null Tue 25 Dec 19:27:57 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 2fqp-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-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/2fqp-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-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 19:28:12 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/2fqp-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-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 222 and 0 Target number of residues in the AU: 222 Target solvent content: 0.6452 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-4.0-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: 4 Cell parameters: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3104 target number of atoms Had to go as low as 0.60 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: 50.895 4.000 Wilson plot Bfac: 74.98 2328 reflections ( 81.71 % complete ) and 0 restraints for refining 3422 atoms. Observations/parameters ratio is 0.17 ------------------------------------------------------ Starting model: R = 0.3198 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2762 (Rfree = 0.000) for 3422 atoms. Found 12 (16 requested) and removed 136 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 4.23 Search for helices and strands: 0 residues in 0 chains, 3334 seeds are put forward NCS extension: 0 residues added, 3334 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.201 Round 2: 80 peptides, 16 chains. Longest chain 9 peptides. Score 0.267 Round 3: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.279 Round 4: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.295 Round 5: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.271 Taking the results from Round 4 Chains 14, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 7194 restraints for refining 2803 atoms. 6960 conditional restraints added. Observations/parameters ratio is 0.21 ------------------------------------------------------ Cycle 1: After refmac, R = 0.1934 (Rfree = 0.000) for 2803 atoms. Found 9 (13 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.1504 (Rfree = 0.000) for 2773 atoms. Found 2 (13 requested) and removed 11 (6 requested) atoms. Cycle 3: After refmac, R = 0.1344 (Rfree = 0.000) for 2740 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.1301 (Rfree = 0.000) for 2722 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.1187 (Rfree = 0.000) for 2715 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 4.19 Search for helices and strands: 0 residues in 0 chains, 2760 seeds are put forward NCS extension: 0 residues added, 2760 seeds are put forward Round 1: 82 peptides, 19 chains. Longest chain 6 peptides. Score 0.204 Round 2: 105 peptides, 22 chains. Longest chain 10 peptides. Score 0.265 Round 3: 121 peptides, 23 chains. Longest chain 10 peptides. Score 0.328 Round 4: 119 peptides, 22 chains. Longest chain 14 peptides. Score 0.340 Round 5: 111 peptides, 24 chains. Longest chain 7 peptides. Score 0.253 Taking the results from Round 4 Chains 22, Residues 97, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5671 restraints for refining 2420 atoms. 5291 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1850 (Rfree = 0.000) for 2420 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 7: After refmac, R = 0.1357 (Rfree = 0.000) for 2386 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 8: After refmac, R = 0.1296 (Rfree = 0.000) for 2377 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.1160 (Rfree = 0.000) for 2364 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.1620 (Rfree = 0.000) for 2357 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 4.07 Search for helices and strands: 0 residues in 0 chains, 2424 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 2439 seeds are put forward Round 1: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.290 Round 2: 123 peptides, 22 chains. Longest chain 11 peptides. Score 0.360 Round 3: 111 peptides, 20 chains. Longest chain 12 peptides. Score 0.343 Round 4: 104 peptides, 19 chains. Longest chain 11 peptides. Score 0.329 Round 5: 117 peptides, 18 chains. Longest chain 12 peptides. Score 0.416 Taking the results from Round 5 Chains 18, Residues 99, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5467 restraints for refining 2353 atoms. 5065 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1795 (Rfree = 0.000) for 2353 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 12: After refmac, R = 0.1629 (Rfree = 0.000) for 2335 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 13: After refmac, R = 0.1312 (Rfree = 0.000) for 2326 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 14: After refmac, R = 0.1281 (Rfree = 0.000) for 2317 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.1733 (Rfree = 0.000) for 2314 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 4.16 Search for helices and strands: 0 residues in 0 chains, 2379 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2395 seeds are put forward Round 1: 106 peptides, 23 chains. Longest chain 7 peptides. Score 0.248 Round 2: 137 peptides, 27 chains. Longest chain 9 peptides. Score 0.323 Round 3: 140 peptides, 24 chains. Longest chain 11 peptides. Score 0.401 Round 4: 139 peptides, 23 chains. Longest chain 12 peptides. Score 0.416 Round 5: 123 peptides, 23 chains. Longest chain 12 peptides. Score 0.338 Taking the results from Round 4 Chains 23, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5314 restraints for refining 2354 atoms. 4873 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1445 (Rfree = 0.000) for 2354 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.1307 (Rfree = 0.000) for 2332 atoms. Found 7 (11 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.1104 (Rfree = 0.000) for 2318 atoms. Found 9 (11 requested) and removed 11 (5 requested) atoms. Cycle 19: After refmac, R = 0.1312 (Rfree = 0.000) for 2308 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.1092 (Rfree = 0.000) for 2304 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 4.08 Search for helices and strands: 0 residues in 0 chains, 2378 seeds are put forward NCS extension: 0 residues added, 2378 seeds are put forward Round 1: 104 peptides, 23 chains. Longest chain 7 peptides. Score 0.237 Round 2: 128 peptides, 27 chains. Longest chain 8 peptides. Score 0.277 Round 3: 133 peptides, 25 chains. Longest chain 10 peptides. Score 0.346 Round 4: 137 peptides, 26 chains. Longest chain 9 peptides. Score 0.344 Round 5: 140 peptides, 27 chains. Longest chain 9 peptides. Score 0.338 Taking the results from Round 3 Chains 25, Residues 108, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5321 restraints for refining 2298 atoms. 4894 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1614 (Rfree = 0.000) for 2298 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 22: After refmac, R = 0.1828 (Rfree = 0.000) for 2280 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 23: After refmac, R = 0.1125 (Rfree = 0.000) for 2271 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.1308 (Rfree = 0.000) for 2260 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1428 (Rfree = 0.000) for 2254 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 4.12 Search for helices and strands: 0 residues in 0 chains, 2315 seeds are put forward NCS extension: 0 residues added, 2315 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 7 peptides. Score 0.241 Round 2: 107 peptides, 20 chains. Longest chain 12 peptides. Score 0.322 Round 3: 117 peptides, 21 chains. Longest chain 8 peptides. Score 0.351 Round 4: 122 peptides, 20 chains. Longest chain 12 peptides. Score 0.398 Round 5: 123 peptides, 22 chains. Longest chain 9 peptides. Score 0.360 Taking the results from Round 4 Chains 20, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5010 restraints for refining 2227 atoms. 4622 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1503 (Rfree = 0.000) for 2227 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 27: After refmac, R = 0.1681 (Rfree = 0.000) for 2209 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 28: After refmac, R = 0.1300 (Rfree = 0.000) for 2198 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1260 (Rfree = 0.000) for 2193 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1328 (Rfree = 0.000) for 2189 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 4.27 Search for helices and strands: 0 residues in 0 chains, 2238 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2252 seeds are put forward Round 1: 98 peptides, 23 chains. Longest chain 7 peptides. Score 0.202 Round 2: 106 peptides, 24 chains. Longest chain 7 peptides. Score 0.225 Round 3: 111 peptides, 24 chains. Longest chain 8 peptides. Score 0.253 Round 4: 115 peptides, 24 chains. Longest chain 9 peptides. Score 0.274 Round 5: 123 peptides, 24 chains. Longest chain 9 peptides. Score 0.316 Taking the results from Round 5 Chains 24, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5358 restraints for refining 2283 atoms. 4986 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1582 (Rfree = 0.000) for 2283 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 32: After refmac, R = 0.1391 (Rfree = 0.000) for 2258 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.1342 (Rfree = 0.000) for 2255 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.1394 (Rfree = 0.000) for 2248 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.1078 (Rfree = 0.000) for 2247 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 4.17 Search for helices and strands: 0 residues in 0 chains, 2302 seeds are put forward NCS extension: 0 residues added, 2302 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 6 peptides. Score 0.205 Round 2: 74 peptides, 17 chains. Longest chain 5 peptides. Score 0.206 Round 3: 97 peptides, 21 chains. Longest chain 6 peptides. Score 0.244 Round 4: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.291 Round 5: 85 peptides, 17 chains. Longest chain 7 peptides. Score 0.272 Taking the results from Round 4 Chains 16, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5205 restraints for refining 2214 atoms. 4949 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1442 (Rfree = 0.000) for 2214 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 37: After refmac, R = 0.1286 (Rfree = 0.000) for 2210 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.1267 (Rfree = 0.000) for 2208 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.1263 (Rfree = 0.000) for 2202 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1249 (Rfree = 0.000) for 2197 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 4.11 Search for helices and strands: 0 residues in 0 chains, 2261 seeds are put forward NCS extension: 0 residues added, 2261 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 10 peptides. Score 0.239 Round 2: 105 peptides, 20 chains. Longest chain 9 peptides. Score 0.311 Round 3: 110 peptides, 20 chains. Longest chain 8 peptides. Score 0.338 Round 4: 106 peptides, 19 chains. Longest chain 13 peptides. Score 0.339 Round 5: 105 peptides, 18 chains. Longest chain 12 peptides. Score 0.357 Taking the results from Round 5 Chains 18, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5007 restraints for refining 2212 atoms. 4677 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1591 (Rfree = 0.000) for 2212 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 42: After refmac, R = 0.1532 (Rfree = 0.000) for 2196 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2111 (Rfree = 0.000) for 2187 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1828 (Rfree = 0.000) for 2179 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 45: After refmac, R = 0.1690 (Rfree = 0.000) for 2170 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 2251 seeds are put forward NCS extension: 0 residues added, 2251 seeds are put forward Round 1: 48 peptides, 11 chains. Longest chain 6 peptides. Score 0.197 Round 2: 62 peptides, 14 chains. Longest chain 6 peptides. Score 0.208 Round 3: 65 peptides, 14 chains. Longest chain 6 peptides. Score 0.228 Round 4: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.271 Round 5: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.233 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 58, 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 2fqp-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2328 reflections ( 81.71 % complete ) and 4599 restraints for refining 1997 atoms. 4381 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2443 (Rfree = 0.000) for 1997 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1493 (Rfree = 0.000) for 1983 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1333 (Rfree = 0.000) for 1975 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1228 (Rfree = 0.000) for 1971 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:22:58 GMT 2018 Job finished. TimeTaking 55.01 Used memory is bytes: 20849256