Starting phenix.real_space_refine on Wed Sep 25 00:23:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/09_2024/7s1m_24805.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/09_2024/7s1m_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_24805/09_2024/7s1m_24805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/09_2024/7s1m_24805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/09_2024/7s1m_24805.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1m_24805/09_2024/7s1m_24805.cif" } 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. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9160 Number of models: 1 Model: "" Number of chains: 7 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: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 213 Classifications: {'peptide': 26} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 25} 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: 5.87, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DAL P 4 " - " GLU P 3 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 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: 1.24 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 No H-bonds generated for '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 84 469 hydrogen bonds defined for protein. 1335 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: 3.34 Time building geometry restraints manager: 2.91 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: 2978 1.34 - 1.45: 1441 1.45 - 1.57: 4865 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 9361 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 9356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 12450 1.49 - 2.97: 196 2.97 - 4.46: 33 4.46 - 5.95: 14 5.95 - 7.44: 2 Bond angle restraints: 12695 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 12690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5081 17.91 - 35.82: 373 35.82 - 53.74: 65 53.74 - 71.65: 9 71.65 - 89.56: 15 Dihedral angle restraints: 5543 sinusoidal: 2139 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 5540 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: 1631 2.77 - 3.30: 8876 3.30 - 3.83: 15680 3.83 - 4.37: 18882 4.37 - 4.90: 31874 Nonbonded interactions: 76943 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.262 3.040 nonbonded pdb=" O TYR A 318 " pdb=" NH1 ARG A 336 " model vdw 2.270 3.120 nonbonded pdb=" OG1 THR R 175 " pdb=" OE2 GLU R 262 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR A 253 " pdb=" OG SER A 306 " model vdw 2.293 3.040 ... (remaining 76938 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=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: 1.430 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.160 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:15.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- 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 9361 Z= 0.219 Angle : 0.513 7.435 12695 Z= 0.288 Chirality : 0.044 0.302 1411 Planarity : 0.004 0.050 1619 Dihedral : 13.540 89.560 3320 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP R 214 HIS 0.015 0.001 HIS A 357 PHE 0.014 0.001 PHE R 230 TYR 0.014 0.001 TYR B 59 ARG 0.009 0.000 ARG G 62 *********************** 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 : 1.070 Fit side-chains REVERT: P 17 GLU cc_start: 0.8520 (tp30) cc_final: 0.8037 (tp30) REVERT: R 211 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8331 (tp40) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 1.5963 time to fit residues: 222.8322 Evaluate side-chains 109 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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: 0.8980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 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: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9361 Z= 0.193 Angle : 0.501 5.019 12695 Z= 0.278 Chirality : 0.042 0.156 1411 Planarity : 0.004 0.039 1619 Dihedral : 4.250 21.809 1269 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.36 % Allowed : 7.22 % Favored : 91.42 % 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: 1.88 (0.25), residues: 1146 helix: 2.71 (0.23), residues: 467 sheet: 0.78 (0.36), residues: 226 loop : -0.04 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.011 0.001 HIS A 357 PHE 0.012 0.001 PHE R 230 TYR 0.033 0.001 TYR R 148 ARG 0.005 0.000 ARG R 421 *********************** 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 136 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.121 Fit side-chains REVERT: N 5 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: P 17 GLU cc_start: 0.8508 (tp30) cc_final: 0.8012 (tp30) REVERT: R 71 CYS cc_start: 0.5586 (t) cc_final: 0.5175 (p) REVERT: R 211 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8453 (tp40) REVERT: R 218 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6374 (tp) outliers start: 13 outliers final: 2 residues processed: 126 average time/residue: 1.4344 time to fit residues: 191.6066 Evaluate side-chains 121 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain R residue 218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 83 optimal weight: 6.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9361 Z= 0.158 Angle : 0.470 7.077 12695 Z= 0.259 Chirality : 0.040 0.163 1411 Planarity : 0.003 0.039 1619 Dihedral : 4.077 20.362 1269 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.05 % Allowed : 9.00 % Favored : 89.96 % 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: 1.82 (0.25), residues: 1146 helix: 2.78 (0.23), residues: 467 sheet: 0.58 (0.35), residues: 225 loop : -0.11 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.011 0.001 PHE B 151 TYR 0.028 0.001 TYR R 148 ARG 0.002 0.000 ARG N 72 *********************** 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 131 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.117 Fit side-chains REVERT: P 17 GLU cc_start: 0.8495 (tp30) cc_final: 0.7992 (tp30) REVERT: P 24 GLU cc_start: 0.8898 (tp30) cc_final: 0.8340 (tm-30) REVERT: R 211 GLN cc_start: 0.8638 (tp-100) cc_final: 0.8309 (tp40) outliers start: 10 outliers final: 2 residues processed: 123 average time/residue: 1.4903 time to fit residues: 193.9484 Evaluate side-chains 116 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 14 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9361 Z= 0.196 Angle : 0.485 7.606 12695 Z= 0.266 Chirality : 0.041 0.165 1411 Planarity : 0.003 0.038 1619 Dihedral : 4.127 19.256 1269 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.05 % Allowed : 11.40 % Favored : 87.55 % 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: 1.76 (0.25), residues: 1146 helix: 2.77 (0.23), residues: 467 sheet: 0.49 (0.35), residues: 226 loop : -0.16 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 33 HIS 0.008 0.001 HIS A 357 PHE 0.012 0.001 PHE B 151 TYR 0.026 0.001 TYR R 148 ARG 0.002 0.000 ARG G 62 *********************** 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 129 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 1.447 Fit side-chains REVERT: B 217 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7800 (pmt) REVERT: P 17 GLU cc_start: 0.8511 (tp30) cc_final: 0.8006 (tp30) REVERT: P 24 GLU cc_start: 0.8890 (tp30) cc_final: 0.8266 (tm-30) REVERT: R 71 CYS cc_start: 0.5709 (t) cc_final: 0.5392 (p) REVERT: R 211 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8169 (tp40) outliers start: 10 outliers final: 3 residues processed: 125 average time/residue: 1.5800 time to fit residues: 208.7991 Evaluate side-chains 115 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain R residue 228 LEU 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: 5.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 6 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9361 Z= 0.340 Angle : 0.557 8.758 12695 Z= 0.307 Chirality : 0.045 0.167 1411 Planarity : 0.004 0.039 1619 Dihedral : 4.505 20.082 1269 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.67 % Allowed : 12.03 % Favored : 86.30 % 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: 1.50 (0.25), residues: 1146 helix: 2.41 (0.23), residues: 472 sheet: 0.43 (0.35), residues: 226 loop : -0.21 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 33 HIS 0.009 0.001 HIS A 357 PHE 0.016 0.002 PHE R 230 TYR 0.027 0.002 TYR R 148 ARG 0.003 0.000 ARG G 62 *********************** 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 130 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.089 Fit side-chains REVERT: N 46 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6386 (mm-30) REVERT: P 17 GLU cc_start: 0.8511 (tp30) cc_final: 0.8011 (tp30) REVERT: R 71 CYS cc_start: 0.5652 (t) cc_final: 0.5402 (p) REVERT: R 210 GLN cc_start: 0.8669 (pt0) cc_final: 0.8260 (pt0) REVERT: R 211 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8198 (tp40) outliers start: 16 outliers final: 5 residues processed: 121 average time/residue: 1.5049 time to fit residues: 192.7215 Evaluate side-chains 115 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 228 LEU 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: 0.7980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9361 Z= 0.172 Angle : 0.481 9.487 12695 Z= 0.264 Chirality : 0.041 0.150 1411 Planarity : 0.003 0.038 1619 Dihedral : 4.163 19.224 1269 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.36 % Allowed : 12.97 % Favored : 85.67 % 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: 1.61 (0.25), residues: 1146 helix: 2.60 (0.24), residues: 473 sheet: 0.37 (0.34), residues: 226 loop : -0.21 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 33 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 230 TYR 0.024 0.001 TYR R 148 ARG 0.002 0.000 ARG A 265 *********************** 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 128 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.093 Fit side-chains REVERT: B 59 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8394 (t80) REVERT: P 17 GLU cc_start: 0.8495 (tp30) cc_final: 0.8005 (tp30) REVERT: R 211 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8071 (tp40) REVERT: R 320 ASN cc_start: 0.8368 (m-40) cc_final: 0.8164 (t0) outliers start: 13 outliers final: 4 residues processed: 124 average time/residue: 1.4867 time to fit residues: 195.4228 Evaluate side-chains 115 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8377 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9361 Z= 0.173 Angle : 0.489 10.288 12695 Z= 0.267 Chirality : 0.040 0.149 1411 Planarity : 0.003 0.037 1619 Dihedral : 4.110 19.421 1269 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.46 % Allowed : 13.70 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1146 helix: 2.63 (0.24), residues: 473 sheet: 0.40 (0.34), residues: 225 loop : -0.25 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 33 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 230 TYR 0.024 0.001 TYR R 148 ARG 0.003 0.000 ARG G 62 *********************** 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 124 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.075 Fit side-chains REVERT: B 59 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8379 (t80) REVERT: B 234 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8570 (m-80) REVERT: P 17 GLU cc_start: 0.8497 (tp30) cc_final: 0.8007 (tp30) REVERT: R 211 GLN cc_start: 0.8507 (tp-100) cc_final: 0.8074 (tp40) outliers start: 14 outliers final: 5 residues processed: 119 average time/residue: 1.5059 time to fit residues: 189.9769 Evaluate side-chains 116 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 210 GLN R 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9361 Z= 0.187 Angle : 0.493 10.435 12695 Z= 0.270 Chirality : 0.041 0.149 1411 Planarity : 0.003 0.037 1619 Dihedral : 4.115 19.179 1269 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.36 % Allowed : 14.54 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1146 helix: 2.63 (0.24), residues: 473 sheet: 0.51 (0.35), residues: 220 loop : -0.30 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 33 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 260 TYR 0.027 0.001 TYR R 69 ARG 0.001 0.000 ARG N 98 *********************** 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 124 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.115 Fit side-chains REVERT: B 59 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8388 (t80) REVERT: P 17 GLU cc_start: 0.8496 (tp30) cc_final: 0.8008 (tp30) REVERT: P 24 GLU cc_start: 0.8825 (tp30) cc_final: 0.8177 (tm-30) REVERT: R 211 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8194 (tp40) outliers start: 13 outliers final: 7 residues processed: 120 average time/residue: 1.5798 time to fit residues: 200.4353 Evaluate side-chains 118 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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: 0.8379 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9361 Z= 0.184 Angle : 0.497 10.981 12695 Z= 0.271 Chirality : 0.041 0.149 1411 Planarity : 0.003 0.037 1619 Dihedral : 4.087 19.317 1269 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.57 % Allowed : 14.75 % 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: 1.62 (0.25), residues: 1146 helix: 2.68 (0.24), residues: 470 sheet: 0.37 (0.34), residues: 225 loop : -0.26 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 33 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 230 TYR 0.023 0.001 TYR R 148 ARG 0.001 0.000 ARG R 310 *********************** 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 126 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.134 Fit side-chains REVERT: B 59 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8384 (t80) REVERT: B 234 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: P 17 GLU cc_start: 0.8494 (tp30) cc_final: 0.8004 (tp30) REVERT: P 24 GLU cc_start: 0.8839 (tp30) cc_final: 0.8180 (tm-30) REVERT: R 211 GLN cc_start: 0.8497 (tp-100) cc_final: 0.8033 (tp40) outliers start: 15 outliers final: 7 residues processed: 122 average time/residue: 1.4410 time to fit residues: 186.4210 Evaluate side-chains 117 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain R residue 228 LEU 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: 7.9990 chunk 113 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9361 Z= 0.199 Angle : 0.510 12.129 12695 Z= 0.278 Chirality : 0.041 0.150 1411 Planarity : 0.003 0.037 1619 Dihedral : 4.125 19.978 1269 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.26 % Allowed : 15.27 % Favored : 83.47 % 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: 1.62 (0.25), residues: 1146 helix: 2.67 (0.24), residues: 470 sheet: 0.50 (0.35), residues: 219 loop : -0.32 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 33 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 230 TYR 0.028 0.001 TYR R 69 ARG 0.002 0.000 ARG N 105 ********************** 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 120 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.118 Fit side-chains REVERT: B 59 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8390 (t80) REVERT: B 234 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8589 (m-80) REVERT: P 17 GLU cc_start: 0.8493 (tp30) cc_final: 0.8000 (tp30) REVERT: P 24 GLU cc_start: 0.8858 (tp30) cc_final: 0.8201 (tm-30) REVERT: R 211 GLN cc_start: 0.8489 (tp-100) cc_final: 0.7979 (tp40) outliers start: 12 outliers final: 7 residues processed: 116 average time/residue: 1.4985 time to fit residues: 185.1174 Evaluate side-chains 116 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.114394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080167 restraints weight = 14287.474| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.21 r_work: 0.2939 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9361 Z= 0.251 Angle : 0.534 12.079 12695 Z= 0.291 Chirality : 0.042 0.157 1411 Planarity : 0.004 0.038 1619 Dihedral : 4.286 20.075 1269 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.26 % Allowed : 15.17 % Favored : 83.58 % 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: 2.58 (0.23), residues: 470 sheet: 0.36 (0.34), residues: 226 loop : -0.28 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 33 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.002 PHE R 230 TYR 0.024 0.002 TYR R 148 ARG 0.001 0.000 ARG N 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4017.40 seconds wall clock time: 71 minutes 4.80 seconds (4264.80 seconds total)