Starting phenix.real_space_refine on Thu Feb 13 03:21:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j19_35914/02_2025/8j19_35914_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j19_35914/02_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_35914/02_2025/8j19_35914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j19_35914/02_2025/8j19_35914.map" model { file = "/net/cci-nas-00/data/ceres_data/8j19_35914/02_2025/8j19_35914_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j19_35914/02_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-5592/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: 5.73, per 1000 atoms: 0.65 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: 1.06 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: 2.77 Time building geometry restraints manager: 2.66 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.200 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- 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 : 0.942 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: 0.2530 time to fit residues: 40.4201 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 : 0.950 ------------------------------------------------------------------------------- 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 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 : 0.911 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: 0.2239 time to fit residues: 44.0106 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 : 1.062 ------------------------------------------------------------------------------- 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 8984 Z= 0.260 Angle : 0.562 8.046 12174 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 *********************** 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 : 0.895 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: 0.2104 time to fit residues: 39.1075 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 : 0.987 ------------------------------------------------------------------------------- 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 8984 Z= 0.319 Angle : 0.584 7.741 12174 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 *********************** 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 : 0.912 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: 0.2221 time to fit residues: 43.5548 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 : 0.912 ------------------------------------------------------------------------------- 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 8984 Z= 0.175 Angle : 0.523 7.925 12174 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 *********************** 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 : 0.901 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: 0.2130 time to fit residues: 40.7767 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 : 0.965 ------------------------------------------------------------------------------- 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 8984 Z= 0.197 Angle : 0.530 8.286 12174 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 *********************** 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 : 0.922 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: 0.2098 time to fit residues: 39.7696 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 : 0.921 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.173781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133165 restraints weight = 9939.160| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.04 r_work: 0.3336 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8984 Z= 0.376 Angle : 0.611 9.257 12174 Z= 0.317 Chirality : 0.045 0.140 1391 Planarity : 0.004 0.035 1533 Dihedral : 5.190 59.806 1237 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.54 % Allowed : 18.90 % Favored : 76.56 % 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: 0.18 (0.25), residues: 1111 helix: 1.79 (0.27), residues: 367 sheet: -0.73 (0.30), residues: 287 loop : -0.61 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.004 0.001 HIS A 213 PHE 0.019 0.002 PHE B 235 TYR 0.018 0.002 TYR B 59 ARG 0.008 0.001 ARG S 160 *********************** 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 160 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.924 Fit side-chains REVERT: R 203 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.6853 (mtp-110) REVERT: R 316 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7471 (ttmt) REVERT: R 326 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7382 (tp) REVERT: A 8 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7824 (pt0) REVERT: A 255 ASN cc_start: 0.8388 (m-40) cc_final: 0.8181 (m110) REVERT: A 306 GLN cc_start: 0.7155 (mp10) cc_final: 0.6767 (mm110) REVERT: B 13 GLN cc_start: 0.7539 (mp10) cc_final: 0.7231 (pt0) REVERT: B 19 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8098 (ttp80) REVERT: S 204 SER cc_start: 0.8999 (t) cc_final: 0.8755 (t) outliers start: 43 outliers final: 29 residues processed: 150 average time/residue: 0.2252 time to fit residues: 45.9192 Evaluate side-chains 141 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 91 THR 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: 0.9980 chunk 36 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 0.0070 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.180193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140240 restraints weight = 9967.634| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.98 r_work: 0.3477 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8984 Z= 0.157 Angle : 0.521 9.146 12174 Z= 0.265 Chirality : 0.040 0.133 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.815 58.361 1237 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.17 % Allowed : 20.27 % Favored : 76.56 % 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: 0.47 (0.26), residues: 1111 helix: 2.05 (0.28), residues: 369 sheet: -0.53 (0.31), residues: 277 loop : -0.50 (0.28), residues: 465 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 0.012 0.001 PHE R 101 TYR 0.009 0.001 TYR S 190 ARG 0.006 0.000 ARG S 160 *********************** 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 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.963 Fit side-chains REVERT: R 316 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7396 (ttmt) REVERT: R 326 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7096 (mt) REVERT: A 8 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7197 (pt0) REVERT: A 255 ASN cc_start: 0.8185 (m-40) cc_final: 0.7932 (m110) REVERT: A 348 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7796 (mp) REVERT: B 19 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8093 (ttp80) REVERT: S 204 SER cc_start: 0.8973 (t) cc_final: 0.8700 (t) outliers start: 30 outliers final: 24 residues processed: 128 average time/residue: 0.2213 time to fit residues: 39.4930 Evaluate side-chains 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 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 165 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 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: 0.9990 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.177583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137316 restraints weight = 9887.528| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.97 r_work: 0.3438 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8984 Z= 0.229 Angle : 0.547 9.671 12174 Z= 0.282 Chirality : 0.041 0.135 1391 Planarity : 0.004 0.033 1533 Dihedral : 4.838 57.259 1237 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.27 % Allowed : 20.38 % Favored : 76.35 % 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: 0.41 (0.26), residues: 1111 helix: 1.99 (0.28), residues: 372 sheet: -0.64 (0.30), residues: 286 loop : -0.48 (0.29), residues: 453 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 0.013 0.001 PHE B 235 TYR 0.011 0.001 TYR S 190 ARG 0.006 0.000 ARG S 160 *********************** 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 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.969 Fit side-chains REVERT: R 316 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7429 (ttmt) REVERT: R 326 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7125 (mt) REVERT: A 8 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: A 20 ASP cc_start: 0.8601 (t70) cc_final: 0.8276 (m-30) REVERT: A 255 ASN cc_start: 0.8249 (m-40) cc_final: 0.8020 (m110) REVERT: A 348 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7810 (mp) REVERT: B 19 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8070 (ttp80) REVERT: S 11 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8219 (tt) REVERT: S 204 SER cc_start: 0.8936 (t) cc_final: 0.8271 (p) outliers start: 31 outliers final: 26 residues processed: 126 average time/residue: 0.2202 time to fit residues: 38.4760 Evaluate side-chains 130 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 165 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 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: 0.5980 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 95 optimal weight: 0.0170 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.181889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142564 restraints weight = 9885.756| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.08 r_work: 0.3509 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2748 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= 0.138 Angle : 0.509 10.007 12174 Z= 0.261 Chirality : 0.040 0.144 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.633 55.438 1237 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.96 % Allowed : 21.22 % Favored : 75.82 % 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: 2.18 (0.28), residues: 372 sheet: -0.56 (0.31), residues: 280 loop : -0.41 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 26 HIS 0.003 0.001 HIS A 213 PHE 0.009 0.001 PHE R 101 TYR 0.009 0.001 TYR S 190 ARG 0.006 0.000 ARG S 160 ********************** 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 134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.065 Fit side-chains REVERT: R 183 MET cc_start: 0.7835 (mtm) cc_final: 0.7588 (mtt) REVERT: R 316 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7390 (ttmt) REVERT: R 320 MET cc_start: 0.7299 (tpt) cc_final: 0.7016 (tpp) REVERT: R 326 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7108 (mt) REVERT: A 8 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: A 20 ASP cc_start: 0.8568 (t70) cc_final: 0.8243 (m-30) REVERT: A 348 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7795 (mp) REVERT: B 19 ARG cc_start: 0.8674 (ttp80) cc_final: 0.8075 (ttp80) REVERT: S 11 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8237 (tt) REVERT: S 204 SER cc_start: 0.8858 (t) cc_final: 0.8188 (p) outliers start: 28 outliers final: 21 residues processed: 129 average time/residue: 0.2391 time to fit residues: 42.6777 Evaluate side-chains 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 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 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 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: 4.9990 chunk 24 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.180727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140551 restraints weight = 9962.652| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.08 r_work: 0.3456 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8984 Z= 0.167 Angle : 0.522 10.430 12174 Z= 0.267 Chirality : 0.040 0.133 1391 Planarity : 0.003 0.034 1533 Dihedral : 4.608 55.022 1237 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.96 % Allowed : 21.44 % 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: 0.65 (0.26), residues: 1111 helix: 2.15 (0.28), residues: 379 sheet: -0.53 (0.31), residues: 285 loop : -0.33 (0.29), residues: 447 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 0.010 0.001 PHE B 235 TYR 0.010 0.001 TYR S 190 ARG 0.005 0.000 ARG S 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4888.63 seconds wall clock time: 87 minutes 26.91 seconds (5246.91 seconds total)