null Sun 23 Dec 22:23:05 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 2gpj-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-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/2gpj-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-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/2gpj-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-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 212 and 0 Target number of residues in the AU: 212 Target solvent content: 0.6637 Checking the provided sequence file Detected sequence length: 252 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 252 Adjusted target solvent content: 0.60 Input MTZ file: 2gpj-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: 92 Cell parameters: 100.540 100.540 67.510 90.000 90.000 90.000 Input sequence file: 2gpj-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2016 target number of atoms Had to go as low as 0.75 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: 71.093 4.000 Wilson plot Bfac: 87.29 3166 reflections ( 99.28 % complete ) and 0 restraints for refining 2239 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3957 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3776 (Rfree = 0.000) for 2239 atoms. Found 6 (10 requested) and removed 24 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.26 Search for helices and strands: 0 residues in 0 chains, 2246 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 7 peptides. Score 0.215 Round 2: 79 peptides, 16 chains. Longest chain 10 peptides. Score 0.261 Round 3: 88 peptides, 17 chains. Longest chain 10 peptides. Score 0.288 Round 4: 89 peptides, 17 chains. Longest chain 10 peptides. Score 0.294 Round 5: 102 peptides, 20 chains. Longest chain 10 peptides. Score 0.295 Taking the results from Round 5 Chains 20, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3166 reflections ( 99.28 % complete ) and 4399 restraints for refining 1820 atoms. 4091 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3298 (Rfree = 0.000) for 1820 atoms. Found 2 (8 requested) and removed 12 (4 requested) atoms. Cycle 2: After refmac, R = 0.3121 (Rfree = 0.000) for 1773 atoms. Found 6 (8 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.2765 (Rfree = 0.000) for 1754 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 4: After refmac, R = 0.2824 (Rfree = 0.000) for 1740 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 5: After refmac, R = 0.2752 (Rfree = 0.000) for 1733 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.81 3.33 Search for helices and strands: 0 residues in 0 chains, 1768 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.263 Round 2: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.330 Round 3: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.352 Round 4: 105 peptides, 19 chains. Longest chain 12 peptides. Score 0.333 Round 5: 101 peptides, 19 chains. Longest chain 11 peptides. Score 0.312 Taking the results from Round 3 Chains 20, Residues 93, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3166 reflections ( 99.28 % complete ) and 4125 restraints for refining 1791 atoms. 3746 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2961 (Rfree = 0.000) for 1791 atoms. Found 7 (8 requested) and removed 12 (4 requested) atoms. Cycle 7: After refmac, R = 0.2871 (Rfree = 0.000) for 1777 atoms. Found 2 (8 requested) and removed 12 (4 requested) atoms. Cycle 8: After refmac, R = 0.2807 (Rfree = 0.000) for 1765 atoms. Found 2 (8 requested) and removed 14 (4 requested) atoms. Cycle 9: After refmac, R = 0.2834 (Rfree = 0.000) for 1748 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2815 (Rfree = 0.000) for 1741 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.81 3.33 Search for helices and strands: 0 residues in 0 chains, 1767 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 10 peptides. Score 0.293 Round 2: 124 peptides, 23 chains. Longest chain 13 peptides. Score 0.342 Round 3: 113 peptides, 18 chains. Longest chain 15 peptides. Score 0.396 Round 4: 111 peptides, 18 chains. Longest chain 13 peptides. Score 0.386 Round 5: 119 peptides, 20 chains. Longest chain 12 peptides. Score 0.382 Taking the results from Round 3 Chains 18, Residues 95, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3166 reflections ( 99.28 % complete ) and 4188 restraints for refining 1820 atoms. 3786 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3021 (Rfree = 0.000) for 1820 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 12: After refmac, R = 0.2991 (Rfree = 0.000) for 1815 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.3013 (Rfree = 0.000) for 1810 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2996 (Rfree = 0.000) for 1805 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2993 (Rfree = 0.000) for 1801 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.83 3.35 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.290 Round 2: 95 peptides, 16 chains. Longest chain 12 peptides. Score 0.350 Round 3: 100 peptides, 17 chains. Longest chain 12 peptides. Score 0.353 Round 4: 100 peptides, 15 chains. Longest chain 12 peptides. Score 0.398 Round 5: 100 peptides, 16 chains. Longest chain 15 peptides. Score 0.376 Taking the results from Round 4 Chains 15, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3166 reflections ( 99.28 % complete ) and 4383 restraints for refining 1819 atoms. 4058 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3400 (Rfree = 0.000) for 1819 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 17: After refmac, R = 0.2914 (Rfree = 0.000) for 1809 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 18: After refmac, R = 0.3477 (Rfree = 0.000) for 1800 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2750 (Rfree = 0.000) for 1794 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2801 (Rfree = 0.000) for 1790 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.33 Search for helices and strands: 0 residues in 0 chains, 1813 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.294 Round 2: 98 peptides, 16 chains. Longest chain 11 peptides. Score 0.365 Round 3: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.346 Round 4: 93 peptides, 14 chains. Longest chain 14 peptides. Score 0.386 Round 5: 99 peptides, 18 chains. Longest chain 10 peptides. Score 0.325 Taking the results from Round 4 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3166 reflections ( 99.28 % complete ) and 4430 restraints for refining 1820 atoms. 4128 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3019 (Rfree = 0.000) for 1820 atoms. Found 4 (8 requested) and removed 12 (4 requested) atoms. Cycle 22: After refmac, R = 0.3082 (Rfree = 0.000) for 1798 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2731 (Rfree = 0.000) for 1791 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2666 (Rfree = 0.000) for 1786 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2677 (Rfree = 0.000) for 1782 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 3.32 Search for helices and strands: 0 residues in 0 chains, 1809 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 9 peptides. Score 0.268 Round 2: 93 peptides, 16 chains. Longest chain 10 peptides. Score 0.339 Round 3: 97 peptides, 16 chains. Longest chain 10 peptides. Score 0.360 Round 4: 98 peptides, 16 chains. Longest chain 11 peptides. Score 0.365 Round 5: 96 peptides, 15 chains. Longest chain 13 peptides. Score 0.378 Taking the results from Round 5 Chains 15, Residues 81, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3166 reflections ( 99.28 % complete ) and 4267 restraints for refining 1820 atoms. 3918 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2952 (Rfree = 0.000) for 1820 atoms. Found 2 (8 requested) and removed 22 (4 requested) atoms. Cycle 27: After refmac, R = 0.3215 (Rfree = 0.000) for 1790 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.2713 (Rfree = 0.000) for 1786 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.2561 (Rfree = 0.000) for 1780 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2550 (Rfree = 0.000) for 1772 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 3.35 Search for helices and strands: 0 residues in 0 chains, 1803 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 8 peptides. Score 0.274 Round 2: 99 peptides, 18 chains. Longest chain 9 peptides. Score 0.325 Round 3: 102 peptides, 16 chains. Longest chain 10 peptides. Score 0.386 Round 4: 92 peptides, 14 chains. Longest chain 15 peptides. Score 0.381 Round 5: 90 peptides, 14 chains. Longest chain 9 peptides. Score 0.370 Taking the results from Round 3 Chains 16, Residues 86, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3166 reflections ( 99.28 % complete ) and 4392 restraints for refining 1820 atoms. 4042 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2757 (Rfree = 0.000) for 1820 atoms. Found 6 (8 requested) and removed 4 (4 requested) atoms. Cycle 32: After refmac, R = 0.2649 (Rfree = 0.000) for 1812 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 33: After refmac, R = 0.2553 (Rfree = 0.000) for 1808 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2528 (Rfree = 0.000) for 1802 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2671 (Rfree = 0.000) for 1795 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 3.29 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward Round 1: 82 peptides, 16 chains. Longest chain 10 peptides. Score 0.279 Round 2: 83 peptides, 16 chains. Longest chain 9 peptides. Score 0.284 Round 3: 89 peptides, 15 chains. Longest chain 13 peptides. Score 0.342 Round 4: 95 peptides, 17 chains. Longest chain 8 peptides. Score 0.327 Round 5: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 3 Chains 15, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3166 reflections ( 99.28 % complete ) and 4543 restraints for refining 1820 atoms. 4262 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3078 (Rfree = 0.000) for 1820 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. Cycle 37: After refmac, R = 0.2675 (Rfree = 0.000) for 1803 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.3422 (Rfree = 0.000) for 1794 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 39: After refmac, R = 0.2629 (Rfree = 0.000) for 1786 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.2573 (Rfree = 0.000) for 1783 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.34 Search for helices and strands: 0 residues in 0 chains, 1802 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.243 Round 2: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.283 Round 3: 87 peptides, 16 chains. Longest chain 11 peptides. Score 0.307 Round 4: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.316 Round 5: 89 peptides, 16 chains. Longest chain 10 peptides. Score 0.318 Taking the results from Round 5 Chains 16, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3166 reflections ( 99.28 % complete ) and 4406 restraints for refining 1820 atoms. 4130 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2838 (Rfree = 0.000) for 1820 atoms. Found 7 (8 requested) and removed 10 (4 requested) atoms. Cycle 42: After refmac, R = 0.2608 (Rfree = 0.000) for 1812 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2576 (Rfree = 0.000) for 1805 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.2494 (Rfree = 0.000) for 1803 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2383 (Rfree = 0.000) for 1800 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 3.34 Search for helices and strands: 0 residues in 0 chains, 1819 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 7 peptides. Score 0.240 Round 2: 87 peptides, 18 chains. Longest chain 10 peptides. Score 0.258 Round 3: 90 peptides, 19 chains. Longest chain 8 peptides. Score 0.251 Round 4: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.264 Round 5: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.275 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 72, 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 2gpj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3166 reflections ( 99.28 % complete ) and 4461 restraints for refining 1820 atoms. 4191 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2922 (Rfree = 0.000) for 1820 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2969 (Rfree = 0.000) for 1815 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3314 (Rfree = 0.000) for 1810 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2678 (Rfree = 0.000) for 1805 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:55:10 GMT 2018 Job finished. TimeTaking 32.09 Used memory is bytes: 19741624