Starting phenix.real_space_refine on Fri Jul 19 17:31:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/07_2024/8jkz_36384.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/07_2024/8jkz_36384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/07_2024/8jkz_36384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/07_2024/8jkz_36384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/07_2024/8jkz_36384.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/07_2024/8jkz_36384.cif" } resolution = 3.6 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 33 5.16 5 C 5404 2.51 5 N 1443 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 313": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8444 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4674 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 23, 'TRANS': 560} Chain: "B" Number of atoms: 3726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3726 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 28, 'TRANS': 440} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.13, per 1000 atoms: 0.61 Number of scatterers: 8444 At special positions: 0 Unit cell: (78.12, 98.28, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 2 15.00 O 1562 8.00 N 1443 7.00 C 5404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.76 Conformation dependent library (CDL) restraints added in 1.8 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 11 sheets defined 41.5% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 removed outlier: 3.550A pdb=" N GLN A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 33 removed outlier: 3.621A pdb=" N THR A 28 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 29 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 30 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 33 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.600A pdb=" N SER A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 98 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.826A pdb=" N SER A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 198 through 217 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 286 through 297 removed outlier: 4.075A pdb=" N GLN A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.547A pdb=" N ARG A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 406 through 414 removed outlier: 3.965A pdb=" N SER A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 532 through 548 removed outlier: 3.574A pdb=" N GLN A 538 " --> pdb=" O GLN A 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.837A pdb=" N LEU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.699A pdb=" N ARG B 106 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.948A pdb=" N VAL B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.602A pdb=" N ALA B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 184 through 189 removed outlier: 4.118A pdb=" N LEU B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.547A pdb=" N VAL B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 276 through 295 Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.514A pdb=" N GLN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 4.150A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 458 removed outlier: 3.624A pdb=" N VAL B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184 removed outlier: 6.404A pdb=" N VAL A 138 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N MET A 20 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N PHE A 139 " --> pdb=" O MET A 20 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TRP A 22 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 252 removed outlier: 6.546A pdb=" N LEU A 251 " --> pdb=" O TYR A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 580 removed outlier: 3.610A pdb=" N ALA A 330 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 345 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.550A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 removed outlier: 3.611A pdb=" N CYS A 345 " --> pdb=" O TYR A 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 561 removed outlier: 3.548A pdb=" N ALA A 569 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.331A pdb=" N ILE B 303 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 332 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 305 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE B 334 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS B 307 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.331A pdb=" N ILE B 303 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 332 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 305 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE B 334 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS B 307 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.748A pdb=" N ARG B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.669A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 51 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU B 147 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA B 53 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N TYR B 149 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 55 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 146 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE B 183 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 148 " --> pdb=" O ILE B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 265 through 267 346 hydrogen bonds defined for protein. 990 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: 2.72 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1378 1.31 - 1.43: 2382 1.43 - 1.56: 4838 1.56 - 1.68: 8 1.68 - 1.81: 51 Bond restraints: 8657 Sorted by residual: bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.243 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C4B NAD A 601 " pdb=" O4B NAD A 601 " ideal model delta sigma weight residual 1.433 1.681 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C3B NAD A 601 " pdb=" C4B NAD A 601 " ideal model delta sigma weight residual 1.523 1.281 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C4D NAD A 601 " pdb=" O4D NAD A 601 " ideal model delta sigma weight residual 1.445 1.274 0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" C7N NAD A 601 " pdb=" N7N NAD A 601 " ideal model delta sigma weight residual 1.328 1.473 -0.145 2.00e-02 2.50e+03 5.25e+01 ... (remaining 8652 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.60: 267 106.60 - 113.83: 4773 113.83 - 121.07: 4178 121.07 - 128.30: 2459 128.30 - 135.53: 71 Bond angle restraints: 11748 Sorted by residual: angle pdb=" C ILE A 390 " pdb=" N PHE A 391 " pdb=" CA PHE A 391 " ideal model delta sigma weight residual 121.54 131.43 -9.89 1.91e+00 2.74e-01 2.68e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.43 13.21 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C ALA B 9 " pdb=" CA ALA B 9 " pdb=" CB ALA B 9 " ideal model delta sigma weight residual 116.34 110.45 5.89 1.40e+00 5.10e-01 1.77e+01 angle pdb=" O3 NAD A 601 " pdb=" PN NAD A 601 " pdb=" O5D NAD A 601 " ideal model delta sigma weight residual 98.00 109.75 -11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O1N NAD A 601 " pdb=" PN NAD A 601 " pdb=" O2N NAD A 601 " ideal model delta sigma weight residual 120.02 109.43 10.59 3.00e+00 1.11e-01 1.25e+01 ... (remaining 11743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4401 17.98 - 35.96: 593 35.96 - 53.95: 154 53.95 - 71.93: 32 71.93 - 89.91: 15 Dihedral angle restraints: 5195 sinusoidal: 2120 harmonic: 3075 Sorted by residual: dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N PRO B 47 " pdb=" CA PRO B 47 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA TYR A 374 " pdb=" C TYR A 374 " pdb=" N THR A 375 " pdb=" CA THR A 375 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA MET A 132 " pdb=" C MET A 132 " pdb=" N ASN A 133 " pdb=" CA ASN A 133 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1141 0.070 - 0.140: 130 0.140 - 0.210: 8 0.210 - 0.280: 1 0.280 - 0.351: 1 Chirality restraints: 1281 Sorted by residual: chirality pdb=" C3D NAD A 601 " pdb=" C2D NAD A 601 " pdb=" C4D NAD A 601 " pdb=" O3D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C3B NAD A 601 " pdb=" C2B NAD A 601 " pdb=" C4B NAD A 601 " pdb=" O3B NAD A 601 " both_signs ideal model delta sigma weight residual False -2.71 -2.44 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2D NAD A 601 " pdb=" C1D NAD A 601 " pdb=" C3D NAD A 601 " pdb=" O2D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.56 -2.37 -0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 1278 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 206 " 0.187 9.50e-02 1.11e+02 8.39e-02 4.33e+00 pdb=" NE ARG A 206 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 206 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 206 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 206 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 391 " -0.011 2.00e-02 2.50e+03 1.52e-02 4.06e+00 pdb=" CG PHE A 391 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 391 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 391 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 391 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 391 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 391 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 390 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ILE A 390 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE A 390 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 391 " 0.010 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1203 2.76 - 3.29: 8017 3.29 - 3.83: 13547 3.83 - 4.36: 15536 4.36 - 4.90: 27371 Nonbonded interactions: 65674 Sorted by model distance: nonbonded pdb=" OH TYR B 83 " pdb=" O ASN B 436 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR B 277 " pdb=" OD2 ASP B 321 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR A 333 " pdb=" O ALA A 578 " model vdw 2.233 2.440 nonbonded pdb=" OE2 GLU B 330 " pdb=" NH1 ARG B 411 " model vdw 2.267 2.520 nonbonded pdb=" ND2 ASN B 389 " pdb=" OE1 GLN B 392 " model vdw 2.267 2.520 ... (remaining 65669 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 group one per residue 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: 0.690 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: 26.690 Find NCS groups from input model: 0.080 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.007 0.288 8657 Z= 0.369 Angle : 0.735 13.209 11748 Z= 0.398 Chirality : 0.045 0.351 1281 Planarity : 0.004 0.084 1505 Dihedral : 17.975 89.910 3219 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.01 % Favored : 89.90 % Rotamer: Outliers : 1.00 % Allowed : 26.00 % Favored : 73.01 % 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: -1.21 (0.27), residues: 1049 helix: 0.80 (0.27), residues: 388 sheet: -0.76 (0.40), residues: 189 loop : -2.25 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.007 0.001 HIS A 52 PHE 0.035 0.002 PHE A 391 TYR 0.013 0.001 TYR B 149 ARG 0.006 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 0.2552 time to fit residues: 31.1614 Evaluate side-chains 78 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain B residue 257 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-dev-5388/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-dev-5388/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-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-dev-5388/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-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-dev-5388/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-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.502 > 50: distance: 48 - 61: 7.301 distance: 54 - 70: 19.442 distance: 57 - 61: 8.060 distance: 61 - 62: 5.735 distance: 62 - 65: 3.562 distance: 63 - 64: 13.707 distance: 63 - 70: 12.649 distance: 65 - 66: 6.144 distance: 66 - 67: 11.007 distance: 67 - 68: 10.198 distance: 68 - 69: 24.545 distance: 70 - 71: 14.541 distance: 71 - 72: 13.637 distance: 71 - 74: 8.002 distance: 72 - 76: 16.965 distance: 74 - 75: 4.338 distance: 76 - 77: 10.374 distance: 77 - 78: 23.569 distance: 77 - 80: 15.704 distance: 78 - 79: 18.287 distance: 78 - 85: 4.544 distance: 79 - 104: 21.406 distance: 80 - 81: 16.666 distance: 82 - 83: 7.585 distance: 85 - 86: 8.489 distance: 85 - 91: 18.218 distance: 86 - 87: 3.351 distance: 86 - 89: 3.321 distance: 87 - 88: 11.321 distance: 87 - 92: 12.279 distance: 88 - 113: 6.644 distance: 89 - 90: 11.424 distance: 90 - 91: 16.331 distance: 92 - 93: 7.500 distance: 93 - 94: 3.755 distance: 93 - 96: 9.146 distance: 94 - 97: 6.323 distance: 95 - 121: 9.890 distance: 97 - 98: 4.295 distance: 98 - 99: 6.076 distance: 98 - 101: 7.815 distance: 99 - 100: 4.503 distance: 99 - 104: 4.456 distance: 100 - 129: 17.121 distance: 101 - 102: 15.829 distance: 101 - 103: 4.961 distance: 105 - 106: 6.733 distance: 105 - 108: 6.761 distance: 106 - 107: 4.683 distance: 106 - 113: 3.126 distance: 107 - 137: 14.145 distance: 109 - 110: 6.791 distance: 110 - 111: 10.906 distance: 110 - 112: 12.362 distance: 113 - 114: 7.893 distance: 114 - 115: 3.910 distance: 114 - 117: 5.753 distance: 115 - 116: 5.194 distance: 115 - 121: 7.782 distance: 116 - 144: 13.759 distance: 117 - 118: 17.832 distance: 118 - 119: 10.232 distance: 118 - 120: 4.461 distance: 121 - 122: 4.968 distance: 122 - 123: 6.239 distance: 122 - 125: 3.553 distance: 123 - 124: 7.023 distance: 123 - 129: 4.981 distance: 124 - 151: 15.091 distance: 125 - 126: 5.063 distance: 126 - 127: 5.540 distance: 126 - 128: 6.014 distance: 129 - 130: 4.775 distance: 130 - 131: 4.474 distance: 130 - 133: 5.001 distance: 132 - 156: 4.516 distance: 133 - 135: 9.107 distance: 134 - 136: 11.419