Starting phenix.real_space_refine on Mon Mar 11 03:00:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/03_2024/8ovx_17225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/03_2024/8ovx_17225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/03_2024/8ovx_17225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/03_2024/8ovx_17225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/03_2024/8ovx_17225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/03_2024/8ovx_17225.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.062 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 29 5.16 5 C 4320 2.51 5 N 1163 2.21 5 O 1251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 227": "NH1" <-> "NH2" Residue "O ASP 298": "OD1" <-> "OD2" Residue "O PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 159": "OD1" <-> "OD2" Residue "P TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 173": "OD1" <-> "OD2" Residue "P TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 209": "OD1" <-> "OD2" Residue "P GLU 216": "OE1" <-> "OE2" Residue "P PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 347": "OE1" <-> "OE2" Residue "Q GLU 289": "OE1" <-> "OE2" Residue "Q ASP 345": "OD1" <-> "OD2" Residue "Q PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 248": "OD1" <-> "OD2" Residue "U ASP 286": "OD1" <-> "OD2" Residue "U GLU 314": "OE1" <-> "OE2" Residue "Y PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y GLU 70": "OE1" <-> "OE2" Residue "Y PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6763 Number of models: 1 Model: "" Number of chains: 6 Chain: "O" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1564 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "Q" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 732 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'HIS:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "U" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 585 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 33 Chain: "Y" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1473 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 3, 'TRANS': 199} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 11, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 76 Chain: "Z" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1062 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 4.18, per 1000 atoms: 0.62 Number of scatterers: 6763 At special positions: 0 Unit cell: (97.468, 80.948, 123.9, 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 29 16.00 O 1251 8.00 N 1163 7.00 C 4320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.4 seconds 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1718 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 5 sheets defined 64.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'O' and resid 162 through 172 removed outlier: 3.866A pdb=" N LEU O 166 " --> pdb=" O ASP O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 257 Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.549A pdb=" N ALA O 264 " --> pdb=" O SER O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 353 through 364 removed outlier: 3.651A pdb=" N LEU O 357 " --> pdb=" O ASP O 353 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN O 360 " --> pdb=" O GLU O 356 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N HIS O 361 " --> pdb=" O LEU O 357 " (cutoff:3.500A) Processing helix chain 'P' and resid 154 through 160 Processing helix chain 'P' and resid 226 through 231 removed outlier: 3.986A pdb=" N GLN P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 226 through 231' Processing helix chain 'P' and resid 232 through 234 No H-bonds generated for 'chain 'P' and resid 232 through 234' Processing helix chain 'P' and resid 236 through 240 Processing helix chain 'P' and resid 244 through 263 Processing helix chain 'P' and resid 333 through 348 removed outlier: 3.904A pdb=" N LEU P 337 " --> pdb=" O ASN P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 349 through 363 removed outlier: 3.605A pdb=" N LEU P 354 " --> pdb=" O VAL P 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 278 through 291 removed outlier: 3.822A pdb=" N LYS Q 285 " --> pdb=" O THR Q 281 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG Q 286 " --> pdb=" O ASN Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 332 removed outlier: 4.429A pdb=" N HIS Q 330 " --> pdb=" O ARG Q 326 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU Q 331 " --> pdb=" O ASN Q 327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 358 through 380 removed outlier: 4.085A pdb=" N GLU Q 362 " --> pdb=" O PRO Q 358 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS Q 365 " --> pdb=" O LYS Q 361 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN Q 376 " --> pdb=" O GLU Q 372 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET Q 377 " --> pdb=" O THR Q 373 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 391 Processing helix chain 'U' and resid 234 through 266 removed outlier: 3.805A pdb=" N ASN U 247 " --> pdb=" O GLN U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 299 removed outlier: 3.753A pdb=" N LEU U 290 " --> pdb=" O ASP U 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP U 297 " --> pdb=" O ALA U 293 " (cutoff:3.500A) Processing helix chain 'U' and resid 305 through 321 removed outlier: 3.898A pdb=" N ASN U 315 " --> pdb=" O LYS U 311 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 31 Processing helix chain 'Y' and resid 35 through 50 Processing helix chain 'Y' and resid 51 through 54 removed outlier: 3.717A pdb=" N MET Y 54 " --> pdb=" O LYS Y 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 51 through 54' Processing helix chain 'Y' and resid 55 through 86 removed outlier: 3.671A pdb=" N ASP Y 60 " --> pdb=" O ARG Y 56 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY Y 86 " --> pdb=" O MET Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 119 Processing helix chain 'Y' and resid 137 through 186 removed outlier: 3.647A pdb=" N LYS Y 153 " --> pdb=" O ASP Y 149 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN Y 158 " --> pdb=" O CYS Y 154 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER Y 169 " --> pdb=" O SER Y 165 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER Y 185 " --> pdb=" O ILE Y 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 194 removed outlier: 3.552A pdb=" N TYR Y 193 " --> pdb=" O ASP Y 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE Y 194 " --> pdb=" O ILE Y 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 189 through 194' Processing helix chain 'Y' and resid 196 through 219 Processing helix chain 'Y' and resid 221 through 238 removed outlier: 4.175A pdb=" N GLU Y 235 " --> pdb=" O LYS Y 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU Y 236 " --> pdb=" O ILE Y 232 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS Y 237 " --> pdb=" O LEU Y 233 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 13 removed outlier: 3.559A pdb=" N LEU Z 6 " --> pdb=" O ASN Z 2 " (cutoff:3.500A) Processing helix chain 'Z' and resid 21 through 29 removed outlier: 3.602A pdb=" N PHE Z 25 " --> pdb=" O SER Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 37 through 71 removed outlier: 4.126A pdb=" N HIS Z 41 " --> pdb=" O GLN Z 37 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER Z 55 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU Z 58 " --> pdb=" O THR Z 54 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA Z 59 " --> pdb=" O SER Z 55 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG Z 60 " --> pdb=" O GLU Z 56 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 126 removed outlier: 4.239A pdb=" N ASP Z 92 " --> pdb=" O GLU Z 88 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA Z 93 " --> pdb=" O THR Z 89 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN Z 103 " --> pdb=" O ASP Z 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE Z 107 " --> pdb=" O GLN Z 103 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU Z 108 " --> pdb=" O ARG Z 104 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU Z 114 " --> pdb=" O ASP Z 110 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS Z 115 " --> pdb=" O ALA Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 153 Proline residue: Z 137 - end of helix Processing sheet with id=AA1, first strand: chain 'O' and resid 175 through 179 removed outlier: 6.923A pdb=" N TYR O 221 " --> pdb=" O HIS O 238 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N HIS O 238 " --> pdb=" O TYR O 221 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU O 223 " --> pdb=" O PHE O 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 297 through 298 removed outlier: 3.540A pdb=" N SER O 307 " --> pdb=" O ASP O 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 315 through 320 removed outlier: 6.577A pdb=" N GLU O 316 " --> pdb=" O CYS O 327 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS O 327 " --> pdb=" O GLU O 316 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE O 318 " --> pdb=" O VAL O 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 165 through 174 removed outlier: 6.730A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG P 172 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL P 182 " --> pdb=" O ARG P 172 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 270 through 273 447 hydrogen bonds defined for protein. 1308 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: 1.79 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1585 1.33 - 1.45: 1222 1.45 - 1.57: 3989 1.57 - 1.69: 1 1.69 - 1.81: 48 Bond restraints: 6845 Sorted by residual: bond pdb=" CA LEU Q 291 " pdb=" C LEU Q 291 " ideal model delta sigma weight residual 1.523 1.574 -0.051 1.34e-02 5.57e+03 1.44e+01 bond pdb=" CA MET Q 335 " pdb=" CB MET Q 335 " ideal model delta sigma weight residual 1.528 1.568 -0.040 1.51e-02 4.39e+03 6.96e+00 bond pdb=" CB GLU U 314 " pdb=" CG GLU U 314 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" N PHE P 207 " pdb=" CA PHE P 207 " ideal model delta sigma weight residual 1.456 1.472 -0.016 1.23e-02 6.61e+03 1.61e+00 bond pdb=" C PHE O 177 " pdb=" N PHE O 178 " ideal model delta sigma weight residual 1.331 1.311 0.021 1.63e-02 3.76e+03 1.59e+00 ... (remaining 6840 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.22: 58 104.22 - 111.73: 3184 111.73 - 119.24: 2477 119.24 - 126.75: 3467 126.75 - 134.25: 50 Bond angle restraints: 9236 Sorted by residual: angle pdb=" C ALA Z 135 " pdb=" N ILE Z 136 " pdb=" CA ILE Z 136 " ideal model delta sigma weight residual 120.24 123.78 -3.54 6.30e-01 2.52e+00 3.15e+01 angle pdb=" CA ARG Z 52 " pdb=" CB ARG Z 52 " pdb=" CG ARG Z 52 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.83e+01 angle pdb=" C PHE O 177 " pdb=" N PHE O 178 " pdb=" CA PHE O 178 " ideal model delta sigma weight residual 121.61 128.35 -6.74 1.39e+00 5.18e-01 2.35e+01 angle pdb=" C THR Q 373 " pdb=" N MET Q 374 " pdb=" CA MET Q 374 " ideal model delta sigma weight residual 122.37 115.64 6.73 1.54e+00 4.22e-01 1.91e+01 angle pdb=" N GLU Z 44 " pdb=" CA GLU Z 44 " pdb=" CB GLU Z 44 " ideal model delta sigma weight residual 110.28 116.82 -6.54 1.55e+00 4.16e-01 1.78e+01 ... (remaining 9231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3822 17.86 - 35.72: 313 35.72 - 53.59: 51 53.59 - 71.45: 8 71.45 - 89.31: 4 Dihedral angle restraints: 4198 sinusoidal: 1587 harmonic: 2611 Sorted by residual: dihedral pdb=" CA LEU Q 334 " pdb=" C LEU Q 334 " pdb=" N MET Q 335 " pdb=" CA MET Q 335 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA MET Q 374 " pdb=" C MET Q 374 " pdb=" N GLY Q 375 " pdb=" CA GLY Q 375 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ASN Z 2 " pdb=" C ASN Z 2 " pdb=" N SER Z 3 " pdb=" CA SER Z 3 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 4195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 849 0.056 - 0.111: 212 0.111 - 0.167: 45 0.167 - 0.222: 8 0.222 - 0.278: 2 Chirality restraints: 1116 Sorted by residual: chirality pdb=" CG LEU Y 26 " pdb=" CB LEU Y 26 " pdb=" CD1 LEU Y 26 " pdb=" CD2 LEU Y 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB ILE Q 292 " pdb=" CA ILE Q 292 " pdb=" CG1 ILE Q 292 " pdb=" CG2 ILE Q 292 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ARG Z 52 " pdb=" N ARG Z 52 " pdb=" C ARG Z 52 " pdb=" CB ARG Z 52 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1113 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE P 207 " -0.017 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE P 207 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE P 207 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE P 207 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE P 207 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE P 207 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE P 207 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 215 " -0.013 2.00e-02 2.50e+03 1.62e-02 6.54e+00 pdb=" CG TRP P 215 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP P 215 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP P 215 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP P 215 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP P 215 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP P 215 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 215 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 215 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 215 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE O 240 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO O 241 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO O 241 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO O 241 " -0.028 5.00e-02 4.00e+02 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 619 2.75 - 3.29: 6915 3.29 - 3.82: 11673 3.82 - 4.36: 12687 4.36 - 4.90: 21051 Nonbonded interactions: 52945 Sorted by model distance: nonbonded pdb=" OH TYR U 302 " pdb=" OE2 GLU Y 183 " model vdw 2.209 2.440 nonbonded pdb=" OG SER O 210 " pdb=" OG1 THR O 213 " model vdw 2.275 2.440 nonbonded pdb=" OD1 ASN Q 337 " pdb=" NH2 ARG U 284 " model vdw 2.297 2.520 nonbonded pdb=" O PRO P 163 " pdb=" OH TYR P 245 " model vdw 2.304 2.440 nonbonded pdb=" NZ LYS P 229 " pdb=" OH TYR U 302 " model vdw 2.313 2.520 ... (remaining 52940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.280 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: 1.350 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.760 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 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 : 0.004 0.051 6845 Z= 0.252 Angle : 0.984 14.658 9236 Z= 0.518 Chirality : 0.053 0.278 1116 Planarity : 0.004 0.052 1159 Dihedral : 13.526 89.310 2480 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.28), residues: 853 helix: -0.11 (0.21), residues: 538 sheet: -0.25 (0.51), residues: 103 loop : -2.14 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP P 215 HIS 0.003 0.001 HIS U 237 PHE 0.056 0.002 PHE P 207 TYR 0.024 0.003 TYR Z 43 ARG 0.012 0.001 ARG Z 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: O 201 MET cc_start: 0.7283 (mmp) cc_final: 0.6624 (tpp) REVERT: O 320 LYS cc_start: 0.9136 (mmpt) cc_final: 0.8907 (mmmt) REVERT: P 262 ILE cc_start: 0.6820 (mm) cc_final: 0.6460 (mm) REVERT: Z 1 MET cc_start: 0.7414 (tmm) cc_final: 0.6983 (tpt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2166 time to fit residues: 34.7891 Evaluate side-chains 87 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.0370 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 288 ASN U 294 HIS ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 GLN Y 170 GLN ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6845 Z= 0.167 Angle : 0.626 8.937 9236 Z= 0.320 Chirality : 0.041 0.167 1116 Planarity : 0.003 0.042 1159 Dihedral : 4.616 27.781 927 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.71 % Allowed : 10.40 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 853 helix: 0.86 (0.22), residues: 539 sheet: -0.18 (0.52), residues: 105 loop : -2.10 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 215 HIS 0.002 0.000 HIS Z 8 PHE 0.014 0.001 PHE Z 25 TYR 0.016 0.002 TYR Z 43 ARG 0.006 0.000 ARG Y 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 172 MET cc_start: 0.7555 (ptt) cc_final: 0.7057 (ptt) REVERT: O 267 PHE cc_start: 0.7813 (t80) cc_final: 0.7394 (t80) REVERT: P 262 ILE cc_start: 0.6629 (mm) cc_final: 0.6274 (mm) REVERT: U 288 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7345 (t0) REVERT: U 299 MET cc_start: 0.7101 (mtm) cc_final: 0.6759 (mtt) REVERT: Z 1 MET cc_start: 0.7634 (tmm) cc_final: 0.7086 (tpt) outliers start: 12 outliers final: 10 residues processed: 105 average time/residue: 0.2146 time to fit residues: 29.4779 Evaluate side-chains 91 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 287 ASP Chi-restraints excluded: chain P residue 205 TYR Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain Q residue 346 VAL Chi-restraints excluded: chain U residue 288 ASN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 173 SER Chi-restraints excluded: chain Z residue 44 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 160 HIS ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 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 : 0.003 0.031 6845 Z= 0.185 Angle : 0.607 11.275 9236 Z= 0.308 Chirality : 0.041 0.153 1116 Planarity : 0.003 0.037 1159 Dihedral : 4.448 28.224 927 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.14 % Allowed : 13.82 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 853 helix: 1.18 (0.23), residues: 540 sheet: -0.13 (0.52), residues: 105 loop : -2.12 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 215 HIS 0.001 0.000 HIS U 294 PHE 0.018 0.001 PHE P 207 TYR 0.014 0.002 TYR U 302 ARG 0.005 0.000 ARG Y 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 172 MET cc_start: 0.7937 (ptt) cc_final: 0.7185 (ptt) REVERT: O 201 MET cc_start: 0.7695 (mmp) cc_final: 0.6613 (tpp) REVERT: O 267 PHE cc_start: 0.8145 (t80) cc_final: 0.7607 (t80) REVERT: P 262 ILE cc_start: 0.6915 (mm) cc_final: 0.6637 (mm) REVERT: U 299 MET cc_start: 0.7040 (mtm) cc_final: 0.6725 (mtt) REVERT: Y 119 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8075 (mtmm) REVERT: Z 1 MET cc_start: 0.7172 (tmm) cc_final: 0.6126 (tpp) outliers start: 15 outliers final: 10 residues processed: 91 average time/residue: 0.1923 time to fit residues: 23.5631 Evaluate side-chains 84 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 287 ASP Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain Q residue 346 VAL Chi-restraints excluded: chain U residue 257 ASN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Z residue 44 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 261 HIS ** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6845 Z= 0.286 Angle : 0.658 8.789 9236 Z= 0.339 Chirality : 0.043 0.142 1116 Planarity : 0.003 0.032 1159 Dihedral : 4.664 28.957 927 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.99 % Allowed : 15.95 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.30), residues: 853 helix: 1.08 (0.23), residues: 544 sheet: 0.28 (0.56), residues: 98 loop : -2.22 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 326 HIS 0.003 0.001 HIS O 361 PHE 0.018 0.002 PHE Y 194 TYR 0.024 0.002 TYR Y 25 ARG 0.009 0.001 ARG Y 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 172 MET cc_start: 0.8359 (ptt) cc_final: 0.7913 (ptt) REVERT: O 201 MET cc_start: 0.7677 (mmp) cc_final: 0.6609 (tpp) REVERT: P 262 ILE cc_start: 0.7369 (mm) cc_final: 0.7123 (mm) REVERT: Q 338 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8304 (m-30) REVERT: Q 374 MET cc_start: 0.6002 (ppp) cc_final: 0.5531 (ppp) REVERT: U 299 MET cc_start: 0.7040 (mtm) cc_final: 0.6656 (mtt) REVERT: Y 119 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8289 (mtmt) REVERT: Z 1 MET cc_start: 0.7284 (tmm) cc_final: 0.6325 (tpp) outliers start: 21 outliers final: 12 residues processed: 97 average time/residue: 0.2301 time to fit residues: 29.0618 Evaluate side-chains 91 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 287 ASP Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain P residue 205 TYR Chi-restraints excluded: chain P residue 237 PHE Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain Q residue 346 VAL Chi-restraints excluded: chain U residue 257 ASN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 44 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.0070 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 56 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 73 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 223 ASN ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6845 Z= 0.149 Angle : 0.607 11.768 9236 Z= 0.301 Chirality : 0.040 0.134 1116 Planarity : 0.003 0.034 1159 Dihedral : 4.375 27.429 927 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.71 % Allowed : 17.09 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.30), residues: 853 helix: 1.44 (0.23), residues: 538 sheet: 0.17 (0.51), residues: 109 loop : -2.14 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 326 HIS 0.001 0.000 HIS U 237 PHE 0.016 0.001 PHE P 189 TYR 0.017 0.001 TYR O 170 ARG 0.008 0.001 ARG Z 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 167 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.9074 (pp20) REVERT: O 172 MET cc_start: 0.8070 (ptt) cc_final: 0.7767 (ptt) REVERT: O 201 MET cc_start: 0.7705 (mmp) cc_final: 0.6857 (tpp) REVERT: O 267 PHE cc_start: 0.8235 (t80) cc_final: 0.8003 (t80) REVERT: P 262 ILE cc_start: 0.6800 (mm) cc_final: 0.6573 (mm) REVERT: Q 338 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8208 (m-30) REVERT: Q 374 MET cc_start: 0.5665 (ppp) cc_final: 0.5247 (ppp) REVERT: U 299 MET cc_start: 0.7040 (mtm) cc_final: 0.6697 (mtt) REVERT: Y 119 LYS cc_start: 0.8417 (mtmm) cc_final: 0.8202 (mtmt) REVERT: Y 162 SER cc_start: 0.8261 (m) cc_final: 0.7993 (m) REVERT: Z 1 MET cc_start: 0.7232 (tmm) cc_final: 0.6679 (tpp) outliers start: 19 outliers final: 10 residues processed: 97 average time/residue: 0.2074 time to fit residues: 26.4304 Evaluate side-chains 89 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 287 ASP Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain U residue 257 ASN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 173 SER Chi-restraints excluded: chain Z residue 44 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 0.0970 chunk 43 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 155 GLN ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6845 Z= 0.153 Angle : 0.588 10.495 9236 Z= 0.298 Chirality : 0.040 0.138 1116 Planarity : 0.003 0.034 1159 Dihedral : 4.265 28.205 927 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.13 % Allowed : 17.38 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.30), residues: 853 helix: 1.52 (0.23), residues: 538 sheet: 0.24 (0.51), residues: 109 loop : -2.22 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 326 HIS 0.001 0.000 HIS U 237 PHE 0.018 0.001 PHE P 207 TYR 0.018 0.001 TYR O 170 ARG 0.010 0.000 ARG Z 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 167 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.9113 (pp20) REVERT: O 172 MET cc_start: 0.7898 (ptt) cc_final: 0.7694 (ptt) REVERT: O 201 MET cc_start: 0.7641 (mmp) cc_final: 0.6895 (tpp) REVERT: P 242 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7829 (mm) REVERT: P 262 ILE cc_start: 0.6846 (mm) cc_final: 0.6597 (mm) REVERT: Q 277 MET cc_start: 0.4155 (tpp) cc_final: 0.3803 (mmp) REVERT: Q 336 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8518 (pp) REVERT: Q 338 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8302 (m-30) REVERT: Q 374 MET cc_start: 0.5300 (ppp) cc_final: 0.4888 (ppp) REVERT: U 299 MET cc_start: 0.6968 (mtm) cc_final: 0.6648 (mtt) REVERT: Z 1 MET cc_start: 0.7139 (tmm) cc_final: 0.6637 (tpp) REVERT: Z 52 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8340 (ptt90) outliers start: 22 outliers final: 12 residues processed: 94 average time/residue: 0.2385 time to fit residues: 29.7208 Evaluate side-chains 95 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 287 ASP Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain Q residue 336 LEU Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 346 VAL Chi-restraints excluded: chain U residue 257 ASN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 44 GLU Chi-restraints excluded: chain Z residue 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 283 ASN ** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6845 Z= 0.177 Angle : 0.601 9.869 9236 Z= 0.309 Chirality : 0.040 0.145 1116 Planarity : 0.003 0.054 1159 Dihedral : 4.348 28.222 927 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.28 % Allowed : 18.23 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.30), residues: 853 helix: 1.57 (0.23), residues: 538 sheet: 0.29 (0.52), residues: 109 loop : -2.11 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 215 HIS 0.001 0.000 HIS U 294 PHE 0.011 0.001 PHE P 207 TYR 0.019 0.001 TYR O 170 ARG 0.009 0.001 ARG P 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 167 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.9150 (pp20) REVERT: O 201 MET cc_start: 0.7636 (mmp) cc_final: 0.6871 (tpp) REVERT: P 242 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7886 (mm) REVERT: Q 277 MET cc_start: 0.4083 (tpp) cc_final: 0.3777 (mmp) REVERT: Q 336 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8359 (pp) REVERT: Q 338 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: U 299 MET cc_start: 0.7003 (mtm) cc_final: 0.6777 (mtt) REVERT: Y 80 GLN cc_start: 0.8419 (pp30) cc_final: 0.8134 (mm-40) REVERT: Y 119 LYS cc_start: 0.8429 (mtmt) cc_final: 0.8033 (mtmm) REVERT: Z 1 MET cc_start: 0.7062 (tmm) cc_final: 0.6562 (tpp) outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 0.2312 time to fit residues: 29.2795 Evaluate side-chains 95 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 276 VAL Chi-restraints excluded: chain O residue 287 ASP Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 348 TYR Chi-restraints excluded: chain Q residue 336 LEU Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 346 VAL Chi-restraints excluded: chain U residue 257 ASN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 173 SER Chi-restraints excluded: chain Z residue 44 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 294 HIS ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6845 Z= 0.232 Angle : 0.650 10.203 9236 Z= 0.340 Chirality : 0.043 0.192 1116 Planarity : 0.003 0.040 1159 Dihedral : 4.477 29.050 927 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.28 % Allowed : 19.52 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.30), residues: 853 helix: 1.49 (0.23), residues: 534 sheet: 0.27 (0.52), residues: 109 loop : -1.96 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 215 HIS 0.003 0.001 HIS U 294 PHE 0.029 0.002 PHE U 295 TYR 0.014 0.002 TYR Y 25 ARG 0.010 0.001 ARG Z 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 167 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.9077 (pp20) REVERT: O 201 MET cc_start: 0.7627 (mmp) cc_final: 0.6842 (tpp) REVERT: P 242 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7812 (mm) REVERT: Q 277 MET cc_start: 0.4345 (tpp) cc_final: 0.4131 (mmp) REVERT: Q 338 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8399 (m-30) REVERT: U 299 MET cc_start: 0.7045 (mtm) cc_final: 0.6839 (mtt) REVERT: U 314 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7621 (mm-30) REVERT: Z 1 MET cc_start: 0.7766 (tmm) cc_final: 0.7208 (tpp) outliers start: 23 outliers final: 16 residues processed: 92 average time/residue: 0.2061 time to fit residues: 24.9938 Evaluate side-chains 95 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 276 VAL Chi-restraints excluded: chain O residue 287 ASP Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 205 TYR Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 348 TYR Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 346 VAL Chi-restraints excluded: chain U residue 257 ASN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 44 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6845 Z= 0.186 Angle : 0.645 10.534 9236 Z= 0.331 Chirality : 0.041 0.174 1116 Planarity : 0.003 0.056 1159 Dihedral : 4.456 29.324 927 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.85 % Allowed : 19.37 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.30), residues: 853 helix: 1.56 (0.23), residues: 532 sheet: 0.35 (0.52), residues: 109 loop : -1.92 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 215 HIS 0.001 0.000 HIS U 237 PHE 0.043 0.002 PHE U 295 TYR 0.013 0.001 TYR Y 25 ARG 0.013 0.001 ARG Z 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 167 GLU cc_start: 0.9469 (OUTLIER) cc_final: 0.9161 (pp20) REVERT: O 201 MET cc_start: 0.7627 (mmp) cc_final: 0.6830 (tpp) REVERT: P 242 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7705 (mm) REVERT: Q 338 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: U 257 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8662 (m-40) REVERT: U 299 MET cc_start: 0.7122 (mtm) cc_final: 0.6864 (mtt) REVERT: U 314 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7330 (mm-30) REVERT: Y 80 GLN cc_start: 0.8405 (pp30) cc_final: 0.8150 (mm-40) REVERT: Y 119 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8113 (mtmm) REVERT: Z 1 MET cc_start: 0.7874 (tmm) cc_final: 0.7326 (tpp) REVERT: Z 52 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7999 (ttp80) outliers start: 20 outliers final: 14 residues processed: 95 average time/residue: 0.2137 time to fit residues: 26.5279 Evaluate side-chains 104 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 276 VAL Chi-restraints excluded: chain O residue 287 ASP Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 348 TYR Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 346 VAL Chi-restraints excluded: chain U residue 257 ASN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 44 GLU Chi-restraints excluded: chain Z residue 52 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6845 Z= 0.194 Angle : 0.664 10.481 9236 Z= 0.342 Chirality : 0.043 0.248 1116 Planarity : 0.003 0.050 1159 Dihedral : 4.525 30.184 927 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.85 % Allowed : 19.94 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.82 (0.30), residues: 853 helix: 1.52 (0.23), residues: 533 sheet: 0.38 (0.52), residues: 109 loop : -1.91 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 215 HIS 0.001 0.000 HIS U 294 PHE 0.026 0.002 PHE P 207 TYR 0.013 0.001 TYR P 187 ARG 0.011 0.001 ARG Z 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 167 GLU cc_start: 0.9475 (OUTLIER) cc_final: 0.9159 (pp20) REVERT: O 201 MET cc_start: 0.7632 (mmp) cc_final: 0.6822 (tpp) REVERT: P 242 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7707 (mm) REVERT: Q 338 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8406 (m-30) REVERT: Q 374 MET cc_start: 0.7190 (ppp) cc_final: 0.6396 (ppp) REVERT: U 257 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8655 (m-40) REVERT: U 299 MET cc_start: 0.7189 (mtm) cc_final: 0.6571 (mtt) REVERT: Y 80 GLN cc_start: 0.8429 (pp30) cc_final: 0.8195 (mm110) REVERT: Y 119 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8084 (mtmm) REVERT: Z 1 MET cc_start: 0.7987 (tmm) cc_final: 0.7423 (tpp) REVERT: Z 52 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.8032 (ttp80) outliers start: 20 outliers final: 15 residues processed: 99 average time/residue: 0.2141 time to fit residues: 27.9132 Evaluate side-chains 97 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 167 GLU Chi-restraints excluded: chain O residue 276 VAL Chi-restraints excluded: chain O residue 287 ASP Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 348 TYR Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 346 VAL Chi-restraints excluded: chain U residue 257 ASN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 73 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 44 GLU Chi-restraints excluded: chain Z residue 52 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.118950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.086468 restraints weight = 26240.444| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 5.72 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6845 Z= 0.200 Angle : 0.698 14.054 9236 Z= 0.352 Chirality : 0.045 0.474 1116 Planarity : 0.004 0.051 1159 Dihedral : 4.571 30.590 927 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.85 % Allowed : 20.37 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.84 (0.30), residues: 853 helix: 1.51 (0.23), residues: 535 sheet: 0.37 (0.53), residues: 109 loop : -1.86 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP P 215 HIS 0.002 0.000 HIS U 237 PHE 0.026 0.002 PHE P 207 TYR 0.013 0.001 TYR Y 25 ARG 0.012 0.001 ARG Z 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.42 seconds wall clock time: 30 minutes 18.56 seconds (1818.56 seconds total)