Sun 23 Dec 22:23:10 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fqp-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.8-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 22:23:19 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fqp-3.8-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 225 and 0 Target number of residues in the AU: 225 Target solvent content: 0.6404 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-3.8-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-3.8-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 3.801 Wilson plot Bfac: 71.89 2715 reflections ( 81.65 % complete ) and 0 restraints for refining 3444 atoms. Observations/parameters ratio is 0.20 ------------------------------------------------------ Starting model: R = 0.3223 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2901 (Rfree = 0.000) for 3444 atoms. Found 16 (18 requested) and removed 73 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 3412 seeds are put forward NCS extension: 0 residues added, 3412 seeds are put forward Round 1: 79 peptides, 19 chains. Longest chain 5 peptides. Score 0.186 Round 2: 110 peptides, 22 chains. Longest chain 8 peptides. Score 0.293 Round 3: 106 peptides, 21 chains. Longest chain 8 peptides. Score 0.294 Round 4: 120 peptides, 22 chains. Longest chain 9 peptides. Score 0.345 Round 5: 111 peptides, 22 chains. Longest chain 10 peptides. Score 0.298 Taking the results from Round 4 Chains 22, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6902 restraints for refining 2806 atoms. 6532 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2083 (Rfree = 0.000) for 2806 atoms. Found 13 (15 requested) and removed 38 (7 requested) atoms. Cycle 2: After refmac, R = 0.1978 (Rfree = 0.000) for 2748 atoms. Found 4 (15 requested) and removed 25 (7 requested) atoms. Cycle 3: After refmac, R = 0.1842 (Rfree = 0.000) for 2706 atoms. Found 6 (14 requested) and removed 16 (7 requested) atoms. Cycle 4: After refmac, R = 0.1207 (Rfree = 0.000) for 2685 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.1034 (Rfree = 0.000) for 2673 atoms. Found 0 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.95 Search for helices and strands: 0 residues in 0 chains, 2724 seeds are put forward NCS extension: 0 residues added, 2724 seeds are put forward Round 1: 126 peptides, 28 chains. Longest chain 7 peptides. Score 0.244 Round 2: 134 peptides, 27 chains. Longest chain 8 peptides. Score 0.308 Round 3: 153 peptides, 29 chains. Longest chain 13 peptides. Score 0.361 Round 4: 155 peptides, 31 chains. Longest chain 8 peptides. Score 0.330 Round 5: 163 peptides, 30 chains. Longest chain 9 peptides. Score 0.388 Taking the results from Round 5 Chains 30, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6249 restraints for refining 2666 atoms. 5747 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1554 (Rfree = 0.000) for 2666 atoms. Found 8 (14 requested) and removed 13 (7 requested) atoms. Cycle 7: After refmac, R = 0.1846 (Rfree = 0.000) for 2628 atoms. Found 11 (14 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.1772 (Rfree = 0.000) for 2610 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 9: After refmac, R = 0.1683 (Rfree = 0.000) for 2599 atoms. Found 12 (14 requested) and removed 15 (7 requested) atoms. Cycle 10: After refmac, R = 0.1586 (Rfree = 0.000) for 2591 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.95 Search for helices and strands: 0 residues in 0 chains, 2649 seeds are put forward NCS extension: 0 residues added, 2649 seeds are put forward Round 1: 131 peptides, 27 chains. Longest chain 10 peptides. Score 0.293 Round 2: 149 peptides, 28 chains. Longest chain 10 peptides. Score 0.362 Round 3: 145 peptides, 27 chains. Longest chain 11 peptides. Score 0.363 Round 4: 154 peptides, 28 chains. Longest chain 11 peptides. Score 0.386 Round 5: 159 peptides, 27 chains. Longest chain 11 peptides. Score 0.429 Taking the results from Round 5 Chains 27, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5993 restraints for refining 2599 atoms. 5492 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1933 (Rfree = 0.000) for 2599 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 12: After refmac, R = 0.1671 (Rfree = 0.000) for 2572 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.1987 (Rfree = 0.000) for 2555 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 14: After refmac, R = 0.1869 (Rfree = 0.000) for 2538 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 15: After refmac, R = 0.1717 (Rfree = 0.000) for 2521 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.87 Search for helices and strands: 0 residues in 0 chains, 2605 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2619 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 7 peptides. Score 0.237 Round 2: 114 peptides, 23 chains. Longest chain 10 peptides. Score 0.291 Round 3: 121 peptides, 23 chains. Longest chain 12 peptides. Score 0.328 Round 4: 122 peptides, 23 chains. Longest chain 11 peptides. Score 0.333 Round 5: 127 peptides, 22 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 5 Chains 22, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5390 restraints for refining 2399 atoms. 4992 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1780 (Rfree = 0.000) for 2399 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 17: After refmac, R = 0.1784 (Rfree = 0.000) for 2384 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.1629 (Rfree = 0.000) for 2375 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.1074 (Rfree = 0.000) for 2371 atoms. Found 12 (13 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.0938 (Rfree = 0.000) for 2375 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 2455 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 2459 seeds are put forward Round 1: 113 peptides, 23 chains. Longest chain 8 peptides. Score 0.286 Round 2: 139 peptides, 25 chains. Longest chain 11 peptides. Score 0.375 Round 3: 161 peptides, 28 chains. Longest chain 11 peptides. Score 0.418 Round 4: 158 peptides, 25 chains. Longest chain 11 peptides. Score 0.463 Round 5: 146 peptides, 22 chains. Longest chain 17 peptides. Score 0.468 Taking the results from Round 5 Chains 22, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5424 restraints for refining 2427 atoms. 4950 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1571 (Rfree = 0.000) for 2427 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.1765 (Rfree = 0.000) for 2408 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 23: After refmac, R = 0.1308 (Rfree = 0.000) for 2396 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.1192 (Rfree = 0.000) for 2390 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1118 (Rfree = 0.000) for 2380 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.93 Search for helices and strands: 0 residues in 0 chains, 2447 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 2475 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 8 peptides. Score 0.264 Round 2: 133 peptides, 25 chains. Longest chain 12 peptides. Score 0.346 Round 3: 128 peptides, 24 chains. Longest chain 12 peptides. Score 0.342 Round 4: 125 peptides, 23 chains. Longest chain 12 peptides. Score 0.348 Round 5: 132 peptides, 25 chains. Longest chain 11 peptides. Score 0.341 Taking the results from Round 4 Chains 23, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5557 restraints for refining 2390 atoms. 5172 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1670 (Rfree = 0.000) for 2390 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 27: After refmac, R = 0.1636 (Rfree = 0.000) for 2384 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 28: After refmac, R = 0.1682 (Rfree = 0.000) for 2382 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.1633 (Rfree = 0.000) for 2383 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1087 (Rfree = 0.000) for 2386 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.92 Search for helices and strands: 0 residues in 0 chains, 2435 seeds are put forward NCS extension: 0 residues added, 2435 seeds are put forward Round 1: 110 peptides, 25 chains. Longest chain 6 peptides. Score 0.224 Round 2: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.326 Round 3: 126 peptides, 23 chains. Longest chain 9 peptides. Score 0.353 Round 4: 126 peptides, 22 chains. Longest chain 10 peptides. Score 0.375 Round 5: 115 peptides, 21 chains. Longest chain 9 peptides. Score 0.341 Taking the results from Round 4 Chains 22, Residues 104, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5390 restraints for refining 2396 atoms. 4951 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1824 (Rfree = 0.000) for 2396 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 32: After refmac, R = 0.1767 (Rfree = 0.000) for 2386 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.1826 (Rfree = 0.000) for 2384 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.1317 (Rfree = 0.000) for 2381 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1644 (Rfree = 0.000) for 2374 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 2436 seeds are put forward NCS extension: 0 residues added, 2436 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 7 peptides. Score 0.199 Round 2: 102 peptides, 21 chains. Longest chain 8 peptides. Score 0.272 Round 3: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.307 Round 4: 103 peptides, 18 chains. Longest chain 9 peptides. Score 0.346 Round 5: 101 peptides, 18 chains. Longest chain 8 peptides. Score 0.336 Taking the results from Round 4 Chains 18, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5230 restraints for refining 2302 atoms. 4908 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1694 (Rfree = 0.000) for 2302 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.1752 (Rfree = 0.000) for 2299 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.1806 (Rfree = 0.000) for 2299 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.1278 (Rfree = 0.000) for 2300 atoms. Found 11 (12 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1522 (Rfree = 0.000) for 2303 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.90 Search for helices and strands: 0 residues in 0 chains, 2395 seeds are put forward NCS extension: 0 residues added, 2395 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 8 peptides. Score 0.222 Round 2: 96 peptides, 21 chains. Longest chain 8 peptides. Score 0.238 Round 3: 116 peptides, 24 chains. Longest chain 8 peptides. Score 0.280 Round 4: 108 peptides, 23 chains. Longest chain 8 peptides. Score 0.259 Round 5: 114 peptides, 24 chains. Longest chain 8 peptides. Score 0.269 Taking the results from Round 3 Chains 24, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5172 restraints for refining 2292 atoms. 4828 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1832 (Rfree = 0.000) for 2292 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 42: After refmac, R = 0.1664 (Rfree = 0.000) for 2284 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.1172 (Rfree = 0.000) for 2285 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1067 (Rfree = 0.000) for 2279 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.0987 (Rfree = 0.000) for 2276 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.93 Search for helices and strands: 0 residues in 0 chains, 2338 seeds are put forward NCS extension: 0 residues added, 2338 seeds are put forward Round 1: 77 peptides, 19 chains. Longest chain 5 peptides. Score 0.173 Round 2: 94 peptides, 21 chains. Longest chain 8 peptides. Score 0.227 Round 3: 86 peptides, 18 chains. Longest chain 10 peptides. Score 0.253 Round 4: 88 peptides, 20 chains. Longest chain 7 peptides. Score 0.216 Round 5: 86 peptides, 17 chains. Longest chain 10 peptides. Score 0.277 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 69, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2715 reflections ( 81.65 % complete ) and 5037 restraints for refining 2236 atoms. 4778 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2721 (Rfree = 0.000) for 2236 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1644 (Rfree = 0.000) for 2222 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1599 (Rfree = 0.000) for 2210 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1458 (Rfree = 0.000) for 2201 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 46.23