10) outliers start: 21 outliers final: 15 residues processed: 158 average time/residue: 1.5168 time to fit residues: 252.6350 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 : 0.987 ------------------------------------------------------------------------------- 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 113 GLN 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 206 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 318 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 58 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.170655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118687 restraints weight = 10124.036| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.04 r_work: 0.3228 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9010 Z= 0.163 Angle : 0.499 12.655 12233 Z= 0.256 Chirality : 0.042 0.155 1406 Planarity : 0.004 0.058 1547 Dihedral : 4.036 39.183 1232 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.58 % Allowed : 17.12 % Favored : 81.30 % 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: 1.67 (0.25), residues: 1129 helix: 2.57 (0.26), residues: 403 sheet: 0.44 (0.30), residues: 275 loop : 0.27 (0.29), residues: 451 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 0.010 0.001 PHE R 161 TYR 0.013 0.001 TYR E 190 ARG 0.014 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 165 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.049 Fit side-chains REVERT: A 29 LYS cc_start: 0.8132 (tttt) cc_final: 0.7627 (ttmm) REVERT: A 186 GLU cc_start: 0.8403 (tt0) cc_final: 0.7662 (tt0) REVERT: A 197 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7954 (mtpp) REVERT: A 208 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7494 (ttp80) REVERT: A 209 LYS cc_start: 0.8362 (pttt) cc_final: 0.8062 (ptmt) REVERT: A 251 ASP cc_start: 0.7978 (t70) cc_final: 0.7700 (OUTLIER) REVERT: A 255 ASN cc_start: 0.8380 (m-40) cc_final: 0.8111 (m110) REVERT: A 306 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7307 (mm110) REVERT: A 310 LEU cc_start: 0.8929 (mt) cc_final: 0.8528 (mt) REVERT: A 330 LYS cc_start: 0.7611 (mttt) cc_final: 0.7012 (mtpt) REVERT: B 19 ARG cc_start: 0.7021 (ttp80) cc_final: 0.6651 (ttp80) REVERT: B 32 GLN cc_start: 0.8269 (mt0) cc_final: 0.8030 (mt0) REVERT: B 46 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7350 (mmt-90) REVERT: B 129 ARG cc_start: 0.8258 (mtp180) cc_final: 0.7694 (mmt180) REVERT: B 134 ARG cc_start: 0.8470 (ptm-80) cc_final: 0.8212 (ptt-90) REVERT: B 226 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8040 (mp0) REVERT: C 21 MET cc_start: 0.8792 (mmm) cc_final: 0.7918 (ttt) REVERT: E 43 LYS cc_start: 0.8236 (mptm) cc_final: 0.7901 (mptt) REVERT: E 77 ASN cc_start: 0.8528 (m-40) cc_final: 0.8315 (m-40) REVERT: E 83 MET cc_start: 0.8558 (mtp) cc_final: 0.8282 (mtp) REVERT: E 89 GLU cc_start: 0.7842 (mp0) cc_final: 0.7463 (mm-30) REVERT: E 145 SER cc_start: 0.8217 (m) cc_final: 0.7879 (p) REVERT: E 160 ARG cc_start: 0.7037 (ttp-110) cc_final: 0.6808 (ttp-110) REVERT: E 223 ASP cc_start: 0.7938 (m-30) cc_final: 0.7729 (m-30) REVERT: E 230 MET cc_start: 0.9122 (ttp) cc_final: 0.8760 (ttp) REVERT: R 165 MET cc_start: 0.8453 (ttm) cc_final: 0.7989 (tmm) REVERT: R 173 MET cc_start: 0.6783 (tmm) cc_final: 0.6460 (tpt) REVERT: R 250 TYR cc_start: 0.8105 (m-10) cc_final: 0.7379 (m-10) outliers start: 15 outliers final: 11 residues processed: 156 average time/residue: 1.5342 time to fit residues: 252.4741 Evaluate side-chains 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 246 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 184 MET Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 318 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 41 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 50.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 346 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.170646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118599 restraints weight = 10164.741| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.05 r_work: 0.3230 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2798 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= 0.165 Angle : 0.483 9.047 12233 Z= 0.251 Chirality : 0.042 0.176 1406 Planarity : 0.004 0.055 1547 Dihedral : 4.013 37.830 1232 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.89 % Allowed : 16.60 % Favored : 81.51 % 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: 1.67 (0.25), residues: 1129 helix: 2.54 (0.26), residues: 405 sheet: 0.47 (0.30), residues: 275 loop : 0.28 (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 0.010 0.001 PHE R 161 TYR 0.013 0.001 TYR R 380 ARG 0.013 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7333.51 seconds wall clock time: 130 minutes 34.51 seconds (7834.51 seconds total)