Starting phenix.real_space_refine on Wed Jan 15 17:51:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x17_37986/01_2025/8x17_37986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x17_37986/01_2025/8x17_37986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x17_37986/01_2025/8x17_37986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x17_37986/01_2025/8x17_37986.map" model { file = "/net/cci-nas-00/data/ceres_data/8x17_37986/01_2025/8x17_37986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x17_37986/01_2025/8x17_37986.cif" } resolution = 3.19 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= 0.007 sd= 0.087 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: 6 Type Number sf(0) Gaussians I 1 10.91 5 S 68 5.16 5 Cl 1 4.86 5 C 5615 2.51 5 N 1469 2.21 5 O 1599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8753 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2269 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'XS0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.97, per 1000 atoms: 0.57 Number of scatterers: 8753 At special positions: 0 Unit cell: (116.184, 88.992, 135.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 1 52.95 Cl 1 17.00 S 68 16.00 O 1599 8.00 N 1469 7.00 C 5615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 166 " distance=2.04 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: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 39.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.599A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.738A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 40 removed outlier: 3.597A pdb=" N ASN R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 45 through 75 removed outlier: 3.501A pdb=" N PHE R 50 " --> pdb=" O THR R 46 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET R 66 " --> pdb=" O GLY R 62 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 79 through 114 removed outlier: 3.507A pdb=" N THR R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 143 Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 157 through 161 Processing helix chain 'R' and resid 167 through 172 Processing helix chain 'R' and resid 173 through 180 Processing helix chain 'R' and resid 180 through 186 Processing helix chain 'R' and resid 186 through 209 Processing helix chain 'R' and resid 224 through 253 removed outlier: 3.586A pdb=" N PHE R 239 " --> pdb=" O VAL R 235 " (cutoff:3.500A) Proline residue: R 245 - end of helix Processing helix chain 'R' and resid 260 through 273 Processing helix chain 'R' and resid 273 through 283 Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 286 through 300 Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.595A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.509A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.676A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.777A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.832A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.753A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.832A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.825A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.811A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.984A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.156A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.096A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.515A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.746A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 141 through 142 removed outlier: 3.941A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.526A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.872A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 3333 1.38 - 1.57: 5498 1.57 - 1.75: 3 1.75 - 1.93: 102 1.93 - 2.11: 1 Bond restraints: 8937 Sorted by residual: bond pdb=" C06 XS0 R 401 " pdb=" C07 XS0 R 401 " ideal model delta sigma weight residual 1.533 1.289 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C16 XS0 R 401 " pdb="CL19 XS0 R 401 " ideal model delta sigma weight residual 1.737 1.889 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C03 XS0 R 401 " pdb=" N02 XS0 R 401 " ideal model delta sigma weight residual 1.334 1.471 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C05 XS0 R 401 " pdb=" O09 XS0 R 401 " ideal model delta sigma weight residual 1.411 1.527 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C07 XS0 R 401 " pdb=" C08 XS0 R 401 " ideal model delta sigma weight residual 1.529 1.640 -0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 8932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 12033 2.66 - 5.33: 73 5.33 - 7.99: 8 7.99 - 10.66: 3 10.66 - 13.32: 2 Bond angle restraints: 12119 Sorted by residual: angle pdb=" N ILE R 248 " pdb=" CA ILE R 248 " pdb=" C ILE R 248 " ideal model delta sigma weight residual 111.45 105.38 6.07 9.30e-01 1.16e+00 4.26e+01 angle pdb=" C LEU R 84 " pdb=" N PHE R 85 " pdb=" CA PHE R 85 " ideal model delta sigma weight residual 120.31 113.51 6.80 1.52e+00 4.33e-01 2.00e+01 angle pdb=" N10 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" O09 XS0 R 401 " ideal model delta sigma weight residual 109.29 95.97 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C07 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" N10 XS0 R 401 " ideal model delta sigma weight residual 112.51 124.11 -11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C SER R 165 " pdb=" N CYS R 166 " pdb=" CA CYS R 166 " ideal model delta sigma weight residual 122.84 117.87 4.97 1.30e+00 5.92e-01 1.46e+01 ... (remaining 12114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4865 17.35 - 34.71: 335 34.71 - 52.06: 69 52.06 - 69.41: 11 69.41 - 86.76: 5 Dihedral angle restraints: 5285 sinusoidal: 2009 harmonic: 3276 Sorted by residual: dihedral pdb=" CB CYS R 83 " pdb=" SG CYS R 83 " pdb=" SG CYS R 166 " pdb=" CB CYS R 166 " ideal model delta sinusoidal sigma weight residual -86.00 -136.59 50.59 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " pdb=" CG ASP A 261 " pdb=" OD1 ASP A 261 " ideal model delta sinusoidal sigma weight residual -30.00 -88.10 58.10 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" N LYS B 15 " pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " ideal model delta sinusoidal sigma weight residual -60.00 -117.05 57.05 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 5282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1333 0.093 - 0.186: 68 0.186 - 0.280: 0 0.280 - 0.373: 0 0.373 - 0.466: 3 Chirality restraints: 1404 Sorted by residual: chirality pdb=" C05 XS0 R 401 " pdb=" C03 XS0 R 401 " pdb=" C06 XS0 R 401 " pdb=" O09 XS0 R 401 " both_signs ideal model delta sigma weight residual False 2.57 3.04 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" C07 XS0 R 401 " pdb=" C06 XS0 R 401 " pdb=" C08 XS0 R 401 " pdb=" O29 XS0 R 401 " both_signs ideal model delta sigma weight residual False 2.75 2.29 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C06 XS0 R 401 " pdb=" C05 XS0 R 401 " pdb=" C07 XS0 R 401 " pdb=" O30 XS0 R 401 " both_signs ideal model delta sigma weight residual False 2.59 2.21 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1401 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 81 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C TYR R 81 " -0.047 2.00e-02 2.50e+03 pdb=" O TYR R 81 " 0.018 2.00e-02 2.50e+03 pdb=" N SER R 82 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 250 " -0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C ASN R 250 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN R 250 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS R 251 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 235 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO H 236 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO H 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 236 " 0.026 5.00e-02 4.00e+02 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.63: 116 2.63 - 3.22: 8488 3.22 - 3.80: 14248 3.80 - 4.38: 20078 4.38 - 4.96: 33618 Nonbonded interactions: 76548 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.053 3.040 nonbonded pdb=" ND2 ASN B 155 " pdb=" OD1 ASP B 170 " model vdw 2.227 3.120 nonbonded pdb=" OE1 GLU A 318 " pdb=" NZ LYS A 345 " model vdw 2.259 3.120 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.264 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.269 3.040 ... (remaining 76543 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: 1.090 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.770 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 0.005 0.244 8937 Z= 0.354 Angle : 0.555 13.321 12119 Z= 0.321 Chirality : 0.043 0.466 1404 Planarity : 0.003 0.047 1507 Dihedral : 12.618 86.763 3168 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.32 % Allowed : 4.37 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1109 helix: 0.15 (0.25), residues: 406 sheet: -0.91 (0.29), residues: 273 loop : -1.05 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 339 HIS 0.002 0.000 HIS B 142 PHE 0.006 0.000 PHE R 48 TYR 0.005 0.000 TYR H 190 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 1.110 Fit side-chains REVERT: B 243 THR cc_start: 0.7925 (p) cc_final: 0.7543 (p) REVERT: R 99 MET cc_start: 0.8433 (mmm) cc_final: 0.8219 (mmm) REVERT: R 288 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7848 (tttp) REVERT: H 59 TYR cc_start: 0.5904 (m-80) cc_final: 0.5632 (m-80) REVERT: H 94 TYR cc_start: 0.8419 (m-80) cc_final: 0.7989 (m-80) REVERT: H 106 SER cc_start: 0.8681 (t) cc_final: 0.8374 (p) REVERT: A 305 CYS cc_start: 0.8386 (m) cc_final: 0.7990 (m) outliers start: 3 outliers final: 1 residues processed: 242 average time/residue: 0.2376 time to fit residues: 76.5473 Evaluate side-chains 159 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 247 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.0980 chunk 99 optimal weight: 4.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN R 12 ASN R 256 ASN C 24 ASN H 179 GLN H 186 GLN A 255 ASN A 294 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125504 restraints weight = 9253.843| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.16 r_work: 0.3364 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8937 Z= 0.161 Angle : 0.504 6.439 12119 Z= 0.270 Chirality : 0.041 0.137 1404 Planarity : 0.004 0.051 1507 Dihedral : 4.642 56.184 1241 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.71 % Allowed : 12.26 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1109 helix: 1.30 (0.26), residues: 411 sheet: -0.40 (0.30), residues: 262 loop : -0.52 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.034 0.001 PHE R 147 TYR 0.010 0.001 TYR H 190 ARG 0.006 0.001 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.926 Fit side-chains REVERT: B 17 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7457 (tm-30) REVERT: B 20 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8552 (m-30) REVERT: B 228 ASP cc_start: 0.8486 (p0) cc_final: 0.7803 (p0) REVERT: B 243 THR cc_start: 0.8418 (p) cc_final: 0.8144 (p) REVERT: R 146 MET cc_start: 0.8180 (mmm) cc_final: 0.7980 (mmm) REVERT: R 277 MET cc_start: 0.8411 (tpp) cc_final: 0.8200 (mmt) REVERT: R 288 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7861 (tttp) REVERT: C 42 GLU cc_start: 0.8354 (pp20) cc_final: 0.8052 (pp20) REVERT: H 59 TYR cc_start: 0.7395 (m-80) cc_final: 0.7122 (m-80) REVERT: H 77 ASN cc_start: 0.8199 (t0) cc_final: 0.7956 (t0) REVERT: H 106 SER cc_start: 0.8845 (t) cc_final: 0.8514 (p) REVERT: H 183 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8122 (mm-40) REVERT: A 251 ASP cc_start: 0.8737 (t70) cc_final: 0.8470 (t0) REVERT: A 305 CYS cc_start: 0.8422 (m) cc_final: 0.7992 (m) REVERT: A 349 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8097 (mttt) REVERT: A 351 CYS cc_start: 0.7728 (t) cc_final: 0.7410 (p) outliers start: 16 outliers final: 9 residues processed: 171 average time/residue: 0.2185 time to fit residues: 51.2090 Evaluate side-chains 149 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 0.0470 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN R 44 GLN H 179 GLN A 244 HIS A 269 ASN A 311 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113174 restraints weight = 8490.580| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.01 r_work: 0.3191 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8937 Z= 0.248 Angle : 0.524 6.035 12119 Z= 0.281 Chirality : 0.043 0.146 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.722 53.085 1240 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.35 % Allowed : 13.11 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1109 helix: 1.62 (0.26), residues: 414 sheet: -0.26 (0.30), residues: 269 loop : -0.31 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.037 0.002 PHE R 147 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.015 Fit side-chains REVERT: B 243 THR cc_start: 0.8799 (p) cc_final: 0.8559 (p) REVERT: R 288 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7925 (tttp) REVERT: C 42 GLU cc_start: 0.8409 (pp20) cc_final: 0.8078 (pp20) REVERT: H 77 ASN cc_start: 0.8176 (t0) cc_final: 0.7916 (t0) REVERT: H 234 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7410 (mt-10) REVERT: A 231 ASP cc_start: 0.6736 (m-30) cc_final: 0.6351 (m-30) REVERT: A 305 CYS cc_start: 0.8418 (m) cc_final: 0.8042 (m) outliers start: 22 outliers final: 16 residues processed: 156 average time/residue: 0.2261 time to fit residues: 48.0648 Evaluate side-chains 145 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 206 ASN Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 266 HIS R 44 GLN H 39 GLN A 244 HIS A 269 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113597 restraints weight = 8494.188| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.02 r_work: 0.3185 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8937 Z= 0.218 Angle : 0.501 6.620 12119 Z= 0.268 Chirality : 0.041 0.138 1404 Planarity : 0.004 0.053 1507 Dihedral : 4.677 53.132 1240 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.45 % Allowed : 14.82 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1109 helix: 1.76 (0.26), residues: 413 sheet: -0.14 (0.30), residues: 275 loop : -0.30 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 185 HIS 0.003 0.001 HIS B 91 PHE 0.034 0.001 PHE R 147 TYR 0.013 0.001 TYR H 190 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: B 243 THR cc_start: 0.8759 (p) cc_final: 0.8520 (p) REVERT: R 288 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7934 (tttp) REVERT: C 42 GLU cc_start: 0.8366 (pp20) cc_final: 0.8014 (pp20) REVERT: H 77 ASN cc_start: 0.8058 (t0) cc_final: 0.7775 (t0) REVERT: A 231 ASP cc_start: 0.6738 (m-30) cc_final: 0.6304 (m-30) REVERT: A 305 CYS cc_start: 0.8476 (m) cc_final: 0.8118 (m) REVERT: A 327 THR cc_start: 0.7581 (OUTLIER) cc_final: 0.7311 (p) REVERT: A 351 CYS cc_start: 0.7924 (p) cc_final: 0.7507 (p) outliers start: 23 outliers final: 17 residues processed: 148 average time/residue: 0.2229 time to fit residues: 45.0852 Evaluate side-chains 144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 206 ASN Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 7 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 266 HIS R 44 GLN A 244 HIS A 269 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.154771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115841 restraints weight = 8568.312| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.28 r_work: 0.3200 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8937 Z= 0.174 Angle : 0.481 6.864 12119 Z= 0.256 Chirality : 0.040 0.135 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.596 53.133 1240 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.13 % Allowed : 17.27 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1109 helix: 1.89 (0.27), residues: 413 sheet: 0.04 (0.30), residues: 273 loop : -0.31 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 185 HIS 0.002 0.001 HIS B 91 PHE 0.035 0.001 PHE R 147 TYR 0.013 0.001 TYR H 190 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: B 161 SER cc_start: 0.8947 (m) cc_final: 0.8669 (t) REVERT: B 243 THR cc_start: 0.8797 (p) cc_final: 0.8497 (p) REVERT: R 238 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7565 (mp) REVERT: R 288 LYS cc_start: 0.8232 (ttpt) cc_final: 0.8001 (tttp) REVERT: C 42 GLU cc_start: 0.8373 (pp20) cc_final: 0.8025 (pp20) REVERT: H 77 ASN cc_start: 0.8042 (t0) cc_final: 0.7756 (t0) REVERT: A 231 ASP cc_start: 0.6824 (m-30) cc_final: 0.6376 (m-30) REVERT: A 305 CYS cc_start: 0.8459 (m) cc_final: 0.8099 (m) REVERT: A 327 THR cc_start: 0.7548 (OUTLIER) cc_final: 0.7337 (p) REVERT: A 351 CYS cc_start: 0.7882 (p) cc_final: 0.7481 (p) outliers start: 20 outliers final: 13 residues processed: 146 average time/residue: 0.2296 time to fit residues: 45.9459 Evaluate side-chains 139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 327 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 0.0060 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 266 HIS R 167 GLN H 39 GLN A 244 HIS A 269 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.151185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109279 restraints weight = 9114.876| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.21 r_work: 0.3125 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8937 Z= 0.301 Angle : 0.535 7.149 12119 Z= 0.285 Chirality : 0.043 0.170 1404 Planarity : 0.004 0.055 1507 Dihedral : 4.789 51.143 1240 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.73 % Allowed : 17.48 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1109 helix: 1.68 (0.26), residues: 414 sheet: -0.07 (0.30), residues: 273 loop : -0.39 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 185 HIS 0.014 0.002 HIS B 266 PHE 0.016 0.002 PHE R 48 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 1.035 Fit side-chains REVERT: B 161 SER cc_start: 0.9061 (m) cc_final: 0.8844 (t) REVERT: B 243 THR cc_start: 0.8924 (p) cc_final: 0.8702 (p) REVERT: B 312 ASP cc_start: 0.8482 (p0) cc_final: 0.8223 (p0) REVERT: R 56 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7457 (mp) REVERT: R 238 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7742 (mp) REVERT: R 288 LYS cc_start: 0.8262 (ttpt) cc_final: 0.8010 (tttp) REVERT: H 77 ASN cc_start: 0.8106 (t0) cc_final: 0.7786 (t0) REVERT: A 231 ASP cc_start: 0.6871 (m-30) cc_final: 0.6469 (m-30) REVERT: A 305 CYS cc_start: 0.8575 (m) cc_final: 0.8219 (m) outliers start: 35 outliers final: 20 residues processed: 165 average time/residue: 0.2375 time to fit residues: 53.9728 Evaluate side-chains 155 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 206 ASN Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 0.0370 chunk 12 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112522 restraints weight = 8855.109| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.31 r_work: 0.3154 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8937 Z= 0.205 Angle : 0.501 6.390 12119 Z= 0.267 Chirality : 0.041 0.163 1404 Planarity : 0.004 0.050 1507 Dihedral : 4.841 59.160 1240 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.67 % Allowed : 18.87 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1109 helix: 1.79 (0.27), residues: 414 sheet: 0.04 (0.30), residues: 271 loop : -0.36 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 185 HIS 0.003 0.001 HIS B 225 PHE 0.038 0.001 PHE R 147 TYR 0.013 0.001 TYR H 190 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.038 Fit side-chains REVERT: B 161 SER cc_start: 0.9052 (m) cc_final: 0.8767 (t) REVERT: B 243 THR cc_start: 0.8910 (p) cc_final: 0.8684 (p) REVERT: R 56 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7324 (mp) REVERT: R 147 PHE cc_start: 0.5461 (p90) cc_final: 0.5051 (m-80) REVERT: R 172 MET cc_start: 0.7514 (tpp) cc_final: 0.6830 (tpp) REVERT: R 238 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7645 (mp) REVERT: R 288 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7955 (tttp) REVERT: H 77 ASN cc_start: 0.8008 (t0) cc_final: 0.7690 (t0) REVERT: A 231 ASP cc_start: 0.6856 (m-30) cc_final: 0.6411 (m-30) REVERT: A 305 CYS cc_start: 0.8484 (m) cc_final: 0.8133 (m) REVERT: A 351 CYS cc_start: 0.8019 (p) cc_final: 0.7582 (p) outliers start: 25 outliers final: 18 residues processed: 150 average time/residue: 0.2358 time to fit residues: 47.6635 Evaluate side-chains 150 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 2 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN H 39 GLN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108050 restraints weight = 9744.053| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.27 r_work: 0.3071 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8937 Z= 0.230 Angle : 0.506 6.617 12119 Z= 0.269 Chirality : 0.042 0.168 1404 Planarity : 0.004 0.055 1507 Dihedral : 4.839 58.373 1240 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.56 % Allowed : 19.51 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1109 helix: 1.74 (0.27), residues: 414 sheet: 0.03 (0.30), residues: 271 loop : -0.33 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 185 HIS 0.003 0.001 HIS B 142 PHE 0.034 0.001 PHE R 147 TYR 0.013 0.001 TYR H 190 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.005 Fit side-chains REVERT: B 17 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7609 (pp30) REVERT: B 161 SER cc_start: 0.9082 (m) cc_final: 0.8818 (t) REVERT: B 243 THR cc_start: 0.8945 (p) cc_final: 0.8732 (p) REVERT: R 44 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7733 (mp10) REVERT: R 56 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7315 (mp) REVERT: R 147 PHE cc_start: 0.5561 (p90) cc_final: 0.5169 (m-80) REVERT: R 172 MET cc_start: 0.7565 (tpp) cc_final: 0.6944 (tpp) REVERT: R 238 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7533 (mp) REVERT: R 288 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7949 (tttp) REVERT: H 77 ASN cc_start: 0.7974 (t0) cc_final: 0.7636 (t0) REVERT: A 231 ASP cc_start: 0.6892 (m-30) cc_final: 0.6470 (m-30) REVERT: A 305 CYS cc_start: 0.8459 (m) cc_final: 0.8099 (m) REVERT: A 351 CYS cc_start: 0.8040 (p) cc_final: 0.7591 (p) outliers start: 24 outliers final: 18 residues processed: 148 average time/residue: 0.2421 time to fit residues: 48.6582 Evaluate side-chains 148 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN H 39 GLN A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109531 restraints weight = 9622.903| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.20 r_work: 0.3121 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8937 Z= 0.244 Angle : 0.514 6.394 12119 Z= 0.273 Chirality : 0.042 0.179 1404 Planarity : 0.004 0.051 1507 Dihedral : 4.862 57.868 1240 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.67 % Allowed : 19.72 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1109 helix: 1.72 (0.27), residues: 414 sheet: -0.00 (0.30), residues: 271 loop : -0.31 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 185 HIS 0.003 0.001 HIS B 91 PHE 0.032 0.001 PHE R 147 TYR 0.013 0.001 TYR H 190 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.983 Fit side-chains REVERT: B 17 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7700 (pp30) REVERT: B 161 SER cc_start: 0.9100 (m) cc_final: 0.8805 (t) REVERT: B 243 THR cc_start: 0.8944 (p) cc_final: 0.8733 (p) REVERT: R 32 LEU cc_start: 0.8241 (tt) cc_final: 0.8012 (tt) REVERT: R 44 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7679 (mp10) REVERT: R 56 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7250 (mp) REVERT: R 147 PHE cc_start: 0.5481 (p90) cc_final: 0.5186 (m-80) REVERT: R 172 MET cc_start: 0.7561 (tpp) cc_final: 0.7005 (tpp) REVERT: R 238 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7438 (mp) REVERT: R 288 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7952 (tttp) REVERT: H 77 ASN cc_start: 0.7947 (t0) cc_final: 0.7601 (t0) REVERT: A 231 ASP cc_start: 0.6900 (m-30) cc_final: 0.6474 (m-30) REVERT: A 305 CYS cc_start: 0.8454 (m) cc_final: 0.8108 (m) outliers start: 25 outliers final: 19 residues processed: 150 average time/residue: 0.2250 time to fit residues: 45.8190 Evaluate side-chains 148 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 206 ASN Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 230 ASN H 39 GLN A 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.153992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112793 restraints weight = 9403.071| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.18 r_work: 0.3182 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8937 Z= 0.150 Angle : 0.483 6.396 12119 Z= 0.257 Chirality : 0.040 0.155 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.738 59.639 1240 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.92 % Allowed : 20.36 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1109 helix: 1.89 (0.27), residues: 414 sheet: 0.13 (0.30), residues: 270 loop : -0.22 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 185 HIS 0.002 0.001 HIS B 54 PHE 0.028 0.001 PHE R 147 TYR 0.014 0.001 TYR H 190 ARG 0.009 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.056 Fit side-chains REVERT: B 17 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7686 (pp30) REVERT: B 217 MET cc_start: 0.8118 (mmt) cc_final: 0.7917 (mmm) REVERT: B 243 THR cc_start: 0.8913 (p) cc_final: 0.8686 (p) REVERT: R 32 LEU cc_start: 0.8262 (tt) cc_final: 0.8002 (tt) REVERT: R 44 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7585 (mp10) REVERT: R 56 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7281 (mp) REVERT: R 172 MET cc_start: 0.7484 (tpp) cc_final: 0.6950 (tpp) REVERT: R 288 LYS cc_start: 0.8261 (ttpt) cc_final: 0.7994 (tttp) REVERT: H 77 ASN cc_start: 0.7873 (t0) cc_final: 0.7537 (t0) REVERT: A 231 ASP cc_start: 0.6813 (m-30) cc_final: 0.6452 (m-30) REVERT: A 305 CYS cc_start: 0.8432 (m) cc_final: 0.8092 (m) outliers start: 18 outliers final: 13 residues processed: 149 average time/residue: 0.2310 time to fit residues: 46.7139 Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 230 ASN H 39 GLN A 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113227 restraints weight = 9375.072| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.18 r_work: 0.3170 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8937 Z= 0.153 Angle : 0.479 6.549 12119 Z= 0.254 Chirality : 0.040 0.154 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.651 59.956 1240 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.92 % Allowed : 20.36 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1109 helix: 1.93 (0.27), residues: 414 sheet: 0.20 (0.31), residues: 270 loop : -0.16 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 185 HIS 0.002 0.001 HIS B 225 PHE 0.012 0.001 PHE A 189 TYR 0.013 0.001 TYR H 190 ARG 0.007 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5120.02 seconds wall clock time: 91 minutes 29.07 seconds (5489.07 seconds total)