Mon 24 Dec 01:12:46 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.4-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 ============================================================ Mon 24 Dec 01:12:51 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-3.4-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 173 and 0 Target number of residues in the AU: 173 Target solvent content: 0.6164 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 59.44 3355 reflections ( 92.37 % complete ) and 0 restraints for refining 2401 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3444 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3433 (Rfree = 0.000) for 2401 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 3.65 Search for helices and strands: 0 residues in 0 chains, 2421 seeds are put forward NCS extension: 0 residues added, 2421 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 8 peptides. Score 0.241 Round 2: 66 peptides, 14 chains. Longest chain 6 peptides. Score 0.251 Round 3: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.308 Round 4: 86 peptides, 18 chains. Longest chain 11 peptides. Score 0.276 Round 5: 106 peptides, 20 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 5 Chains 20, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4528 restraints for refining 1978 atoms. 4204 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2993 (Rfree = 0.000) for 1978 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 2: After refmac, R = 0.2816 (Rfree = 0.000) for 1956 atoms. Found 11 (14 requested) and removed 7 (7 requested) atoms. Cycle 3: After refmac, R = 0.2633 (Rfree = 0.000) for 1954 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 4: After refmac, R = 0.2507 (Rfree = 0.000) for 1946 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 5: After refmac, R = 0.2459 (Rfree = 0.000) for 1939 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.69 Search for helices and strands: 0 residues in 0 chains, 1969 seeds are put forward NCS extension: 0 residues added, 1969 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 7 peptides. Score 0.252 Round 2: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.322 Round 3: 120 peptides, 24 chains. Longest chain 10 peptides. Score 0.339 Round 4: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.384 Round 5: 122 peptides, 23 chains. Longest chain 13 peptides. Score 0.380 Taking the results from Round 4 Chains 20, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4141 restraints for refining 1814 atoms. 3801 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2858 (Rfree = 0.000) for 1814 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. Cycle 7: After refmac, R = 0.2654 (Rfree = 0.000) for 1799 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.2712 (Rfree = 0.000) for 1785 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2529 (Rfree = 0.000) for 1779 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2592 (Rfree = 0.000) for 1771 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward NCS extension: 0 residues added, 1805 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 7 peptides. Score 0.280 Round 2: 125 peptides, 25 chains. Longest chain 12 peptides. Score 0.345 Round 3: 133 peptides, 24 chains. Longest chain 12 peptides. Score 0.423 Round 4: 115 peptides, 19 chains. Longest chain 14 peptides. Score 0.444 Round 5: 119 peptides, 19 chains. Longest chain 16 peptides. Score 0.468 Taking the results from Round 5 Chains 19, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 3950 restraints for refining 1757 atoms. 3569 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2912 (Rfree = 0.000) for 1757 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 12: After refmac, R = 0.2829 (Rfree = 0.000) for 1751 atoms. Found 9 (13 requested) and removed 6 (6 requested) atoms. Cycle 13: After refmac, R = 0.2802 (Rfree = 0.000) for 1746 atoms. Found 12 (13 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2476 (Rfree = 0.000) for 1747 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.2451 (Rfree = 0.000) for 1744 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 1784 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 1807 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 7 peptides. Score 0.250 Round 2: 117 peptides, 21 chains. Longest chain 12 peptides. Score 0.402 Round 3: 113 peptides, 21 chains. Longest chain 11 peptides. Score 0.376 Round 4: 110 peptides, 17 chains. Longest chain 23 peptides. Score 0.466 Round 5: 120 peptides, 21 chains. Longest chain 14 peptides. Score 0.421 Taking the results from Round 4 Chains 17, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 3909 restraints for refining 1761 atoms. 3554 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2968 (Rfree = 0.000) for 1761 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.2885 (Rfree = 0.000) for 1748 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 18: After refmac, R = 0.2739 (Rfree = 0.000) for 1739 atoms. Found 10 (13 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.2494 (Rfree = 0.000) for 1736 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.2643 (Rfree = 0.000) for 1726 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.70 Search for helices and strands: 0 residues in 0 chains, 1769 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 1806 seeds are put forward Round 1: 84 peptides, 19 chains. Longest chain 7 peptides. Score 0.229 Round 2: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.384 Round 3: 113 peptides, 21 chains. Longest chain 12 peptides. Score 0.376 Round 4: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.399 Round 5: 102 peptides, 17 chains. Longest chain 12 peptides. Score 0.416 Taking the results from Round 5 Chains 17, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 3924 restraints for refining 1774 atoms. 3601 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3017 (Rfree = 0.000) for 1774 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 22: After refmac, R = 0.2878 (Rfree = 0.000) for 1759 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 23: After refmac, R = 0.2689 (Rfree = 0.000) for 1755 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.2479 (Rfree = 0.000) for 1750 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.2414 (Rfree = 0.000) for 1742 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.59 Search for helices and strands: 0 residues in 0 chains, 1768 seeds are put forward NCS extension: 0 residues added, 1768 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 7 peptides. Score 0.252 Round 2: 103 peptides, 19 chains. Longest chain 7 peptides. Score 0.366 Round 3: 101 peptides, 18 chains. Longest chain 8 peptides. Score 0.381 Round 4: 105 peptides, 18 chains. Longest chain 9 peptides. Score 0.408 Round 5: 99 peptides, 18 chains. Longest chain 8 peptides. Score 0.368 Taking the results from Round 4 Chains 18, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 3926 restraints for refining 1750 atoms. 3596 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2617 (Rfree = 0.000) for 1750 atoms. Found 9 (13 requested) and removed 21 (6 requested) atoms. Cycle 27: After refmac, R = 0.2481 (Rfree = 0.000) for 1735 atoms. Found 8 (13 requested) and removed 13 (6 requested) atoms. Cycle 28: After refmac, R = 0.2321 (Rfree = 0.000) for 1729 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.2411 (Rfree = 0.000) for 1725 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.2246 (Rfree = 0.000) for 1717 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.63 Search for helices and strands: 0 residues in 0 chains, 1765 seeds are put forward NCS extension: 0 residues added, 1765 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.268 Round 2: 93 peptides, 18 chains. Longest chain 8 peptides. Score 0.326 Round 3: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.375 Round 4: 99 peptides, 18 chains. Longest chain 7 peptides. Score 0.368 Round 5: 110 peptides, 21 chains. Longest chain 8 peptides. Score 0.356 Taking the results from Round 3 Chains 18, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4079 restraints for refining 1757 atoms. 3769 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2555 (Rfree = 0.000) for 1757 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.2609 (Rfree = 0.000) for 1747 atoms. Found 11 (13 requested) and removed 15 (6 requested) atoms. Cycle 33: After refmac, R = 0.2493 (Rfree = 0.000) for 1740 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 34: After refmac, R = 0.2439 (Rfree = 0.000) for 1739 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.2321 (Rfree = 0.000) for 1734 atoms. Found 10 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.91 Search for helices and strands: 0 residues in 0 chains, 1785 seeds are put forward NCS extension: 0 residues added, 1785 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 8 peptides. Score 0.246 Round 2: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.317 Round 3: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.319 Round 4: 86 peptides, 17 chains. Longest chain 7 peptides. Score 0.306 Round 5: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.282 Taking the results from Round 3 Chains 18, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 3878 restraints for refining 1754 atoms. 3600 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2213 (Rfree = 0.000) for 1754 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. Cycle 37: After refmac, R = 0.2118 (Rfree = 0.000) for 1754 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2137 (Rfree = 0.000) for 1750 atoms. Found 11 (13 requested) and removed 14 (6 requested) atoms. Cycle 39: After refmac, R = 0.1988 (Rfree = 0.000) for 1742 atoms. Found 3 (13 requested) and removed 11 (6 requested) atoms. Cycle 40: After refmac, R = 0.2054 (Rfree = 0.000) for 1733 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 3.56 Search for helices and strands: 0 residues in 0 chains, 1769 seeds are put forward NCS extension: 0 residues added, 1769 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 6 peptides. Score 0.222 Round 2: 92 peptides, 17 chains. Longest chain 9 peptides. Score 0.349 Round 3: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.318 Round 4: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.364 Round 5: 104 peptides, 19 chains. Longest chain 10 peptides. Score 0.373 Taking the results from Round 5 Chains 19, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3355 reflections ( 92.37 % complete ) and 4010 restraints for refining 1803 atoms. 3689 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2450 (Rfree = 0.000) for 1803 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. Cycle 42: After refmac, R = 0.2097 (Rfree = 0.000) for 1797 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.2049 (Rfree = 0.000) for 1782 atoms. Found 5 (13 requested) and removed 10 (6 requested) atoms. Cycle 44: After refmac, R = 0.2077 (Rfree = 0.000) for 1774 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.2044 (Rfree = 0.000) for 1768 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 3.53 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: 77 peptides, 18 chains. Longest chain 6 peptides. Score 0.207 Round 2: 82 peptides, 17 chains. Longest chain 10 peptides. Score 0.277 Round 3: 82 peptides, 15 chains. Longest chain 12 peptides. Score 0.339 Round 4: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.303 Round 5: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 67, 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. 3355 reflections ( 92.37 % complete ) and 3910 restraints for refining 1756 atoms. 3657 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2330 (Rfree = 0.000) for 1756 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2330 (Rfree = 0.000) for 1748 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2273 (Rfree = 0.000) for 1741 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2234 (Rfree = 0.000) for 1735 atoms. TimeTaking 23.22