Starting phenix.real_space_refine on Sat Aug 3 10:57:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/08_2024/8wc8_37434_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/08_2024/8wc8_37434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/08_2024/8wc8_37434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/08_2024/8wc8_37434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/08_2024/8wc8_37434_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/08_2024/8wc8_37434_neut.cif" } resolution = 2.9 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= 0.003 sd= 0.098 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 55 5.16 5 C 5174 2.51 5 N 1372 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8062 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1695 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 218} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 7, 'PHE:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2333 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 119 Chain: "R" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2030 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 2, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "S" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1666 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "Y" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 328 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.61 Number of scatterers: 8062 At special positions: 0 Unit cell: (86.92, 117.26, 121.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 55 16.00 O 1460 8.00 N 1372 7.00 C 5174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.00 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.5% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.563A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.655A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.932A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.990A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 4.280A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 16 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.585A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 51 Processing helix chain 'R' and resid 52 through 55 removed outlier: 3.772A pdb=" N HIS R 55 " --> pdb=" O LYS R 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 52 through 55' Processing helix chain 'R' and resid 56 through 86 removed outlier: 3.933A pdb=" N LEU R 61 " --> pdb=" O PRO R 57 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE R 62 " --> pdb=" O THR R 58 " (cutoff:3.500A) Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 92 through 127 removed outlier: 3.543A pdb=" N ASP R 127 " --> pdb=" O TYR R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix removed outlier: 3.534A pdb=" N LEU R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 179 Processing helix chain 'R' and resid 187 through 200 removed outlier: 3.722A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 227 Processing helix chain 'R' and resid 248 through 277 removed outlier: 4.051A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.679A pdb=" N GLY R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 315 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'Y' and resid 16 through 24 Processing helix chain 'Y' and resid 29 through 45 Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.170A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.708A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.636A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.327A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.626A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.627A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.454A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.634A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 11 removed outlier: 5.414A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.434A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.631A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1236 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: 2.44 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.41: 3495 1.41 - 1.65: 4668 1.65 - 1.89: 81 1.89 - 2.13: 1 2.13 - 2.37: 1 Bond restraints: 8246 Sorted by residual: bond pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 1.331 2.375 -1.044 1.46e-02 4.69e+03 5.12e+03 bond pdb=" C LEU R 289 " pdb=" O LEU R 289 " ideal model delta sigma weight residual 1.237 1.169 0.067 1.17e-02 7.31e+03 3.33e+01 bond pdb=" C TYR R 294 " pdb=" O TYR R 294 " ideal model delta sigma weight residual 1.237 1.170 0.067 1.17e-02 7.31e+03 3.26e+01 bond pdb=" C PHE R 292 " pdb=" O PHE R 292 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.16e-02 7.43e+03 2.94e+01 bond pdb=" C PHE R 185 " pdb=" O PHE R 185 " ideal model delta sigma weight residual 1.234 1.170 0.064 1.22e-02 6.72e+03 2.75e+01 ... (remaining 8241 not shown) Histogram of bond angle deviations from ideal: 87.02 - 101.69: 28 101.69 - 116.36: 5457 116.36 - 131.04: 5716 131.04 - 145.71: 43 145.71 - 160.38: 1 Bond angle restraints: 11245 Sorted by residual: angle pdb=" O GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 123.05 87.02 36.03 1.03e+00 9.43e-01 1.22e+03 angle pdb=" C GLY A 320 " pdb=" N GLY A 322 " pdb=" CA GLY A 322 " ideal model delta sigma weight residual 121.41 160.38 -38.97 1.96e+00 2.60e-01 3.95e+02 angle pdb=" N PRO S 236 " pdb=" CA PRO S 236 " pdb=" C PRO S 236 " ideal model delta sigma weight residual 112.47 97.97 14.50 2.06e+00 2.36e-01 4.96e+01 angle pdb=" C THR R 37 " pdb=" CA THR R 37 " pdb=" CB THR R 37 " ideal model delta sigma weight residual 110.96 100.82 10.14 1.54e+00 4.22e-01 4.33e+01 angle pdb=" CA GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 114.28 123.01 -8.73 1.56e+00 4.11e-01 3.13e+01 ... (remaining 11240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4384 17.31 - 34.62: 315 34.62 - 51.93: 53 51.93 - 69.23: 5 69.23 - 86.54: 5 Dihedral angle restraints: 4762 sinusoidal: 1563 harmonic: 3199 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -162.39 76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CA GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " pdb=" CA GLY A 322 " ideal model delta harmonic sigma weight residual -180.00 -148.86 -31.14 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" C PHE R 292 " pdb=" N PHE R 292 " pdb=" CA PHE R 292 " pdb=" CB PHE R 292 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.03e+01 ... (remaining 4759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1293 0.136 - 0.273: 10 0.273 - 0.409: 1 0.409 - 0.546: 2 0.546 - 0.682: 4 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA LEU R 289 " pdb=" N LEU R 289 " pdb=" C LEU R 289 " pdb=" CB LEU R 289 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PHE R 292 " pdb=" N PHE R 292 " pdb=" C PHE R 292 " pdb=" CB PHE R 292 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA TRP R 291 " pdb=" N TRP R 291 " pdb=" C TRP R 291 " pdb=" CB TRP R 291 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.74e+00 ... (remaining 1307 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 320 " -0.146 2.00e-02 2.50e+03 2.03e-01 4.13e+02 pdb=" C GLY A 320 " 0.347 2.00e-02 2.50e+03 pdb=" O GLY A 320 " -0.142 2.00e-02 2.50e+03 pdb=" N GLY A 322 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL S 199 " 0.055 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO S 200 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO S 200 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 200 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 56 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO R 57 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 57 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 57 " -0.044 5.00e-02 4.00e+02 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1841 2.78 - 3.31: 7558 3.31 - 3.84: 13764 3.84 - 4.37: 15780 4.37 - 4.90: 28412 Nonbonded interactions: 67355 Sorted by model distance: nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.252 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.258 3.040 nonbonded pdb=" O ARG A 250 " pdb=" OG1 THR A 251 " model vdw 2.288 3.040 nonbonded pdb=" O SER S 52 " pdb=" NH1 ARG S 72 " model vdw 2.295 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.297 3.040 ... (remaining 67350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.013 1.044 8246 Z= 0.986 Angle : 0.854 38.971 11245 Z= 0.555 Chirality : 0.060 0.682 1310 Planarity : 0.008 0.203 1417 Dihedral : 12.531 86.543 2692 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1077 helix: 2.57 (0.26), residues: 362 sheet: 0.07 (0.31), residues: 266 loop : -0.50 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 291 HIS 0.004 0.001 HIS B 225 PHE 0.036 0.002 PHE R 292 TYR 0.030 0.002 TYR S 235 ARG 0.008 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.876 Fit side-chains REVERT: A 17 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7537 (mtmt) REVERT: R 218 LYS cc_start: 0.7698 (ttpp) cc_final: 0.7218 (pttp) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 1.0152 time to fit residues: 170.4051 Evaluate side-chains 118 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8246 Z= 0.185 Angle : 0.529 7.309 11245 Z= 0.282 Chirality : 0.042 0.167 1310 Planarity : 0.005 0.066 1417 Dihedral : 4.188 24.664 1178 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.22 % Allowed : 11.36 % Favored : 86.42 % 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: 1.11 (0.26), residues: 1079 helix: 2.71 (0.26), residues: 368 sheet: 0.33 (0.32), residues: 255 loop : -0.68 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 291 HIS 0.004 0.001 HIS R 113 PHE 0.016 0.001 PHE S 29 TYR 0.012 0.001 TYR S 190 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 0.912 Fit side-chains REVERT: A 17 LYS cc_start: 0.7764 (mtmt) cc_final: 0.7534 (mtmt) REVERT: A 237 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8237 (mm) REVERT: B 52 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7662 (ptm160) REVERT: R 105 MET cc_start: 0.8312 (ttp) cc_final: 0.8078 (ttt) REVERT: R 218 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7255 (pttp) outliers start: 17 outliers final: 7 residues processed: 140 average time/residue: 1.1289 time to fit residues: 168.2030 Evaluate side-chains 131 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain Y residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8246 Z= 0.220 Angle : 0.523 7.132 11245 Z= 0.281 Chirality : 0.042 0.171 1310 Planarity : 0.005 0.058 1417 Dihedral : 4.178 26.124 1178 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.61 % Allowed : 14.10 % Favored : 83.29 % 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: 1.01 (0.26), residues: 1079 helix: 2.63 (0.26), residues: 371 sheet: 0.23 (0.32), residues: 266 loop : -0.76 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 291 HIS 0.007 0.001 HIS A 197 PHE 0.015 0.001 PHE A 189 TYR 0.013 0.001 TYR A 30 ARG 0.007 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.915 Fit side-chains REVERT: A 17 LYS cc_start: 0.7763 (mtmt) cc_final: 0.7511 (mtmt) REVERT: B 52 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7769 (ptm160) REVERT: R 105 MET cc_start: 0.8319 (ttp) cc_final: 0.8098 (ttt) REVERT: R 196 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6991 (mpt) REVERT: R 218 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7237 (pttp) outliers start: 20 outliers final: 8 residues processed: 137 average time/residue: 1.1682 time to fit residues: 169.9936 Evaluate side-chains 129 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 0.0040 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN R 41 ASN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8246 Z= 0.173 Angle : 0.498 6.885 11245 Z= 0.267 Chirality : 0.041 0.156 1310 Planarity : 0.005 0.057 1417 Dihedral : 4.042 21.810 1178 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.00 % Allowed : 16.32 % Favored : 80.68 % 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: 1079 helix: 2.64 (0.26), residues: 373 sheet: 0.34 (0.32), residues: 254 loop : -0.80 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 197 PHE 0.015 0.001 PHE A 189 TYR 0.012 0.001 TYR A 30 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.877 Fit side-chains REVERT: A 17 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7482 (mtmt) REVERT: B 52 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7759 (ptm160) REVERT: R 105 MET cc_start: 0.8299 (ttp) cc_final: 0.8095 (ttt) REVERT: R 196 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6882 (mpt) REVERT: R 218 LYS cc_start: 0.7658 (ttpp) cc_final: 0.7138 (pttp) outliers start: 23 outliers final: 11 residues processed: 143 average time/residue: 1.0708 time to fit residues: 163.5158 Evaluate side-chains 134 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 220 GLN R 59 ASN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8246 Z= 0.270 Angle : 0.556 7.389 11245 Z= 0.297 Chirality : 0.043 0.182 1310 Planarity : 0.005 0.062 1417 Dihedral : 4.190 23.958 1178 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.52 % Allowed : 17.36 % Favored : 79.11 % 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: 1079 helix: 2.52 (0.26), residues: 373 sheet: 0.13 (0.31), residues: 268 loop : -0.81 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.014 0.002 HIS B 225 PHE 0.015 0.001 PHE A 189 TYR 0.015 0.001 TYR R 79 ARG 0.007 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.887 Fit side-chains REVERT: A 17 LYS cc_start: 0.7763 (mtmt) cc_final: 0.7520 (mtmt) REVERT: B 52 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7833 (ptm160) REVERT: R 123 TYR cc_start: 0.7989 (m-80) cc_final: 0.7745 (m-80) REVERT: R 196 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6786 (mpt) REVERT: R 218 LYS cc_start: 0.7764 (ttpp) cc_final: 0.7228 (pttp) outliers start: 27 outliers final: 16 residues processed: 144 average time/residue: 1.1248 time to fit residues: 172.2749 Evaluate side-chains 140 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 259 ASN B 220 GLN S 186 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8246 Z= 0.264 Angle : 0.551 7.037 11245 Z= 0.295 Chirality : 0.043 0.191 1310 Planarity : 0.005 0.066 1417 Dihedral : 4.208 21.093 1178 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.39 % Allowed : 17.89 % Favored : 78.72 % 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: 0.83 (0.26), residues: 1079 helix: 2.45 (0.26), residues: 371 sheet: 0.08 (0.31), residues: 266 loop : -0.80 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.016 0.002 HIS B 225 PHE 0.015 0.001 PHE A 189 TYR 0.013 0.001 TYR A 30 ARG 0.007 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.857 Fit side-chains REVERT: A 17 LYS cc_start: 0.7735 (mtmt) cc_final: 0.7491 (mtmt) REVERT: B 52 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7841 (ptm160) REVERT: R 123 TYR cc_start: 0.7952 (m-80) cc_final: 0.7681 (m-80) REVERT: R 196 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6691 (mpt) REVERT: R 218 LYS cc_start: 0.7778 (ttpp) cc_final: 0.7221 (pttp) REVERT: S 245 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8027 (mp) outliers start: 26 outliers final: 15 residues processed: 148 average time/residue: 1.0458 time to fit residues: 165.1837 Evaluate side-chains 141 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 213 GLN A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN S 186 GLN S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8246 Z= 0.171 Angle : 0.517 7.317 11245 Z= 0.277 Chirality : 0.042 0.209 1310 Planarity : 0.005 0.067 1417 Dihedral : 4.073 20.568 1178 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.13 % Allowed : 19.06 % Favored : 77.81 % 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: 1079 helix: 2.54 (0.26), residues: 372 sheet: 0.07 (0.32), residues: 258 loop : -0.82 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 211 HIS 0.015 0.001 HIS B 225 PHE 0.016 0.001 PHE A 189 TYR 0.013 0.001 TYR R 79 ARG 0.007 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.892 Fit side-chains REVERT: A 17 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7465 (mtmt) REVERT: B 52 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7804 (ptm160) REVERT: R 123 TYR cc_start: 0.7878 (m-80) cc_final: 0.7550 (m-80) REVERT: R 196 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6570 (mpt) REVERT: R 218 LYS cc_start: 0.7757 (ttpp) cc_final: 0.7208 (pttp) outliers start: 24 outliers final: 16 residues processed: 150 average time/residue: 1.0531 time to fit residues: 168.6084 Evaluate side-chains 142 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.0020 chunk 81 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 261 GLN B 220 GLN S 186 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8246 Z= 0.176 Angle : 0.522 7.944 11245 Z= 0.281 Chirality : 0.042 0.212 1310 Planarity : 0.005 0.069 1417 Dihedral : 4.026 20.006 1178 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.52 % Allowed : 19.06 % Favored : 77.42 % 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: 0.87 (0.26), residues: 1079 helix: 2.56 (0.26), residues: 372 sheet: 0.10 (0.32), residues: 257 loop : -0.84 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.014 0.001 HIS B 225 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.001 TYR A 30 ARG 0.007 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.928 Fit side-chains REVERT: A 17 LYS cc_start: 0.7736 (mtmt) cc_final: 0.7472 (mtmt) REVERT: A 313 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7910 (mm) REVERT: B 52 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7789 (ptm160) REVERT: R 123 TYR cc_start: 0.7879 (m-80) cc_final: 0.7586 (m-80) REVERT: R 196 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6508 (mpt) REVERT: R 218 LYS cc_start: 0.7744 (ttpp) cc_final: 0.7202 (pttp) REVERT: S 245 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8044 (mp) outliers start: 27 outliers final: 16 residues processed: 147 average time/residue: 1.0189 time to fit residues: 160.2974 Evaluate side-chains 143 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 98 optimal weight: 0.0270 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 101 optimal weight: 0.3980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 259 ASN A 261 GLN B 220 GLN S 186 GLN S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8246 Z= 0.155 Angle : 0.504 7.609 11245 Z= 0.273 Chirality : 0.042 0.218 1310 Planarity : 0.005 0.070 1417 Dihedral : 3.947 19.432 1178 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.13 % Allowed : 20.37 % Favored : 76.50 % 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: 0.87 (0.26), residues: 1079 helix: 2.47 (0.26), residues: 378 sheet: 0.17 (0.32), residues: 250 loop : -0.84 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 211 HIS 0.011 0.001 HIS B 225 PHE 0.015 0.001 PHE A 189 TYR 0.016 0.001 TYR R 79 ARG 0.007 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 0.885 Fit side-chains REVERT: A 17 LYS cc_start: 0.7745 (mtmt) cc_final: 0.7493 (mtmt) REVERT: A 313 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 52 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7770 (ptm160) REVERT: R 48 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7218 (mp) REVERT: R 123 TYR cc_start: 0.7828 (m-80) cc_final: 0.7522 (m-80) REVERT: R 196 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6518 (mpt) REVERT: R 218 LYS cc_start: 0.7746 (ttpp) cc_final: 0.7236 (pttp) REVERT: S 245 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8009 (mp) outliers start: 24 outliers final: 15 residues processed: 144 average time/residue: 1.0420 time to fit residues: 160.5080 Evaluate side-chains 143 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.0870 chunk 67 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8246 Z= 0.173 Angle : 0.529 8.277 11245 Z= 0.283 Chirality : 0.042 0.220 1310 Planarity : 0.005 0.073 1417 Dihedral : 3.967 19.595 1178 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.87 % Allowed : 20.89 % Favored : 76.24 % 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: 0.87 (0.26), residues: 1079 helix: 2.49 (0.26), residues: 378 sheet: 0.14 (0.32), residues: 250 loop : -0.83 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.011 0.001 HIS B 225 PHE 0.022 0.001 PHE R 307 TYR 0.012 0.001 TYR S 190 ARG 0.009 0.001 ARG S 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.928 Fit side-chains REVERT: A 17 LYS cc_start: 0.7746 (mtmt) cc_final: 0.7493 (mtmt) REVERT: A 313 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7907 (mm) REVERT: B 52 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7755 (ptm160) REVERT: R 48 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7208 (mp) REVERT: R 123 TYR cc_start: 0.7836 (m-80) cc_final: 0.7504 (m-80) REVERT: R 196 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6512 (mpt) REVERT: R 218 LYS cc_start: 0.7745 (ttpp) cc_final: 0.7237 (pttp) REVERT: S 245 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8029 (mp) outliers start: 22 outliers final: 15 residues processed: 137 average time/residue: 1.0190 time to fit residues: 149.6579 Evaluate side-chains 139 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 0.0770 chunk 23 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.158227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122966 restraints weight = 9469.433| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.98 r_work: 0.3277 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 8246 Z= 0.433 Angle : 0.658 9.255 11245 Z= 0.353 Chirality : 0.047 0.231 1310 Planarity : 0.005 0.069 1417 Dihedral : 4.530 25.472 1178 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.26 % Allowed : 20.63 % Favored : 76.11 % 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: 0.60 (0.26), residues: 1079 helix: 2.26 (0.26), residues: 372 sheet: -0.32 (0.30), residues: 282 loop : -0.74 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 36 HIS 0.019 0.002 HIS B 225 PHE 0.021 0.002 PHE S 68 TYR 0.015 0.002 TYR A 306 ARG 0.008 0.001 ARG S 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3344.81 seconds wall clock time: 58 minutes 51.33 seconds (3531.33 seconds total)