INPUT Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwq_30882/12_2022/7dwq_30882.pdb Reading option "hydrogens=False" from command line Writing effective parameters to 7dwq_30882.eff Ligand restraint generation using eLBOW, phenix.elbow Build ligand and use monomer library to name atoms : LHG Using monomer library entry LHG as template Build ligand and use monomer library to name atoms : PHO Using monomer library entry PHO as template Processing a loop Build ligand and use chemical components : SF4 MoleculeClass : S: 4 Fe: 4 (CHEMICAL COMPONENTS format) 8 atoms 12 bonds 0 angles 0 dihedrals 0 rings 0 chirals Mapped the ligand (SF4) to the monomer library restraints Build ligand and use monomer library to name atoms : PQN Using monomer library entry PQN as template group index 1 change? False ChiralClass Atom H18(53) xyz:( 0.802, 0.342, -1.080) Atom C18(21) xyz:( 1.035, 0.750, -0.105) R Atom C17(20) xyz:(-0.204, 0.676, 0.788) Atom C19(22) xyz:( 1.469, 2.206, -0.253) Atom C20(23) xyz:( 2.167, -0.057, 0.527) not correct chiralisation group index 2 change? False ChiralClass Atom H23(63) xyz:( 4.510, -2.469, -1.415) Atom C23(26) xyz:( 5.117, -2.032, -0.631) R Atom C22(25) xyz:( 4.472, -0.735, -0.151) Atom C24(27) xyz:( 5.223, -3.010, 0.535) Atom C25(28) xyz:( 6.516, -1.735, -1.176) not correct chiralisation Build ligand and use monomer library to name atoms : G9R Using monomer library entry G9R as template Residue has metal at the centre of a coordination sphere. Using input geometry to generate restraints. Hydrogens may not be added. Processing a loop Suspicious bonds Bond between Atom MG ( 1) xyz:(139.513, 219.908, 166.477) and Atom NB (17) xyz:(13.979, 11.967, 9.137) should be unknown, not 289.40 Bond between Atom CHB( 3) xyz:( 8.964, 6.933, 12.770) and Atom C4A(10) xyz:(136.930, 219.756, 171.985) should be unknown, not 294.99 Bond between Atom CHD( 5) xyz:(11.352, 8.488, 13.498) and Atom C4C(28) xyz:(10.749, 6.143, 9.589) should be unknown, not 4.60 Bond between Atom CHD( 5) xyz:(11.352, 8.488, 13.498) and Atom C1D(33) xyz:(137.155, 218.661, 165.823) should be unknown, not 288.45 Bond between Atom NA ( 6) xyz:(11.281, 6.486, 12.007) and Atom C1A( 7) xyz:(138.298, 218.986, 169.069) should be unknown, not 293.19 Bond between Atom NA ( 6) xyz:(11.281, 6.486, 12.007) and Atom C4A(10) xyz:(136.930, 219.756, 171.985) should be unknown, not 294.73 Bond between Atom NB (17) xyz:(13.979, 11.967, 9.137) and Atom C1B(18) xyz:( 8.964, 6.208, 11.408) should be unknown, not 7.97 Bond between Atom C1B(18) xyz:( 8.964, 6.208, 11.408) and Atom C2B(19) xyz:(-0.494, 1.522, 0.000) should be unknown, not 15.54 Bond between Atom C2B(19) xyz:(-0.494, 1.522, 0.000) and Atom CMB(22) xyz:(142.647, 222.307, 170.441) should be unknown, not 313.51 Bond between Atom C3B(20) xyz:( 0.800, 2.462, 0.000) and Atom C4B(21) xyz:(13.704, 13.161, 8.194) should be unknown, not 18.66 Bond between Atom C3B(20) xyz:( 0.800, 2.462, 0.000) and Atom CAB(23) xyz:(143.938, 223.069, 167.887) should be unknown, not 312.00 Bond between Atom NC (24) xyz:(13.863, 10.710, 8.380) and Atom C4C(28) xyz:(10.749, 6.143, 9.589) should be unknown, not 5.66 Bond between Atom C2C(26) xyz:(10.742, 8.468, 8.689) and Atom CMC(29) xyz:(142.954, 222.011, 162.524) should be unknown, not 294.53 Bond between Atom C3C(27) xyz:(10.398, 5.745, 11.072) and Atom CAC(30) xyz:(140.841, 220.138, 160.894) should be unknown, not 292.28 Bond between Atom C1D(33) xyz:(137.155, 218.661, 165.823) and Atom C2D(34) xyz:( 0.703, -0.114, -0.966) should be unknown, not 307.08 Bond between Atom C2D(34) xyz:( 0.703, -0.114, -0.966) and Atom CMD(37) xyz:(137.135, 216.374, 162.543) should be unknown, not 303.67 Bond between Atom C3D(35) xyz:(-0.223, -0.409, 0.177) and Atom C4D(36) xyz:(137.153, 219.842, 167.881) should be unknown, not 309.04 Bond between Atom C3D(35) xyz:(-0.223, -0.409, 0.177) and Atom CAD(38) xyz:(135.650, 217.802, 168.834) should be unknown, not 307.45 Bond between Atom CAD(38) xyz:(135.650, 217.802, 168.834) and Atom OBD(39) xyz:(135.710, 214.845, 165.505) should be unknown, not 4.45 Bond between Atom CGD(41) xyz:(135.659, 217.829, 170.623) and Atom O1D(42) xyz:(138.366, 214.345, 167.589) should be unknown, not 5.35 Bond between Atom CGD(41) xyz:(135.659, 217.829, 170.623) and Atom O2D(43) xyz:(136.485, 213.942, 168.847) should be unknown, not 4.35 Bond between Atom C10(54) xyz:(143.654, 211.394, 169.837) and Atom C11(55) xyz:(143.650, 208.052, 166.589) should be unknown, not 4.66 Bond between Atom CHB( 3) xyz:( 8.964, 6.933, 12.770) and Atom H1 (66) xyz:(140.214, 220.709, 170.750) should be unknown, not 296.45 Bond between Atom CHC( 4) xyz:(13.054, 12.481, 6.964) and Atom H2 (67) xyz:(143.272, 222.116, 165.273) should be unknown, not 293.20 Bond between Atom CHD( 5) xyz:(11.352, 8.488, 13.498) and Atom H3 (68) xyz:(139.467, 218.198, 162.001) should be unknown, not 287.13 Bond between Atom CMA(11) xyz:(138.969, 219.756, 173.426) and Atom H5 (70) xyz:(137.034, 220.146, 169.301) should be unknown, not 4.57 Bond between Atom C9 (53) xyz:(141.615, 211.394, 168.396) and Atom H44(108) xyz:(145.037, 210.179, 165.893) should be unknown, not 4.41 Bond between Atom C9 (53) xyz:(141.615, 211.394, 168.396) and Atom H45(109) xyz:(143.744, 210.769, 164.794) should be unknown, not 4.23 Bond between Atom C10(54) xyz:(143.654, 211.394, 169.837) and Atom H47(111) xyz:(141.684, 208.837, 167.224) should be unknown, not 4.15 Bond between Atom C10(54) xyz:(143.654, 211.394, 169.837) and Atom H48(112) xyz:(142.061, 209.127, 165.491) should be unknown, not 5.15 Bond between Atom C2A( 8) xyz:(138.979, 220.982, 171.250) and Atom H14(134) xyz:(138.134, 216.853, 169.300) should be unknown, not 4.64 G9R MG NB single 289.403 0.020 289.403 1.895092 ******************************************************************************** eLBOW has stopped unexpectedly. Why? : "Bond length too long : 289.40" Will carry on but there may be restraints missing! Try to generate the restraints directly using phenix.elbow --chemical-component=G9R ******************************************************************************** MoleculeClass : C:54 N: 4 O: 6 Mg: 1 (CHEMICAL COMPONENTS format) 135 atoms 141 bonds 0 angles 0 dihedrals 0 rings 0 chirals Processing a loop Difficulties in the ring structures may lead to problems later Build ligand and use monomer library to name atoms : 8CT Using monomer library entry 8CT as template Attempting to download Chemical Components file for CL7 Running eLBOW on CL7.cif Residue has metal at the centre of a coordination sphere. Using input geometry to generate restraints. Hydrogens may not be added. Suspicious bonds Bond between Atom C10(11) xyz:( 8.504, -0.624, -0.074) and Atom C11(12) xyz:(12.518, -0.423, 0.087) should be unknown, not 4.02 Bond between Atom C15(15) xyz:(13.060, 0.139, 1.687) and Atom C16(16) xyz:(17.487, -0.233, 0.503) should be unknown, not 4.60 Bond between Atom CBA(24) xyz:(-0.355, 0.606, -1.046) and Atom CAA(25) xyz:(-2.364, 4.190, -1.880) should be unknown, not 4.19 Bond between Atom C2A(26) xyz:(-2.269, 1.323, -2.454) and Atom C1A(27) xyz:(-6.432, 0.438, -2.544) should be unknown, not 4.26 Bond between Atom C1A(27) xyz:(-6.432, 0.438, -2.544) and Atom CHA(28) xyz:(-3.138, 5.831, 0.771) should be unknown, not 7.14 Bond between Atom CHA(28) xyz:(-3.138, 5.831, 0.771) and Atom C4D(43) xyz:( 2.138, 4.316, 2.889) should be unknown, not 5.88 Bond between Atom C4A(36) xyz:(-6.043, -1.886, -2.269) and Atom CHB(38) xyz:( 4.496, 7.264, 6.017) should be unknown, not 16.23 Bond between Atom NB (40) xyz:( 5.478, 5.918, 3.818) and Atom MG (41) xyz:(-5.023, -2.085, 1.048) should be unknown, not 13.49 Bond between Atom MG (41) xyz:(-5.023, -2.085, 1.048) and Atom ND (42) xyz:( 3.587, 4.222, 2.850) should be unknown, not 10.82 Bond between Atom C2B(44) xyz:( 6.473, 7.802, 4.712) and Atom CMB(45) xyz:(-8.048, -1.539, -4.924) should be unknown, not 19.77 Bond between Atom C3B(46) xyz:( 7.474, 6.973, 4.311) and Atom CAB(47) xyz:(-10.014, -3.019, -2.846) should be unknown, not 21.37 Bond between Atom CHC(50) xyz:( 7.740, 4.566, 4.672) and Atom C1C(51) xyz:(-7.670, -2.778, 0.815) should be unknown, not 17.50 Bond between Atom C1C(51) xyz:(-7.670, -2.778, 0.815) and Atom C2C(53) xyz:( 7.641, 1.984, 4.919) should be unknown, not 16.55 Bond between Atom C2C(53) xyz:( 7.641, 1.984, 4.919) and Atom CMC(54) xyz:(-7.652, -5.043, 2.567) should be unknown, not 16.99 Bond between Atom C3C(55) xyz:( 6.662, 1.061, 4.319) and Atom CAC(56) xyz:(-7.132, -2.884, 4.816) should be unknown, not 14.36 Bond between Atom C3C(55) xyz:( 6.662, 1.061, 4.319) and Atom C4C(58) xyz:(-7.216, -0.450, 0.797) should be unknown, not 14.40 Bond between Atom C4C(58) xyz:(-7.216, -0.450, 0.797) and Atom CHD(59) xyz:( 4.564, 1.635, 2.833) should be unknown, not 12.13 Bond between Atom C2D(61) xyz:( 2.627, 2.501, 1.616) and Atom CMD(62) xyz:(-7.881, 3.125, 3.859) should be unknown, not 10.76 Bond between Atom C3D(63) xyz:( 1.575, 3.259, 2.107) and Atom CAD(64) xyz:(-3.148, 4.605, 2.947) should be unknown, not 4.98 Bond between Atom C15(15) xyz:(13.060, 0.139, 1.687) and Atom H151(91) xyz:(16.347, -1.576, -0.737) should be unknown, not 4.43 Bond between Atom C15(15) xyz:(13.060, 0.139, 1.687) and Atom H152(92) xyz:(16.424, 0.097, -1.341) should be unknown, not 4.53 Bond between Atom CAA(25) xyz:(-2.364, 4.190, -1.880) and Atom HAA1(107) xyz:(-1.910, -0.419, 0.035) should be unknown, not 5.01 Bond between Atom CHB(38) xyz:( 4.496, 7.264, 6.017) and Atom HHB(118) xyz:(-5.163, -0.811, -4.004) should be unknown, not 16.09 Bond between Atom CHC(50) xyz:( 7.740, 4.566, 4.672) and Atom HHC(122) xyz:(-8.839, -3.980, -0.124) should be unknown, not 19.26 Bond between Atom CHD(59) xyz:( 4.564, 1.635, 2.833) and Atom HHD(131) xyz:(-7.752, 0.053, 4.131) should be unknown, not 12.49 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/elbow/elbow/command_line/ready_set.py", line 1108, in run(args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/elbow/elbow/command_line/ready_set.py", line 882, in run random_seed=working_params.ready_set.run_options.random_seed, File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/elbow/elbow/command_line/ready_set.py", line 266, in run_though_all_the_options None), File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2487, in run hydrogens=hydrogens, File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/scripts/elbow_on_pdb_file.py", line 781, in elbow_on_pdb_file silent=True, File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/command_line/builder.py", line 2441, in run call_back_function=call_back_function, File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/command_line/builder.py", line 1833, in post_process molecule = neutron_utils.add_neutron_bond_lengths(molecule) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/utilities/neutron_utils.py", line 21, in add_neutron_bond_lengths molecule, File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/scripts/add_neutron_bond_lengths.py", line 134, in process_molecule_from_hd_distances mol.RelativeHydrogenNames() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/elbow/elbow/chemistry/IOMixins.py", line 960, in RelativeHydrogenNames if atom.name.strip() in names: AttributeError: AtomClass instance has no attribute 'name'