Starting phenix.real_space_refine on Sat Aug 3 17:40:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/08_2024/8x17_37986.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/08_2024/8x17_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/08_2024/8x17_37986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/08_2024/8x17_37986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/08_2024/8x17_37986.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x17_37986/08_2024/8x17_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 Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "R ARG 108": "NH1" <-> "NH2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "R GLU 291": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "H GLU 222": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.34, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.55 Conformation dependent library (CDL) restraints added in 1.6 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: 2.84 Time building geometry restraints manager: 3.80 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: 95.97 - 103.77: 91 103.77 - 111.58: 4232 111.58 - 119.38: 3113 119.38 - 127.19: 4592 127.19 - 135.00: 91 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: 1.000 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.090 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.250 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 1.039 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: 0.2331 time to fit residues: 74.9238 Evaluate side-chains 159 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 0.927 Fit side-chains REVERT: B 17 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 228 ASP cc_start: 0.8285 (p0) cc_final: 0.7663 (p0) REVERT: B 243 THR cc_start: 0.8066 (p) cc_final: 0.7744 (p) REVERT: R 277 MET cc_start: 0.8098 (tpp) cc_final: 0.7877 (mmt) REVERT: C 42 GLU cc_start: 0.8148 (pp20) cc_final: 0.7907 (pp20) REVERT: H 59 TYR cc_start: 0.6741 (m-80) cc_final: 0.6481 (m-80) REVERT: H 106 SER cc_start: 0.8673 (t) cc_final: 0.8336 (p) REVERT: H 183 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7792 (mm-40) REVERT: A 251 ASP cc_start: 0.8812 (t70) cc_final: 0.8524 (t0) REVERT: A 290 TYR cc_start: 0.8026 (t80) cc_final: 0.7824 (t80) REVERT: A 305 CYS cc_start: 0.8291 (m) cc_final: 0.7917 (m) REVERT: A 349 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8079 (mttt) outliers start: 16 outliers final: 9 residues processed: 171 average time/residue: 0.2149 time to fit residues: 50.6527 Evaluate side-chains 147 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8937 Z= 0.260 Angle : 0.526 6.101 12119 Z= 0.282 Chirality : 0.043 0.146 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.730 53.263 1240 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.24 % Allowed : 13.11 % Favored : 84.65 % 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: 0.58 (0.26), residues: 1109 helix: 1.62 (0.26), residues: 414 sheet: -0.21 (0.30), residues: 273 loop : -0.34 (0.31), residues: 422 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 0.036 0.002 PHE R 147 TYR 0.013 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 fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.027 Fit side-chains REVERT: B 243 THR cc_start: 0.8471 (p) cc_final: 0.8193 (p) REVERT: C 42 GLU cc_start: 0.8249 (pp20) cc_final: 0.7988 (pp20) REVERT: H 234 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6749 (mt-10) REVERT: A 231 ASP cc_start: 0.6913 (m-30) cc_final: 0.6612 (m-30) REVERT: A 305 CYS cc_start: 0.8338 (m) cc_final: 0.8011 (m) REVERT: A 351 CYS cc_start: 0.7541 (p) cc_final: 0.7251 (p) outliers start: 21 outliers final: 15 residues processed: 158 average time/residue: 0.2142 time to fit residues: 46.1577 Evaluate side-chains 143 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 261 LEU 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 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 98 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 A 269 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8937 Z= 0.170 Angle : 0.486 6.669 12119 Z= 0.259 Chirality : 0.040 0.129 1404 Planarity : 0.004 0.053 1507 Dihedral : 4.591 53.837 1240 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.03 % Allowed : 14.82 % Favored : 83.16 % 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: 0.79 (0.26), residues: 1109 helix: 1.84 (0.27), residues: 413 sheet: -0.01 (0.30), residues: 269 loop : -0.33 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 185 HIS 0.002 0.001 HIS C 44 PHE 0.033 0.001 PHE R 147 TYR 0.014 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 150 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: B 161 SER cc_start: 0.8648 (m) cc_final: 0.8436 (t) REVERT: B 243 THR cc_start: 0.8360 (p) cc_final: 0.8079 (p) REVERT: R 44 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7939 (mp10) REVERT: C 42 GLU cc_start: 0.8174 (pp20) cc_final: 0.7916 (pp20) REVERT: C 46 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8507 (mmtt) REVERT: A 231 ASP cc_start: 0.6866 (m-30) cc_final: 0.6532 (m-30) REVERT: A 305 CYS cc_start: 0.8307 (m) cc_final: 0.7984 (m) REVERT: A 327 THR cc_start: 0.6901 (OUTLIER) cc_final: 0.6696 (p) outliers start: 19 outliers final: 12 residues processed: 144 average time/residue: 0.2168 time to fit residues: 42.9015 Evaluate side-chains 137 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU 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 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 88 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS R 167 GLN A 244 HIS A 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8937 Z= 0.304 Angle : 0.541 7.008 12119 Z= 0.287 Chirality : 0.043 0.161 1404 Planarity : 0.004 0.055 1507 Dihedral : 4.796 51.583 1240 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.99 % Allowed : 16.52 % Favored : 80.49 % 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: 0.67 (0.26), residues: 1109 helix: 1.69 (0.26), residues: 414 sheet: -0.00 (0.30), residues: 271 loop : -0.40 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 185 HIS 0.004 0.001 HIS R 95 PHE 0.036 0.002 PHE R 147 TYR 0.012 0.001 TYR H 190 ARG 0.007 0.001 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 157 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: B 243 THR cc_start: 0.8550 (p) cc_final: 0.8167 (p) REVERT: R 56 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7352 (mp) REVERT: R 238 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7520 (mp) REVERT: C 42 GLU cc_start: 0.8252 (pp20) cc_final: 0.7972 (pp20) REVERT: A 231 ASP cc_start: 0.6973 (m-30) cc_final: 0.6622 (m-30) REVERT: A 305 CYS cc_start: 0.8352 (m) cc_final: 0.8029 (m) outliers start: 28 outliers final: 20 residues processed: 148 average time/residue: 0.2321 time to fit residues: 47.5010 Evaluate side-chains 146 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 THR 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 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 R residue 238 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 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 52 GLN Chi-restraints excluded: chain A residue 253 ILE 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 35 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.0980 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 102 optimal weight: 0.0980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS A 244 HIS A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8937 Z= 0.141 Angle : 0.473 5.396 12119 Z= 0.253 Chirality : 0.040 0.137 1404 Planarity : 0.004 0.050 1507 Dihedral : 4.568 52.696 1240 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.81 % Allowed : 18.87 % 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: 0.89 (0.26), residues: 1109 helix: 1.92 (0.27), residues: 414 sheet: 0.12 (0.30), residues: 271 loop : -0.35 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 185 HIS 0.002 0.001 HIS B 225 PHE 0.012 0.001 PHE A 189 TYR 0.014 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 147 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.025 Fit side-chains REVERT: R 44 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7647 (mp10) REVERT: A 231 ASP cc_start: 0.6901 (m-30) cc_final: 0.6568 (m-30) REVERT: A 305 CYS cc_start: 0.8291 (m) cc_final: 0.7968 (m) outliers start: 17 outliers final: 12 residues processed: 140 average time/residue: 0.2344 time to fit residues: 45.0496 Evaluate side-chains 134 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 THR 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 116 VAL Chi-restraints excluded: chain R residue 179 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain H residue 118 THR 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 11 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS A 244 HIS A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3772 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= 0.182 Angle : 0.482 6.380 12119 Z= 0.259 Chirality : 0.041 0.144 1404 Planarity : 0.004 0.055 1507 Dihedral : 4.707 59.794 1240 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.03 % Allowed : 18.87 % Favored : 79.10 % 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: 0.93 (0.26), residues: 1109 helix: 1.92 (0.27), residues: 414 sheet: 0.18 (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 0.002 0.001 HIS B 91 PHE 0.039 0.001 PHE R 147 TYR 0.013 0.001 TYR H 190 ARG 0.007 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 144 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.022 Fit side-chains REVERT: B 243 THR cc_start: 0.8487 (p) cc_final: 0.8212 (p) REVERT: R 44 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7661 (mp10) REVERT: R 56 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7355 (mp) REVERT: R 172 MET cc_start: 0.7235 (tpp) cc_final: 0.6340 (tpp) REVERT: R 238 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7454 (mp) REVERT: A 231 ASP cc_start: 0.6855 (m-30) cc_final: 0.6542 (m-30) REVERT: A 305 CYS cc_start: 0.8312 (m) cc_final: 0.7989 (m) outliers start: 19 outliers final: 13 residues processed: 139 average time/residue: 0.2201 time to fit residues: 41.9235 Evaluate side-chains 138 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 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 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 238 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain H residue 118 THR 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 63 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8937 Z= 0.199 Angle : 0.493 6.315 12119 Z= 0.263 Chirality : 0.041 0.149 1404 Planarity : 0.004 0.052 1507 Dihedral : 4.704 58.764 1240 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.24 % Allowed : 18.87 % Favored : 78.89 % 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: 1.90 (0.27), residues: 414 sheet: 0.20 (0.31), residues: 271 loop : -0.29 (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 266 PHE 0.032 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 146 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 0.931 Fit side-chains REVERT: B 243 THR cc_start: 0.8495 (p) cc_final: 0.8216 (p) REVERT: R 44 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7652 (mp10) REVERT: R 56 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7351 (mp) REVERT: R 172 MET cc_start: 0.7284 (tpp) cc_final: 0.6488 (tpp) REVERT: R 238 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7434 (mp) REVERT: A 231 ASP cc_start: 0.6849 (m-30) cc_final: 0.6535 (m-30) REVERT: A 305 CYS cc_start: 0.8319 (m) cc_final: 0.7997 (m) outliers start: 21 outliers final: 15 residues processed: 141 average time/residue: 0.2143 time to fit residues: 41.3047 Evaluate side-chains 138 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 THR 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 266 HIS 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 238 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 VAL 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 98 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.0370 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8937 Z= 0.150 Angle : 0.485 8.624 12119 Z= 0.257 Chirality : 0.040 0.139 1404 Planarity : 0.004 0.053 1507 Dihedral : 4.665 59.940 1240 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.60 % Allowed : 20.26 % Favored : 78.14 % 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: 0.99 (0.26), residues: 1109 helix: 1.96 (0.27), residues: 414 sheet: 0.26 (0.31), residues: 265 loop : -0.30 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 185 HIS 0.006 0.001 HIS B 266 PHE 0.029 0.001 PHE R 147 TYR 0.013 0.001 TYR H 190 ARG 0.009 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 142 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: B 243 THR cc_start: 0.8502 (p) cc_final: 0.8208 (p) REVERT: R 32 LEU cc_start: 0.8221 (tt) cc_final: 0.7906 (tt) REVERT: R 44 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7511 (mp10) REVERT: R 56 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7397 (mp) REVERT: R 172 MET cc_start: 0.7287 (tpp) cc_final: 0.6495 (tpp) REVERT: A 231 ASP cc_start: 0.6778 (m-30) cc_final: 0.6467 (m-30) REVERT: A 305 CYS cc_start: 0.8303 (m) cc_final: 0.7980 (m) outliers start: 15 outliers final: 14 residues processed: 140 average time/residue: 0.2220 time to fit residues: 42.2457 Evaluate side-chains 139 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR 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 244 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 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 49 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3971 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= 0.185 Angle : 0.495 9.290 12119 Z= 0.262 Chirality : 0.041 0.151 1404 Planarity : 0.004 0.054 1507 Dihedral : 4.642 60.046 1240 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.49 % Allowed : 20.47 % Favored : 78.04 % 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: 1.92 (0.27), residues: 414 sheet: 0.23 (0.31), residues: 271 loop : -0.26 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 185 HIS 0.003 0.001 HIS B 142 PHE 0.029 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 135 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: B 243 THR cc_start: 0.8525 (p) cc_final: 0.8237 (p) REVERT: R 32 LEU cc_start: 0.8246 (tt) cc_final: 0.7911 (tt) REVERT: R 44 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7485 (mp10) REVERT: R 56 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7398 (mp) REVERT: R 172 MET cc_start: 0.7271 (tpp) cc_final: 0.6544 (tpp) REVERT: A 231 ASP cc_start: 0.6741 (m-30) cc_final: 0.6469 (m-30) REVERT: A 248 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7847 (ptmt) REVERT: A 305 CYS cc_start: 0.8322 (m) cc_final: 0.7997 (m) outliers start: 14 outliers final: 13 residues processed: 133 average time/residue: 0.2326 time to fit residues: 41.9321 Evaluate side-chains 134 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR 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 244 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 155 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 80 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- 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** A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111295 restraints weight = 8541.635| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.07 r_work: 0.3147 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4151 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= 0.233 Angle : 0.518 8.641 12119 Z= 0.275 Chirality : 0.042 0.181 1404 Planarity : 0.004 0.053 1507 Dihedral : 4.736 58.029 1240 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.81 % Allowed : 20.04 % Favored : 78.14 % 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: 0.90 (0.26), residues: 1109 helix: 1.83 (0.27), residues: 414 sheet: 0.22 (0.31), residues: 271 loop : -0.29 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 185 HIS 0.003 0.001 HIS B 225 PHE 0.030 0.001 PHE R 147 TYR 0.012 0.001 TYR H 190 ARG 0.005 0.000 ARG H 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2197.40 seconds wall clock time: 39 minutes 49.90 seconds (2389.90 seconds total)