null Tue 25 Dec 19:27:56 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 2pn1-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.6-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/2pn1-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.6-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 19:28:10 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/2pn1-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.6-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 240 and 0 Target number of residues in the AU: 240 Target solvent content: 0.6349 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 331 Adjusted target solvent content: 0.50 Input MTZ file: 2pn1-3.6-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: 91.460 61.130 76.770 90.000 124.022 90.000 Input sequence file: 2pn1-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2648 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 Loops will be built when appropriate and at the last cycle Resolution range: 63.629 3.600 Wilson plot Bfac: 68.40 3990 reflections ( 95.61 % complete ) and 0 restraints for refining 2927 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3415 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2961 (Rfree = 0.000) for 2927 atoms. Found 18 (18 requested) and removed 32 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.41 Search for helices and strands: 0 residues in 0 chains, 2958 seeds are put forward Round 1: 109 peptides, 20 chains. Longest chain 11 peptides. Score 0.327 Round 2: 132 peptides, 25 chains. Longest chain 11 peptides. Score 0.334 Round 3: 148 peptides, 25 chains. Longest chain 11 peptides. Score 0.409 Round 4: 149 peptides, 24 chains. Longest chain 12 peptides. Score 0.432 Round 5: 150 peptides, 22 chains. Longest chain 19 peptides. Score 0.474 Taking the results from Round 5 Chains 22, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3990 reflections ( 95.61 % complete ) and 5841 restraints for refining 2397 atoms. 5351 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2231 (Rfree = 0.000) for 2397 atoms. Found 10 (15 requested) and removed 28 (7 requested) atoms. Cycle 2: After refmac, R = 0.2071 (Rfree = 0.000) for 2352 atoms. Found 5 (15 requested) and removed 16 (7 requested) atoms. Cycle 3: After refmac, R = 0.1780 (Rfree = 0.000) for 2334 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.1750 (Rfree = 0.000) for 2327 atoms. Found 3 (14 requested) and removed 13 (7 requested) atoms. Cycle 5: After refmac, R = 0.1791 (Rfree = 0.000) for 2312 atoms. Found 5 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.40 Search for helices and strands: 0 residues in 0 chains, 2375 seeds are put forward Round 1: 142 peptides, 25 chains. Longest chain 12 peptides. Score 0.382 Round 2: 157 peptides, 25 chains. Longest chain 14 peptides. Score 0.448 Round 3: 163 peptides, 22 chains. Longest chain 18 peptides. Score 0.526 Round 4: 166 peptides, 22 chains. Longest chain 15 peptides. Score 0.538 Round 5: 164 peptides, 23 chains. Longest chain 16 peptides. Score 0.513 Taking the results from Round 4 Chains 22, Residues 144, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3990 reflections ( 95.61 % complete ) and 5292 restraints for refining 2371 atoms. 4717 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2016 (Rfree = 0.000) for 2371 atoms. Found 11 (15 requested) and removed 11 (7 requested) atoms. Cycle 7: After refmac, R = 0.1950 (Rfree = 0.000) for 2354 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. Cycle 8: After refmac, R = 0.1959 (Rfree = 0.000) for 2335 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 9: After refmac, R = 0.1916 (Rfree = 0.000) for 2326 atoms. Found 10 (14 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.1763 (Rfree = 0.000) for 2318 atoms. Found 3 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.41 Search for helices and strands: 0 residues in 0 chains, 2363 seeds are put forward Round 1: 139 peptides, 22 chains. Longest chain 14 peptides. Score 0.427 Round 2: 142 peptides, 22 chains. Longest chain 12 peptides. Score 0.440 Round 3: 151 peptides, 22 chains. Longest chain 15 peptides. Score 0.478 Round 4: 145 peptides, 20 chains. Longest chain 13 peptides. Score 0.490 Round 5: 141 peptides, 20 chains. Longest chain 13 peptides. Score 0.474 Taking the results from Round 4 Chains 20, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3990 reflections ( 95.61 % complete ) and 5577 restraints for refining 2353 atoms. 5097 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1999 (Rfree = 0.000) for 2353 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 12: After refmac, R = 0.1819 (Rfree = 0.000) for 2344 atoms. Found 6 (15 requested) and removed 15 (7 requested) atoms. Cycle 13: After refmac, R = 0.1792 (Rfree = 0.000) for 2331 atoms. Found 8 (14 requested) and removed 15 (7 requested) atoms. Cycle 14: After refmac, R = 0.1715 (Rfree = 0.000) for 2324 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.1701 (Rfree = 0.000) for 2319 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.38 Search for helices and strands: 0 residues in 0 chains, 2392 seeds are put forward Round 1: 141 peptides, 24 chains. Longest chain 11 peptides. Score 0.397 Round 2: 148 peptides, 26 chains. Longest chain 12 peptides. Score 0.389 Round 3: 156 peptides, 26 chains. Longest chain 13 peptides. Score 0.425 Round 4: 147 peptides, 22 chains. Longest chain 11 peptides. Score 0.462 Round 5: 148 peptides, 23 chains. Longest chain 13 peptides. Score 0.447 Taking the results from Round 4 Chains 22, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3990 reflections ( 95.61 % complete ) and 5635 restraints for refining 2401 atoms. 5157 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1796 (Rfree = 0.000) for 2401 atoms. Found 13 (15 requested) and removed 10 (7 requested) atoms. Cycle 17: After refmac, R = 0.1766 (Rfree = 0.000) for 2389 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. Cycle 18: After refmac, R = 0.1670 (Rfree = 0.000) for 2383 atoms. Found 5 (15 requested) and removed 11 (7 requested) atoms. Cycle 19: After refmac, R = 0.1558 (Rfree = 0.000) for 2371 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. Cycle 20: After refmac, R = 0.1606 (Rfree = 0.000) for 2369 atoms. Found 10 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.39 Search for helices and strands: 0 residues in 0 chains, 2425 seeds are put forward Round 1: 112 peptides, 22 chains. Longest chain 8 peptides. Score 0.298 Round 2: 116 peptides, 19 chains. Longest chain 10 peptides. Score 0.382 Round 3: 131 peptides, 22 chains. Longest chain 11 peptides. Score 0.391 Round 4: 119 peptides, 19 chains. Longest chain 14 peptides. Score 0.396 Round 5: 128 peptides, 21 chains. Longest chain 10 peptides. Score 0.397 Taking the results from Round 5 Chains 21, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3990 reflections ( 95.61 % complete ) and 5784 restraints for refining 2401 atoms. 5377 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1925 (Rfree = 0.000) for 2401 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.2276 (Rfree = 0.000) for 2397 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.2227 (Rfree = 0.000) for 2391 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 24: After refmac, R = 0.2209 (Rfree = 0.000) for 2384 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.2146 (Rfree = 0.000) for 2379 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.30 Search for helices and strands: 0 residues in 0 chains, 2431 seeds are put forward Round 1: 109 peptides, 24 chains. Longest chain 8 peptides. Score 0.239 Round 2: 149 peptides, 29 chains. Longest chain 10 peptides. Score 0.335 Round 3: 143 peptides, 26 chains. Longest chain 12 peptides. Score 0.366 Round 4: 158 peptides, 27 chains. Longest chain 11 peptides. Score 0.415 Round 5: 157 peptides, 28 chains. Longest chain 10 peptides. Score 0.391 Taking the results from Round 4 Chains 27, Residues 131, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3990 reflections ( 95.61 % complete ) and 5393 restraints for refining 2401 atoms. 4871 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2095 (Rfree = 0.000) for 2401 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 27: After refmac, R = 0.2199 (Rfree = 0.000) for 2389 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 28: After refmac, R = 0.2095 (Rfree = 0.000) for 2379 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 29: After refmac, R = 0.1630 (Rfree = 0.000) for 2371 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1596 (Rfree = 0.000) for 2362 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.34 Search for helices and strands: 0 residues in 0 chains, 2412 seeds are put forward Round 1: 126 peptides, 24 chains. Longest chain 10 peptides. Score 0.326 Round 2: 131 peptides, 21 chains. Longest chain 12 peptides. Score 0.411 Round 3: 128 peptides, 22 chains. Longest chain 13 peptides. Score 0.377 Round 4: 128 peptides, 18 chains. Longest chain 15 peptides. Score 0.457 Round 5: 129 peptides, 20 chains. Longest chain 14 peptides. Score 0.422 Taking the results from Round 4 Chains 19, Residues 110, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 3990 reflections ( 95.61 % complete ) and 5379 restraints for refining 2400 atoms. 4875 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2112 (Rfree = 0.000) for 2400 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 32: After refmac, R = 0.2067 (Rfree = 0.000) for 2392 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 33: After refmac, R = 0.2086 (Rfree = 0.000) for 2382 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 34: After refmac, R = 0.2027 (Rfree = 0.000) for 2384 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 35: After refmac, R = 0.2071 (Rfree = 0.000) for 2378 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.38 Search for helices and strands: 0 residues in 0 chains, 2423 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 8 peptides. Score 0.240 Round 2: 130 peptides, 26 chains. Longest chain 7 peptides. Score 0.304 Round 3: 132 peptides, 25 chains. Longest chain 14 peptides. Score 0.334 Round 4: 127 peptides, 23 chains. Longest chain 9 peptides. Score 0.352 Round 5: 130 peptides, 23 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 5 Chains 23, Residues 107, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3990 reflections ( 95.61 % complete ) and 5616 restraints for refining 2401 atoms. 5183 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2232 (Rfree = 0.000) for 2401 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 37: After refmac, R = 0.2008 (Rfree = 0.000) for 2393 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 38: After refmac, R = 0.1929 (Rfree = 0.000) for 2386 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 39: After refmac, R = 0.2042 (Rfree = 0.000) for 2380 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 40: After refmac, R = 0.1491 (Rfree = 0.000) for 2377 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.38 3.38 Search for helices and strands: 0 residues in 0 chains, 2420 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 8 peptides. Score 0.240 Round 2: 127 peptides, 22 chains. Longest chain 14 peptides. Score 0.372 Round 3: 134 peptides, 25 chains. Longest chain 9 peptides. Score 0.344 Round 4: 123 peptides, 21 chains. Longest chain 15 peptides. Score 0.374 Round 5: 114 peptides, 20 chains. Longest chain 13 peptides. Score 0.351 Taking the results from Round 4 Chains 21, Residues 102, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3990 reflections ( 95.61 % complete ) and 5450 restraints for refining 2351 atoms. 5054 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1955 (Rfree = 0.000) for 2351 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 42: After refmac, R = 0.2110 (Rfree = 0.000) for 2346 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.1506 (Rfree = 0.000) for 2344 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1491 (Rfree = 0.000) for 2337 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.1465 (Rfree = 0.000) for 2339 atoms. Found 12 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.36 Search for helices and strands: 0 residues in 0 chains, 2392 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 8 peptides. Score 0.252 Round 2: 110 peptides, 22 chains. Longest chain 8 peptides. Score 0.288 Round 3: 103 peptides, 20 chains. Longest chain 11 peptides. Score 0.296 Round 4: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.325 Round 5: 103 peptides, 21 chains. Longest chain 7 peptides. Score 0.274 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 82, 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 2pn1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3990 reflections ( 95.61 % complete ) and 5837 restraints for refining 2385 atoms. 5527 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2151 (Rfree = 0.000) for 2385 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2136 (Rfree = 0.000) for 2373 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2070 (Rfree = 0.000) for 2362 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1628 (Rfree = 0.000) for 2350 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:24:55 GMT 2018 Job finished. TimeTaking 56.99 Used memory is bytes: 23680880