Starting phenix.real_space_refine on Thu Mar 13 05:15:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x17_37986/03_2025/8x17_37986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x17_37986/03_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_37986/03_2025/8x17_37986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x17_37986/03_2025/8x17_37986.map" model { file = "/net/cci-nas-00/data/ceres_data/8x17_37986/03_2025/8x17_37986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x17_37986/03_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-5624/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: 5.50, per 1000 atoms: 0.63 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: 2.17 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: 1.01 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: 2.61 Time building geometry restraints manager: 2.54 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.900 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- 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 : 0.882 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: 0.2355 time to fit residues: 76.0519 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 : 0.903 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125667 restraints weight = 9253.842| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.14 r_work: 0.3365 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.853 Fit side-chains REVERT: B 17 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7456 (tm-30) REVERT: B 20 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8552 (m-30) REVERT: B 228 ASP cc_start: 0.8485 (p0) cc_final: 0.7801 (p0) REVERT: B 243 THR cc_start: 0.8416 (p) cc_final: 0.8141 (p) REVERT: R 146 MET cc_start: 0.8180 (mmm) cc_final: 0.7980 (mmm) REVERT: R 277 MET cc_start: 0.8409 (tpp) cc_final: 0.8197 (mmt) REVERT: R 288 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7859 (tttp) REVERT: C 42 GLU cc_start: 0.8353 (pp20) cc_final: 0.8052 (pp20) REVERT: H 59 TYR cc_start: 0.7394 (m-80) cc_final: 0.7121 (m-80) REVERT: H 77 ASN cc_start: 0.8199 (t0) cc_final: 0.7955 (t0) REVERT: H 106 SER cc_start: 0.8844 (t) cc_final: 0.8513 (p) REVERT: H 183 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8119 (mm-40) REVERT: A 251 ASP cc_start: 0.8737 (t70) cc_final: 0.8470 (t0) REVERT: A 305 CYS cc_start: 0.8419 (m) cc_final: 0.7990 (m) REVERT: A 349 LYS cc_start: 0.8434 (mtmm) cc_final: 0.8098 (mttt) REVERT: A 351 CYS cc_start: 0.7729 (t) cc_final: 0.7410 (p) outliers start: 16 outliers final: 9 residues processed: 171 average time/residue: 0.2047 time to fit residues: 48.2222 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 : 0.854 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.0770 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 44 GLN H 179 GLN A 244 HIS A 269 ASN A 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.159083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119445 restraints weight = 8724.824| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.07 r_work: 0.3278 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2764 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= 0.190 Angle : 0.479 6.042 12119 Z= 0.257 Chirality : 0.041 0.126 1404 Planarity : 0.004 0.050 1507 Dihedral : 4.489 54.666 1240 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.71 % Allowed : 12.69 % Favored : 85.61 % 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: 0.68 (0.26), residues: 1109 helix: 1.77 (0.26), residues: 412 sheet: -0.18 (0.31), residues: 258 loop : -0.33 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS C 44 PHE 0.034 0.001 PHE R 147 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG A 313 *********************** 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 158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.905 Fit side-chains REVERT: B 243 THR cc_start: 0.8654 (p) cc_final: 0.8397 (p) REVERT: R 288 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7943 (tttp) REVERT: C 42 GLU cc_start: 0.8409 (pp20) cc_final: 0.8084 (pp20) REVERT: H 77 ASN cc_start: 0.8107 (t0) cc_final: 0.7846 (t0) REVERT: A 231 ASP cc_start: 0.6662 (m-30) cc_final: 0.6368 (m-30) REVERT: A 269 ASN cc_start: 0.8892 (m-40) cc_final: 0.8657 (m110) REVERT: A 305 CYS cc_start: 0.8412 (m) cc_final: 0.8011 (m) outliers start: 16 outliers final: 11 residues processed: 152 average time/residue: 0.2149 time to fit residues: 45.1528 Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 262 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain H residue 118 THR 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: 4.9990 chunk 75 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 61 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- 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 H 39 GLN A 244 HIS A 255 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.151761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113104 restraints weight = 8409.270| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.16 r_work: 0.3168 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8937 Z= 0.301 Angle : 0.554 7.031 12119 Z= 0.295 Chirality : 0.043 0.158 1404 Planarity : 0.004 0.054 1507 Dihedral : 4.874 51.715 1240 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.99 % Allowed : 13.54 % Favored : 83.48 % 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: 0.62 (0.25), residues: 1109 helix: 1.60 (0.26), residues: 413 sheet: -0.02 (0.30), residues: 271 loop : -0.38 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 185 HIS 0.004 0.001 HIS B 183 PHE 0.038 0.002 PHE R 147 TYR 0.012 0.001 TYR B 105 ARG 0.006 0.001 ARG H 18 *********************** 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 163 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 161 SER cc_start: 0.8983 (m) cc_final: 0.8699 (t) REVERT: B 243 THR cc_start: 0.8896 (p) cc_final: 0.8664 (p) REVERT: R 238 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7619 (mp) REVERT: R 288 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7903 (tttp) REVERT: C 42 GLU cc_start: 0.8364 (pp20) cc_final: 0.8007 (pp20) REVERT: H 77 ASN cc_start: 0.8129 (t0) cc_final: 0.7858 (t0) REVERT: A 231 ASP cc_start: 0.6844 (m-30) cc_final: 0.6456 (m-30) REVERT: A 269 ASN cc_start: 0.8897 (m-40) cc_final: 0.8667 (m110) REVERT: A 305 CYS cc_start: 0.8500 (m) cc_final: 0.8129 (m) REVERT: A 327 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7305 (p) outliers start: 28 outliers final: 17 residues processed: 156 average time/residue: 0.2271 time to fit residues: 48.4637 Evaluate side-chains 145 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL 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 238 LEU 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 H residue 63 THR 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: 0.6980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 230 ASN B 266 HIS A 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.155107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116515 restraints weight = 8472.879| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.19 r_work: 0.3196 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8937 Z= 0.157 Angle : 0.476 7.225 12119 Z= 0.253 Chirality : 0.040 0.137 1404 Planarity : 0.003 0.050 1507 Dihedral : 4.589 53.151 1240 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.56 % Allowed : 16.84 % 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: 0.85 (0.26), residues: 1109 helix: 1.87 (0.27), residues: 414 sheet: 0.06 (0.30), residues: 273 loop : -0.33 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 185 HIS 0.002 0.001 HIS B 225 PHE 0.033 0.001 PHE R 147 TYR 0.014 0.001 TYR H 190 ARG 0.005 0.000 ARG B 314 *********************** 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 159 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.887 Fit side-chains REVERT: B 20 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8634 (m-30) REVERT: B 243 THR cc_start: 0.8778 (p) cc_final: 0.8460 (p) REVERT: R 56 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7342 (mp) REVERT: R 288 LYS cc_start: 0.8235 (ttpt) cc_final: 0.8016 (tttp) REVERT: C 42 GLU cc_start: 0.8366 (pp20) cc_final: 0.8011 (pp20) REVERT: H 77 ASN cc_start: 0.8031 (t0) cc_final: 0.7763 (t0) REVERT: A 231 ASP cc_start: 0.6832 (m-30) cc_final: 0.6391 (m-30) REVERT: A 269 ASN cc_start: 0.8898 (m-40) cc_final: 0.8665 (m110) REVERT: A 305 CYS cc_start: 0.8481 (m) cc_final: 0.8112 (m) outliers start: 24 outliers final: 14 residues processed: 150 average time/residue: 0.2095 time to fit residues: 43.1282 Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 261 LEU 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 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 0.0570 chunk 67 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 A 244 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116097 restraints weight = 8378.390| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.99 r_work: 0.3232 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8937 Z= 0.138 Angle : 0.467 7.081 12119 Z= 0.249 Chirality : 0.040 0.129 1404 Planarity : 0.003 0.053 1507 Dihedral : 4.492 53.213 1240 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.24 % Allowed : 18.44 % Favored : 79.32 % 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: 0.92 (0.26), residues: 1109 helix: 1.95 (0.27), residues: 414 sheet: 0.21 (0.31), residues: 260 loop : -0.38 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 185 HIS 0.002 0.001 HIS B 266 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 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 156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.774 Fit side-chains REVERT: B 20 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8546 (m-30) REVERT: B 243 THR cc_start: 0.8766 (p) cc_final: 0.8530 (p) REVERT: R 56 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7352 (mp) REVERT: R 288 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7992 (tttp) REVERT: C 42 GLU cc_start: 0.8348 (pp20) cc_final: 0.7993 (pp20) REVERT: H 77 ASN cc_start: 0.7989 (t0) cc_final: 0.7726 (t0) REVERT: A 231 ASP cc_start: 0.6710 (m-30) cc_final: 0.6317 (m-30) REVERT: A 269 ASN cc_start: 0.8908 (m-40) cc_final: 0.8670 (m110) REVERT: A 305 CYS cc_start: 0.8433 (m) cc_final: 0.8070 (m) outliers start: 21 outliers final: 12 residues processed: 148 average time/residue: 0.2457 time to fit residues: 49.9142 Evaluate side-chains 143 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 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 56 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 155 VAL 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: 6.9990 chunk 88 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 266 HIS A 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111456 restraints weight = 9182.634| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.21 r_work: 0.3164 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3743 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 : 0.501 7.307 12119 Z= 0.267 Chirality : 0.041 0.151 1404 Planarity : 0.004 0.054 1507 Dihedral : 4.688 59.707 1240 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.24 % Allowed : 19.40 % Favored : 78.36 % 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: 1.88 (0.27), residues: 414 sheet: 0.10 (0.30), residues: 271 loop : -0.34 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 185 HIS 0.005 0.001 HIS B 266 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG H 18 *********************** 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 151 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.915 Fit side-chains REVERT: B 243 THR cc_start: 0.8919 (p) cc_final: 0.8698 (p) REVERT: R 56 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7391 (mp) REVERT: R 172 MET cc_start: 0.7435 (tpp) cc_final: 0.6549 (tpp) REVERT: R 288 LYS cc_start: 0.8251 (ttpt) cc_final: 0.8015 (tttp) REVERT: C 42 GLU cc_start: 0.8381 (pp20) cc_final: 0.8025 (pp20) REVERT: H 77 ASN cc_start: 0.8041 (t0) cc_final: 0.7748 (t0) REVERT: A 231 ASP cc_start: 0.6773 (m-30) cc_final: 0.6323 (m-30) REVERT: A 305 CYS cc_start: 0.8498 (m) cc_final: 0.8134 (m) outliers start: 21 outliers final: 14 residues processed: 145 average time/residue: 0.2314 time to fit residues: 46.0171 Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR 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 196 ILE Chi-restraints excluded: chain R residue 262 LEU 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: 7.9990 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 0.0060 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.154949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114430 restraints weight = 9123.904| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.12 r_work: 0.3196 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3831 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= 0.173 Angle : 0.487 8.040 12119 Z= 0.258 Chirality : 0.040 0.145 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.631 60.725 1240 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.92 % Allowed : 19.83 % Favored : 78.25 % 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: 0.91 (0.26), residues: 1109 helix: 1.92 (0.27), residues: 414 sheet: 0.07 (0.30), residues: 273 loop : -0.26 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 185 HIS 0.003 0.001 HIS B 142 PHE 0.038 0.001 PHE R 147 TYR 0.012 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 147 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.964 Fit side-chains REVERT: B 243 THR cc_start: 0.8868 (p) cc_final: 0.8634 (p) REVERT: R 44 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7693 (mp10) REVERT: R 56 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7321 (mp) REVERT: R 147 PHE cc_start: 0.5469 (p90) cc_final: 0.4917 (m-80) REVERT: R 172 MET cc_start: 0.7389 (tpp) cc_final: 0.6476 (tpp) REVERT: R 288 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7994 (tttp) REVERT: C 42 GLU cc_start: 0.8358 (pp20) cc_final: 0.8011 (pp20) REVERT: H 77 ASN cc_start: 0.7941 (t0) cc_final: 0.7643 (t0) REVERT: A 231 ASP cc_start: 0.6775 (m-30) cc_final: 0.6301 (m-30) REVERT: A 305 CYS cc_start: 0.8431 (m) cc_final: 0.8087 (m) outliers start: 18 outliers final: 15 residues processed: 143 average time/residue: 0.2363 time to fit residues: 46.2216 Evaluate side-chains 143 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 322 ASP 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 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: 6.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 71 optimal weight: 0.0040 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.153908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112991 restraints weight = 9296.003| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.15 r_work: 0.3188 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3937 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= 0.178 Angle : 0.485 7.089 12119 Z= 0.258 Chirality : 0.040 0.150 1404 Planarity : 0.003 0.053 1507 Dihedral : 4.644 60.951 1240 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.13 % Allowed : 20.04 % Favored : 77.83 % 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: 0.97 (0.26), residues: 1109 helix: 1.95 (0.27), residues: 414 sheet: 0.15 (0.31), residues: 268 loop : -0.25 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 185 HIS 0.004 0.001 HIS B 142 PHE 0.031 0.001 PHE R 147 TYR 0.013 0.001 TYR H 190 ARG 0.008 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 148 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.888 Fit side-chains REVERT: B 20 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: B 243 THR cc_start: 0.8860 (p) cc_final: 0.8633 (p) REVERT: R 28 VAL cc_start: 0.8562 (t) cc_final: 0.8353 (p) REVERT: R 44 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7631 (mp10) REVERT: R 56 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7352 (mp) REVERT: R 172 MET cc_start: 0.7366 (tpp) cc_final: 0.6595 (tpp) REVERT: R 288 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7999 (tttp) REVERT: H 77 ASN cc_start: 0.7907 (t0) cc_final: 0.7582 (t0) REVERT: A 231 ASP cc_start: 0.6648 (m-30) cc_final: 0.6241 (m-30) REVERT: A 248 LYS cc_start: 0.8337 (ttpt) cc_final: 0.7968 (ptmt) REVERT: A 305 CYS cc_start: 0.8441 (m) cc_final: 0.8100 (m) outliers start: 20 outliers final: 14 residues processed: 145 average time/residue: 0.2281 time to fit residues: 44.8218 Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL 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 206 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS 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 = 0.3810 r_free = 0.3810 target = 0.153256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112242 restraints weight = 9086.388| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.14 r_work: 0.3177 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4059 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= 0.208 Angle : 0.503 6.788 12119 Z= 0.267 Chirality : 0.041 0.166 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.670 59.171 1240 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.81 % Allowed : 20.47 % 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: 0.98 (0.26), residues: 1109 helix: 1.95 (0.27), residues: 414 sheet: 0.11 (0.31), residues: 273 loop : -0.21 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 185 HIS 0.005 0.001 HIS B 142 PHE 0.035 0.001 PHE R 147 TYR 0.012 0.001 TYR H 190 ARG 0.010 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 144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.885 Fit side-chains REVERT: B 20 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8569 (m-30) REVERT: B 217 MET cc_start: 0.8109 (mmt) cc_final: 0.7909 (mmm) REVERT: B 243 THR cc_start: 0.8902 (p) cc_final: 0.8666 (p) REVERT: R 28 VAL cc_start: 0.8559 (t) cc_final: 0.8355 (p) REVERT: R 44 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7577 (mp10) REVERT: R 56 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7321 (mp) REVERT: R 172 MET cc_start: 0.7458 (tpp) cc_final: 0.6750 (tpp) REVERT: R 288 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7987 (tttp) REVERT: H 77 ASN cc_start: 0.7911 (t0) cc_final: 0.7569 (t0) REVERT: A 231 ASP cc_start: 0.6665 (m-30) cc_final: 0.6260 (m-30) REVERT: A 305 CYS cc_start: 0.8443 (m) cc_final: 0.8099 (m) outliers start: 17 outliers final: 14 residues processed: 142 average time/residue: 0.2178 time to fit residues: 42.2220 Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 0.0370 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113133 restraints weight = 9057.683| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.12 r_work: 0.3193 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8937 Z= 0.179 Angle : 0.490 6.531 12119 Z= 0.260 Chirality : 0.041 0.161 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.601 59.136 1240 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.71 % Allowed : 21.00 % Favored : 77.29 % 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: 1.03 (0.26), residues: 1109 helix: 1.97 (0.27), residues: 420 sheet: 0.22 (0.31), residues: 268 loop : -0.25 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 185 HIS 0.003 0.001 HIS B 142 PHE 0.031 0.001 PHE R 147 TYR 0.013 0.001 TYR H 190 ARG 0.010 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5188.94 seconds wall clock time: 90 minutes 36.01 seconds (5436.01 seconds total)