Starting phenix.real_space_refine on Sat Aug 3 23:49:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6n_36924/08_2024/8k6n_36924.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6n_36924/08_2024/8k6n_36924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6n_36924/08_2024/8k6n_36924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6n_36924/08_2024/8k6n_36924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6n_36924/08_2024/8k6n_36924.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6n_36924/08_2024/8k6n_36924.cif" } resolution = 3.2 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= 0.029 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 60 5.16 5 C 5915 2.51 5 N 1575 2.21 5 O 1741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 35": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9291 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1807 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" 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: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 267 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 3, 'TRANS': 27} Chain breaks: 1 Chain: "E" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2387 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 10, 'TRANS': 290} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 5.65, per 1000 atoms: 0.61 Number of scatterers: 9291 At special positions: 0 Unit cell: (136, 123.25, 105.4, 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 60 16.00 O 1741 8.00 N 1575 7.00 C 5915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 123 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.83 Conformation dependent library (CDL) restraints added in 1.7 seconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 37.6% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.778A pdb=" N LYS A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.589A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.984A pdb=" N LYS A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.960A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.674A pdb=" N GLN A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.964A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 16 through 32 Processing helix chain 'E' and resid 46 through 78 removed outlier: 3.786A pdb=" N PHE E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 114 removed outlier: 4.183A pdb=" N LEU E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Proline residue: E 105 - end of helix Processing helix chain 'E' and resid 119 through 153 Proline residue: E 127 - end of helix Processing helix chain 'E' and resid 161 through 180 Processing helix chain 'E' and resid 180 through 186 removed outlier: 4.237A pdb=" N ALA E 184 " --> pdb=" O ALA E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 228 removed outlier: 4.520A pdb=" N THR E 217 " --> pdb=" O SER E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 248 Processing helix chain 'E' and resid 256 through 281 removed outlier: 3.976A pdb=" N HIS E 260 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN E 261 " --> pdb=" O ASP E 257 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS E 265 " --> pdb=" O GLN E 261 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR E 266 " --> pdb=" O ARG E 262 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP E 281 " --> pdb=" O PHE E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 292 removed outlier: 3.994A pdb=" N HIS E 285 " --> pdb=" O TRP E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 316 Processing helix chain 'E' and resid 316 through 327 Proline residue: E 322 - end of helix Processing helix chain 'E' and resid 329 through 339 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.559A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.637A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.850A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 235 removed outlier: 6.154A pdb=" N MET A 241 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.844A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.663A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.394A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.536A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.866A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.235A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.885A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 288 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 188 through 194 removed outlier: 4.060A pdb=" N GLU E 188 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 204 " --> pdb=" O GLU E 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.612A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 71 through 73 Processing sheet with id=AB5, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB6, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.860A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER S 208 " --> pdb=" O ALA S 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.824A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1293 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: 2.59 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2716 1.33 - 1.46: 2118 1.46 - 1.58: 4561 1.58 - 1.70: 1 1.70 - 1.83: 88 Bond restraints: 9484 Sorted by residual: bond pdb=" CA SER D 22 " pdb=" CB SER D 22 " ideal model delta sigma weight residual 1.529 1.488 0.041 1.55e-02 4.16e+03 6.89e+00 bond pdb=" N SER D 3 " pdb=" CA SER D 3 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.69e+00 bond pdb=" CA SER D 3 " pdb=" CB SER D 3 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.50e-02 4.44e+03 6.20e+00 bond pdb=" CB PRO C 60 " pdb=" CG PRO C 60 " ideal model delta sigma weight residual 1.492 1.608 -0.116 5.00e-02 4.00e+02 5.42e+00 bond pdb=" N LYS D 4 " pdb=" CA LYS D 4 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.45e-02 4.76e+03 5.34e+00 ... (remaining 9479 not shown) Histogram of bond angle deviations from ideal: 95.74 - 103.40: 81 103.40 - 111.06: 3630 111.06 - 118.72: 3963 118.72 - 126.38: 5030 126.38 - 134.04: 143 Bond angle restraints: 12847 Sorted by residual: angle pdb=" CA PRO C 60 " pdb=" N PRO C 60 " pdb=" CD PRO C 60 " ideal model delta sigma weight residual 112.00 104.94 7.06 1.40e+00 5.10e-01 2.54e+01 angle pdb=" C LYS E 268 " pdb=" N MET E 269 " pdb=" CA MET E 269 " ideal model delta sigma weight residual 121.14 113.34 7.80 1.75e+00 3.27e-01 1.99e+01 angle pdb=" N ILE D 28 " pdb=" CA ILE D 28 " pdb=" C ILE D 28 " ideal model delta sigma weight residual 110.62 106.62 4.00 1.02e+00 9.61e-01 1.54e+01 angle pdb=" CA ASN D 29 " pdb=" C ASN D 29 " pdb=" O ASN D 29 " ideal model delta sigma weight residual 120.82 116.92 3.90 1.05e+00 9.07e-01 1.38e+01 angle pdb=" CA ARG D 35 " pdb=" C ARG D 35 " pdb=" O ARG D 35 " ideal model delta sigma weight residual 120.70 116.90 3.80 1.08e+00 8.57e-01 1.24e+01 ... (remaining 12842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5107 17.31 - 34.62: 440 34.62 - 51.94: 80 51.94 - 69.25: 9 69.25 - 86.56: 6 Dihedral angle restraints: 5642 sinusoidal: 2195 harmonic: 3447 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 60.52 32.48 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA PHE A 268 " pdb=" C PHE A 268 " pdb=" N LEU A 269 " pdb=" CA LEU A 269 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLY S 26 " pdb=" C GLY S 26 " pdb=" N PHE S 27 " pdb=" CA PHE S 27 " ideal model delta harmonic sigma weight residual 180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1248 0.063 - 0.126: 194 0.126 - 0.189: 14 0.189 - 0.252: 8 0.252 - 0.316: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA TYR D 27 " pdb=" N TYR D 27 " pdb=" C TYR D 27 " pdb=" CB TYR D 27 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ARG D 35 " pdb=" N ARG D 35 " pdb=" C ARG D 35 " pdb=" CB ARG D 35 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE D 31 " pdb=" N ILE D 31 " pdb=" C ILE D 31 " pdb=" CB ILE D 31 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1463 not shown) Planarity restraints: 1618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 59 " 0.033 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO C 60 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 111 " -0.012 2.00e-02 2.50e+03 1.14e-02 3.22e+00 pdb=" CG TRP S 111 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP S 111 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP S 111 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP S 111 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP S 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP S 111 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 111 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP S 111 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 251 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO E 252 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 252 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 252 " -0.024 5.00e-02 4.00e+02 ... (remaining 1615 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1038 2.75 - 3.29: 9080 3.29 - 3.82: 14961 3.82 - 4.36: 16897 4.36 - 4.90: 29865 Nonbonded interactions: 71841 Sorted by model distance: nonbonded pdb=" NH1 ARG E 263 " pdb=" OG1 THR E 266 " model vdw 2.211 3.120 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.216 3.040 nonbonded pdb=" O CYS A 255 " pdb=" NZ LYS A 318 " model vdw 2.231 3.120 nonbonded pdb=" OG1 THR E 44 " pdb=" O LYS E 301 " model vdw 2.237 3.040 nonbonded pdb=" NE ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.238 3.120 ... (remaining 71836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.920 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.240 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 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 0.116 9484 Z= 0.262 Angle : 0.662 7.797 12847 Z= 0.384 Chirality : 0.048 0.316 1466 Planarity : 0.004 0.048 1618 Dihedral : 13.234 86.559 3412 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.10 % Allowed : 0.79 % Favored : 99.12 % 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: 0.15 (0.25), residues: 1168 helix: 1.96 (0.26), residues: 408 sheet: -0.15 (0.32), residues: 273 loop : -1.39 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP S 111 HIS 0.007 0.001 HIS D 26 PHE 0.018 0.002 PHE B 235 TYR 0.027 0.002 TYR D 27 ARG 0.002 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 0.999 Fit side-chains REVERT: A 262 ASP cc_start: 0.6790 (t0) cc_final: 0.6548 (t0) REVERT: B 66 ASP cc_start: 0.8367 (p0) cc_final: 0.7777 (p0) REVERT: E 107 THR cc_start: 0.8108 (m) cc_final: 0.7899 (m) REVERT: E 226 ILE cc_start: 0.8028 (tp) cc_final: 0.7760 (tp) REVERT: E 248 ASN cc_start: 0.6941 (m-40) cc_final: 0.6582 (m-40) REVERT: E 267 THR cc_start: 0.7508 (m) cc_final: 0.7307 (m) outliers start: 1 outliers final: 1 residues processed: 162 average time/residue: 0.2335 time to fit residues: 51.2221 Evaluate side-chains 154 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN E 329 ASN S 142 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9484 Z= 0.239 Angle : 0.616 10.121 12847 Z= 0.320 Chirality : 0.043 0.164 1466 Planarity : 0.004 0.041 1618 Dihedral : 5.088 87.185 1284 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.57 % Allowed : 9.22 % Favored : 89.21 % 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: 0.23 (0.25), residues: 1168 helix: 2.13 (0.26), residues: 419 sheet: -0.24 (0.31), residues: 276 loop : -1.46 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 169 HIS 0.004 0.001 HIS D 26 PHE 0.015 0.002 PHE B 235 TYR 0.029 0.002 TYR D 27 ARG 0.004 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.6769 (t0) cc_final: 0.6524 (t0) REVERT: A 341 THR cc_start: 0.8004 (m) cc_final: 0.7795 (m) REVERT: B 323 ASP cc_start: 0.7965 (p0) cc_final: 0.7753 (p0) REVERT: B 340 ASN cc_start: 0.7150 (t0) cc_final: 0.6873 (t0) REVERT: E 179 LEU cc_start: 0.7616 (tp) cc_final: 0.7399 (tt) REVERT: E 226 ILE cc_start: 0.8127 (tp) cc_final: 0.7802 (tp) REVERT: E 248 ASN cc_start: 0.6822 (m-40) cc_final: 0.6491 (m-40) REVERT: S 140 MET cc_start: 0.4655 (mtp) cc_final: 0.4394 (mtp) outliers start: 16 outliers final: 12 residues processed: 161 average time/residue: 0.2670 time to fit residues: 59.2271 Evaluate side-chains 167 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-dev-5409/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-dev-5409/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: 65.4874 > 50: distance: 46 - 110: 30.732 distance: 49 - 107: 22.682 distance: 59 - 97: 29.027 distance: 62 - 94: 29.549 distance: 81 - 86: 27.913 distance: 86 - 87: 51.528 distance: 86 - 174: 31.459 distance: 87 - 88: 8.558 distance: 87 - 90: 10.322 distance: 88 - 89: 42.199 distance: 88 - 94: 39.807 distance: 89 - 171: 24.453 distance: 94 - 95: 26.353 distance: 95 - 96: 31.553 distance: 95 - 98: 11.656 distance: 96 - 97: 27.432 distance: 96 - 101: 30.768 distance: 98 - 99: 15.687 distance: 98 - 100: 21.643 distance: 101 - 102: 38.722 distance: 101 - 159: 23.830 distance: 102 - 103: 37.751 distance: 102 - 105: 17.620 distance: 103 - 104: 43.254 distance: 103 - 107: 27.884 distance: 104 - 156: 27.722 distance: 105 - 106: 40.891 distance: 107 - 108: 8.963 distance: 108 - 109: 11.736 distance: 108 - 111: 8.066 distance: 109 - 110: 34.358 distance: 109 - 112: 19.241 distance: 112 - 113: 7.223 distance: 113 - 114: 5.814 distance: 113 - 116: 6.783 distance: 114 - 118: 11.357 distance: 116 - 117: 42.472 distance: 118 - 119: 21.306 distance: 119 - 120: 25.673 distance: 119 - 122: 20.388 distance: 120 - 121: 25.060 distance: 120 - 127: 22.343 distance: 122 - 123: 35.899 distance: 123 - 124: 21.800 distance: 124 - 125: 11.664 distance: 124 - 126: 57.247 distance: 127 - 128: 32.444 distance: 128 - 129: 7.175 distance: 128 - 131: 31.750 distance: 129 - 130: 36.621 distance: 129 - 135: 36.328 distance: 131 - 132: 43.669 distance: 132 - 133: 14.265 distance: 132 - 134: 22.832 distance: 135 - 136: 17.761 distance: 136 - 137: 18.228 distance: 137 - 138: 33.622 distance: 137 - 139: 12.763 distance: 139 - 140: 6.407 distance: 140 - 141: 12.495 distance: 140 - 143: 23.046 distance: 141 - 142: 9.099 distance: 141 - 148: 31.416 distance: 143 - 144: 8.382 distance: 144 - 145: 33.555 distance: 145 - 146: 19.008 distance: 146 - 147: 42.068 distance: 148 - 149: 9.012 distance: 148 - 190: 30.902 distance: 149 - 150: 12.337 distance: 149 - 152: 25.294 distance: 150 - 151: 6.691 distance: 150 - 156: 25.765 distance: 151 - 187: 28.360 distance: 152 - 153: 6.343 distance: 153 - 154: 28.695 distance: 153 - 155: 13.777