Starting phenix.real_space_refine on Tue Nov 14 17:37:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/11_2023/7s1m_24805.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/11_2023/7s1m_24805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/11_2023/7s1m_24805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/11_2023/7s1m_24805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/11_2023/7s1m_24805.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/11_2023/7s1m_24805.pdb" } resolution = 2.41 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5825 2.51 5 N 1592 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "P GLU 15": "OE1" <-> "OE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9160 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1929 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Chain: "B" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2615 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2963 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 13, 'TRANS': 367} Chain breaks: 2 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 143 Time building chain proxies: 5.16, per 1000 atoms: 0.56 Number of scatterers: 9160 At special positions: 0 Unit cell: (87.15, 171.81, 97.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1686 8.00 N 1592 7.00 C 5825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 3.34 Conformation dependent library (CDL) restraints added in 1.7 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL P 4 " Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 44.8% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.745A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.503A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.556A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.622A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.037A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.274A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.644A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.546A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'R' and resid 32 through 52 Processing helix chain 'R' and resid 91 through 95 Processing helix chain 'R' and resid 139 through 169 Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.508A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 215 removed outlier: 3.574A pdb=" N GLN R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TRP R 214 " --> pdb=" O GLN R 210 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP R 215 " --> pdb=" O GLN R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 255 removed outlier: 4.157A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 291 removed outlier: 3.695A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix removed outlier: 4.056A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 302 through 338 removed outlier: 3.894A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 342 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.712A pdb=" N PHE R 369 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 404 removed outlier: 4.153A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.235A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.537A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.732A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.939A 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: 6.452A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.501A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.955A 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: 4.291A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.575A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.510A 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: 3.894A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.830A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 80 through 84 493 hydrogen bonds defined for protein. 1407 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: 2.64 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2979 1.34 - 1.45: 1441 1.45 - 1.57: 4865 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 9362 Sorted by residual: bond pdb=" N SER R 258 " pdb=" CA SER R 258 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.77e+00 bond pdb=" CA ASP R 372 " pdb=" C ASP R 372 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.27e-02 6.20e+03 1.50e+00 bond pdb=" CG GLN R 37 " pdb=" CD GLN R 37 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" CA SER R 261 " pdb=" C SER R 261 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.29e-02 6.01e+03 1.34e+00 bond pdb=" CA MET R 371 " pdb=" C MET R 371 " ideal model delta sigma weight residual 1.525 1.511 0.013 1.28e-02 6.10e+03 1.09e+00 ... (remaining 9357 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.65: 125 105.65 - 112.78: 4952 112.78 - 119.90: 3149 119.90 - 127.03: 4351 127.03 - 134.16: 121 Bond angle restraints: 12698 Sorted by residual: angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 109.59 102.48 7.11 1.61e+00 3.86e-01 1.95e+01 angle pdb=" N MET R 371 " pdb=" CA MET R 371 " pdb=" C MET R 371 " ideal model delta sigma weight residual 110.35 115.98 -5.63 1.36e+00 5.41e-01 1.71e+01 angle pdb=" N SER R 258 " pdb=" CA SER R 258 " pdb=" C SER R 258 " ideal model delta sigma weight residual 110.80 118.24 -7.44 2.13e+00 2.20e-01 1.22e+01 angle pdb=" N PHE R 257 " pdb=" CA PHE R 257 " pdb=" C PHE R 257 " ideal model delta sigma weight residual 111.30 115.38 -4.08 1.43e+00 4.89e-01 8.14e+00 angle pdb=" N SER R 261 " pdb=" CA SER R 261 " pdb=" C SER R 261 " ideal model delta sigma weight residual 109.15 105.08 4.07 1.44e+00 4.82e-01 7.97e+00 ... (remaining 12693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5080 17.91 - 35.82: 372 35.82 - 53.74: 65 53.74 - 71.65: 9 71.65 - 89.56: 15 Dihedral angle restraints: 5541 sinusoidal: 2137 harmonic: 3404 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual -86.00 -116.56 30.56 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 5538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1216 0.060 - 0.121: 178 0.121 - 0.181: 14 0.181 - 0.242: 1 0.242 - 0.302: 2 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA SER R 258 " pdb=" N SER R 258 " pdb=" C SER R 258 " pdb=" CB SER R 258 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA PHE R 257 " pdb=" N PHE R 257 " pdb=" C PHE R 257 " pdb=" CB PHE R 257 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1408 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 214 " -0.016 2.00e-02 2.50e+03 1.46e-02 5.30e+00 pdb=" CG TRP R 214 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP R 214 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP R 214 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 214 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 214 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 214 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 214 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 214 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP R 214 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 259 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C VAL R 259 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL R 259 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE R 260 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO R 277 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " -0.024 5.00e-02 4.00e+02 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1630 2.77 - 3.30: 8855 3.30 - 3.83: 15642 3.83 - 4.37: 18850 4.37 - 4.90: 31870 Nonbonded interactions: 76847 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.233 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.262 2.440 nonbonded pdb=" O TYR A 318 " pdb=" NH1 ARG A 336 " model vdw 2.270 2.520 nonbonded pdb=" OG1 THR R 175 " pdb=" OE2 GLU R 262 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR A 253 " pdb=" OG SER A 306 " model vdw 2.293 2.440 ... (remaining 76842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.220 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.010 Find NCS groups from input model: 0.270 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.003 0.030 9362 Z= 0.216 Angle : 0.513 7.435 12698 Z= 0.288 Chirality : 0.044 0.302 1411 Planarity : 0.004 0.050 1620 Dihedral : 13.538 89.560 3321 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.10 % Allowed : 0.52 % Favored : 99.37 % 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: 1.84 (0.25), residues: 1146 helix: 2.62 (0.24), residues: 456 sheet: 0.99 (0.36), residues: 225 loop : -0.05 (0.28), residues: 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.082 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 1.4763 time to fit residues: 206.1214 Evaluate side-chains 109 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN R 212 HIS R 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9362 Z= 0.186 Angle : 0.486 5.748 12698 Z= 0.269 Chirality : 0.041 0.148 1411 Planarity : 0.004 0.040 1620 Dihedral : 4.204 21.887 1270 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.36 % Allowed : 7.74 % Favored : 90.90 % 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: 2.01 (0.25), residues: 1146 helix: 2.81 (0.23), residues: 466 sheet: 0.85 (0.36), residues: 225 loop : 0.04 (0.29), residues: 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.022 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 126 average time/residue: 1.4025 time to fit residues: 187.7811 Evaluate side-chains 117 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.5925 time to fit residues: 3.2800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9362 Z= 0.146 Angle : 0.449 6.663 12698 Z= 0.248 Chirality : 0.040 0.167 1411 Planarity : 0.003 0.038 1620 Dihedral : 4.022 20.281 1270 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.15 % Allowed : 9.21 % Favored : 89.64 % 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: 1.95 (0.25), residues: 1146 helix: 2.91 (0.24), residues: 467 sheet: 0.67 (0.35), residues: 220 loop : -0.09 (0.28), residues: 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.070 Fit side-chains outliers start: 11 outliers final: 2 residues processed: 127 average time/residue: 1.4594 time to fit residues: 196.8338 Evaluate side-chains 114 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.2612 time to fit residues: 1.6613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 210 GLN R 211 GLN R 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9362 Z= 0.172 Angle : 0.460 8.086 12698 Z= 0.254 Chirality : 0.040 0.154 1411 Planarity : 0.003 0.038 1620 Dihedral : 4.005 19.322 1270 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.15 % Allowed : 11.72 % Favored : 87.13 % 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: 1.91 (0.25), residues: 1146 helix: 2.93 (0.23), residues: 467 sheet: 0.47 (0.34), residues: 227 loop : -0.08 (0.29), residues: 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.186 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 124 average time/residue: 1.4963 time to fit residues: 196.9428 Evaluate side-chains 115 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.2567 time to fit residues: 1.6176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.0670 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 213 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9362 Z= 0.289 Angle : 0.514 8.123 12698 Z= 0.284 Chirality : 0.043 0.154 1411 Planarity : 0.004 0.039 1620 Dihedral : 4.355 19.683 1270 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.99 % Allowed : 11.82 % Favored : 86.19 % 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: 1.72 (0.25), residues: 1146 helix: 2.67 (0.23), residues: 472 sheet: 0.43 (0.34), residues: 228 loop : -0.12 (0.29), residues: 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.090 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 125 average time/residue: 1.4987 time to fit residues: 198.6225 Evaluate side-chains 119 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1836 time to fit residues: 2.0294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 210 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9362 Z= 0.195 Angle : 0.475 9.186 12698 Z= 0.262 Chirality : 0.040 0.145 1411 Planarity : 0.003 0.037 1620 Dihedral : 4.176 19.379 1270 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.36 % Allowed : 13.39 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.25), residues: 1146 helix: 2.75 (0.23), residues: 472 sheet: 0.38 (0.34), residues: 229 loop : -0.14 (0.29), residues: 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.057 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 122 average time/residue: 1.5654 time to fit residues: 202.6471 Evaluate side-chains 119 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1350 time to fit residues: 1.6763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9362 Z= 0.342 Angle : 0.548 9.899 12698 Z= 0.301 Chirality : 0.044 0.161 1411 Planarity : 0.004 0.039 1620 Dihedral : 4.504 20.337 1270 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.99 % Allowed : 13.70 % Favored : 84.31 % 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: 1.54 (0.25), residues: 1146 helix: 2.53 (0.23), residues: 473 sheet: 0.38 (0.34), residues: 227 loop : -0.25 (0.28), residues: 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.085 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 123 average time/residue: 1.5052 time to fit residues: 195.9820 Evaluate side-chains 116 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.1936 time to fit residues: 2.1273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9362 Z= 0.177 Angle : 0.479 9.948 12698 Z= 0.263 Chirality : 0.040 0.142 1411 Planarity : 0.003 0.038 1620 Dihedral : 4.193 20.274 1270 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.67 % Allowed : 14.64 % Favored : 83.68 % 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: 1.64 (0.25), residues: 1146 helix: 2.70 (0.23), residues: 473 sheet: 0.30 (0.34), residues: 228 loop : -0.23 (0.29), residues: 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.112 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 124 average time/residue: 1.5328 time to fit residues: 201.6235 Evaluate side-chains 118 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.4798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9362 Z= 0.169 Angle : 0.485 10.782 12698 Z= 0.264 Chirality : 0.040 0.140 1411 Planarity : 0.003 0.037 1620 Dihedral : 4.074 20.775 1270 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.36 % Allowed : 15.27 % Favored : 83.37 % 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: 1.71 (0.25), residues: 1146 helix: 2.77 (0.23), residues: 473 sheet: 0.32 (0.34), residues: 226 loop : -0.19 (0.29), residues: 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.075 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 125 average time/residue: 1.4541 time to fit residues: 192.4594 Evaluate side-chains 121 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1966 time to fit residues: 1.5660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 6 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9362 Z= 0.255 Angle : 0.524 11.109 12698 Z= 0.286 Chirality : 0.042 0.149 1411 Planarity : 0.004 0.039 1620 Dihedral : 4.306 21.241 1270 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.46 % Allowed : 15.48 % Favored : 83.05 % 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: 1.64 (0.25), residues: 1146 helix: 2.71 (0.23), residues: 467 sheet: 0.34 (0.34), residues: 226 loop : -0.22 (0.28), residues: 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.081 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 1.4998 time to fit residues: 193.8287 Evaluate side-chains 118 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1124 time to fit residues: 1.4760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN R 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.115580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081580 restraints weight = 14242.375| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.21 r_work: 0.2960 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9362 Z= 0.202 Angle : 0.504 11.020 12698 Z= 0.275 Chirality : 0.041 0.142 1411 Planarity : 0.003 0.037 1620 Dihedral : 4.207 23.175 1270 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.26 % Allowed : 15.79 % Favored : 82.95 % 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: 1.68 (0.25), residues: 1146 helix: 2.80 (0.23), residues: 467 sheet: 0.25 (0.34), residues: 228 loop : -0.20 (0.29), residues: 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3923.89 seconds wall clock time: 70 minutes 23.02 seconds (4223.02 seconds total)