null Mon 24 Dec 08:08:09 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2od6-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2od6-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2od6-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 08:08:14 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/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.4-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.70 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 3874 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3442 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3256 (Rfree = 0.000) for 3874 atoms. Found 25 (29 requested) and removed 40 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 3958 seeds are put forward NCS extension: 0 residues added, 3958 seeds are put forward Round 1: 221 peptides, 40 chains. Longest chain 13 peptides. Score 0.387 Round 2: 250 peptides, 38 chains. Longest chain 16 peptides. Score 0.503 Round 3: 269 peptides, 42 chains. Longest chain 15 peptides. Score 0.507 Round 4: 266 peptides, 36 chains. Longest chain 20 peptides. Score 0.570 Round 5: 274 peptides, 37 chains. Longest chain 20 peptides. Score 0.579 Taking the results from Round 5 Chains 37, Residues 237, Estimated correctness of the model 21.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7176 restraints for refining 3197 atoms. 6265 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2733 (Rfree = 0.000) for 3197 atoms. Found 12 (24 requested) and removed 24 (12 requested) atoms. Cycle 2: After refmac, R = 0.2686 (Rfree = 0.000) for 3146 atoms. Found 8 (24 requested) and removed 16 (12 requested) atoms. Cycle 3: After refmac, R = 0.2620 (Rfree = 0.000) for 3123 atoms. Found 13 (23 requested) and removed 16 (11 requested) atoms. Cycle 4: After refmac, R = 0.2554 (Rfree = 0.000) for 3111 atoms. Found 7 (23 requested) and removed 15 (11 requested) atoms. Cycle 5: After refmac, R = 0.2515 (Rfree = 0.000) for 3096 atoms. Found 14 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 3236 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 3260 seeds are put forward Round 1: 212 peptides, 34 chains. Longest chain 14 peptides. Score 0.441 Round 2: 242 peptides, 36 chains. Longest chain 24 peptides. Score 0.505 Round 3: 236 peptides, 32 chains. Longest chain 19 peptides. Score 0.538 Round 4: 247 peptides, 32 chains. Longest chain 25 peptides. Score 0.567 Round 5: 245 peptides, 31 chains. Longest chain 19 peptides. Score 0.574 Taking the results from Round 5 Chains 31, Residues 214, Estimated correctness of the model 20.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7204 restraints for refining 3200 atoms. 6379 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2765 (Rfree = 0.000) for 3200 atoms. Found 13 (24 requested) and removed 15 (12 requested) atoms. Cycle 7: After refmac, R = 0.2563 (Rfree = 0.000) for 3185 atoms. Found 14 (24 requested) and removed 16 (12 requested) atoms. Cycle 8: After refmac, R = 0.2460 (Rfree = 0.000) for 3173 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. Cycle 9: After refmac, R = 0.2521 (Rfree = 0.000) for 3166 atoms. Found 9 (23 requested) and removed 14 (11 requested) atoms. Cycle 10: After refmac, R = 0.2445 (Rfree = 0.000) for 3159 atoms. Found 14 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 3280 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3297 seeds are put forward Round 1: 221 peptides, 36 chains. Longest chain 15 peptides. Score 0.442 Round 2: 239 peptides, 35 chains. Longest chain 18 peptides. Score 0.509 Round 3: 235 peptides, 29 chains. Longest chain 17 peptides. Score 0.571 Round 4: 235 peptides, 34 chains. Longest chain 19 peptides. Score 0.510 Round 5: 251 peptides, 29 chains. Longest chain 19 peptides. Score 0.611 Taking the results from Round 5 Chains 29, Residues 222, Estimated correctness of the model 32.2 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7003 restraints for refining 3200 atoms. 6082 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2583 (Rfree = 0.000) for 3200 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. Cycle 12: After refmac, R = 0.2432 (Rfree = 0.000) for 3185 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. Cycle 13: After refmac, R = 0.2372 (Rfree = 0.000) for 3167 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 14: After refmac, R = 0.2419 (Rfree = 0.000) for 3151 atoms. Found 2 (23 requested) and removed 14 (11 requested) atoms. Cycle 15: After refmac, R = 0.2377 (Rfree = 0.000) for 3133 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 3226 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3240 seeds are put forward Round 1: 230 peptides, 40 chains. Longest chain 18 peptides. Score 0.416 Round 2: 256 peptides, 34 chains. Longest chain 20 peptides. Score 0.567 Round 3: 250 peptides, 36 chains. Longest chain 26 peptides. Score 0.527 Round 4: 237 peptides, 33 chains. Longest chain 36 peptides. Score 0.528 Round 5: 245 peptides, 33 chains. Longest chain 31 peptides. Score 0.550 Taking the results from Round 2 Chains 34, Residues 222, Estimated correctness of the model 17.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7238 restraints for refining 3201 atoms. 6384 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2571 (Rfree = 0.000) for 3201 atoms. Found 13 (24 requested) and removed 14 (12 requested) atoms. Cycle 17: After refmac, R = 0.2433 (Rfree = 0.000) for 3192 atoms. Found 9 (24 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.2367 (Rfree = 0.000) for 3184 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.2336 (Rfree = 0.000) for 3172 atoms. Found 9 (23 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.2302 (Rfree = 0.000) for 3168 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.37 Search for helices and strands: 0 residues in 0 chains, 3266 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3285 seeds are put forward Round 1: 203 peptides, 34 chains. Longest chain 14 peptides. Score 0.413 Round 2: 243 peptides, 32 chains. Longest chain 21 peptides. Score 0.556 Round 3: 250 peptides, 33 chains. Longest chain 18 peptides. Score 0.563 Round 4: 245 peptides, 33 chains. Longest chain 19 peptides. Score 0.550 Round 5: 254 peptides, 31 chains. Longest chain 18 peptides. Score 0.596 Taking the results from Round 5 Chains 32, Residues 223, Estimated correctness of the model 27.4 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7072 restraints for refining 3199 atoms. 6157 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2627 (Rfree = 0.000) for 3199 atoms. Found 22 (24 requested) and removed 12 (12 requested) atoms. Cycle 22: After refmac, R = 0.2441 (Rfree = 0.000) for 3204 atoms. Found 3 (24 requested) and removed 15 (12 requested) atoms. Cycle 23: After refmac, R = 0.2375 (Rfree = 0.000) for 3190 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.2344 (Rfree = 0.000) for 3177 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.2318 (Rfree = 0.000) for 3165 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 3269 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3292 seeds are put forward Round 1: 196 peptides, 37 chains. Longest chain 14 peptides. Score 0.346 Round 2: 227 peptides, 32 chains. Longest chain 18 peptides. Score 0.512 Round 3: 231 peptides, 31 chains. Longest chain 16 peptides. Score 0.536 Round 4: 231 peptides, 32 chains. Longest chain 17 peptides. Score 0.524 Round 5: 244 peptides, 30 chains. Longest chain 19 peptides. Score 0.583 Taking the results from Round 5 Chains 30, Residues 214, Estimated correctness of the model 23.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7208 restraints for refining 3201 atoms. 6382 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2511 (Rfree = 0.000) for 3201 atoms. Found 16 (24 requested) and removed 14 (12 requested) atoms. Cycle 27: After refmac, R = 0.2360 (Rfree = 0.000) for 3194 atoms. Found 3 (24 requested) and removed 13 (12 requested) atoms. Cycle 28: After refmac, R = 0.2303 (Rfree = 0.000) for 3181 atoms. Found 3 (24 requested) and removed 13 (12 requested) atoms. Cycle 29: After refmac, R = 0.2235 (Rfree = 0.000) for 3166 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.2187 (Rfree = 0.000) for 3156 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 3231 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3254 seeds are put forward Round 1: 197 peptides, 33 chains. Longest chain 15 peptides. Score 0.407 Round 2: 219 peptides, 34 chains. Longest chain 16 peptides. Score 0.463 Round 3: 230 peptides, 34 chains. Longest chain 17 peptides. Score 0.496 Round 4: 231 peptides, 35 chains. Longest chain 21 peptides. Score 0.486 Round 5: 236 peptides, 31 chains. Longest chain 19 peptides. Score 0.550 Taking the results from Round 5 Chains 31, Residues 205, Estimated correctness of the model 11.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7222 restraints for refining 3201 atoms. 6433 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2419 (Rfree = 0.000) for 3201 atoms. Found 18 (24 requested) and removed 14 (12 requested) atoms. Cycle 32: After refmac, R = 0.2331 (Rfree = 0.000) for 3201 atoms. Found 9 (24 requested) and removed 14 (12 requested) atoms. Cycle 33: After refmac, R = 0.2371 (Rfree = 0.000) for 3189 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. Cycle 34: After refmac, R = 0.2285 (Rfree = 0.000) for 3178 atoms. Found 3 (24 requested) and removed 14 (12 requested) atoms. Cycle 35: After refmac, R = 0.2264 (Rfree = 0.000) for 3166 atoms. Found 2 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 3255 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3271 seeds are put forward Round 1: 202 peptides, 38 chains. Longest chain 12 peptides. Score 0.352 Round 2: 216 peptides, 33 chains. Longest chain 20 peptides. Score 0.467 Round 3: 209 peptides, 34 chains. Longest chain 14 peptides. Score 0.432 Round 4: 225 peptides, 33 chains. Longest chain 17 peptides. Score 0.494 Round 5: 208 peptides, 34 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 4 Chains 33, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7299 restraints for refining 3201 atoms. 6564 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2487 (Rfree = 0.000) for 3201 atoms. Found 16 (24 requested) and removed 12 (12 requested) atoms. Cycle 37: After refmac, R = 0.2392 (Rfree = 0.000) for 3198 atoms. Found 8 (24 requested) and removed 14 (12 requested) atoms. Cycle 38: After refmac, R = 0.2315 (Rfree = 0.000) for 3185 atoms. Found 2 (24 requested) and removed 15 (12 requested) atoms. Cycle 39: After refmac, R = 0.2324 (Rfree = 0.000) for 3169 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.2290 (Rfree = 0.000) for 3162 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 3253 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3268 seeds are put forward Round 1: 168 peptides, 35 chains. Longest chain 9 peptides. Score 0.276 Round 2: 203 peptides, 34 chains. Longest chain 12 peptides. Score 0.413 Round 3: 206 peptides, 35 chains. Longest chain 13 peptides. Score 0.408 Round 4: 220 peptides, 34 chains. Longest chain 15 peptides. Score 0.466 Round 5: 215 peptides, 31 chains. Longest chain 17 peptides. Score 0.490 Taking the results from Round 5 Chains 31, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7188 reflections ( 98.95 % complete ) and 7308 restraints for refining 3201 atoms. 6603 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2479 (Rfree = 0.000) for 3201 atoms. Found 9 (24 requested) and removed 12 (12 requested) atoms. Cycle 42: After refmac, R = 0.2449 (Rfree = 0.000) for 3191 atoms. Found 5 (24 requested) and removed 14 (12 requested) atoms. Cycle 43: After refmac, R = 0.2375 (Rfree = 0.000) for 3175 atoms. Found 2 (24 requested) and removed 14 (12 requested) atoms. Cycle 44: After refmac, R = 0.2347 (Rfree = 0.000) for 3159 atoms. Found 5 (23 requested) and removed 14 (11 requested) atoms. Cycle 45: After refmac, R = 0.2534 (Rfree = 0.000) for 3148 atoms. Found 9 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.29 Search for helices and strands: 0 residues in 0 chains, 3231 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3244 seeds are put forward Round 1: 168 peptides, 29 chains. Longest chain 16 peptides. Score 0.368 Round 2: 188 peptides, 29 chains. Longest chain 19 peptides. Score 0.435 Round 3: 177 peptides, 26 chains. Longest chain 19 peptides. Score 0.442 Round 4: 175 peptides, 30 chains. Longest chain 12 peptides. Score 0.377 Round 5: 184 peptides, 29 chains. Longest chain 19 peptides. Score 0.422 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 151, Estimated correctness of the model 0.0 % 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 7198 restraints for refining 3201 atoms. 6620 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2323 (Rfree = 0.000) for 3201 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2472 (Rfree = 0.000) for 3182 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2553 (Rfree = 0.000) for 3163 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2922 (Rfree = 0.000) for 3145 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:44:47 GMT 2018 Job finished. TimeTaking 36.63 Used memory is bytes: 8316552