null Sun 23 Dec 22:22:46 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 2a3n-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a3n-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a3n-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-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/2a3n-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-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 ============================================================ Sun 23 Dec 22:22:56 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/2a3n-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-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 209 and 0 Target number of residues in the AU: 209 Target solvent content: 0.6709 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.44 Input MTZ file: 2a3n-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: 5 Cell parameters: 81.220 102.610 49.296 90.000 123.209 90.000 Input sequence file: 2a3n-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 target number of atoms Had to go as low as 0.80 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 Loops will be built when appropriate and at the last cycle Resolution range: 56.657 4.000 Wilson plot Bfac: 92.26 2888 reflections ( 99.69 % complete ) and 0 restraints for refining 3157 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3459 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3113 (Rfree = 0.000) for 3157 atoms. Found 15 (15 requested) and removed 40 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 4.16 Search for helices and strands: 0 residues in 0 chains, 3192 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 7 peptides. Score 0.233 Round 2: 119 peptides, 20 chains. Longest chain 12 peptides. Score 0.381 Round 3: 140 peptides, 24 chains. Longest chain 13 peptides. Score 0.398 Round 4: 152 peptides, 22 chains. Longest chain 14 peptides. Score 0.490 Round 5: 139 peptides, 19 chains. Longest chain 18 peptides. Score 0.492 Taking the results from Round 5 Chains 20, Residues 120, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2888 reflections ( 99.69 % complete ) and 6206 restraints for refining 2564 atoms. 5719 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2194 (Rfree = 0.000) for 2564 atoms. Found 1 (12 requested) and removed 15 (6 requested) atoms. Cycle 2: After refmac, R = 0.2315 (Rfree = 0.000) for 2513 atoms. Found 2 (12 requested) and removed 18 (6 requested) atoms. Cycle 3: After refmac, R = 0.1933 (Rfree = 0.000) for 2474 atoms. Found 6 (11 requested) and removed 17 (5 requested) atoms. Cycle 4: After refmac, R = 0.1626 (Rfree = 0.000) for 2454 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.2325 (Rfree = 0.000) for 2435 atoms. Found 9 (11 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 4.04 Search for helices and strands: 0 residues in 0 chains, 2528 seeds are put forward Round 1: 126 peptides, 26 chains. Longest chain 8 peptides. Score 0.287 Round 2: 148 peptides, 25 chains. Longest chain 12 peptides. Score 0.415 Round 3: 162 peptides, 27 chains. Longest chain 10 peptides. Score 0.439 Round 4: 159 peptides, 27 chains. Longest chain 10 peptides. Score 0.426 Round 5: 159 peptides, 27 chains. Longest chain 10 peptides. Score 0.426 Taking the results from Round 3 Chains 27, Residues 135, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2888 reflections ( 99.69 % complete ) and 5412 restraints for refining 2404 atoms. 4883 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2116 (Rfree = 0.000) for 2404 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 7: After refmac, R = 0.2023 (Rfree = 0.000) for 2370 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 8: After refmac, R = 0.2106 (Rfree = 0.000) for 2335 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 9: After refmac, R = 0.1940 (Rfree = 0.000) for 2324 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2241 (Rfree = 0.000) for 2316 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.87 4.19 Search for helices and strands: 0 residues in 0 chains, 2435 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 8 peptides. Score 0.265 Round 2: 156 peptides, 31 chains. Longest chain 11 peptides. Score 0.332 Round 3: 158 peptides, 27 chains. Longest chain 11 peptides. Score 0.421 Round 4: 164 peptides, 28 chains. Longest chain 11 peptides. Score 0.429 Round 5: 164 peptides, 28 chains. Longest chain 11 peptides. Score 0.429 Taking the results from Round 5 Chains 28, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2888 reflections ( 99.69 % complete ) and 5626 restraints for refining 2421 atoms. 5110 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2112 (Rfree = 0.000) for 2421 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 12: After refmac, R = 0.1999 (Rfree = 0.000) for 2395 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.1735 (Rfree = 0.000) for 2368 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.1944 (Rfree = 0.000) for 2363 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.1835 (Rfree = 0.000) for 2357 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 4.11 Search for helices and strands: 0 residues in 0 chains, 2452 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 8 peptides. Score 0.239 Round 2: 142 peptides, 28 chains. Longest chain 8 peptides. Score 0.325 Round 3: 145 peptides, 23 chains. Longest chain 13 peptides. Score 0.441 Round 4: 149 peptides, 26 chains. Longest chain 10 peptides. Score 0.400 Round 5: 143 peptides, 22 chains. Longest chain 18 peptides. Score 0.451 Taking the results from Round 5 Chains 22, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2888 reflections ( 99.69 % complete ) and 5654 restraints for refining 2427 atoms. 5192 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2257 (Rfree = 0.000) for 2427 atoms. Found 6 (11 requested) and removed 26 (5 requested) atoms. Cycle 17: After refmac, R = 0.2145 (Rfree = 0.000) for 2389 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.1824 (Rfree = 0.000) for 2374 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. Cycle 19: After refmac, R = 0.1767 (Rfree = 0.000) for 2357 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 20: After refmac, R = 0.1274 (Rfree = 0.000) for 2354 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 4.16 Search for helices and strands: 0 residues in 0 chains, 2423 seeds are put forward Round 1: 113 peptides, 25 chains. Longest chain 6 peptides. Score 0.240 Round 2: 135 peptides, 27 chains. Longest chain 8 peptides. Score 0.311 Round 3: 142 peptides, 28 chains. Longest chain 11 peptides. Score 0.325 Round 4: 136 peptides, 26 chains. Longest chain 11 peptides. Score 0.337 Round 5: 128 peptides, 25 chains. Longest chain 14 peptides. Score 0.319 Taking the results from Round 4 Chains 26, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2888 reflections ( 99.69 % complete ) and 5734 restraints for refining 2418 atoms. 5320 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2224 (Rfree = 0.000) for 2418 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 22: After refmac, R = 0.1909 (Rfree = 0.000) for 2389 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.1901 (Rfree = 0.000) for 2378 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 24: After refmac, R = 0.1656 (Rfree = 0.000) for 2364 atoms. Found 8 (11 requested) and removed 11 (5 requested) atoms. Cycle 25: After refmac, R = 0.1964 (Rfree = 0.000) for 2351 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 4.07 Search for helices and strands: 0 residues in 0 chains, 2460 seeds are put forward Round 1: 92 peptides, 22 chains. Longest chain 5 peptides. Score 0.191 Round 2: 116 peptides, 23 chains. Longest chain 9 peptides. Score 0.300 Round 3: 110 peptides, 23 chains. Longest chain 9 peptides. Score 0.269 Round 4: 114 peptides, 22 chains. Longest chain 8 peptides. Score 0.312 Round 5: 122 peptides, 21 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 5 Chains 21, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2888 reflections ( 99.69 % complete ) and 5795 restraints for refining 2414 atoms. 5412 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2096 (Rfree = 0.000) for 2414 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 27: After refmac, R = 0.1983 (Rfree = 0.000) for 2395 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 28: After refmac, R = 0.2029 (Rfree = 0.000) for 2372 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.1854 (Rfree = 0.000) for 2361 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 30: After refmac, R = 0.1724 (Rfree = 0.000) for 2350 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 4.11 Search for helices and strands: 0 residues in 0 chains, 2455 seeds are put forward Round 1: 86 peptides, 20 chains. Longest chain 5 peptides. Score 0.203 Round 2: 111 peptides, 22 chains. Longest chain 11 peptides. Score 0.296 Round 3: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.353 Round 4: 104 peptides, 21 chains. Longest chain 7 peptides. Score 0.282 Round 5: 113 peptides, 20 chains. Longest chain 12 peptides. Score 0.351 Taking the results from Round 3 Chains 19, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2888 reflections ( 99.69 % complete ) and 5370 restraints for refining 2306 atoms. 5029 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2202 (Rfree = 0.000) for 2306 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 32: After refmac, R = 0.1804 (Rfree = 0.000) for 2295 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.1917 (Rfree = 0.000) for 2285 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 34: After refmac, R = 0.1629 (Rfree = 0.000) for 2270 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.1622 (Rfree = 0.000) for 2270 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 4.07 Search for helices and strands: 0 residues in 0 chains, 2349 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 7 peptides. Score 0.211 Round 2: 98 peptides, 21 chains. Longest chain 8 peptides. Score 0.249 Round 3: 111 peptides, 24 chains. Longest chain 10 peptides. Score 0.252 Round 4: 113 peptides, 22 chains. Longest chain 11 peptides. Score 0.307 Round 5: 105 peptides, 20 chains. Longest chain 9 peptides. Score 0.310 Taking the results from Round 5 Chains 20, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2888 reflections ( 99.69 % complete ) and 5435 restraints for refining 2305 atoms. 5115 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1995 (Rfree = 0.000) for 2305 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 37: After refmac, R = 0.1650 (Rfree = 0.000) for 2283 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.1922 (Rfree = 0.000) for 2277 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 39: After refmac, R = 0.1654 (Rfree = 0.000) for 2269 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 40: After refmac, R = 0.1452 (Rfree = 0.000) for 2260 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 4.12 Search for helices and strands: 0 residues in 0 chains, 2358 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 8 peptides. Score 0.221 Round 2: 106 peptides, 22 chains. Longest chain 7 peptides. Score 0.270 Round 3: 97 peptides, 20 chains. Longest chain 7 peptides. Score 0.266 Round 4: 108 peptides, 21 chains. Longest chain 9 peptides. Score 0.303 Round 5: 114 peptides, 23 chains. Longest chain 7 peptides. Score 0.290 Taking the results from Round 4 Chains 21, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2888 reflections ( 99.69 % complete ) and 5238 restraints for refining 2263 atoms. 4911 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1999 (Rfree = 0.000) for 2263 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 42: After refmac, R = 0.1905 (Rfree = 0.000) for 2254 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.1722 (Rfree = 0.000) for 2253 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.1607 (Rfree = 0.000) for 2251 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.1824 (Rfree = 0.000) for 2241 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 4.11 Search for helices and strands: 0 residues in 0 chains, 2344 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 7 peptides. Score 0.221 Round 2: 101 peptides, 21 chains. Longest chain 9 peptides. Score 0.265 Round 3: 120 peptides, 23 chains. Longest chain 9 peptides. Score 0.321 Round 4: 106 peptides, 21 chains. Longest chain 9 peptides. Score 0.292 Round 5: 117 peptides, 21 chains. Longest chain 12 peptides. Score 0.349 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 96, 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 2a3n-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2888 reflections ( 99.69 % complete ) and 5247 restraints for refining 2279 atoms. 4884 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1847 (Rfree = 0.000) for 2279 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2048 (Rfree = 0.000) for 2264 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1808 (Rfree = 0.000) for 2249 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1631 (Rfree = 0.000) for 2238 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:28 GMT 2018 Job finished. TimeTaking 47.7 Used memory is bytes: 1490736