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 2pw4-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pw4-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.4-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/2pw4-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.4-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/2pw4-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pw4-3.4-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 143 and 0 Target number of residues in the AU: 143 Target solvent content: 0.6299 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: 2pw4-3.4-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: 2pw4-3.4-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 3.400 Wilson plot Bfac: 65.84 2833 reflections ( 97.59 % complete ) and 0 restraints for refining 1675 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3093 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2658 (Rfree = 0.000) for 1675 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 1722 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.348 Round 2: 104 peptides, 17 chains. Longest chain 10 peptides. Score 0.461 Round 3: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.466 Round 4: 117 peptides, 17 chains. Longest chain 12 peptides. Score 0.547 Round 5: 117 peptides, 16 chains. Longest chain 16 peptides. Score 0.574 Taking the results from Round 5 Chains 16, Residues 101, Estimated correctness of the model 20.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2833 reflections ( 97.59 % complete ) and 3067 restraints for refining 1368 atoms. 2679 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2285 (Rfree = 0.000) for 1368 atoms. Found 8 (10 requested) and removed 13 (5 requested) atoms. Cycle 2: After refmac, R = 0.2076 (Rfree = 0.000) for 1354 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.1880 (Rfree = 0.000) for 1348 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 4: After refmac, R = 0.1798 (Rfree = 0.000) for 1338 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.1722 (Rfree = 0.000) for 1336 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.21 Search for helices and strands: 0 residues in 0 chains, 1391 seeds are put forward Round 1: 87 peptides, 16 chains. Longest chain 8 peptides. Score 0.366 Round 2: 115 peptides, 17 chains. Longest chain 13 peptides. Score 0.535 Round 3: 120 peptides, 18 chains. Longest chain 12 peptides. Score 0.539 Round 4: 118 peptides, 17 chains. Longest chain 12 peptides. Score 0.553 Round 5: 114 peptides, 18 chains. Longest chain 11 peptides. Score 0.500 Taking the results from Round 4 Chains 17, Residues 101, Estimated correctness of the model 12.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2833 reflections ( 97.59 % complete ) and 2986 restraints for refining 1368 atoms. 2599 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2070 (Rfree = 0.000) for 1368 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 7: After refmac, R = 0.1863 (Rfree = 0.000) for 1363 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.1816 (Rfree = 0.000) for 1359 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.1720 (Rfree = 0.000) for 1353 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.1667 (Rfree = 0.000) for 1347 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 1411 seeds are put forward Round 1: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.370 Round 2: 116 peptides, 17 chains. Longest chain 13 peptides. Score 0.541 Round 3: 106 peptides, 16 chains. Longest chain 14 peptides. Score 0.505 Round 4: 105 peptides, 16 chains. Longest chain 11 peptides. Score 0.498 Round 5: 103 peptides, 14 chains. Longest chain 11 peptides. Score 0.543 Taking the results from Round 5 Chains 14, Residues 89, Estimated correctness of the model 9.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2833 reflections ( 97.59 % complete ) and 3118 restraints for refining 1368 atoms. 2776 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1990 (Rfree = 0.000) for 1368 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 12: After refmac, R = 0.1855 (Rfree = 0.000) for 1362 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.1793 (Rfree = 0.000) for 1360 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.1935 (Rfree = 0.000) for 1359 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.1717 (Rfree = 0.000) for 1358 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 1415 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.334 Round 2: 105 peptides, 16 chains. Longest chain 14 peptides. Score 0.498 Round 3: 98 peptides, 16 chains. Longest chain 12 peptides. Score 0.449 Round 4: 99 peptides, 15 chains. Longest chain 11 peptides. Score 0.487 Round 5: 97 peptides, 15 chains. Longest chain 10 peptides. Score 0.473 Taking the results from Round 2 Chains 17, Residues 89, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2833 reflections ( 97.59 % complete ) and 2988 restraints for refining 1368 atoms. 2610 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1896 (Rfree = 0.000) for 1368 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. Cycle 17: After refmac, R = 0.1917 (Rfree = 0.000) for 1363 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 18: After refmac, R = 0.1811 (Rfree = 0.000) for 1361 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.1841 (Rfree = 0.000) for 1359 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.1800 (Rfree = 0.000) for 1354 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 1411 seeds are put forward Round 1: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.376 Round 2: 112 peptides, 17 chains. Longest chain 13 peptides. Score 0.515 Round 3: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.430 Round 4: 114 peptides, 16 chains. Longest chain 14 peptides. Score 0.556 Round 5: 102 peptides, 14 chains. Longest chain 13 peptides. Score 0.536 Taking the results from Round 4 Chains 16, Residues 98, Estimated correctness of the model 13.7 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2833 reflections ( 97.59 % complete ) and 2934 restraints for refining 1368 atoms. 2527 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2012 (Rfree = 0.000) for 1368 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 22: After refmac, R = 0.1942 (Rfree = 0.000) for 1368 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.1876 (Rfree = 0.000) for 1365 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.1850 (Rfree = 0.000) for 1357 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.1751 (Rfree = 0.000) for 1356 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 1402 seeds are put forward Round 1: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.336 Round 2: 82 peptides, 13 chains. Longest chain 11 peptides. Score 0.427 Round 3: 86 peptides, 13 chains. Longest chain 13 peptides. Score 0.457 Round 4: 87 peptides, 13 chains. Longest chain 14 peptides. Score 0.464 Round 5: 90 peptides, 14 chains. Longest chain 13 peptides. Score 0.454 Taking the results from Round 4 Chains 13, Residues 74, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2833 reflections ( 97.59 % complete ) and 3050 restraints for refining 1367 atoms. 2724 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2000 (Rfree = 0.000) for 1367 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 27: After refmac, R = 0.1814 (Rfree = 0.000) for 1362 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.1753 (Rfree = 0.000) for 1355 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.1727 (Rfree = 0.000) for 1352 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1707 (Rfree = 0.000) for 1349 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 1392 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 7 peptides. Score 0.255 Round 2: 70 peptides, 11 chains. Longest chain 12 peptides. Score 0.403 Round 3: 63 peptides, 10 chains. Longest chain 10 peptides. Score 0.383 Round 4: 75 peptides, 13 chains. Longest chain 10 peptides. Score 0.373 Round 5: 67 peptides, 11 chains. Longest chain 10 peptides. Score 0.379 Taking the results from Round 2 Chains 11, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2833 reflections ( 97.59 % complete ) and 3307 restraints for refining 1358 atoms. 3082 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1846 (Rfree = 0.000) for 1358 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.1725 (Rfree = 0.000) for 1357 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.1668 (Rfree = 0.000) for 1357 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1651 (Rfree = 0.000) for 1353 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1645 (Rfree = 0.000) for 1350 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 1392 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.280 Round 2: 72 peptides, 12 chains. Longest chain 10 peptides. Score 0.384 Round 3: 70 peptides, 12 chains. Longest chain 12 peptides. Score 0.368 Round 4: 78 peptides, 11 chains. Longest chain 16 peptides. Score 0.464 Round 5: 68 peptides, 11 chains. Longest chain 14 peptides. Score 0.387 Taking the results from Round 4 Chains 11, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2833 reflections ( 97.59 % complete ) and 3268 restraints for refining 1368 atoms. 3011 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1894 (Rfree = 0.000) for 1368 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 37: After refmac, R = 0.1737 (Rfree = 0.000) for 1372 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.1699 (Rfree = 0.000) for 1371 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1645 (Rfree = 0.000) for 1365 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1649 (Rfree = 0.000) for 1358 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.21 Search for helices and strands: 0 residues in 0 chains, 1416 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 9 peptides. Score 0.285 Round 2: 83 peptides, 13 chains. Longest chain 12 peptides. Score 0.435 Round 3: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.378 Round 4: 90 peptides, 13 chains. Longest chain 12 peptides. Score 0.486 Round 5: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 4 Chains 13, Residues 77, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2833 reflections ( 97.59 % complete ) and 2980 restraints for refining 1367 atoms. 2649 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1972 (Rfree = 0.000) for 1367 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.1878 (Rfree = 0.000) for 1368 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.1857 (Rfree = 0.000) for 1364 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1780 (Rfree = 0.000) for 1360 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2145 (Rfree = 0.000) for 1356 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 1418 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.340 Round 2: 77 peptides, 12 chains. Longest chain 13 peptides. Score 0.423 Round 3: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.423 Round 4: 78 peptides, 12 chains. Longest chain 13 peptides. Score 0.431 Round 5: 76 peptides, 11 chains. Longest chain 17 peptides. Score 0.449 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 65, 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 2pw4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2833 reflections ( 97.59 % complete ) and 3283 restraints for refining 1368 atoms. 3034 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1969 (Rfree = 0.000) for 1368 atoms. Found 0 (10 requested) and removed 4 (5 requested) atoms. Cycle 47: After refmac, R = 0.1863 (Rfree = 0.000) for 1364 atoms. Found 0 (10 requested) and removed 2 (5 requested) atoms. Cycle 48: After refmac, R = 0.1823 (Rfree = 0.000) for 1361 atoms. Found 0 (10 requested) and removed 0 (5 requested) atoms. Cycle 49: After refmac, R = 0.1830 (Rfree = 0.000) for 1360 atoms. TimeTaking 28.07