null Sun 23 Dec 22:23:02 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 2oc6-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oc6-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oc6-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-4.0-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/2oc6-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-4.0-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 22:23:12 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/2oc6-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-4.0-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 168 and 0 Target number of residues in the AU: 168 Target solvent content: 0.6724 Checking the provided sequence file Detected sequence length: 124 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 248 Adjusted target solvent content: 0.52 Input MTZ file: 2oc6-4.0-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: 3 Cell parameters: 48.794 46.883 64.576 90.000 110.073 90.000 Input sequence file: 2oc6-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.90 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: 60.653 4.001 Wilson plot Bfac: 94.12 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2411 reflections ( 99.55 % complete ) and 0 restraints for refining 2219 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3678 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3477 (Rfree = 0.000) for 2219 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.70 Search for helices and strands: 0 residues in 0 chains, 2266 seeds are put forward NCS extension: 0 residues added, 2266 seeds are put forward Round 1: 75 peptides, 18 chains. Longest chain 5 peptides. Score 0.189 Round 2: 96 peptides, 18 chains. Longest chain 10 peptides. Score 0.331 Round 3: 101 peptides, 19 chains. Longest chain 10 peptides. Score 0.336 Round 4: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.337 Round 5: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.292 Taking the results from Round 4 Chains 18, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4400 restraints for refining 1790 atoms. 4102 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3095 (Rfree = 0.000) for 1790 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 2: After refmac, R = 0.3098 (Rfree = 0.000) for 1761 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 3: After refmac, R = 0.2714 (Rfree = 0.000) for 1738 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2132 (Rfree = 0.000) for 1728 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2346 (Rfree = 0.000) for 1722 atoms. Found 6 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.81 3.71 Search for helices and strands: 0 residues in 0 chains, 1783 seeds are put forward NCS extension: 0 residues added, 1783 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 6 peptides. Score 0.264 Round 2: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.337 Round 3: 105 peptides, 16 chains. Longest chain 13 peptides. Score 0.437 Round 4: 107 peptides, 17 chains. Longest chain 12 peptides. Score 0.423 Round 5: 103 peptides, 17 chains. Longest chain 10 peptides. Score 0.400 Taking the results from Round 3 Chains 16, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4047 restraints for refining 1736 atoms. 3707 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2143 (Rfree = 0.000) for 1736 atoms. Found 2 (8 requested) and removed 9 (4 requested) atoms. Cycle 7: After refmac, R = 0.1778 (Rfree = 0.000) for 1716 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.1699 (Rfree = 0.000) for 1704 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.1582 (Rfree = 0.000) for 1697 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.1618 (Rfree = 0.000) for 1687 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.69 Search for helices and strands: 0 residues in 0 chains, 1752 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1771 seeds are put forward Round 1: 102 peptides, 23 chains. Longest chain 7 peptides. Score 0.235 Round 2: 113 peptides, 20 chains. Longest chain 11 peptides. Score 0.382 Round 3: 112 peptides, 21 chains. Longest chain 8 peptides. Score 0.351 Round 4: 111 peptides, 17 chains. Longest chain 16 peptides. Score 0.446 Round 5: 112 peptides, 16 chains. Longest chain 12 peptides. Score 0.475 Taking the results from Round 5 Chains 16, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4184 restraints for refining 1791 atoms. 3816 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2608 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 12: After refmac, R = 0.2340 (Rfree = 0.000) for 1764 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2098 (Rfree = 0.000) for 1743 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.1797 (Rfree = 0.000) for 1734 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.1955 (Rfree = 0.000) for 1729 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward NCS extension: 0 residues added, 1818 seeds are put forward Round 1: 99 peptides, 20 chains. Longest chain 11 peptides. Score 0.296 Round 2: 107 peptides, 19 chains. Longest chain 10 peptides. Score 0.372 Round 3: 115 peptides, 15 chains. Longest chain 19 peptides. Score 0.515 Round 4: 118 peptides, 18 chains. Longest chain 13 peptides. Score 0.460 Round 5: 109 peptides, 17 chains. Longest chain 17 peptides. Score 0.434 Taking the results from Round 3 Chains 15, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4006 restraints for refining 1791 atoms. 3621 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1942 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 17: After refmac, R = 0.1618 (Rfree = 0.000) for 1778 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.1435 (Rfree = 0.000) for 1774 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.1407 (Rfree = 0.000) for 1772 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.1270 (Rfree = 0.000) for 1770 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.79 3.69 Search for helices and strands: 0 residues in 0 chains, 1835 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1854 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 6 peptides. Score 0.229 Round 2: 108 peptides, 19 chains. Longest chain 12 peptides. Score 0.378 Round 3: 107 peptides, 20 chains. Longest chain 12 peptides. Score 0.346 Round 4: 104 peptides, 18 chains. Longest chain 10 peptides. Score 0.380 Round 5: 109 peptides, 16 chains. Longest chain 14 peptides. Score 0.459 Taking the results from Round 5 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4174 restraints for refining 1790 atoms. 3818 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2633 (Rfree = 0.000) for 1790 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.2076 (Rfree = 0.000) for 1762 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 23: After refmac, R = 0.1785 (Rfree = 0.000) for 1753 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.1506 (Rfree = 0.000) for 1740 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.1322 (Rfree = 0.000) for 1738 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 1800 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1818 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 8 peptides. Score 0.259 Round 2: 104 peptides, 20 chains. Longest chain 12 peptides. Score 0.328 Round 3: 103 peptides, 18 chains. Longest chain 12 peptides. Score 0.374 Round 4: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.374 Round 5: 103 peptides, 17 chains. Longest chain 14 peptides. Score 0.400 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 ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4174 restraints for refining 1791 atoms. 3847 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2365 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.1930 (Rfree = 0.000) for 1778 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.1632 (Rfree = 0.000) for 1774 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.1596 (Rfree = 0.000) for 1773 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.1379 (Rfree = 0.000) for 1771 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 1857 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.248 Round 2: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.278 Round 3: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.305 Round 4: 106 peptides, 20 chains. Longest chain 9 peptides. Score 0.340 Round 5: 97 peptides, 19 chains. Longest chain 7 peptides. Score 0.310 Taking the results from Round 4 Chains 20, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4106 restraints for refining 1791 atoms. 3782 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1973 (Rfree = 0.000) for 1791 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 32: After refmac, R = 0.1791 (Rfree = 0.000) for 1771 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.1730 (Rfree = 0.000) for 1768 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.1714 (Rfree = 0.000) for 1764 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.1518 (Rfree = 0.000) for 1757 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 1814 seeds are put forward NCS extension: 0 residues added, 1814 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 6 peptides. Score 0.237 Round 2: 103 peptides, 19 chains. Longest chain 8 peptides. Score 0.348 Round 3: 96 peptides, 16 chains. Longest chain 10 peptides. Score 0.384 Round 4: 99 peptides, 16 chains. Longest chain 11 peptides. Score 0.402 Round 5: 104 peptides, 17 chains. Longest chain 13 peptides. Score 0.406 Taking the results from Round 5 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4154 restraints for refining 1791 atoms. 3823 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2032 (Rfree = 0.000) for 1791 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.1645 (Rfree = 0.000) for 1780 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.1559 (Rfree = 0.000) for 1771 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.1461 (Rfree = 0.000) for 1766 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.1569 (Rfree = 0.000) for 1757 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 1803 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1819 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.279 Round 2: 93 peptides, 17 chains. Longest chain 9 peptides. Score 0.339 Round 3: 88 peptides, 16 chains. Longest chain 8 peptides. Score 0.335 Round 4: 92 peptides, 16 chains. Longest chain 12 peptides. Score 0.360 Round 5: 92 peptides, 15 chains. Longest chain 12 peptides. Score 0.387 Taking the results from Round 5 Chains 15, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2411 reflections ( 99.55 % complete ) and 4231 restraints for refining 1791 atoms. 3938 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1923 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.1634 (Rfree = 0.000) for 1789 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.1540 (Rfree = 0.000) for 1786 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.1474 (Rfree = 0.000) for 1780 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.1612 (Rfree = 0.000) for 1770 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1832 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 7 peptides. Score 0.212 Round 2: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.315 Round 3: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.331 Round 4: 102 peptides, 18 chains. Longest chain 11 peptides. Score 0.368 Round 5: 97 peptides, 16 chains. Longest chain 9 peptides. Score 0.390 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 81, 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 2oc6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2411 reflections ( 99.55 % complete ) and 4179 restraints for refining 1791 atoms. 3871 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2206 (Rfree = 0.000) for 1791 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2253 (Rfree = 0.000) for 1773 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1788 (Rfree = 0.000) for 1762 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1720 (Rfree = 0.000) for 1751 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:58 GMT 2018 Job finished. TimeTaking 29.93 Used memory is bytes: 17773664