Sun 23 Dec 23:50:45 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1zko-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.8-parrot-mrncs ############### 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 23:50:49 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/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.8-parrot-mrncs/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 172 and 0 Target number of residues in the AU: 172 Target solvent content: 0.6187 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-3.8-parrot-mrncs.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: 19 Cell parameters: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2176 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: 47.500 3.801 Wilson plot Bfac: 60.61 2442 reflections ( 92.68 % complete ) and 0 restraints for refining 2412 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3641 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3707 (Rfree = 0.000) for 2412 atoms. Found 13 (13 requested) and removed 41 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.88 Search for helices and strands: 0 residues in 0 chains, 2404 seeds are put forward NCS extension: 0 residues added, 2404 seeds are put forward Round 1: 26 peptides, 6 chains. Longest chain 5 peptides. Score 0.191 Round 2: 42 peptides, 9 chains. Longest chain 7 peptides. Score 0.226 Round 3: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.222 Round 4: 45 peptides, 10 chains. Longest chain 7 peptides. Score 0.215 Round 5: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.267 Taking the results from Round 5 Chains 10, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 4923 restraints for refining 1967 atoms. 4769 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3649 (Rfree = 0.000) for 1967 atoms. Found 10 (10 requested) and removed 53 (5 requested) atoms. Cycle 2: After refmac, R = 0.3552 (Rfree = 0.000) for 1912 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 3: After refmac, R = 0.3124 (Rfree = 0.000) for 1895 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.3503 (Rfree = 0.000) for 1884 atoms. Found 8 (10 requested) and removed 13 (5 requested) atoms. Cycle 5: After refmac, R = 0.3417 (Rfree = 0.000) for 1874 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.82 Search for helices and strands: 0 residues in 0 chains, 1904 seeds are put forward NCS extension: 0 residues added, 1904 seeds are put forward Round 1: 33 peptides, 8 chains. Longest chain 5 peptides. Score 0.178 Round 2: 41 peptides, 10 chains. Longest chain 5 peptides. Score 0.177 Round 3: 57 peptides, 13 chains. Longest chain 8 peptides. Score 0.211 Round 4: 68 peptides, 15 chains. Longest chain 8 peptides. Score 0.233 Round 5: 63 peptides, 13 chains. Longest chain 8 peptides. Score 0.260 Taking the results from Round 5 Chains 13, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3222 restraints for refining 1449 atoms. 3035 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3403 (Rfree = 0.000) for 1449 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 7: After refmac, R = 0.3155 (Rfree = 0.000) for 1431 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 8: After refmac, R = 0.3291 (Rfree = 0.000) for 1418 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.2901 (Rfree = 0.000) for 1411 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.2447 (Rfree = 0.000) for 1407 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 1448 seeds are put forward NCS extension: 0 residues added, 1448 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 6 peptides. Score 0.222 Round 2: 90 peptides, 18 chains. Longest chain 7 peptides. Score 0.305 Round 3: 97 peptides, 18 chains. Longest chain 10 peptides. Score 0.354 Round 4: 94 peptides, 18 chains. Longest chain 8 peptides. Score 0.333 Round 5: 103 peptides, 17 chains. Longest chain 11 peptides. Score 0.423 Taking the results from Round 5 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3370 restraints for refining 1520 atoms. 3043 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2857 (Rfree = 0.000) for 1520 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 12: After refmac, R = 0.2752 (Rfree = 0.000) for 1494 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2887 (Rfree = 0.000) for 1484 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2774 (Rfree = 0.000) for 1479 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2762 (Rfree = 0.000) for 1468 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.83 Search for helices and strands: 0 residues in 0 chains, 1503 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1506 seeds are put forward Round 1: 101 peptides, 23 chains. Longest chain 7 peptides. Score 0.234 Round 2: 102 peptides, 21 chains. Longest chain 8 peptides. Score 0.301 Round 3: 99 peptides, 20 chains. Longest chain 8 peptides. Score 0.309 Round 4: 99 peptides, 20 chains. Longest chain 9 peptides. Score 0.309 Round 5: 88 peptides, 17 chains. Longest chain 10 peptides. Score 0.321 Taking the results from Round 5 Chains 17, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3687 restraints for refining 1593 atoms. 3420 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2809 (Rfree = 0.000) for 1593 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 17: After refmac, R = 0.2917 (Rfree = 0.000) for 1579 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 18: After refmac, R = 0.2324 (Rfree = 0.000) for 1569 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2378 (Rfree = 0.000) for 1568 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2391 (Rfree = 0.000) for 1563 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.96 Search for helices and strands: 0 residues in 0 chains, 1587 seeds are put forward NCS extension: 0 residues added, 1587 seeds are put forward Round 1: 89 peptides, 19 chains. Longest chain 6 peptides. Score 0.267 Round 2: 108 peptides, 22 chains. Longest chain 7 peptides. Score 0.314 Round 3: 120 peptides, 22 chains. Longest chain 9 peptides. Score 0.394 Round 4: 120 peptides, 22 chains. Longest chain 9 peptides. Score 0.394 Round 5: 116 peptides, 18 chains. Longest chain 9 peptides. Score 0.476 Taking the results from Round 5 Chains 18, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3808 restraints for refining 1722 atoms. 3434 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2795 (Rfree = 0.000) for 1722 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 22: After refmac, R = 0.2270 (Rfree = 0.000) for 1702 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. Cycle 23: After refmac, R = 0.2199 (Rfree = 0.000) for 1693 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.2277 (Rfree = 0.000) for 1686 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2213 (Rfree = 0.000) for 1683 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.93 Search for helices and strands: 0 residues in 0 chains, 1723 seeds are put forward NCS extension: 0 residues added, 1723 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 8 peptides. Score 0.262 Round 2: 100 peptides, 21 chains. Longest chain 9 peptides. Score 0.287 Round 3: 99 peptides, 20 chains. Longest chain 8 peptides. Score 0.309 Round 4: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.312 Round 5: 95 peptides, 18 chains. Longest chain 8 peptides. Score 0.340 Taking the results from Round 5 Chains 18, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 4125 restraints for refining 1773 atoms. 3835 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2530 (Rfree = 0.000) for 1773 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. Cycle 27: After refmac, R = 0.2186 (Rfree = 0.000) for 1763 atoms. Found 6 (9 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.2033 (Rfree = 0.000) for 1762 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.2065 (Rfree = 0.000) for 1755 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2049 (Rfree = 0.000) for 1754 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.95 Search for helices and strands: 0 residues in 0 chains, 1795 seeds are put forward NCS extension: 0 residues added, 1795 seeds are put forward Round 1: 87 peptides, 20 chains. Longest chain 5 peptides. Score 0.221 Round 2: 93 peptides, 17 chains. Longest chain 10 peptides. Score 0.356 Round 3: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.319 Round 4: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.347 Round 5: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.333 Taking the results from Round 2 Chains 17, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 4047 restraints for refining 1759 atoms. 3760 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3025 (Rfree = 0.000) for 1759 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 32: After refmac, R = 0.2016 (Rfree = 0.000) for 1746 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 33: After refmac, R = 0.2293 (Rfree = 0.000) for 1737 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.2358 (Rfree = 0.000) for 1732 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2214 (Rfree = 0.000) for 1726 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 1754 seeds are put forward NCS extension: 0 residues added, 1754 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.239 Round 2: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.353 Round 3: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.323 Round 4: 72 peptides, 14 chains. Longest chain 7 peptides. Score 0.297 Round 5: 86 peptides, 17 chains. Longest chain 8 peptides. Score 0.306 Taking the results from Round 2 Chains 15, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3835 restraints for refining 1704 atoms. 3574 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2231 (Rfree = 0.000) for 1704 atoms. Found 6 (9 requested) and removed 14 (4 requested) atoms. Cycle 37: After refmac, R = 0.2055 (Rfree = 0.000) for 1691 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 38: After refmac, R = 0.1929 (Rfree = 0.000) for 1685 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.1832 (Rfree = 0.000) for 1675 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.1832 (Rfree = 0.000) for 1674 atoms. Found 2 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.99 Search for helices and strands: 0 residues in 0 chains, 1693 seeds are put forward NCS extension: 0 residues added, 1693 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 7 peptides. Score 0.208 Round 2: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.266 Round 3: 74 peptides, 15 chains. Longest chain 8 peptides. Score 0.280 Round 4: 74 peptides, 14 chains. Longest chain 9 peptides. Score 0.312 Round 5: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.278 Taking the results from Round 4 Chains 14, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3801 restraints for refining 1681 atoms. 3575 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2520 (Rfree = 0.000) for 1681 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2314 (Rfree = 0.000) for 1675 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.2797 (Rfree = 0.000) for 1666 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.2415 (Rfree = 0.000) for 1657 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.1982 (Rfree = 0.000) for 1649 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.97 Search for helices and strands: 0 residues in 0 chains, 1672 seeds are put forward NCS extension: 0 residues added, 1672 seeds are put forward Round 1: 53 peptides, 13 chains. Longest chain 5 peptides. Score 0.176 Round 2: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.252 Round 3: 71 peptides, 15 chains. Longest chain 6 peptides. Score 0.257 Round 4: 68 peptides, 14 chains. Longest chain 6 peptides. Score 0.266 Round 5: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 58, 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 1zko-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2442 reflections ( 92.68 % complete ) and 3825 restraints for refining 1663 atoms. 3605 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2643 (Rfree = 0.000) for 1663 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2636 (Rfree = 0.000) for 1645 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2260 (Rfree = 0.000) for 1629 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1999 (Rfree = 0.000) for 1620 atoms. TimeTaking 21.75