Starting phenix.real_space_refine on Mon May 12 02:10:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j19_35914/05_2025/8j19_35914_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j19_35914/05_2025/8j19_35914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j19_35914/05_2025/8j19_35914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j19_35914/05_2025/8j19_35914.map" model { file = "/net/cci-nas-00/data/ceres_data/8j19_35914/05_2025/8j19_35914_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j19_35914/05_2025/8j19_35914_neut.cif" } resolution = 3.23 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= 0.038 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 59 5.16 5 C 5619 2.51 5 N 1509 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8801 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2232 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "S" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'SWO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.04, per 1000 atoms: 0.57 Number of scatterers: 8801 At special positions: 0 Unit cell: (96.408, 117.832, 124.424, 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 59 16.00 O 1614 8.00 N 1509 7.00 C 5619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 166 " distance=2.12 Simple disulfide: pdb=" SG CYS R 93 " - pdb=" SG CYS R 168 " distance=1.66 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " 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: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 39.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'R' and resid 14 through 18 removed outlier: 4.094A pdb=" N GLY R 18 " --> pdb=" O SER R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 48 Processing helix chain 'R' and resid 49 through 52 removed outlier: 3.579A pdb=" N ARG R 52 " --> pdb=" O PRO R 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 49 through 52' Processing helix chain 'R' and resid 55 through 84 removed outlier: 4.054A pdb=" N ILE R 59 " --> pdb=" O PHE R 55 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN R 74 " --> pdb=" O CYS R 70 " (cutoff:3.500A) Proline residue: R 75 - end of helix Processing helix chain 'R' and resid 89 through 124 removed outlier: 3.873A pdb=" N VAL R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU R 98 " --> pdb=" O ARG R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 133 through 151 removed outlier: 4.658A pdb=" N VAL R 138 " --> pdb=" O ALA R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 157 Proline residue: R 157 - end of helix Processing helix chain 'R' and resid 175 through 212 removed outlier: 3.851A pdb=" N PHE R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU R 212 " --> pdb=" O ALA R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 316 through 342 Proline residue: R 334 - end of helix Processing helix chain 'R' and resid 348 through 371 removed outlier: 4.306A pdb=" N HIS R 352 " --> pdb=" O PRO R 348 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET R 353 " --> pdb=" O ARG R 349 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY R 363 " --> pdb=" O THR R 359 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS R 364 " --> pdb=" O TRP R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 385 removed outlier: 3.696A pdb=" N GLN R 379 " --> pdb=" O ARG R 375 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA R 380 " --> pdb=" O GLN R 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.734A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 260 removed outlier: 4.203A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.331A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.920A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.013A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.625A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.586A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.569A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'R' and resid 159 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.665A pdb=" N PHE A 196 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.084A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.668A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.764A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.976A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.536A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.140A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.319A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.866A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.537A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1239 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: 2.39 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1409 1.32 - 1.44: 2494 1.44 - 1.57: 4997 1.57 - 1.69: 2 1.69 - 1.81: 82 Bond restraints: 8984 Sorted by residual: bond pdb=" C ILE R 185 " pdb=" N TYR R 186 " ideal model delta sigma weight residual 1.334 1.434 -0.100 1.49e-02 4.50e+03 4.52e+01 bond pdb=" C03 SWO R 401 " pdb=" N04 SWO R 401 " ideal model delta sigma weight residual 1.348 1.240 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" CA TRP R 156 " pdb=" C TRP R 156 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.00e-02 1.00e+04 2.51e+01 bond pdb=" C TRP R 156 " pdb=" N PRO R 157 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.11e-02 8.12e+03 1.59e+01 bond pdb=" C ILE R 333 " pdb=" O ILE R 333 " ideal model delta sigma weight residual 1.240 1.198 0.042 1.26e-02 6.30e+03 1.12e+01 ... (remaining 8979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 12043 2.42 - 4.85: 108 4.85 - 7.27: 16 7.27 - 9.69: 4 9.69 - 12.11: 3 Bond angle restraints: 12174 Sorted by residual: angle pdb=" N GLY R 315 " pdb=" CA GLY R 315 " pdb=" C GLY R 315 " ideal model delta sigma weight residual 114.37 102.26 12.11 1.26e+00 6.30e-01 9.24e+01 angle pdb=" O ILE R 185 " pdb=" C ILE R 185 " pdb=" N TYR R 186 " ideal model delta sigma weight residual 121.87 112.94 8.93 1.01e+00 9.80e-01 7.82e+01 angle pdb=" N ILE R 340 " pdb=" CA ILE R 340 " pdb=" C ILE R 340 " ideal model delta sigma weight residual 111.56 105.89 5.67 8.60e-01 1.35e+00 4.35e+01 angle pdb=" CA ILE R 185 " pdb=" C ILE R 185 " pdb=" N TYR R 186 " ideal model delta sigma weight residual 117.53 123.82 -6.29 1.19e+00 7.06e-01 2.79e+01 angle pdb=" N VAL S 5 " pdb=" CA VAL S 5 " pdb=" C VAL S 5 " ideal model delta sigma weight residual 109.17 101.82 7.35 1.54e+00 4.22e-01 2.28e+01 ... (remaining 12169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4676 17.72 - 35.44: 482 35.44 - 53.16: 119 53.16 - 70.88: 27 70.88 - 88.60: 13 Dihedral angle restraints: 5317 sinusoidal: 2048 harmonic: 3269 Sorted by residual: dihedral pdb=" CB CYS R 93 " pdb=" SG CYS R 93 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual 93.00 19.08 73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" C ILE R 333 " pdb=" N ILE R 333 " pdb=" CA ILE R 333 " pdb=" CB ILE R 333 " ideal model delta harmonic sigma weight residual -122.00 -133.36 11.36 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N ILE R 333 " pdb=" C ILE R 333 " pdb=" CA ILE R 333 " pdb=" CB ILE R 333 " ideal model delta harmonic sigma weight residual 123.40 132.76 -9.36 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 5314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1207 0.058 - 0.117: 156 0.117 - 0.175: 22 0.175 - 0.233: 4 0.233 - 0.291: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA VAL S 5 " pdb=" N VAL S 5 " pdb=" C VAL S 5 " pdb=" CB VAL S 5 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ILE R 333 " pdb=" N ILE R 333 " pdb=" C ILE R 333 " pdb=" CB ILE R 333 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE R 340 " pdb=" N ILE R 340 " pdb=" C ILE R 340 " pdb=" CB ILE R 340 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 1388 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 185 " -0.030 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C ILE R 185 " 0.092 2.00e-02 2.50e+03 pdb=" O ILE R 185 " -0.033 2.00e-02 2.50e+03 pdb=" N TYR R 186 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 SWO R 401 " -0.003 2.00e-02 2.50e+03 2.26e-02 1.15e+01 pdb=" C02 SWO R 401 " 0.017 2.00e-02 2.50e+03 pdb=" C03 SWO R 401 " -0.033 2.00e-02 2.50e+03 pdb=" C05 SWO R 401 " 0.007 2.00e-02 2.50e+03 pdb=" C06 SWO R 401 " -0.001 2.00e-02 2.50e+03 pdb=" C07 SWO R 401 " -0.012 2.00e-02 2.50e+03 pdb=" N04 SWO R 401 " 0.050 2.00e-02 2.50e+03 pdb=" O16 SWO R 401 " -0.003 2.00e-02 2.50e+03 pdb=" O17 SWO R 401 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 175 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLY R 175 " -0.055 2.00e-02 2.50e+03 pdb=" O GLY R 175 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG R 176 " 0.018 2.00e-02 2.50e+03 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1360 2.76 - 3.29: 8581 3.29 - 3.83: 14329 3.83 - 4.36: 17107 4.36 - 4.90: 30885 Nonbonded interactions: 72262 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.274 3.040 nonbonded pdb=" O ALA R 31 " pdb=" OG1 THR R 35 " model vdw 2.275 3.040 nonbonded pdb=" ND1 HIS S 167 " pdb=" OD1 ASN S 169 " model vdw 2.289 3.120 nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.290 3.040 ... (remaining 72257 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: 0.700 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.006 0.371 8987 Z= 0.312 Angle : 0.787 45.307 12180 Z= 0.437 Chirality : 0.043 0.291 1391 Planarity : 0.005 0.078 1533 Dihedral : 15.950 88.596 3202 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.74 % Allowed : 17.11 % Favored : 82.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % 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: 0.90 (0.26), residues: 1111 helix: 2.32 (0.28), residues: 368 sheet: -0.11 (0.32), residues: 292 loop : -0.30 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 156 HIS 0.002 0.001 HIS A 322 PHE 0.009 0.001 PHE S 80 TYR 0.009 0.001 TYR S 190 ARG 0.010 0.000 ARG R 54 Details of bonding type rmsd hydrogen bonds : bond 0.17794 ( 445) hydrogen bonds : angle 7.10602 ( 1239) SS BOND : bond 0.22001 ( 3) SS BOND : angle 20.61707 ( 6) covalent geometry : bond 0.00407 ( 8984) covalent geometry : angle 0.64043 (12174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.995 Fit side-chains REVERT: R 88 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6562 (p) REVERT: R 313 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: R 316 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7876 (tptt) REVERT: R 349 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.5572 (mtp180) REVERT: A 255 ASN cc_start: 0.8380 (m-40) cc_final: 0.8161 (m110) REVERT: B 323 ASP cc_start: 0.8538 (p0) cc_final: 0.8317 (p0) REVERT: S 179 GLN cc_start: 0.8824 (tt0) cc_final: 0.8621 (tt0) outliers start: 7 outliers final: 0 residues processed: 119 average time/residue: 0.2409 time to fit residues: 38.4545 Evaluate side-chains 109 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 313 GLU Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 349 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 352 HIS A 269 ASN B 75 GLN B 125 ASN B 340 ASN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.182155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143193 restraints weight = 9752.655| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.11 r_work: 0.3495 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8987 Z= 0.132 Angle : 0.561 9.840 12180 Z= 0.293 Chirality : 0.042 0.157 1391 Planarity : 0.004 0.046 1533 Dihedral : 5.755 58.468 1245 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.06 % Allowed : 16.26 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.95 (0.26), residues: 1111 helix: 2.33 (0.27), residues: 372 sheet: -0.18 (0.31), residues: 279 loop : -0.19 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS R 83 PHE 0.013 0.001 PHE S 68 TYR 0.011 0.001 TYR R 370 ARG 0.004 0.000 ARG R 172 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 445) hydrogen bonds : angle 5.11307 ( 1239) SS BOND : bond 0.00607 ( 3) SS BOND : angle 0.99218 ( 6) covalent geometry : bond 0.00303 ( 8984) covalent geometry : angle 0.56058 (12174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.916 Fit side-chains REVERT: R 88 THR cc_start: 0.6631 (OUTLIER) cc_final: 0.6332 (p) REVERT: R 316 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7334 (tptt) REVERT: A 20 ASP cc_start: 0.8694 (t0) cc_final: 0.8370 (m-30) REVERT: A 255 ASN cc_start: 0.8221 (m-40) cc_final: 0.7961 (m110) REVERT: A 306 GLN cc_start: 0.7065 (mp10) cc_final: 0.6810 (mm110) REVERT: B 237 ASN cc_start: 0.8448 (t0) cc_final: 0.8197 (t0) REVERT: S 113 GLN cc_start: 0.8672 (tp40) cc_final: 0.8427 (mm-40) REVERT: S 159 CYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8194 (t) REVERT: S 179 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: S 204 SER cc_start: 0.8988 (t) cc_final: 0.8513 (p) outliers start: 29 outliers final: 14 residues processed: 139 average time/residue: 0.1967 time to fit residues: 38.6006 Evaluate side-chains 132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain G residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.177986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137710 restraints weight = 9933.384| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.11 r_work: 0.3428 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8987 Z= 0.168 Angle : 0.564 8.046 12180 Z= 0.294 Chirality : 0.043 0.143 1391 Planarity : 0.004 0.043 1533 Dihedral : 5.117 57.088 1238 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.48 % Allowed : 16.58 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1111 helix: 2.07 (0.27), residues: 371 sheet: -0.40 (0.30), residues: 280 loop : -0.29 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS A 322 PHE 0.015 0.002 PHE B 235 TYR 0.017 0.001 TYR B 59 ARG 0.004 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 445) hydrogen bonds : angle 4.91361 ( 1239) SS BOND : bond 0.00396 ( 3) SS BOND : angle 1.71629 ( 6) covalent geometry : bond 0.00406 ( 8984) covalent geometry : angle 0.56240 (12174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.949 Fit side-chains REVERT: R 316 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7381 (ttmt) REVERT: A 8 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7561 (pt0) REVERT: A 255 ASN cc_start: 0.8241 (m-40) cc_final: 0.7992 (m110) REVERT: A 306 GLN cc_start: 0.7130 (mp10) cc_final: 0.6823 (mm110) REVERT: B 57 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8457 (mttp) REVERT: S 38 ARG cc_start: 0.8523 (ptt180) cc_final: 0.8313 (ptt90) REVERT: S 204 SER cc_start: 0.9041 (t) cc_final: 0.8600 (p) outliers start: 33 outliers final: 19 residues processed: 134 average time/residue: 0.2032 time to fit residues: 37.8170 Evaluate side-chains 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain G residue 9 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.176091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136237 restraints weight = 9925.706| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.03 r_work: 0.3412 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8987 Z= 0.204 Angle : 0.584 7.741 12180 Z= 0.305 Chirality : 0.044 0.142 1391 Planarity : 0.004 0.040 1533 Dihedral : 5.196 59.662 1237 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.22 % Allowed : 17.21 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.44 (0.25), residues: 1111 helix: 1.94 (0.27), residues: 367 sheet: -0.59 (0.30), residues: 279 loop : -0.39 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.004 0.001 HIS A 213 PHE 0.016 0.002 PHE B 235 TYR 0.017 0.002 TYR B 59 ARG 0.003 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 445) hydrogen bonds : angle 4.90973 ( 1239) SS BOND : bond 0.00733 ( 3) SS BOND : angle 1.23856 ( 6) covalent geometry : bond 0.00496 ( 8984) covalent geometry : angle 0.58361 (12174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.918 Fit side-chains REVERT: R 88 THR cc_start: 0.7204 (p) cc_final: 0.6937 (p) REVERT: R 316 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7459 (ttmt) REVERT: R 326 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7335 (tp) REVERT: A 8 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: A 255 ASN cc_start: 0.8323 (m-40) cc_final: 0.8100 (m110) REVERT: B 57 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8479 (mttp) REVERT: S 38 ARG cc_start: 0.8497 (ptt180) cc_final: 0.8270 (ptt90) REVERT: S 193 SER cc_start: 0.8171 (t) cc_final: 0.7966 (t) REVERT: S 204 SER cc_start: 0.8988 (t) cc_final: 0.8517 (p) outliers start: 40 outliers final: 23 residues processed: 143 average time/residue: 0.2228 time to fit residues: 43.5909 Evaluate side-chains 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139648 restraints weight = 9767.296| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.02 r_work: 0.3456 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8987 Z= 0.117 Angle : 0.524 7.925 12180 Z= 0.269 Chirality : 0.041 0.134 1391 Planarity : 0.004 0.038 1533 Dihedral : 4.966 58.507 1237 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.48 % Allowed : 18.80 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.52 (0.26), residues: 1111 helix: 2.09 (0.28), residues: 368 sheet: -0.61 (0.30), residues: 276 loop : -0.39 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS A 213 PHE 0.011 0.001 PHE S 27 TYR 0.010 0.001 TYR S 190 ARG 0.007 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 445) hydrogen bonds : angle 4.71564 ( 1239) SS BOND : bond 0.00321 ( 3) SS BOND : angle 1.11458 ( 6) covalent geometry : bond 0.00273 ( 8984) covalent geometry : angle 0.52349 (12174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.984 Fit side-chains REVERT: R 88 THR cc_start: 0.6967 (p) cc_final: 0.6721 (p) REVERT: R 316 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7450 (ttmt) REVERT: R 326 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7168 (mt) REVERT: A 8 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7290 (pt0) REVERT: A 20 ASP cc_start: 0.8656 (t70) cc_final: 0.8313 (m-30) REVERT: A 255 ASN cc_start: 0.8260 (m-40) cc_final: 0.7994 (m110) REVERT: A 306 GLN cc_start: 0.7092 (mp10) cc_final: 0.6792 (mm110) REVERT: B 57 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8314 (mttp) REVERT: B 130 GLU cc_start: 0.8889 (mp0) cc_final: 0.8659 (mp0) REVERT: S 38 ARG cc_start: 0.8504 (ptt180) cc_final: 0.8261 (ptt90) REVERT: S 58 ILE cc_start: 0.8981 (mt) cc_final: 0.8750 (mt) REVERT: S 204 SER cc_start: 0.9004 (t) cc_final: 0.8535 (p) outliers start: 33 outliers final: 23 residues processed: 138 average time/residue: 0.2133 time to fit residues: 40.7164 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139322 restraints weight = 9792.556| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.09 r_work: 0.3445 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8987 Z= 0.130 Angle : 0.531 8.286 12180 Z= 0.272 Chirality : 0.041 0.134 1391 Planarity : 0.004 0.035 1533 Dihedral : 4.903 57.707 1237 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.12 % Allowed : 18.37 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.52 (0.25), residues: 1111 helix: 2.09 (0.28), residues: 371 sheet: -0.63 (0.31), residues: 266 loop : -0.40 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS A 213 PHE 0.011 0.001 PHE B 235 TYR 0.011 0.001 TYR S 190 ARG 0.010 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 445) hydrogen bonds : angle 4.64194 ( 1239) SS BOND : bond 0.00300 ( 3) SS BOND : angle 1.10624 ( 6) covalent geometry : bond 0.00308 ( 8984) covalent geometry : angle 0.53014 (12174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.952 Fit side-chains REVERT: R 316 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7441 (ttmt) REVERT: R 326 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7176 (mt) REVERT: A 8 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: A 255 ASN cc_start: 0.8232 (m-40) cc_final: 0.7918 (m110) REVERT: A 306 GLN cc_start: 0.7066 (mp10) cc_final: 0.6767 (mm110) REVERT: B 19 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8157 (ttp80) REVERT: S 58 ILE cc_start: 0.8990 (mt) cc_final: 0.8757 (mt) REVERT: S 204 SER cc_start: 0.8996 (t) cc_final: 0.8293 (p) outliers start: 39 outliers final: 30 residues processed: 136 average time/residue: 0.2077 time to fit residues: 39.4296 Evaluate side-chains 139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.175377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134062 restraints weight = 9911.894| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.08 r_work: 0.3351 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8987 Z= 0.197 Angle : 0.578 9.189 12180 Z= 0.299 Chirality : 0.043 0.137 1391 Planarity : 0.004 0.034 1533 Dihedral : 5.063 59.582 1237 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.54 % Allowed : 18.59 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.30 (0.25), residues: 1111 helix: 1.92 (0.28), residues: 368 sheet: -0.74 (0.30), residues: 291 loop : -0.49 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.004 0.001 HIS A 213 PHE 0.017 0.002 PHE B 235 TYR 0.016 0.001 TYR B 59 ARG 0.008 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 445) hydrogen bonds : angle 4.80631 ( 1239) SS BOND : bond 0.00406 ( 3) SS BOND : angle 1.41057 ( 6) covalent geometry : bond 0.00483 ( 8984) covalent geometry : angle 0.57767 (12174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.928 Fit side-chains REVERT: R 203 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.6820 (mtp180) REVERT: R 316 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7485 (ttmt) REVERT: R 326 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7167 (mt) REVERT: A 8 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: A 20 ASP cc_start: 0.8668 (t70) cc_final: 0.8342 (m-30) REVERT: A 255 ASN cc_start: 0.8315 (m-40) cc_final: 0.8090 (m110) REVERT: A 306 GLN cc_start: 0.7081 (mp10) cc_final: 0.6712 (mm110) REVERT: B 13 GLN cc_start: 0.7478 (mp10) cc_final: 0.7185 (pt0) REVERT: B 19 ARG cc_start: 0.8702 (ttp80) cc_final: 0.8107 (ttp80) REVERT: S 204 SER cc_start: 0.8992 (t) cc_final: 0.8738 (t) outliers start: 43 outliers final: 29 residues processed: 149 average time/residue: 0.2311 time to fit residues: 46.4604 Evaluate side-chains 140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain G residue 9 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 2.9990 chunk 109 optimal weight: 0.0050 chunk 36 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.180286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140064 restraints weight = 9969.079| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.00 r_work: 0.3475 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8987 Z= 0.106 Angle : 0.518 9.438 12180 Z= 0.263 Chirality : 0.040 0.133 1391 Planarity : 0.003 0.035 1533 Dihedral : 4.786 58.977 1237 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.38 % Allowed : 19.85 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.50 (0.26), residues: 1111 helix: 2.09 (0.28), residues: 371 sheet: -0.60 (0.31), residues: 280 loop : -0.45 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS A 213 PHE 0.010 0.001 PHE R 101 TYR 0.010 0.001 TYR S 190 ARG 0.006 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 445) hydrogen bonds : angle 4.60320 ( 1239) SS BOND : bond 0.00305 ( 3) SS BOND : angle 1.35633 ( 6) covalent geometry : bond 0.00242 ( 8984) covalent geometry : angle 0.51767 (12174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.980 Fit side-chains REVERT: R 316 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7385 (ttmt) REVERT: R 326 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7094 (mt) REVERT: A 8 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7226 (pt0) REVERT: A 20 ASP cc_start: 0.8620 (t70) cc_final: 0.8287 (m-30) REVERT: A 255 ASN cc_start: 0.8071 (m-40) cc_final: 0.7779 (m110) REVERT: A 306 GLN cc_start: 0.6866 (mp10) cc_final: 0.6599 (mm110) REVERT: A 348 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7793 (mp) REVERT: B 13 GLN cc_start: 0.7423 (mp10) cc_final: 0.7148 (pt0) REVERT: B 19 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8075 (ttp80) REVERT: S 58 ILE cc_start: 0.8886 (mt) cc_final: 0.8634 (mt) REVERT: S 204 SER cc_start: 0.8945 (t) cc_final: 0.8673 (t) outliers start: 32 outliers final: 24 residues processed: 130 average time/residue: 0.2034 time to fit residues: 37.1927 Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 0.0770 chunk 107 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.181039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140987 restraints weight = 9916.556| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.05 r_work: 0.3467 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8987 Z= 0.109 Angle : 0.518 10.192 12180 Z= 0.263 Chirality : 0.040 0.134 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.675 57.492 1237 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.17 % Allowed : 19.96 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.59 (0.26), residues: 1111 helix: 2.17 (0.28), residues: 373 sheet: -0.55 (0.31), residues: 280 loop : -0.40 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS A 213 PHE 0.009 0.001 PHE S 27 TYR 0.010 0.001 TYR S 190 ARG 0.006 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 445) hydrogen bonds : angle 4.51384 ( 1239) SS BOND : bond 0.00298 ( 3) SS BOND : angle 1.22440 ( 6) covalent geometry : bond 0.00251 ( 8984) covalent geometry : angle 0.51700 (12174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.046 Fit side-chains REVERT: R 316 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7448 (ttmt) REVERT: R 326 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7176 (mt) REVERT: A 8 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: A 20 ASP cc_start: 0.8622 (t70) cc_final: 0.8304 (m-30) REVERT: A 255 ASN cc_start: 0.8042 (m-40) cc_final: 0.7710 (m110) REVERT: A 348 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7913 (mp) REVERT: B 13 GLN cc_start: 0.7526 (mp10) cc_final: 0.7201 (pt0) REVERT: B 19 ARG cc_start: 0.8710 (ttp80) cc_final: 0.8117 (ttp80) REVERT: S 11 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8225 (tt) REVERT: S 204 SER cc_start: 0.8934 (t) cc_final: 0.8289 (p) outliers start: 30 outliers final: 24 residues processed: 130 average time/residue: 0.2161 time to fit residues: 39.0806 Evaluate side-chains 130 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 98 optimal weight: 0.0050 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 269 ASN S 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.183750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143284 restraints weight = 9959.065| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.03 r_work: 0.3512 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8987 Z= 0.094 Angle : 0.507 10.653 12180 Z= 0.258 Chirality : 0.039 0.144 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.550 56.378 1237 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.85 % Allowed : 21.54 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 373 sheet: -0.48 (0.31), residues: 280 loop : -0.29 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.003 0.000 HIS A 213 PHE 0.008 0.001 PHE S 27 TYR 0.009 0.001 TYR S 190 ARG 0.006 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.02844 ( 445) hydrogen bonds : angle 4.40272 ( 1239) SS BOND : bond 0.00282 ( 3) SS BOND : angle 0.95824 ( 6) covalent geometry : bond 0.00207 ( 8984) covalent geometry : angle 0.50710 (12174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.937 Fit side-chains REVERT: R 183 MET cc_start: 0.7836 (mtm) cc_final: 0.7592 (mtt) REVERT: R 316 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7461 (ttmt) REVERT: R 326 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7166 (mt) REVERT: A 20 ASP cc_start: 0.8589 (t70) cc_final: 0.8273 (m-30) REVERT: A 348 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7888 (mp) REVERT: B 13 GLN cc_start: 0.7533 (mp10) cc_final: 0.7210 (pt0) REVERT: B 19 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8197 (ttp80) REVERT: S 11 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8256 (tt) REVERT: S 204 SER cc_start: 0.8866 (t) cc_final: 0.8225 (p) outliers start: 27 outliers final: 23 residues processed: 125 average time/residue: 0.2098 time to fit residues: 36.3853 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 316 LYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.182947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143294 restraints weight = 9916.487| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.97 r_work: 0.3507 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8987 Z= 0.129 Angle : 0.879 59.197 12180 Z= 0.507 Chirality : 0.043 0.584 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.556 56.376 1237 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.06 % Allowed : 21.01 % Favored : 75.92 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 373 sheet: -0.47 (0.31), residues: 280 loop : -0.29 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 47 HIS 0.003 0.000 HIS A 213 PHE 0.008 0.001 PHE S 27 TYR 0.010 0.001 TYR S 190 ARG 0.005 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.02873 ( 445) hydrogen bonds : angle 4.40144 ( 1239) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.86695 ( 6) covalent geometry : bond 0.00288 ( 8984) covalent geometry : angle 0.87927 (12174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5092.14 seconds wall clock time: 88 minutes 39.57 seconds (5319.57 seconds total)