Starting phenix.real_space_refine on Wed Feb 12 23:30:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e33_30975/02_2025/7e33_30975_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e33_30975/02_2025/7e33_30975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e33_30975/02_2025/7e33_30975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e33_30975/02_2025/7e33_30975.map" model { file = "/net/cci-nas-00/data/ceres_data/7e33_30975/02_2025/7e33_30975_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e33_30975/02_2025/7e33_30975_neut.cif" } resolution = 2.9 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= -0.000 sd= 0.014 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 62 5.16 5 C 5446 2.51 5 N 1438 2.21 5 O 1592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8538 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "E" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1762 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 391 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "R" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2060 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'HVU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.24, per 1000 atoms: 0.61 Number of scatterers: 8538 At special positions: 0 Unit cell: (107.635, 112.86, 114.95, 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 62 16.00 O 1592 8.00 N 1438 7.00 C 5446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 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 95 " - pdb=" SG CYS R 173 " 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: 2.19 Conformation dependent library (CDL) restraints added in 975.2 milliseconds 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 40.1% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.595A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 211 through 218 removed outlier: 4.574A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.351A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.685A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.572A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.791A 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 Processing helix chain 'A' and resid 327 through 351 Processing helix chain 'B' and resid 8 through 26 removed outlier: 4.396A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.826A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.592A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 46 removed outlier: 3.597A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 50 Processing helix chain 'R' and resid 51 through 54 Processing helix chain 'R' and resid 55 through 75 Processing helix chain 'R' and resid 75 through 85 Processing helix chain 'R' and resid 93 through 126 Processing helix chain 'R' and resid 128 through 134 removed outlier: 4.111A pdb=" N ARG R 132 " --> pdb=" O ILE R 128 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS R 133 " --> pdb=" O GLU R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 155 Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 191 through 212 Processing helix chain 'R' and resid 283 through 316 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 322 through 346 removed outlier: 4.087A pdb=" N ASN R 336 " --> pdb=" O LEU R 332 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER R 337 " --> pdb=" O GLY R 333 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU R 338 " --> pdb=" O TYR R 334 " (cutoff:3.500A) Proline residue: R 341 - end of helix Processing helix chain 'R' and resid 348 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.567A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.534A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.516A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.725A 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 148 removed outlier: 3.568A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.339A 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: 6.850A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.413A 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: 6.341A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.282A 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: 3.894A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.509A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.772A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.772A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.029A 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 194 through 195 removed outlier: 6.384A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.384A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1266 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: 2.45 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2724 1.35 - 1.47: 2151 1.47 - 1.58: 3748 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 8713 Sorted by residual: bond pdb=" NZ HVU R 501 " pdb=" CA1 HVU R 501 " ideal model delta sigma weight residual 1.454 1.318 0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" NZ HVU R 501 " pdb=" CJ HVU R 501 " ideal model delta sigma weight residual 1.441 1.310 0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" NZ HVU R 501 " pdb=" CF1 HVU R 501 " ideal model delta sigma weight residual 1.449 1.342 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" CD1 HVU R 501 " pdb=" NE1 HVU R 501 " ideal model delta sigma weight residual 1.364 1.282 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CD2 HVU R 501 " pdb=" CE2 HVU R 501 " ideal model delta sigma weight residual 1.412 1.489 -0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 8708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 11739 2.37 - 4.73: 52 4.73 - 7.10: 9 7.10 - 9.47: 0 9.47 - 11.84: 1 Bond angle restraints: 11801 Sorted by residual: angle pdb=" CD1 HVU R 501 " pdb=" NE1 HVU R 501 " pdb=" CE2 HVU R 501 " ideal model delta sigma weight residual 108.93 120.77 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N ARG E 67 " pdb=" CA ARG E 67 " pdb=" C ARG E 67 " ideal model delta sigma weight residual 114.04 110.75 3.29 1.24e+00 6.50e-01 7.05e+00 angle pdb=" CG HVU R 501 " pdb=" CD1 HVU R 501 " pdb=" NE1 HVU R 501 " ideal model delta sigma weight residual 110.60 104.25 6.35 3.00e+00 1.11e-01 4.48e+00 angle pdb=" NE1 HVU R 501 " pdb=" CE2 HVU R 501 " pdb=" CZ2 HVU R 501 " ideal model delta sigma weight residual 130.54 136.63 -6.09 3.00e+00 1.11e-01 4.12e+00 angle pdb=" CD2 HVU R 501 " pdb=" CE2 HVU R 501 " pdb=" NE1 HVU R 501 " ideal model delta sigma weight residual 107.63 101.78 5.85 3.00e+00 1.11e-01 3.81e+00 ... (remaining 11796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 5004 26.44 - 52.89: 164 52.89 - 79.33: 10 79.33 - 105.78: 4 105.78 - 132.22: 1 Dihedral angle restraints: 5183 sinusoidal: 2026 harmonic: 3157 Sorted by residual: dihedral pdb=" CB1 HVU R 501 " pdb=" NZ HVU R 501 " pdb=" CF1 HVU R 501 " pdb=" CA1 HVU R 501 " ideal model delta sinusoidal sigma weight residual -69.87 62.35 -132.22 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CA HVU R 501 " pdb=" NZ HVU R 501 " pdb=" CA1 HVU R 501 " pdb=" CF1 HVU R 501 " ideal model delta sinusoidal sigma weight residual 39.14 -59.98 99.12 1 3.00e+01 1.11e-03 1.24e+01 dihedral pdb=" CB HVU R 501 " pdb=" CB1 HVU R 501 " pdb=" CF1 HVU R 501 " pdb=" NZ HVU R 501 " ideal model delta sinusoidal sigma weight residual -29.70 60.47 -90.17 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 5180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1165 0.051 - 0.101: 137 0.101 - 0.152: 51 0.152 - 0.202: 0 0.202 - 0.253: 1 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CB HVU R 501 " pdb=" CA HVU R 501 " pdb=" CB1 HVU R 501 " pdb=" CG HVU R 501 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1351 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO B 236 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 340 " 0.015 5.00e-02 4.00e+02 2.33e-02 8.68e-01 pdb=" N PRO R 341 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO R 341 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 341 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 192 " 0.004 2.00e-02 2.50e+03 7.04e-03 4.96e-01 pdb=" C MET E 192 " -0.012 2.00e-02 2.50e+03 pdb=" O MET E 192 " 0.005 2.00e-02 2.50e+03 pdb=" N SER E 193 " 0.004 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 63 2.51 - 3.11: 6529 3.11 - 3.71: 13515 3.71 - 4.30: 19320 4.30 - 4.90: 32848 Nonbonded interactions: 72275 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 1.918 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD2 ASP B 247 " model vdw 2.035 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.043 3.040 nonbonded pdb=" O ALA A 203 " pdb=" NH1 ARG A 205 " model vdw 2.130 3.120 nonbonded pdb=" O PRO R 341 " pdb=" OG1 THR R 345 " model vdw 2.153 3.040 ... (remaining 72270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.220 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 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 0.136 8713 Z= 0.248 Angle : 0.449 11.836 11801 Z= 0.239 Chirality : 0.038 0.253 1354 Planarity : 0.002 0.033 1470 Dihedral : 12.839 132.220 3133 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.41 (0.27), residues: 1066 helix: 2.93 (0.27), residues: 379 sheet: 1.23 (0.31), residues: 269 loop : 0.69 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 331 HIS 0.002 0.000 HIS G 44 PHE 0.008 0.001 PHE R 152 TYR 0.008 0.001 TYR R 192 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.883 Fit side-chains REVERT: A 243 MET cc_start: 0.8133 (tpp) cc_final: 0.7689 (tpt) REVERT: B 188 MET cc_start: 0.7847 (mmm) cc_final: 0.7638 (mmm) REVERT: B 221 THR cc_start: 0.7828 (m) cc_final: 0.7606 (m) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.1533 time to fit residues: 216.9778 Evaluate side-chains 134 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.0060 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 255 ASN B 155 ASN E 77 ASN E 186 GLN R 112 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.189740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.153698 restraints weight = 9516.008| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.24 r_work: 0.3577 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8713 Z= 0.203 Angle : 0.547 7.243 11801 Z= 0.292 Chirality : 0.042 0.143 1354 Planarity : 0.004 0.059 1470 Dihedral : 6.456 114.702 1185 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.96 % Allowed : 12.41 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.99 (0.26), residues: 1066 helix: 2.31 (0.27), residues: 381 sheet: 1.08 (0.32), residues: 263 loop : 0.67 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.003 0.001 HIS B 62 PHE 0.026 0.002 PHE E 212 TYR 0.012 0.001 TYR R 192 ARG 0.007 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.948 Fit side-chains REVERT: A 216 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: A 248 LYS cc_start: 0.7865 (mmtm) cc_final: 0.7453 (mmtm) REVERT: A 297 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.5746 (tm-30) REVERT: A 337 ASP cc_start: 0.7145 (m-30) cc_final: 0.6838 (m-30) REVERT: B 189 SER cc_start: 0.8959 (p) cc_final: 0.8379 (t) REVERT: E 179 GLN cc_start: 0.8639 (tt0) cc_final: 0.8434 (tt0) REVERT: G 21 MET cc_start: 0.7750 (tmt) cc_final: 0.7462 (tmt) REVERT: R 27 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6405 (mpp) REVERT: R 85 MET cc_start: 0.6266 (ppp) cc_final: 0.5933 (ppp) REVERT: R 144 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5821 (mt) REVERT: R 350 ASP cc_start: 0.8553 (m-30) cc_final: 0.8335 (m-30) outliers start: 9 outliers final: 2 residues processed: 157 average time/residue: 1.1426 time to fit residues: 192.3175 Evaluate side-chains 143 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 144 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 94 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 295 ASN E 77 ASN E 82 GLN E 186 GLN R 40 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.178778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.141510 restraints weight = 9561.444| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.23 r_work: 0.3403 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8713 Z= 0.319 Angle : 0.582 8.071 11801 Z= 0.312 Chirality : 0.044 0.143 1354 Planarity : 0.004 0.043 1470 Dihedral : 6.922 117.397 1185 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.57 % Allowed : 14.01 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.54 (0.26), residues: 1066 helix: 2.02 (0.26), residues: 374 sheet: 0.63 (0.31), residues: 274 loop : 0.51 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 99 HIS 0.007 0.001 HIS B 62 PHE 0.019 0.002 PHE E 212 TYR 0.013 0.002 TYR R 192 ARG 0.005 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.976 Fit side-chains REVERT: A 208 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7462 (ttp80) REVERT: A 216 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: A 248 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7438 (mmtm) REVERT: A 297 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5798 (tm-30) REVERT: B 175 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7136 (mp10) REVERT: B 217 MET cc_start: 0.8489 (mtp) cc_final: 0.7068 (mmp) REVERT: B 256 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7433 (mtm180) REVERT: E 43 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7538 (mmtm) REVERT: E 179 GLN cc_start: 0.8780 (tt0) cc_final: 0.8573 (tt0) REVERT: R 27 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6595 (mpp) outliers start: 24 outliers final: 10 residues processed: 152 average time/residue: 1.2674 time to fit residues: 205.8319 Evaluate side-chains 141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 0.0570 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 269 ASN B 259 GLN E 39 GLN E 82 GLN E 113 GLN E 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141061 restraints weight = 9628.025| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.26 r_work: 0.3411 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8713 Z= 0.258 Angle : 0.557 7.770 11801 Z= 0.298 Chirality : 0.042 0.131 1354 Planarity : 0.004 0.037 1470 Dihedral : 6.825 116.401 1185 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.35 % Allowed : 15.72 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1066 helix: 1.81 (0.26), residues: 382 sheet: 0.45 (0.31), residues: 271 loop : 0.49 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS B 62 PHE 0.016 0.002 PHE E 212 TYR 0.013 0.001 TYR E 190 ARG 0.006 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.968 Fit side-chains REVERT: A 9 ASP cc_start: 0.7986 (m-30) cc_final: 0.7663 (m-30) REVERT: A 208 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7413 (ttp80) REVERT: A 243 MET cc_start: 0.7826 (mmm) cc_final: 0.7625 (tpt) REVERT: A 248 LYS cc_start: 0.7899 (mmtm) cc_final: 0.7487 (mmtm) REVERT: A 297 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5787 (tm-30) REVERT: A 318 GLU cc_start: 0.7180 (tp30) cc_final: 0.6864 (tp30) REVERT: A 337 ASP cc_start: 0.7182 (m-30) cc_final: 0.6965 (m-30) REVERT: B 134 ARG cc_start: 0.7913 (ptp-110) cc_final: 0.7444 (ptt90) REVERT: B 217 MET cc_start: 0.8161 (mtp) cc_final: 0.6961 (mmp) REVERT: B 256 ARG cc_start: 0.7783 (mtm180) cc_final: 0.7452 (mtm180) REVERT: E 43 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7623 (mmtm) REVERT: R 27 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6514 (mpp) REVERT: R 85 MET cc_start: 0.6689 (ppp) cc_final: 0.6335 (ppp) outliers start: 22 outliers final: 7 residues processed: 146 average time/residue: 1.2223 time to fit residues: 190.2412 Evaluate side-chains 133 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 23 MET Chi-restraints excluded: chain R residue 27 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 69 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 269 ASN B 259 GLN E 82 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.171960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135361 restraints weight = 9707.452| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.17 r_work: 0.3406 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8713 Z= 0.239 Angle : 0.543 7.264 11801 Z= 0.291 Chirality : 0.042 0.190 1354 Planarity : 0.004 0.037 1470 Dihedral : 6.838 117.237 1185 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.57 % Allowed : 17.86 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.27 (0.26), residues: 1066 helix: 1.79 (0.26), residues: 382 sheet: 0.31 (0.32), residues: 272 loop : 0.49 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 112 PHE 0.011 0.001 PHE A 334 TYR 0.012 0.001 TYR E 190 ARG 0.008 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.874 Fit side-chains REVERT: A 9 ASP cc_start: 0.7943 (m-30) cc_final: 0.7619 (m-30) REVERT: A 208 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7410 (ttp80) REVERT: A 216 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: A 252 SER cc_start: 0.8459 (m) cc_final: 0.8001 (p) REVERT: A 297 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.5773 (tm-30) REVERT: A 308 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: A 318 GLU cc_start: 0.7287 (tp30) cc_final: 0.7015 (tp30) REVERT: A 324 THR cc_start: 0.7070 (t) cc_final: 0.6818 (m) REVERT: A 337 ASP cc_start: 0.7395 (m-30) cc_final: 0.7132 (m-30) REVERT: B 43 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8333 (mp) REVERT: B 175 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: B 217 MET cc_start: 0.8283 (mtp) cc_final: 0.6888 (mmp) REVERT: B 256 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7501 (mtm180) REVERT: E 43 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7574 (mmtm) REVERT: R 27 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6626 (mpp) REVERT: R 85 MET cc_start: 0.6153 (ppp) cc_final: 0.5925 (ppp) outliers start: 24 outliers final: 12 residues processed: 145 average time/residue: 1.2101 time to fit residues: 187.0922 Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 198 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 331 ASN B 259 GLN E 82 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134713 restraints weight = 9763.445| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.18 r_work: 0.3397 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8713 Z= 0.245 Angle : 0.546 7.275 11801 Z= 0.292 Chirality : 0.042 0.176 1354 Planarity : 0.004 0.038 1470 Dihedral : 6.990 120.550 1185 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.57 % Allowed : 18.40 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1066 helix: 1.77 (0.26), residues: 384 sheet: 0.27 (0.32), residues: 271 loop : 0.45 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 112 PHE 0.011 0.001 PHE A 334 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.957 Fit side-chains REVERT: A 9 ASP cc_start: 0.7940 (m-30) cc_final: 0.7588 (m-30) REVERT: A 208 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7410 (ttp80) REVERT: A 216 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: A 252 SER cc_start: 0.8468 (m) cc_final: 0.8013 (p) REVERT: A 270 LYS cc_start: 0.8400 (mtmp) cc_final: 0.7773 (ptpp) REVERT: A 308 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: A 318 GLU cc_start: 0.7290 (tp30) cc_final: 0.7005 (tp30) REVERT: A 324 THR cc_start: 0.6934 (t) cc_final: 0.6721 (m) REVERT: B 43 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8276 (mp) REVERT: B 175 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7104 (mp10) REVERT: B 217 MET cc_start: 0.8282 (mtp) cc_final: 0.6919 (mmp) REVERT: B 256 ARG cc_start: 0.7816 (mtm180) cc_final: 0.7491 (mtm180) REVERT: E 43 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7598 (mmtm) REVERT: E 140 MET cc_start: 0.8696 (mmt) cc_final: 0.7649 (mmt) REVERT: R 27 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6632 (mpp) outliers start: 24 outliers final: 14 residues processed: 140 average time/residue: 1.2623 time to fit residues: 188.4496 Evaluate side-chains 147 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 198 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 269 ASN A 331 ASN B 259 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.172450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.135749 restraints weight = 9857.934| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.19 r_work: 0.3411 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8713 Z= 0.212 Angle : 0.550 7.232 11801 Z= 0.292 Chirality : 0.042 0.153 1354 Planarity : 0.004 0.037 1470 Dihedral : 7.025 121.504 1185 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.67 % Allowed : 18.72 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1066 helix: 1.73 (0.26), residues: 384 sheet: 0.27 (0.33), residues: 269 loop : 0.50 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS R 112 PHE 0.010 0.001 PHE A 334 TYR 0.012 0.001 TYR E 190 ARG 0.009 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.906 Fit side-chains REVERT: A 9 ASP cc_start: 0.7933 (m-30) cc_final: 0.7588 (m-30) REVERT: A 208 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7531 (ttp80) REVERT: A 216 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: A 252 SER cc_start: 0.8453 (m) cc_final: 0.8055 (p) REVERT: A 270 LYS cc_start: 0.8385 (mtmp) cc_final: 0.7784 (ptpp) REVERT: A 297 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.5720 (tm-30) REVERT: A 308 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: A 318 GLU cc_start: 0.7287 (tp30) cc_final: 0.6996 (tp30) REVERT: A 324 THR cc_start: 0.6936 (t) cc_final: 0.6531 (m) REVERT: A 330 LYS cc_start: 0.7551 (ttmm) cc_final: 0.7100 (mttp) REVERT: A 331 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7326 (m110) REVERT: B 130 GLU cc_start: 0.7589 (mp0) cc_final: 0.6955 (tt0) REVERT: B 134 ARG cc_start: 0.8151 (ptp-110) cc_final: 0.7522 (ptt90) REVERT: B 175 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: B 217 MET cc_start: 0.8272 (mtp) cc_final: 0.6924 (mmp) REVERT: B 256 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7496 (mtm180) REVERT: E 43 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7608 (mmtm) REVERT: E 93 MET cc_start: 0.8308 (ttm) cc_final: 0.8043 (tpp) REVERT: R 27 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6620 (mpp) REVERT: R 85 MET cc_start: 0.6700 (ppp) cc_final: 0.6407 (ppp) outliers start: 25 outliers final: 14 residues processed: 143 average time/residue: 1.2008 time to fit residues: 183.3498 Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 198 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 331 ASN B 259 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.172982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136652 restraints weight = 9933.932| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.17 r_work: 0.3416 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8713 Z= 0.208 Angle : 0.548 7.221 11801 Z= 0.290 Chirality : 0.042 0.174 1354 Planarity : 0.004 0.037 1470 Dihedral : 6.758 115.318 1185 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.78 % Allowed : 18.82 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.24 (0.27), residues: 1066 helix: 1.73 (0.26), residues: 384 sheet: 0.27 (0.33), residues: 269 loop : 0.52 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS R 112 PHE 0.013 0.001 PHE E 68 TYR 0.011 0.001 TYR R 192 ARG 0.008 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.853 Fit side-chains REVERT: A 9 ASP cc_start: 0.7938 (m-30) cc_final: 0.7616 (m-30) REVERT: A 208 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7464 (ttp80) REVERT: A 216 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: A 252 SER cc_start: 0.8466 (m) cc_final: 0.8072 (p) REVERT: A 270 LYS cc_start: 0.8398 (mtmp) cc_final: 0.7811 (ptpp) REVERT: A 308 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: A 318 GLU cc_start: 0.7308 (tp30) cc_final: 0.6934 (tp30) REVERT: A 324 THR cc_start: 0.6922 (t) cc_final: 0.6517 (m) REVERT: A 330 LYS cc_start: 0.7646 (ttmm) cc_final: 0.7170 (mttp) REVERT: A 331 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7377 (m110) REVERT: B 130 GLU cc_start: 0.7606 (mp0) cc_final: 0.6971 (tt0) REVERT: B 134 ARG cc_start: 0.8176 (ptp-110) cc_final: 0.7549 (ptt90) REVERT: B 175 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7131 (mp10) REVERT: B 217 MET cc_start: 0.8307 (mtp) cc_final: 0.7020 (mmp) REVERT: B 256 ARG cc_start: 0.7848 (mtm180) cc_final: 0.7527 (mtm180) REVERT: B 262 MET cc_start: 0.8434 (tpp) cc_final: 0.8225 (mmt) REVERT: E 43 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7629 (mmtm) REVERT: E 91 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8189 (t) REVERT: E 93 MET cc_start: 0.8299 (ttm) cc_final: 0.8055 (tpp) REVERT: R 27 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6617 (mpp) REVERT: R 85 MET cc_start: 0.6673 (ppp) cc_final: 0.6449 (ppp) outliers start: 26 outliers final: 11 residues processed: 136 average time/residue: 1.2558 time to fit residues: 181.8785 Evaluate side-chains 137 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 198 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN A 331 ASN B 259 GLN E 82 GLN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.174403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138170 restraints weight = 9808.252| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.14 r_work: 0.3441 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8713 Z= 0.188 Angle : 0.542 7.719 11801 Z= 0.286 Chirality : 0.042 0.157 1354 Planarity : 0.004 0.037 1470 Dihedral : 6.718 115.587 1185 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.93 % Allowed : 19.89 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 1066 helix: 1.76 (0.26), residues: 384 sheet: 0.33 (0.33), residues: 267 loop : 0.56 (0.33), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 112 PHE 0.011 0.001 PHE E 68 TYR 0.011 0.001 TYR E 190 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.954 Fit side-chains REVERT: A 9 ASP cc_start: 0.7910 (m-30) cc_final: 0.7597 (m-30) REVERT: A 208 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7451 (ttp80) REVERT: A 252 SER cc_start: 0.8269 (m) cc_final: 0.7890 (p) REVERT: A 270 LYS cc_start: 0.8392 (mtmp) cc_final: 0.7850 (ptpp) REVERT: A 308 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: A 318 GLU cc_start: 0.7277 (tp30) cc_final: 0.6896 (tp30) REVERT: A 324 THR cc_start: 0.6899 (t) cc_final: 0.6665 (m) REVERT: A 330 LYS cc_start: 0.7588 (ttmm) cc_final: 0.7219 (mtmt) REVERT: B 130 GLU cc_start: 0.7584 (mp0) cc_final: 0.6944 (tt0) REVERT: B 134 ARG cc_start: 0.8182 (ptp-110) cc_final: 0.7557 (ptt90) REVERT: B 175 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7111 (mp10) REVERT: B 217 MET cc_start: 0.8274 (mtp) cc_final: 0.6973 (mmp) REVERT: B 249 THR cc_start: 0.8598 (p) cc_final: 0.8283 (t) REVERT: E 43 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7640 (mmtm) REVERT: E 93 MET cc_start: 0.8332 (ttm) cc_final: 0.8101 (tpp) REVERT: R 27 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6634 (mpp) REVERT: R 85 MET cc_start: 0.6612 (ppp) cc_final: 0.6382 (ppp) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 1.1966 time to fit residues: 173.9568 Evaluate side-chains 135 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 198 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 0.0770 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.0170 chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 331 ASN E 82 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.174394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138066 restraints weight = 9781.816| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.18 r_work: 0.3438 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8713 Z= 0.196 Angle : 0.561 9.838 11801 Z= 0.293 Chirality : 0.042 0.161 1354 Planarity : 0.004 0.036 1470 Dihedral : 6.740 116.509 1185 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.82 % Allowed : 20.11 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.29 (0.27), residues: 1066 helix: 1.79 (0.26), residues: 384 sheet: 0.29 (0.33), residues: 267 loop : 0.53 (0.33), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS R 112 PHE 0.011 0.001 PHE A 334 TYR 0.011 0.001 TYR R 192 ARG 0.008 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.959 Fit side-chains REVERT: A 9 ASP cc_start: 0.7900 (m-30) cc_final: 0.7555 (m-30) REVERT: A 208 ARG cc_start: 0.7750 (ttm-80) cc_final: 0.7529 (ttp80) REVERT: A 216 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: A 252 SER cc_start: 0.8243 (m) cc_final: 0.7898 (p) REVERT: A 270 LYS cc_start: 0.8398 (mtmp) cc_final: 0.7905 (ptpp) REVERT: A 308 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: A 318 GLU cc_start: 0.7304 (tp30) cc_final: 0.6925 (tp30) REVERT: A 324 THR cc_start: 0.6894 (t) cc_final: 0.6539 (m) REVERT: A 330 LYS cc_start: 0.7724 (ttmm) cc_final: 0.7189 (mttp) REVERT: B 130 GLU cc_start: 0.7595 (mp0) cc_final: 0.6961 (tt0) REVERT: B 134 ARG cc_start: 0.8180 (ptp-110) cc_final: 0.7562 (ptt90) REVERT: B 175 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7072 (mp10) REVERT: B 217 MET cc_start: 0.8268 (mtp) cc_final: 0.6977 (mmp) REVERT: E 43 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7603 (mmtm) REVERT: E 93 MET cc_start: 0.8365 (ttm) cc_final: 0.8132 (tpp) REVERT: R 27 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6627 (mpp) REVERT: R 85 MET cc_start: 0.6686 (ppp) cc_final: 0.6424 (ppp) REVERT: R 144 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6348 (mt) outliers start: 17 outliers final: 9 residues processed: 133 average time/residue: 1.1889 time to fit residues: 169.1016 Evaluate side-chains 133 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN E 39 GLN E 77 ASN E 82 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.173724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136937 restraints weight = 9963.993| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.21 r_work: 0.3420 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8713 Z= 0.210 Angle : 0.568 9.842 11801 Z= 0.296 Chirality : 0.042 0.169 1354 Planarity : 0.004 0.037 1470 Dihedral : 6.679 114.779 1185 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.82 % Allowed : 20.43 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.26 (0.27), residues: 1066 helix: 1.76 (0.26), residues: 385 sheet: 0.27 (0.33), residues: 267 loop : 0.51 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS R 112 PHE 0.010 0.001 PHE E 68 TYR 0.011 0.001 TYR R 192 ARG 0.008 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7250.30 seconds wall clock time: 128 minutes 34.99 seconds (7714.99 seconds total)