Starting phenix.real_space_refine on Thu Jan 18 08:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3s_30566/01_2024/7d3s_30566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3s_30566/01_2024/7d3s_30566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3s_30566/01_2024/7d3s_30566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3s_30566/01_2024/7d3s_30566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3s_30566/01_2024/7d3s_30566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3s_30566/01_2024/7d3s_30566.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 50 5.16 5 C 5286 2.51 5 N 1473 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 9": "OE1" <-> "OE2" Residue "R GLU 133": "OE1" <-> "OE2" Residue "R ARG 169": "NH1" <-> "NH2" Residue "R ARG 174": "NH1" <-> "NH2" Residue "R GLU 373": "OE1" <-> "OE2" Residue "R GLU 398": "OE1" <-> "OE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8338 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2179 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 4, 'TRANS': 261} Chain breaks: 2 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1921 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} 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} Time building chain proxies: 4.91, per 1000 atoms: 0.59 Number of scatterers: 8338 At special positions: 0 Unit cell: (122.84, 98.4936, 107.347, 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 50 16.00 O 1529 8.00 N 1473 7.00 C 5286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " distance=2.02 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 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: 3.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'P' and resid 1 through 27 Processing helix chain 'R' and resid 132 through 166 Processing helix chain 'R' and resid 167 through 171 removed outlier: 3.509A pdb=" N LEU R 170 " --> pdb=" O PHE R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 200 removed outlier: 3.527A pdb=" N ILE R 177 " --> pdb=" O THR R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 246 Processing helix chain 'R' and resid 250 through 281 removed outlier: 3.832A pdb=" N GLN R 256 " --> pdb=" O ARG R 252 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY R 257 " --> pdb=" O LYS R 253 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 291 through 327 removed outlier: 4.202A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Proline residue: R 301 - end of helix removed outlier: 3.867A pdb=" N GLN R 327 " --> pdb=" O LYS R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'R' and resid 347 through 352 Processing helix chain 'R' and resid 365 through 377 Processing helix chain 'R' and resid 379 through 391 Processing helix chain 'R' and resid 392 through 405 removed outlier: 3.560A pdb=" N LYS R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.724A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 252 through 268 removed outlier: 4.212A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.026A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.591A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.886A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.659A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.286A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.574A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.819A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.791A 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: 5.939A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.927A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.985A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.444A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.857A 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: 3.644A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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: 6.898A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1284 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: 2.52 Time building geometry restraints manager: 3.42 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: 2750 1.34 - 1.46: 1906 1.46 - 1.58: 3780 1.58 - 1.70: 0 1.70 - 1.81: 71 Bond restraints: 8507 Sorted by residual: bond pdb=" CA TYR A 381 " pdb=" C TYR A 381 " ideal model delta sigma weight residual 1.523 1.490 0.033 1.41e-02 5.03e+03 5.38e+00 bond pdb=" CB TRP B 63 " pdb=" CG TRP B 63 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.72e+00 bond pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.33e+00 bond pdb=" N CYS R 389 " pdb=" CA CYS R 389 " ideal model delta sigma weight residual 1.460 1.446 0.014 1.27e-02 6.20e+03 1.21e+00 bond pdb=" CA PHE R 371 " pdb=" C PHE R 371 " ideal model delta sigma weight residual 1.525 1.510 0.015 1.37e-02 5.33e+03 1.17e+00 ... (remaining 8502 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.50: 95 105.50 - 112.65: 4408 112.65 - 119.79: 2830 119.79 - 126.93: 4058 126.93 - 134.08: 108 Bond angle restraints: 11499 Sorted by residual: angle pdb=" N HIS R 211 " pdb=" CA HIS R 211 " pdb=" C HIS R 211 " ideal model delta sigma weight residual 112.58 108.88 3.70 1.22e+00 6.72e-01 9.19e+00 angle pdb=" C LEU R 374 " pdb=" N ALA R 375 " pdb=" CA ALA R 375 " ideal model delta sigma weight residual 122.06 116.46 5.60 1.86e+00 2.89e-01 9.07e+00 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 114.80 118.98 -4.18 1.42e+00 4.96e-01 8.65e+00 angle pdb=" CA TYR R 146 " pdb=" CB TYR R 146 " pdb=" CG TYR R 146 " ideal model delta sigma weight residual 113.90 118.91 -5.01 1.80e+00 3.09e-01 7.75e+00 angle pdb=" N ALA R 245 " pdb=" CA ALA R 245 " pdb=" C ALA R 245 " ideal model delta sigma weight residual 114.31 111.14 3.17 1.29e+00 6.01e-01 6.02e+00 ... (remaining 11494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4560 17.79 - 35.57: 431 35.57 - 53.36: 50 53.36 - 71.14: 17 71.14 - 88.93: 7 Dihedral angle restraints: 5065 sinusoidal: 2025 harmonic: 3040 Sorted by residual: dihedral pdb=" CA LEU B 70 " pdb=" C LEU B 70 " pdb=" N VAL B 71 " pdb=" CA VAL B 71 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 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 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA PHE R 358 " pdb=" C PHE R 358 " pdb=" N ALA R 359 " pdb=" CA ALA R 359 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 788 0.036 - 0.071: 365 0.071 - 0.107: 97 0.107 - 0.142: 26 0.142 - 0.178: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1274 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 372 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C PHE R 372 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE R 372 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU R 373 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 387 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU R 387 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU R 387 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR R 388 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 386 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C VAL R 386 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL R 386 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU R 387 " -0.017 2.00e-02 2.50e+03 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1551 2.77 - 3.30: 7877 3.30 - 3.83: 14171 3.83 - 4.37: 17502 4.37 - 4.90: 29472 Nonbonded interactions: 70573 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.237 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.241 2.440 nonbonded pdb=" NZ LYS R 323 " pdb=" OE1 GLN A 374 " model vdw 2.266 2.520 nonbonded pdb=" NE2 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.277 2.520 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.285 2.520 ... (remaining 70568 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 2.300 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.640 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.004 0.048 8507 Z= 0.271 Angle : 0.643 7.026 11499 Z= 0.394 Chirality : 0.043 0.178 1277 Planarity : 0.005 0.058 1469 Dihedral : 13.878 88.926 3090 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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: -2.28 (0.23), residues: 1030 helix: -0.99 (0.23), residues: 423 sheet: -0.95 (0.32), residues: 219 loop : -2.31 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.008 0.001 HIS R 178 PHE 0.025 0.002 PHE R 313 TYR 0.016 0.002 TYR R 146 ARG 0.011 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.936 Fit side-chains REVERT: R 346 LEU cc_start: 0.8167 (mp) cc_final: 0.7678 (mt) REVERT: R 368 ILE cc_start: 0.7624 (tt) cc_final: 0.7414 (tp) REVERT: A 27 GLU cc_start: 0.6300 (tp30) cc_final: 0.5629 (tp30) REVERT: A 60 MET cc_start: 0.7722 (mmm) cc_final: 0.7407 (mmt) REVERT: A 209 GLU cc_start: 0.7343 (tt0) cc_final: 0.7071 (tt0) REVERT: A 258 GLU cc_start: 0.7778 (pt0) cc_final: 0.7489 (pt0) REVERT: A 321 ASP cc_start: 0.7469 (t70) cc_final: 0.7076 (t0) REVERT: A 382 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7336 (mt-10) REVERT: B 96 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7541 (mtt180) REVERT: B 124 TYR cc_start: 0.7729 (m-80) cc_final: 0.7314 (m-80) REVERT: B 138 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6323 (mt-10) REVERT: N 5 GLN cc_start: 0.6876 (tp-100) cc_final: 0.6434 (mt0) REVERT: N 82 GLN cc_start: 0.7193 (tp40) cc_final: 0.6925 (tp-100) REVERT: N 94 TYR cc_start: 0.7943 (m-80) cc_final: 0.7627 (m-80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 1.3207 time to fit residues: 219.3164 Evaluate side-chains 120 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 GLN P 24 GLN R 132 ASN R 241 HIS R 336 HIS R 354 HIS A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 269 ASN B 88 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN N 31 ASN N 39 GLN N 82 GLN N 120 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8507 Z= 0.201 Angle : 0.525 8.076 11499 Z= 0.289 Chirality : 0.042 0.139 1277 Planarity : 0.005 0.071 1469 Dihedral : 4.666 23.528 1148 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.67 % Allowed : 12.47 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1030 helix: 0.73 (0.25), residues: 420 sheet: -0.47 (0.33), residues: 216 loop : -1.73 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.017 0.002 PHE R 313 TYR 0.029 0.002 TYR R 146 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.954 Fit side-chains REVERT: R 246 ILE cc_start: 0.7645 (mt) cc_final: 0.7420 (mp) REVERT: R 367 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6490 (mp0) REVERT: A 27 GLU cc_start: 0.6390 (tp30) cc_final: 0.5692 (tp30) REVERT: A 58 LYS cc_start: 0.6768 (ttpp) cc_final: 0.6058 (mmmt) REVERT: A 301 TYR cc_start: 0.8188 (m-80) cc_final: 0.7735 (m-80) REVERT: A 346 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6146 (mtp180) REVERT: A 382 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7315 (mt-10) REVERT: B 124 TYR cc_start: 0.7729 (m-80) cc_final: 0.7282 (m-80) REVERT: B 175 GLN cc_start: 0.7738 (mm110) cc_final: 0.7529 (mm110) REVERT: N 5 GLN cc_start: 0.6796 (tp-100) cc_final: 0.6402 (mt0) REVERT: N 94 TYR cc_start: 0.7848 (m-80) cc_final: 0.7614 (m-80) outliers start: 24 outliers final: 10 residues processed: 141 average time/residue: 1.3066 time to fit residues: 195.0431 Evaluate side-chains 129 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain N residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.0170 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 400 GLN A 254 ASN B 91 HIS ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 8507 Z= 0.199 Angle : 0.481 7.471 11499 Z= 0.266 Chirality : 0.040 0.144 1277 Planarity : 0.004 0.051 1469 Dihedral : 4.341 18.268 1148 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.34 % Allowed : 16.04 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1030 helix: 1.39 (0.25), residues: 425 sheet: -0.25 (0.34), residues: 214 loop : -1.55 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.015 0.001 PHE R 313 TYR 0.023 0.001 TYR R 146 ARG 0.002 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 0.945 Fit side-chains REVERT: R 156 MET cc_start: 0.7161 (mmp) cc_final: 0.6910 (mmp) REVERT: R 246 ILE cc_start: 0.7481 (mt) cc_final: 0.7232 (mp) REVERT: R 344 THR cc_start: 0.8097 (m) cc_final: 0.7711 (m) REVERT: R 348 ILE cc_start: 0.8003 (mt) cc_final: 0.7757 (mt) REVERT: R 367 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6567 (mp0) REVERT: A 27 GLU cc_start: 0.6396 (tp30) cc_final: 0.5951 (tp30) REVERT: A 58 LYS cc_start: 0.7068 (ttpp) cc_final: 0.6438 (mmmt) REVERT: A 60 MET cc_start: 0.7233 (mmt) cc_final: 0.6834 (mmt) REVERT: A 301 TYR cc_start: 0.8053 (m-80) cc_final: 0.7571 (m-80) REVERT: A 346 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.5982 (mtp180) REVERT: A 382 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6709 (mt-10) REVERT: B 96 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7257 (mtt-85) REVERT: B 124 TYR cc_start: 0.7613 (m-80) cc_final: 0.7170 (m-80) REVERT: B 146 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8131 (tt) REVERT: B 175 GLN cc_start: 0.7610 (mm110) cc_final: 0.7374 (mm110) REVERT: N 5 GLN cc_start: 0.6828 (tp-100) cc_final: 0.6451 (mt0) REVERT: N 94 TYR cc_start: 0.7815 (m-80) cc_final: 0.7551 (m-80) outliers start: 21 outliers final: 9 residues processed: 131 average time/residue: 1.3285 time to fit residues: 184.3165 Evaluate side-chains 128 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2762 > 50: distance: 24 - 163: 21.917 distance: 27 - 160: 23.366 distance: 42 - 146: 6.291 distance: 45 - 143: 7.371 distance: 89 - 154: 4.001 distance: 92 - 151: 7.214 distance: 102 - 134: 6.793 distance: 105 - 131: 4.992 distance: 125 - 131: 3.159 distance: 132 - 133: 4.840 distance: 132 - 135: 6.273 distance: 133 - 134: 6.425 distance: 133 - 143: 3.134 distance: 135 - 136: 7.773 distance: 136 - 137: 3.428 distance: 136 - 138: 5.679 distance: 141 - 142: 4.217 distance: 144 - 145: 6.106 distance: 144 - 147: 10.032 distance: 145 - 146: 7.498 distance: 145 - 151: 7.055 distance: 147 - 148: 18.698 distance: 148 - 149: 13.344 distance: 148 - 150: 6.423 distance: 151 - 152: 10.300 distance: 152 - 155: 9.772 distance: 153 - 154: 9.841 distance: 153 - 160: 9.575 distance: 155 - 156: 9.230 distance: 156 - 157: 7.428 distance: 157 - 158: 7.370 distance: 157 - 159: 9.349 distance: 160 - 161: 13.017 distance: 161 - 162: 14.830 distance: 161 - 164: 8.722 distance: 162 - 163: 10.131 distance: 162 - 168: 10.367 distance: 164 - 165: 12.915 distance: 165 - 166: 19.269 distance: 166 - 167: 20.053 distance: 168 - 169: 7.613 distance: 169 - 170: 10.253 distance: 170 - 171: 5.513 distance: 170 - 176: 4.713 distance: 172 - 173: 28.691 distance: 173 - 174: 6.970 distance: 173 - 175: 20.242 distance: 176 - 177: 13.931 distance: 177 - 178: 13.013 distance: 177 - 180: 20.175 distance: 178 - 179: 27.406 distance: 178 - 182: 20.441 distance: 180 - 181: 21.198 distance: 182 - 183: 12.658 distance: 183 - 184: 12.470 distance: 183 - 186: 29.748 distance: 184 - 185: 30.788 distance: 184 - 190: 21.009 distance: 186 - 187: 16.548 distance: 187 - 188: 20.470 distance: 187 - 189: 20.007 distance: 190 - 191: 13.043 distance: 191 - 192: 10.834 distance: 191 - 194: 10.023 distance: 192 - 193: 18.829 distance: 192 - 199: 21.253 distance: 193 - 215: 25.100 distance: 194 - 195: 7.249 distance: 195 - 196: 12.207 distance: 196 - 197: 18.402 distance: 197 - 198: 5.551 distance: 199 - 200: 24.694 distance: 199 - 205: 20.050 distance: 200 - 201: 15.017 distance: 200 - 203: 8.600 distance: 201 - 202: 21.920 distance: 201 - 206: 11.231 distance: 203 - 204: 6.061 distance: 204 - 205: 30.308 distance: 206 - 207: 17.648 distance: 207 - 208: 8.150 distance: 207 - 210: 24.361 distance: 208 - 209: 5.961 distance: 208 - 215: 10.686 distance: 210 - 211: 4.390 distance: 211 - 212: 4.700 distance: 212 - 213: 7.260 distance: 212 - 214: 4.510