INPUT Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vvz_21408/12_2022/6vvz_21408.pdb Reading option "hydrogens=False" from command line Writing effective parameters to 6vvz_21408.eff Ligand restraint generation using eLBOW, phenix.elbow Attempting to download Chemical Components file for SRN Running eLBOW on SRN.cif 3 ring group 7 5 6 Processing a loop SRN O11 C45 deloc 1.229 0.020 1.229 SRN C45 O10 deloc 1.324 0.020 1.324 SRN C45 C44 single 1.453 0.020 1.453 SRN C44 C43 single 1.547 0.020 1.547 SRN C44 H441 single 0.939 0.020 1.096 SRN C44 H442 single 0.939 0.020 1.096 SRN C43 C42 single 1.597 0.020 1.597 SRN C43 H431 single 0.939 0.020 1.096 SRN C43 H432 single 0.939 0.020 1.096 SRN C42 C41 single 1.451 0.020 1.451 SRN C42 H421 single 0.939 0.020 1.096 SRN C42 H422 single 0.939 0.020 1.096 SRN C41 C39 single 1.479 0.020 1.479 SRN C41 H411 single 0.939 0.020 1.096 SRN C41 H412 single 0.939 0.020 1.096 SRN C39 C40 single 1.669 0.020 1.669 SRN C39 C38 single 1.615 0.020 1.615 SRN C39 H39 single 0.939 0.020 1.096 SRN C40 H401 single 0.939 0.020 1.096 SRN C40 H402 single 0.939 0.020 1.096 SRN C40 H403 single 0.939 0.020 1.096 SRN C38 C36 double 1.430 0.020 1.430 SRN C38 H38 single 0.930 0.020 1.086 SRN C36 C37 single 1.493 0.020 1.493 SRN C36 C32 single 2.117 0.020 2.117 SRN C37 H371 single 0.939 0.020 1.096 SRN C37 H372 single 0.939 0.020 1.096 SRN C37 H373 single 0.939 0.020 1.096 SRN C32 C33 single 1.336 0.020 1.336 SRN C32 O7 single 1.486 0.020 1.486 SRN C32 H32 single 0.939 0.020 1.096 SRN C33 C47 single 1.631 0.020 1.631 SRN C33 O1 single 1.241 0.020 1.241 SRN C33 H33 single 0.939 0.020 1.096 SRN C47 C46 double 1.646 0.020 1.646 SRN C47 H47 single 0.930 0.020 1.086 SRN C46 C31 single 1.393 0.020 1.393 SRN C46 H46 single 0.930 0.020 1.086 SRN O1 C1 single 1.850 0.020 1.850 SRN O7 C31 single 1.675 0.020 1.675 SRN C31 C30 single 1.570 0.020 1.570 SRN C31 H31 single 0.939 0.020 1.096 SRN C30 C29 single 1.736 0.020 1.736 SRN C30 H301 single 0.939 0.020 1.096 SRN C30 H302 single 0.939 0.020 1.096 SRN C29 C28 double 1.918 0.020 1.918 SRN C29 H29 single 0.930 0.020 1.086 SRN C28 C27 single 2.021 0.020 2.021 SRN C28 H28 single 0.930 0.020 1.086 SRN C27 C26 single 1.290 0.020 1.290 SRN C27 H271 single 0.939 0.020 1.096 SRN C27 H272 single 0.939 0.020 1.096 SRN C26 C25 single 1.648 0.020 1.648 SRN C26 H261 single 0.939 0.020 1.096 SRN C26 H262 single 0.939 0.020 1.096 SRN C25 C24 double 0.875 0.020 0.875 SRN C25 H25 single 0.930 0.020 1.086 SRN C24 C23 single 1.446 0.020 1.446 SRN C24 H24 single 0.930 0.020 1.086 SRN C23 O6 single 1.228 0.020 1.228 SRN C23 C22 single 1.821 0.020 1.821 SRN C23 H23 single 0.939 0.020 1.096 SRN O6 HO6 single 0.832 0.020 0.971 SRN C22 O5 single 1.318 0.020 1.318 SRN C22 C21 single 1.559 0.020 1.559 SRN C22 H22 single 0.939 0.020 1.096 SRN O5 HO5 single 0.832 0.020 0.971 SRN C21 O9 single 1.482 0.020 1.482 SRN C21 C20 single 1.476 0.020 1.476 SRN C21 H21 single 0.939 0.020 1.096 SRN O9 C16 single 1.346 0.020 1.346 SRN C20 C19 single 1.483 0.020 1.483 SRN C20 H201 single 0.939 0.020 1.096 SRN C20 H202 single 0.939 0.020 1.096 SRN C19 O4 single 1.511 0.020 1.511 SRN C19 C17 single 1.672 0.020 1.672 SRN C19 H19 single 0.939 0.020 1.096 SRN O4 HO4 single 0.832 0.020 0.971 SRN C17 C18 single 1.606 0.020 1.606 SRN C17 C16 single 1.330 0.020 1.330 SRN C17 H17 single 0.939 0.020 1.096 SRN C18 H181 single 0.939 0.020 1.096 SRN C18 H182 single 0.939 0.020 1.096 SRN C18 H183 single 0.939 0.020 1.096 SRN C16 C15 single 2.001 0.020 2.001 SRN C16 H16 single 0.939 0.020 1.096 SRN C15 C14 single 1.786 0.020 1.786 SRN C15 H151 single 0.939 0.020 1.096 SRN C15 H152 single 0.939 0.020 1.096 SRN C14 C13 double 1.057 0.020 1.057 SRN C14 H14 single 0.930 0.020 1.086 SRN C13 C12 single 1.259 0.020 1.259 SRN C13 H13 single 0.930 0.020 1.086 SRN C12 O8 single 1.160 0.020 1.160 SRN C12 C10 single 1.990 0.020 1.990 SRN C12 H12 single 0.939 0.020 1.096 SRN O8 C35 single 1.391 0.020 1.391 SRN C35 C34 single 1.429 0.020 1.429 SRN C35 C8 single 1.309 0.020 1.309 SRN C35 H35 single 0.939 0.020 1.096 SRN C34 C9 single 1.011 0.020 1.011 SRN C34 H341 single 0.939 0.020 1.096 SRN C34 H342 single 0.939 0.020 1.096 SRN C9 C10 single 1.026 0.020 1.026 SRN C9 O3 single 3.006 0.020 3.006 1.398717 Sorry: Bond length too long : 3.01