null Tue 25 Dec 19:27:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2od6-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od6-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od6-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 325 and 0 Target number of residues in the AU: 325 Target solvent content: 0.6406 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-3.4-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.066 3.400 Wilson plot Bfac: 72.06 7188 reflections ( 98.95 % complete ) and 0 restraints for refining 3901 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3332 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3194 (Rfree = 0.000) for 3901 atoms. Found 20 (29 requested) and removed 35 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 3994 seeds are put forward NCS extension: 0 residues added, 3994 seeds are put forward Round 1: 217 peptides, 40 chains. Longest chain 11 peptides. Score 0.374 Round 2: 250 peptides, 38 chains. Longest chain 12 peptides. Score 0.503 Round 3: 274 peptides, 41 chains. Longest chain 16 peptides. Score 0.533 Round 4: 274 peptides, 36 chains. Longest chain 18 peptides. Score 0.590 Round 5: 288 peptides, 32 chains. Longest chain 25 peptides. Score 0.664 Taking the results from Round 5 Chains 32, Residues 256, Estimated correctness of the model 48.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 6845 restraints for refining 3200 atoms. 5853 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3041 (Rfree = 0.000) for 3200 atoms. Found 17 (24 requested) and removed 20 (12 requested) atoms. Cycle 2: After refmac, R = 0.2515 (Rfree = 0.000) for 3157 atoms. Found 6 (24 requested) and removed 16 (12 requested) atoms. Cycle 3: After refmac, R = 0.2590 (Rfree = 0.000) for 3131 atoms. Found 6 (23 requested) and removed 18 (11 requested) atoms. Cycle 4: After refmac, R = 0.2430 (Rfree = 0.000) for 3117 atoms. Found 6 (23 requested) and removed 14 (11 requested) atoms. Cycle 5: After refmac, R = 0.2389 (Rfree = 0.000) for 3101 atoms. Found 1 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 3201 seeds are put forward NCS extension: 15 residues added (9 deleted due to clashes), 3216 seeds are put forward Round 1: 230 peptides, 36 chains. Longest chain 15 peptides. Score 0.470 Round 2: 274 peptides, 36 chains. Longest chain 15 peptides. Score 0.590 Round 3: 289 peptides, 34 chains. Longest chain 20 peptides. Score 0.646 Round 4: 278 peptides, 30 chains. Longest chain 20 peptides. Score 0.662 Round 5: 277 peptides, 33 chains. Longest chain 18 peptides. Score 0.629 Taking the results from Round 4 Chains 31, Residues 248, Estimated correctness of the model 47.6 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 6973 restraints for refining 3201 atoms. 5953 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2655 (Rfree = 0.000) for 3201 atoms. Found 18 (24 requested) and removed 19 (12 requested) atoms. Cycle 7: After refmac, R = 0.2562 (Rfree = 0.000) for 3175 atoms. Found 8 (24 requested) and removed 16 (12 requested) atoms. Cycle 8: After refmac, R = 0.2413 (Rfree = 0.000) for 3154 atoms. Found 7 (23 requested) and removed 17 (11 requested) atoms. Cycle 9: After refmac, R = 0.2334 (Rfree = 0.000) for 3141 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. Cycle 10: After refmac, R = 0.2237 (Rfree = 0.000) for 3132 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 3278 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3296 seeds are put forward Round 1: 244 peptides, 36 chains. Longest chain 19 peptides. Score 0.510 Round 2: 259 peptides, 31 chains. Longest chain 20 peptides. Score 0.608 Round 3: 266 peptides, 31 chains. Longest chain 21 peptides. Score 0.625 Round 4: 260 peptides, 31 chains. Longest chain 19 peptides. Score 0.611 Round 5: 279 peptides, 29 chains. Longest chain 23 peptides. Score 0.674 Taking the results from Round 5 Chains 32, Residues 250, Estimated correctness of the model 50.9 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 6478 restraints for refining 3201 atoms. 5302 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2708 (Rfree = 0.000) for 3201 atoms. Found 22 (24 requested) and removed 23 (12 requested) atoms. Cycle 12: After refmac, R = 0.2708 (Rfree = 0.000) for 3175 atoms. Found 19 (24 requested) and removed 22 (12 requested) atoms. Cycle 13: After refmac, R = 0.2321 (Rfree = 0.000) for 3155 atoms. Found 8 (23 requested) and removed 17 (11 requested) atoms. Cycle 14: After refmac, R = 0.2401 (Rfree = 0.000) for 3140 atoms. Found 12 (23 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.2434 (Rfree = 0.000) for 3127 atoms. Found 8 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 3233 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3249 seeds are put forward Round 1: 232 peptides, 35 chains. Longest chain 19 peptides. Score 0.489 Round 2: 250 peptides, 29 chains. Longest chain 20 peptides. Score 0.609 Round 3: 269 peptides, 33 chains. Longest chain 21 peptides. Score 0.611 Round 4: 259 peptides, 28 chains. Longest chain 21 peptides. Score 0.641 Round 5: 270 peptides, 32 chains. Longest chain 20 peptides. Score 0.624 Taking the results from Round 4 Chains 28, Residues 231, Estimated correctness of the model 41.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7110 restraints for refining 3200 atoms. 6214 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2502 (Rfree = 0.000) for 3200 atoms. Found 9 (24 requested) and removed 14 (12 requested) atoms. Cycle 17: After refmac, R = 0.2335 (Rfree = 0.000) for 3184 atoms. Found 7 (24 requested) and removed 17 (12 requested) atoms. Cycle 18: After refmac, R = 0.2235 (Rfree = 0.000) for 3171 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.2292 (Rfree = 0.000) for 3159 atoms. Found 9 (23 requested) and removed 14 (11 requested) atoms. Cycle 20: After refmac, R = 0.2189 (Rfree = 0.000) for 3154 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 3262 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3281 seeds are put forward Round 1: 232 peptides, 31 chains. Longest chain 18 peptides. Score 0.539 Round 2: 251 peptides, 28 chains. Longest chain 21 peptides. Score 0.622 Round 3: 269 peptides, 31 chains. Longest chain 22 peptides. Score 0.632 Round 4: 257 peptides, 33 chains. Longest chain 21 peptides. Score 0.581 Round 5: 260 peptides, 30 chains. Longest chain 28 peptides. Score 0.622 Taking the results from Round 3 Chains 31, Residues 238, Estimated correctness of the model 38.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7179 restraints for refining 3201 atoms. 6258 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2540 (Rfree = 0.000) for 3201 atoms. Found 8 (24 requested) and removed 15 (12 requested) atoms. Cycle 22: After refmac, R = 0.2395 (Rfree = 0.000) for 3184 atoms. Found 6 (24 requested) and removed 13 (12 requested) atoms. Cycle 23: After refmac, R = 0.2332 (Rfree = 0.000) for 3172 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.2315 (Rfree = 0.000) for 3161 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.2280 (Rfree = 0.000) for 3154 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 3268 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3290 seeds are put forward Round 1: 235 peptides, 33 chains. Longest chain 22 peptides. Score 0.522 Round 2: 249 peptides, 31 chains. Longest chain 20 peptides. Score 0.584 Round 3: 245 peptides, 30 chains. Longest chain 19 peptides. Score 0.585 Round 4: 247 peptides, 31 chains. Longest chain 21 peptides. Score 0.579 Round 5: 252 peptides, 29 chains. Longest chain 23 peptides. Score 0.614 Taking the results from Round 5 Chains 29, Residues 223, Estimated correctness of the model 33.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7230 restraints for refining 3200 atoms. 6367 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2510 (Rfree = 0.000) for 3200 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. Cycle 27: After refmac, R = 0.2345 (Rfree = 0.000) for 3192 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.2319 (Rfree = 0.000) for 3182 atoms. Found 1 (24 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.2259 (Rfree = 0.000) for 3169 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 30: After refmac, R = 0.2248 (Rfree = 0.000) for 3162 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 3255 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 3278 seeds are put forward Round 1: 218 peptides, 34 chains. Longest chain 15 peptides. Score 0.460 Round 2: 228 peptides, 33 chains. Longest chain 20 peptides. Score 0.503 Round 3: 242 peptides, 34 chains. Longest chain 27 peptides. Score 0.530 Round 4: 228 peptides, 29 chains. Longest chain 18 peptides. Score 0.553 Round 5: 227 peptides, 32 chains. Longest chain 18 peptides. Score 0.512 Taking the results from Round 4 Chains 29, Residues 199, Estimated correctness of the model 12.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7368 restraints for refining 3201 atoms. 6601 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2533 (Rfree = 0.000) for 3201 atoms. Found 9 (24 requested) and removed 14 (12 requested) atoms. Cycle 32: After refmac, R = 0.2436 (Rfree = 0.000) for 3195 atoms. Found 2 (24 requested) and removed 15 (12 requested) atoms. Cycle 33: After refmac, R = 0.2369 (Rfree = 0.000) for 3177 atoms. Found 9 (24 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.2323 (Rfree = 0.000) for 3173 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.2314 (Rfree = 0.000) for 3158 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 3259 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3272 seeds are put forward Round 1: 204 peptides, 32 chains. Longest chain 13 peptides. Score 0.444 Round 2: 233 peptides, 33 chains. Longest chain 19 peptides. Score 0.517 Round 3: 229 peptides, 30 chains. Longest chain 19 peptides. Score 0.543 Round 4: 215 peptides, 28 chains. Longest chain 18 peptides. Score 0.529 Round 5: 222 peptides, 27 chains. Longest chain 22 peptides. Score 0.561 Taking the results from Round 5 Chains 27, Residues 195, Estimated correctness of the model 15.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7391 restraints for refining 3201 atoms. 6638 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2494 (Rfree = 0.000) for 3201 atoms. Found 15 (24 requested) and removed 13 (12 requested) atoms. Cycle 37: After refmac, R = 0.2390 (Rfree = 0.000) for 3200 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 38: After refmac, R = 0.2400 (Rfree = 0.000) for 3188 atoms. Found 10 (24 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.2264 (Rfree = 0.000) for 3182 atoms. Found 8 (24 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.2577 (Rfree = 0.000) for 3175 atoms. Found 23 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 3293 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3318 seeds are put forward Round 1: 183 peptides, 31 chains. Longest chain 14 peptides. Score 0.390 Round 2: 224 peptides, 32 chains. Longest chain 18 peptides. Score 0.504 Round 3: 239 peptides, 31 chains. Longest chain 19 peptides. Score 0.558 Round 4: 225 peptides, 30 chains. Longest chain 18 peptides. Score 0.532 Round 5: 219 peptides, 30 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 3 Chains 31, Residues 208, Estimated correctness of the model 14.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7228 restraints for refining 3201 atoms. 6427 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2570 (Rfree = 0.000) for 3201 atoms. Found 19 (24 requested) and removed 14 (12 requested) atoms. Cycle 42: After refmac, R = 0.2434 (Rfree = 0.000) for 3198 atoms. Found 24 (24 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.2104 (Rfree = 0.000) for 3204 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.2041 (Rfree = 0.000) for 3192 atoms. Found 3 (24 requested) and removed 14 (12 requested) atoms. Cycle 45: After refmac, R = 0.2062 (Rfree = 0.000) for 3180 atoms. Found 3 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 3282 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3300 seeds are put forward Round 1: 186 peptides, 33 chains. Longest chain 13 peptides. Score 0.370 Round 2: 214 peptides, 33 chains. Longest chain 19 peptides. Score 0.461 Round 3: 218 peptides, 33 chains. Longest chain 14 peptides. Score 0.473 Round 4: 215 peptides, 28 chains. Longest chain 21 peptides. Score 0.529 Round 5: 203 peptides, 28 chains. Longest chain 25 peptides. Score 0.495 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 187, Estimated correctness of the model 3.8 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2od6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7188 reflections ( 98.95 % complete ) and 7439 restraints for refining 3201 atoms. 6719 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2664 (Rfree = 0.000) for 3201 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2437 (Rfree = 0.000) for 3182 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2198 (Rfree = 0.000) for 3164 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2301 (Rfree = 0.000) for 3150 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:20:18 GMT 2018 Job finished. TimeTaking 52.39 Used memory is bytes: 9681936