Sun 23 Dec 22:22:52 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 2pw4-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-4.0-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/2pw4-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-4.0-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 22:23:02 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/2pw4-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-4.0-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 130 and 0 Target number of residues in the AU: 130 Target solvent content: 0.6635 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 188 Adjusted target solvent content: 0.51 Input MTZ file: 2pw4-4.0-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: 77.750 59.670 57.820 90.000 128.790 90.000 Input sequence file: 2pw4-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1504 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: 25.783 4.000 Wilson plot Bfac: 87.48 1753 reflections ( 96.85 % complete ) and 0 restraints for refining 1668 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3315 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2950 (Rfree = 0.000) for 1668 atoms. Found 7 (7 requested) and removed 19 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.79 Search for helices and strands: 0 residues in 0 chains, 1694 seeds are put forward Round 1: 58 peptides, 9 chains. Longest chain 10 peptides. Score 0.379 Round 2: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.392 Round 3: 74 peptides, 10 chains. Longest chain 12 peptides. Score 0.468 Round 4: 73 peptides, 11 chains. Longest chain 10 peptides. Score 0.426 Round 5: 70 peptides, 11 chains. Longest chain 10 peptides. Score 0.403 Taking the results from Round 3 Chains 10, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1753 reflections ( 96.85 % complete ) and 3382 restraints for refining 1359 atoms. 3136 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2048 (Rfree = 0.000) for 1359 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 2: After refmac, R = 0.1836 (Rfree = 0.000) for 1334 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.1693 (Rfree = 0.000) for 1322 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 4: After refmac, R = 0.1629 (Rfree = 0.000) for 1314 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.1755 (Rfree = 0.000) for 1311 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.84 3.79 Search for helices and strands: 0 residues in 0 chains, 1367 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.302 Round 2: 74 peptides, 12 chains. Longest chain 9 peptides. Score 0.400 Round 3: 77 peptides, 12 chains. Longest chain 10 peptides. Score 0.423 Round 4: 79 peptides, 12 chains. Longest chain 12 peptides. Score 0.438 Round 5: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 4 Chains 12, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1753 reflections ( 96.85 % complete ) and 3007 restraints for refining 1296 atoms. 2751 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2012 (Rfree = 0.000) for 1296 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 7: After refmac, R = 0.1983 (Rfree = 0.000) for 1286 atoms. Found 4 (6 requested) and removed 10 (3 requested) atoms. Cycle 8: After refmac, R = 0.1737 (Rfree = 0.000) for 1272 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.1501 (Rfree = 0.000) for 1268 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 10: After refmac, R = 0.1547 (Rfree = 0.000) for 1264 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 3.79 Search for helices and strands: 0 residues in 0 chains, 1327 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.273 Round 2: 77 peptides, 11 chains. Longest chain 13 peptides. Score 0.457 Round 3: 74 peptides, 11 chains. Longest chain 11 peptides. Score 0.434 Round 4: 74 peptides, 12 chains. Longest chain 12 peptides. Score 0.400 Round 5: 83 peptides, 14 chains. Longest chain 12 peptides. Score 0.402 Taking the results from Round 2 Chains 11, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1753 reflections ( 96.85 % complete ) and 2841 restraints for refining 1263 atoms. 2588 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1838 (Rfree = 0.000) for 1263 atoms. Found 5 (6 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.1750 (Rfree = 0.000) for 1250 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 13: After refmac, R = 0.1881 (Rfree = 0.000) for 1246 atoms. Found 4 (5 requested) and removed 8 (2 requested) atoms. Cycle 14: After refmac, R = 0.1770 (Rfree = 0.000) for 1238 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2087 (Rfree = 0.000) for 1233 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.88 3.83 Search for helices and strands: 0 residues in 0 chains, 1292 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.289 Round 2: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.332 Round 3: 69 peptides, 11 chains. Longest chain 9 peptides. Score 0.395 Round 4: 73 peptides, 12 chains. Longest chain 9 peptides. Score 0.392 Round 5: 74 peptides, 12 chains. Longest chain 10 peptides. Score 0.400 Taking the results from Round 5 Chains 12, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1753 reflections ( 96.85 % complete ) and 3034 restraints for refining 1291 atoms. 2798 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2111 (Rfree = 0.000) for 1291 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 17: After refmac, R = 0.2033 (Rfree = 0.000) for 1281 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. Cycle 18: After refmac, R = 0.1795 (Rfree = 0.000) for 1275 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.1581 (Rfree = 0.000) for 1275 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 20: After refmac, R = 0.1497 (Rfree = 0.000) for 1270 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.86 3.81 Search for helices and strands: 0 residues in 0 chains, 1312 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.253 Round 2: 66 peptides, 13 chains. Longest chain 7 peptides. Score 0.298 Round 3: 73 peptides, 13 chains. Longest chain 8 peptides. Score 0.357 Round 4: 69 peptides, 13 chains. Longest chain 7 peptides. Score 0.323 Round 5: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.326 Taking the results from Round 3 Chains 13, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1753 reflections ( 96.85 % complete ) and 3082 restraints for refining 1316 atoms. 2855 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1746 (Rfree = 0.000) for 1316 atoms. Found 4 (6 requested) and removed 15 (3 requested) atoms. Cycle 22: After refmac, R = 0.1625 (Rfree = 0.000) for 1300 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.1754 (Rfree = 0.000) for 1299 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.1658 (Rfree = 0.000) for 1292 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.1852 (Rfree = 0.000) for 1286 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.89 3.84 Search for helices and strands: 0 residues in 0 chains, 1325 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.271 Round 2: 63 peptides, 11 chains. Longest chain 8 peptides. Score 0.346 Round 3: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.349 Round 4: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.357 Round 5: 79 peptides, 12 chains. Longest chain 10 peptides. Score 0.438 Taking the results from Round 5 Chains 12, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1753 reflections ( 96.85 % complete ) and 3202 restraints for refining 1359 atoms. 2946 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2107 (Rfree = 0.000) for 1359 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.1701 (Rfree = 0.000) for 1347 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 28: After refmac, R = 0.1724 (Rfree = 0.000) for 1337 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.1583 (Rfree = 0.000) for 1331 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1688 (Rfree = 0.000) for 1325 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 3.78 Search for helices and strands: 0 residues in 0 chains, 1374 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 9 peptides. Score 0.245 Round 2: 68 peptides, 14 chains. Longest chain 10 peptides. Score 0.278 Round 3: 73 peptides, 15 chains. Longest chain 11 peptides. Score 0.285 Round 4: 75 peptides, 14 chains. Longest chain 11 peptides. Score 0.338 Round 5: 74 peptides, 13 chains. Longest chain 14 peptides. Score 0.365 Taking the results from Round 5 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1753 reflections ( 96.85 % complete ) and 3302 restraints for refining 1359 atoms. 3071 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1852 (Rfree = 0.000) for 1359 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.1703 (Rfree = 0.000) for 1355 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.1601 (Rfree = 0.000) for 1353 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.1633 (Rfree = 0.000) for 1349 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.1441 (Rfree = 0.000) for 1345 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.74 Search for helices and strands: 0 residues in 0 chains, 1388 seeds are put forward Round 1: 48 peptides, 9 chains. Longest chain 9 peptides. Score 0.290 Round 2: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.273 Round 3: 56 peptides, 12 chains. Longest chain 6 peptides. Score 0.245 Round 4: 61 peptides, 11 chains. Longest chain 10 peptides. Score 0.329 Round 5: 66 peptides, 11 chains. Longest chain 14 peptides. Score 0.371 Taking the results from Round 5 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1753 reflections ( 96.85 % complete ) and 3265 restraints for refining 1359 atoms. 3043 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1868 (Rfree = 0.000) for 1359 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 37: After refmac, R = 0.1840 (Rfree = 0.000) for 1358 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.1723 (Rfree = 0.000) for 1353 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 39: After refmac, R = 0.1676 (Rfree = 0.000) for 1348 atoms. Found 2 (6 requested) and removed 13 (3 requested) atoms. Cycle 40: After refmac, R = 0.1795 (Rfree = 0.000) for 1334 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.88 3.83 Search for helices and strands: 0 residues in 0 chains, 1379 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 9 peptides. Score 0.266 Round 2: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.302 Round 3: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.284 Round 4: 60 peptides, 11 chains. Longest chain 12 peptides. Score 0.320 Round 5: 61 peptides, 11 chains. Longest chain 11 peptides. Score 0.329 Taking the results from Round 5 Chains 11, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1753 reflections ( 96.85 % complete ) and 3327 restraints for refining 1359 atoms. 3138 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2001 (Rfree = 0.000) for 1359 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.1956 (Rfree = 0.000) for 1353 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.2378 (Rfree = 0.000) for 1346 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 44: After refmac, R = 0.2586 (Rfree = 0.000) for 1342 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.2381 (Rfree = 0.000) for 1342 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 3.76 Search for helices and strands: 0 residues in 0 chains, 1389 seeds are put forward Round 1: 34 peptides, 8 chains. Longest chain 5 peptides. Score 0.190 Round 2: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.230 Round 3: 47 peptides, 9 chains. Longest chain 7 peptides. Score 0.281 Round 4: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.300 Round 5: 40 peptides, 8 chains. Longest chain 7 peptides. Score 0.255 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 40, 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 2pw4-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1753 reflections ( 96.85 % complete ) and 3415 restraints for refining 1359 atoms. 3264 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2470 (Rfree = 0.000) for 1359 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1826 (Rfree = 0.000) for 1355 atoms. Found 0 (6 requested) and removed 2 (3 requested) atoms. Cycle 48: After refmac, R = 0.2252 (Rfree = 0.000) for 1353 atoms. Found 0 (6 requested) and removed 0 (3 requested) atoms. Cycle 49: After refmac, R = 0.1757 (Rfree = 0.000) for 1353 atoms. TimeTaking 26.58