Starting phenix.real_space_refine on Thu Mar 13 05:01:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j19_35914/03_2025/8j19_35914_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j19_35914/03_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_35914/03_2025/8j19_35914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j19_35914/03_2025/8j19_35914.map" model { file = "/net/cci-nas-00/data/ceres_data/8j19_35914/03_2025/8j19_35914_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j19_35914/03_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-5624/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: 5.52, per 1000 atoms: 0.63 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 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: 1.05 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: 2.65 Time building geometry restraints manager: 2.73 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: 0.800 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.720 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.120 ------------------------------------------------------------------------------- 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 : 0.004 0.108 8984 Z= 0.273 Angle : 0.640 12.115 12174 Z= 0.379 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 *********************** 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 : 0.944 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: 0.2498 time to fit residues: 39.8917 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 : 0.927 ------------------------------------------------------------------------------- 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 = 0.143194 restraints weight = 9752.656| |-----------------------------------------------------------------------------| 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: 4.42 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 8984 Z= 0.194 Angle : 0.561 9.840 12174 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 *********************** 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 : 0.880 Fit side-chains REVERT: R 88 THR cc_start: 0.6634 (OUTLIER) cc_final: 0.6336 (p) REVERT: R 316 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7335 (tptt) REVERT: A 20 ASP cc_start: 0.8692 (t0) cc_final: 0.8369 (m-30) REVERT: A 255 ASN cc_start: 0.8219 (m-40) cc_final: 0.7959 (m110) REVERT: A 306 GLN cc_start: 0.7058 (mp10) cc_final: 0.6801 (mm110) REVERT: B 237 ASN cc_start: 0.8448 (t0) cc_final: 0.8199 (t0) REVERT: S 113 GLN cc_start: 0.8671 (tp40) cc_final: 0.8426 (mm-40) REVERT: S 159 CYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8194 (t) REVERT: S 179 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: S 204 SER cc_start: 0.8986 (t) cc_final: 0.8510 (p) outliers start: 29 outliers final: 14 residues processed: 139 average time/residue: 0.1975 time to fit residues: 38.6502 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 : 0.895 ------------------------------------------------------------------------------- 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: 0.1980 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 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: 0.7980 chunk 76 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 S 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139311 restraints weight = 9982.815| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.07 r_work: 0.3443 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8984 Z= 0.232 Angle : 0.550 7.713 12174 Z= 0.287 Chirality : 0.042 0.141 1391 Planarity : 0.004 0.042 1533 Dihedral : 5.079 57.216 1238 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.38 % Allowed : 16.37 % Favored : 80.25 % 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: 0.70 (0.26), residues: 1111 helix: 2.11 (0.27), residues: 371 sheet: -0.37 (0.30), residues: 280 loop : -0.28 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS A 322 PHE 0.014 0.001 PHE B 235 TYR 0.016 0.001 TYR B 59 ARG 0.004 0.000 ARG S 160 *********************** 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 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.955 Fit side-chains REVERT: R 316 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7369 (ttmt) REVERT: A 8 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: A 20 ASP cc_start: 0.8751 (t0) cc_final: 0.8411 (m-30) REVERT: A 255 ASN cc_start: 0.8213 (m-40) cc_final: 0.7957 (m110) REVERT: A 306 GLN cc_start: 0.7063 (mp10) cc_final: 0.6777 (mm110) REVERT: B 57 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8438 (mttp) REVERT: S 38 ARG cc_start: 0.8509 (ptt180) cc_final: 0.8304 (ptt90) REVERT: S 204 SER cc_start: 0.9038 (t) cc_final: 0.8611 (p) outliers start: 32 outliers final: 19 residues processed: 136 average time/residue: 0.1995 time to fit residues: 38.5420 Evaluate side-chains 125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 A residue 8 GLU Chi-restraints excluded: chain A residue 28 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: 0.8980 chunk 91 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140823 restraints weight = 9816.392| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.97 r_work: 0.3492 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8984 Z= 0.186 Angle : 0.522 8.601 12174 Z= 0.271 Chirality : 0.041 0.136 1391 Planarity : 0.004 0.039 1533 Dihedral : 4.954 58.893 1237 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.91 % Allowed : 17.21 % Favored : 78.88 % 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: 0.72 (0.26), residues: 1111 helix: 2.16 (0.28), residues: 371 sheet: -0.38 (0.30), residues: 273 loop : -0.27 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 B 59 ARG 0.005 0.000 ARG S 160 *********************** 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 143 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.849 Fit side-chains REVERT: R 88 THR cc_start: 0.7030 (p) cc_final: 0.6782 (p) REVERT: R 316 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7405 (ttmt) REVERT: R 326 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7165 (mt) REVERT: A 8 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: A 20 ASP cc_start: 0.8670 (t0) cc_final: 0.8340 (m-30) REVERT: A 255 ASN cc_start: 0.8154 (m-40) cc_final: 0.7872 (m110) REVERT: A 306 GLN cc_start: 0.7034 (mp10) cc_final: 0.6829 (mm110) REVERT: B 57 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8309 (mttp) REVERT: S 38 ARG cc_start: 0.8461 (ptt180) cc_final: 0.8226 (ptt90) REVERT: S 204 SER cc_start: 0.9007 (t) cc_final: 0.8534 (p) outliers start: 37 outliers final: 23 residues processed: 134 average time/residue: 0.1972 time to fit residues: 37.4723 Evaluate side-chains 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.181737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143151 restraints weight = 9687.319| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.06 r_work: 0.3497 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8984 Z= 0.158 Angle : 0.508 7.591 12174 Z= 0.261 Chirality : 0.040 0.133 1391 Planarity : 0.003 0.036 1533 Dihedral : 4.813 59.050 1237 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.48 % Allowed : 17.85 % Favored : 78.67 % 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: 0.75 (0.26), residues: 1111 helix: 2.23 (0.28), residues: 374 sheet: -0.47 (0.30), residues: 282 loop : -0.24 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.003 0.001 HIS A 213 PHE 0.010 0.001 PHE S 27 TYR 0.010 0.001 TYR B 111 ARG 0.003 0.000 ARG S 160 *********************** 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 138 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.887 Fit side-chains REVERT: R 316 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7405 (ttmt) REVERT: R 326 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7148 (mt) REVERT: A 8 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7208 (mt-10) REVERT: A 255 ASN cc_start: 0.8033 (m-40) cc_final: 0.7670 (m110) REVERT: A 348 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7899 (mp) REVERT: S 38 ARG cc_start: 0.8494 (ptt180) cc_final: 0.8234 (ptt90) REVERT: S 204 SER cc_start: 0.8984 (t) cc_final: 0.8247 (p) REVERT: S 215 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7718 (p) outliers start: 33 outliers final: 24 residues processed: 129 average time/residue: 0.2116 time to fit residues: 37.7588 Evaluate side-chains 128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 186 GLU Chi-restraints excluded: chain A residue 256 ASN 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 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 25 SER 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 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: 3.9990 chunk 108 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 50 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 98 optimal weight: 0.0000 chunk 73 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.3542 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.184020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144766 restraints weight = 9684.679| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.97 r_work: 0.3526 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8984 Z= 0.128 Angle : 0.496 8.429 12174 Z= 0.254 Chirality : 0.039 0.131 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.691 58.585 1237 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.27 % Allowed : 18.27 % Favored : 78.46 % 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: 0.87 (0.26), residues: 1111 helix: 2.36 (0.28), residues: 373 sheet: -0.40 (0.30), residues: 282 loop : -0.19 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.003 0.000 HIS A 213 PHE 0.009 0.001 PHE S 27 TYR 0.009 0.001 TYR S 190 ARG 0.007 0.000 ARG A 24 *********************** 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 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.882 Fit side-chains REVERT: R 68 LEU cc_start: 0.6849 (tt) cc_final: 0.5777 (tt) REVERT: R 82 LEU cc_start: 0.6951 (tp) cc_final: 0.6643 (tp) REVERT: R 316 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7403 (ttmt) REVERT: R 326 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7132 (mt) REVERT: A 8 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: A 20 ASP cc_start: 0.8561 (t70) cc_final: 0.8229 (m-30) REVERT: A 255 ASN cc_start: 0.7924 (m-40) cc_final: 0.7545 (m110) REVERT: B 19 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8251 (ttp80) REVERT: S 65 LYS cc_start: 0.8304 (tttm) cc_final: 0.7966 (tttm) REVERT: S 204 SER cc_start: 0.8949 (t) cc_final: 0.8235 (p) outliers start: 31 outliers final: 23 residues processed: 135 average time/residue: 0.2022 time to fit residues: 38.1349 Evaluate side-chains 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL 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 186 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 161 SER 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 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 93 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: 0.5980 chunk 92 optimal weight: 0.0970 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.181629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143178 restraints weight = 9839.410| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.02 r_work: 0.3494 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8984 Z= 0.172 Angle : 0.514 9.522 12174 Z= 0.262 Chirality : 0.040 0.133 1391 Planarity : 0.003 0.033 1533 Dihedral : 4.703 58.232 1237 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.38 % Allowed : 19.11 % 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: 0.80 (0.26), residues: 1111 helix: 2.27 (0.28), residues: 376 sheet: -0.40 (0.31), residues: 276 loop : -0.26 (0.29), residues: 459 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 0.010 0.001 PHE S 80 TYR 0.011 0.001 TYR S 190 ARG 0.006 0.000 ARG A 24 *********************** 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 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.974 Fit side-chains REVERT: R 82 LEU cc_start: 0.6961 (tp) cc_final: 0.6653 (tp) REVERT: R 316 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7378 (ttmt) REVERT: R 326 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7117 (mt) REVERT: A 8 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7297 (pt0) REVERT: A 20 ASP cc_start: 0.8570 (t70) cc_final: 0.8230 (m-30) REVERT: A 255 ASN cc_start: 0.7971 (m-40) cc_final: 0.7557 (m110) REVERT: A 348 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7882 (mp) REVERT: B 19 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8211 (ttp80) REVERT: S 204 SER cc_start: 0.8931 (t) cc_final: 0.8652 (t) outliers start: 32 outliers final: 25 residues processed: 126 average time/residue: 0.2016 time to fit residues: 36.1189 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 : 0.933 ------------------------------------------------------------------------------- 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 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 186 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 102 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.183737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.145218 restraints weight = 9950.241| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.17 r_work: 0.3519 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8984 Z= 0.140 Angle : 0.497 9.490 12174 Z= 0.253 Chirality : 0.040 0.132 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.639 59.105 1237 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.27 % Allowed : 19.43 % Favored : 77.30 % 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: 0.83 (0.26), residues: 1111 helix: 2.33 (0.27), residues: 374 sheet: -0.43 (0.31), residues: 273 loop : -0.24 (0.29), residues: 464 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 0.009 0.001 PHE S 27 TYR 0.010 0.001 TYR S 190 ARG 0.004 0.000 ARG A 24 *********************** 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 134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.899 Fit side-chains REVERT: R 82 LEU cc_start: 0.6944 (tp) cc_final: 0.6634 (tp) REVERT: R 316 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7362 (ttmt) REVERT: R 320 MET cc_start: 0.7294 (tpt) cc_final: 0.7023 (tpp) REVERT: R 326 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7136 (mt) REVERT: A 8 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: A 20 ASP cc_start: 0.8548 (t70) cc_final: 0.8222 (m-30) REVERT: A 348 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7890 (mp) REVERT: B 19 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8311 (ttp80) REVERT: S 204 SER cc_start: 0.8905 (t) cc_final: 0.8632 (t) outliers start: 31 outliers final: 25 residues processed: 126 average time/residue: 0.2176 time to fit residues: 38.0774 Evaluate side-chains 128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 186 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 217 MET 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 93 MET Chi-restraints excluded: chain S residue 99 SER 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: 0.8980 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.181404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141468 restraints weight = 9879.380| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.98 r_work: 0.3489 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8984 Z= 0.177 Angle : 0.520 10.010 12174 Z= 0.263 Chirality : 0.040 0.135 1391 Planarity : 0.003 0.033 1533 Dihedral : 4.673 59.975 1237 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.59 % Allowed : 19.22 % Favored : 77.19 % 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: 0.77 (0.26), residues: 1111 helix: 2.26 (0.27), residues: 376 sheet: -0.44 (0.31), residues: 278 loop : -0.27 (0.29), residues: 457 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 0.010 0.001 PHE B 235 TYR 0.010 0.001 TYR S 190 ARG 0.004 0.000 ARG A 24 *********************** 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 139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.965 Fit side-chains REVERT: R 88 THR cc_start: 0.6797 (OUTLIER) cc_final: 0.6573 (p) REVERT: R 316 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7413 (ttmt) REVERT: R 320 MET cc_start: 0.7378 (tpt) cc_final: 0.7170 (tpp) REVERT: R 326 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7129 (mt) REVERT: A 8 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: A 20 ASP cc_start: 0.8586 (t70) cc_final: 0.8276 (m-30) REVERT: A 255 ASN cc_start: 0.7941 (m-40) cc_final: 0.7552 (m110) REVERT: A 348 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7946 (mp) REVERT: B 19 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8305 (ttp80) REVERT: S 204 SER cc_start: 0.8899 (t) cc_final: 0.8620 (t) outliers start: 34 outliers final: 27 residues processed: 131 average time/residue: 0.2260 time to fit residues: 41.1176 Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 88 THR 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 186 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 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 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 99 SER 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: 3.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 41 optimal weight: 0.0030 chunk 98 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.182952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.143087 restraints weight = 9900.132| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.99 r_work: 0.3508 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8984 Z= 0.148 Angle : 0.517 10.558 12174 Z= 0.260 Chirality : 0.040 0.132 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.611 58.844 1237 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.27 % Allowed : 19.64 % Favored : 77.09 % 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: 0.83 (0.26), residues: 1111 helix: 2.29 (0.27), residues: 377 sheet: -0.42 (0.31), residues: 278 loop : -0.22 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 360 HIS 0.003 0.001 HIS A 213 PHE 0.008 0.001 PHE S 27 TYR 0.010 0.001 TYR S 190 ARG 0.004 0.000 ARG A 24 ********************** 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: 31 poor density : 100 time to evaluate : 0.891 Fit side-chains REVERT: R 88 THR cc_start: 0.6724 (OUTLIER) cc_final: 0.6500 (p) REVERT: R 316 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7413 (ttmt) REVERT: R 326 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7120 (mt) REVERT: A 8 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: A 18 MET cc_start: 0.8358 (ttm) cc_final: 0.8144 (mtp) REVERT: A 20 ASP cc_start: 0.8557 (t70) cc_final: 0.8236 (m-30) REVERT: A 348 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7892 (mp) REVERT: B 19 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8301 (ttp80) REVERT: S 204 SER cc_start: 0.8845 (t) cc_final: 0.8587 (t) outliers start: 31 outliers final: 26 residues processed: 123 average time/residue: 0.2040 time to fit residues: 35.1611 Evaluate side-chains 128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL 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 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 186 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 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 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 99 SER 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: 6.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 77 optimal weight: 0.0470 chunk 92 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143776 restraints weight = 9930.403| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.98 r_work: 0.3516 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8984 Z= 0.144 Angle : 0.520 10.488 12174 Z= 0.262 Chirality : 0.040 0.132 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.547 57.515 1237 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.59 % Allowed : 19.43 % Favored : 76.98 % 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: 0.86 (0.26), residues: 1111 helix: 2.33 (0.27), residues: 377 sheet: -0.40 (0.31), residues: 278 loop : -0.21 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 360 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 0.004 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5318.16 seconds wall clock time: 92 minutes 51.67 seconds (5571.67 seconds total)