null Sun 23 Dec 22:22:43 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gpj-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-3.2-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 22:22:53 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gpj-3.2-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 228 and 0 Target number of residues in the AU: 228 Target solvent content: 0.6384 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-3.2-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-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2016 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: 71.093 3.200 Wilson plot Bfac: 70.86 6058 reflections ( 99.61 % complete ) and 0 restraints for refining 2220 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3812 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3890 (Rfree = 0.000) for 2220 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.09 Search for helices and strands: 0 residues in 0 chains, 2239 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 9 peptides. Score 0.268 Round 2: 124 peptides, 22 chains. Longest chain 12 peptides. Score 0.364 Round 3: 131 peptides, 24 chains. Longest chain 9 peptides. Score 0.356 Round 4: 135 peptides, 23 chains. Longest chain 19 peptides. Score 0.396 Round 5: 131 peptides, 21 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 5 Chains 21, Residues 110, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6058 reflections ( 99.61 % complete ) and 4246 restraints for refining 1840 atoms. 3801 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3311 (Rfree = 0.000) for 1840 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 2: After refmac, R = 0.3308 (Rfree = 0.000) for 1824 atoms. Found 14 (16 requested) and removed 16 (8 requested) atoms. Cycle 3: After refmac, R = 0.3186 (Rfree = 0.000) for 1807 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.3461 (Rfree = 0.000) for 1797 atoms. Found 15 (16 requested) and removed 14 (8 requested) atoms. Cycle 5: After refmac, R = 0.3242 (Rfree = 0.000) for 1792 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 2.95 Search for helices and strands: 0 residues in 0 chains, 1819 seeds are put forward Round 1: 127 peptides, 26 chains. Longest chain 8 peptides. Score 0.293 Round 2: 130 peptides, 21 chains. Longest chain 10 peptides. Score 0.414 Round 3: 137 peptides, 22 chains. Longest chain 9 peptides. Score 0.426 Round 4: 141 peptides, 22 chains. Longest chain 11 peptides. Score 0.444 Round 5: 129 peptides, 21 chains. Longest chain 10 peptides. Score 0.409 Taking the results from Round 4 Chains 22, Residues 119, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6058 reflections ( 99.61 % complete ) and 4086 restraints for refining 1839 atoms. 3602 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3537 (Rfree = 0.000) for 1839 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 7: After refmac, R = 0.3418 (Rfree = 0.000) for 1811 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 8: After refmac, R = 0.3206 (Rfree = 0.000) for 1792 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. Cycle 9: After refmac, R = 0.3277 (Rfree = 0.000) for 1771 atoms. Found 9 (16 requested) and removed 38 (8 requested) atoms. Cycle 10: After refmac, R = 0.3322 (Rfree = 0.000) for 1735 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 2.86 Search for helices and strands: 0 residues in 0 chains, 1791 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 10 peptides. Score 0.288 Round 2: 137 peptides, 23 chains. Longest chain 16 peptides. Score 0.406 Round 3: 133 peptides, 25 chains. Longest chain 13 peptides. Score 0.345 Round 4: 136 peptides, 23 chains. Longest chain 14 peptides. Score 0.401 Round 5: 148 peptides, 27 chains. Longest chain 11 peptides. Score 0.376 Taking the results from Round 2 Chains 24, Residues 114, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6058 reflections ( 99.61 % complete ) and 3743 restraints for refining 1768 atoms. 3284 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3650 (Rfree = 0.000) for 1768 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 12: After refmac, R = 0.3192 (Rfree = 0.000) for 1744 atoms. Found 12 (15 requested) and removed 15 (7 requested) atoms. Cycle 13: After refmac, R = 0.3100 (Rfree = 0.000) for 1734 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 14: After refmac, R = 0.3136 (Rfree = 0.000) for 1727 atoms. Found 13 (15 requested) and removed 13 (7 requested) atoms. Cycle 15: After refmac, R = 0.2742 (Rfree = 0.000) for 1716 atoms. Found 6 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 1750 seeds are put forward Round 1: 111 peptides, 23 chains. Longest chain 8 peptides. Score 0.275 Round 2: 148 peptides, 24 chains. Longest chain 12 peptides. Score 0.436 Round 3: 144 peptides, 24 chains. Longest chain 10 peptides. Score 0.418 Round 4: 148 peptides, 24 chains. Longest chain 15 peptides. Score 0.436 Round 5: 151 peptides, 24 chains. Longest chain 16 peptides. Score 0.450 Taking the results from Round 5 Chains 25, Residues 127, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6058 reflections ( 99.61 % complete ) and 3788 restraints for refining 1841 atoms. 3242 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3068 (Rfree = 0.000) for 1841 atoms. Found 15 (16 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.2987 (Rfree = 0.000) for 1832 atoms. Found 14 (16 requested) and removed 12 (8 requested) atoms. Cycle 18: After refmac, R = 0.2714 (Rfree = 0.000) for 1826 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.2884 (Rfree = 0.000) for 1820 atoms. Found 10 (16 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.2696 (Rfree = 0.000) for 1814 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 2.87 Search for helices and strands: 0 residues in 0 chains, 1838 seeds are put forward Round 1: 149 peptides, 26 chains. Longest chain 16 peptides. Score 0.401 Round 2: 135 peptides, 21 chains. Longest chain 12 peptides. Score 0.437 Round 3: 131 peptides, 18 chains. Longest chain 22 peptides. Score 0.479 Round 4: 130 peptides, 18 chains. Longest chain 17 peptides. Score 0.475 Round 5: 140 peptides, 21 chains. Longest chain 14 peptides. Score 0.460 Taking the results from Round 3 Chains 20, Residues 113, Estimated correctness of the model 4.4 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6058 reflections ( 99.61 % complete ) and 3980 restraints for refining 1841 atoms. 3502 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3188 (Rfree = 0.000) for 1841 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 22: After refmac, R = 0.3036 (Rfree = 0.000) for 1830 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.3011 (Rfree = 0.000) for 1822 atoms. Found 13 (16 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.3008 (Rfree = 0.000) for 1817 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.3094 (Rfree = 0.000) for 1817 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 2.88 Search for helices and strands: 0 residues in 0 chains, 1878 seeds are put forward Round 1: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.300 Round 2: 127 peptides, 21 chains. Longest chain 16 peptides. Score 0.400 Round 3: 130 peptides, 21 chains. Longest chain 15 peptides. Score 0.414 Round 4: 135 peptides, 21 chains. Longest chain 15 peptides. Score 0.437 Round 5: 128 peptides, 18 chains. Longest chain 16 peptides. Score 0.466 Taking the results from Round 5 Chains 18, Residues 110, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6058 reflections ( 99.61 % complete ) and 4049 restraints for refining 1841 atoms. 3614 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3238 (Rfree = 0.000) for 1841 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 27: After refmac, R = 0.3168 (Rfree = 0.000) for 1832 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.3015 (Rfree = 0.000) for 1822 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.2677 (Rfree = 0.000) for 1825 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.2647 (Rfree = 0.000) for 1822 atoms. Found 9 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 2.87 Search for helices and strands: 0 residues in 0 chains, 1862 seeds are put forward Round 1: 124 peptides, 24 chains. Longest chain 10 peptides. Score 0.321 Round 2: 138 peptides, 26 chains. Longest chain 11 peptides. Score 0.349 Round 3: 142 peptides, 23 chains. Longest chain 14 peptides. Score 0.429 Round 4: 148 peptides, 26 chains. Longest chain 18 peptides. Score 0.397 Round 5: 140 peptides, 23 chains. Longest chain 12 peptides. Score 0.420 Taking the results from Round 3 Chains 23, Residues 119, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6058 reflections ( 99.61 % complete ) and 3940 restraints for refining 1841 atoms. 3457 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3514 (Rfree = 0.000) for 1841 atoms. Found 15 (16 requested) and removed 13 (8 requested) atoms. Cycle 32: After refmac, R = 0.3180 (Rfree = 0.000) for 1829 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 33: After refmac, R = 0.3110 (Rfree = 0.000) for 1825 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 34: After refmac, R = 0.3056 (Rfree = 0.000) for 1825 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.3085 (Rfree = 0.000) for 1827 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 1875 seeds are put forward Round 1: 118 peptides, 23 chains. Longest chain 11 peptides. Score 0.312 Round 2: 134 peptides, 22 chains. Longest chain 14 peptides. Score 0.412 Round 3: 135 peptides, 24 chains. Longest chain 12 peptides. Score 0.376 Round 4: 122 peptides, 23 chains. Longest chain 10 peptides. Score 0.332 Round 5: 137 peptides, 22 chains. Longest chain 19 peptides. Score 0.426 Taking the results from Round 5 Chains 23, Residues 115, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6058 reflections ( 99.61 % complete ) and 3765 restraints for refining 1841 atoms. 3250 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3046 (Rfree = 0.000) for 1841 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.3108 (Rfree = 0.000) for 1837 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.3114 (Rfree = 0.000) for 1836 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 39: After refmac, R = 0.3096 (Rfree = 0.000) for 1835 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.2893 (Rfree = 0.000) for 1836 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 2.85 Search for helices and strands: 0 residues in 0 chains, 1848 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 9 peptides. Score 0.269 Round 2: 126 peptides, 23 chains. Longest chain 10 peptides. Score 0.353 Round 3: 130 peptides, 23 chains. Longest chain 10 peptides. Score 0.372 Round 4: 137 peptides, 23 chains. Longest chain 10 peptides. Score 0.406 Round 5: 131 peptides, 24 chains. Longest chain 11 peptides. Score 0.356 Taking the results from Round 4 Chains 23, Residues 114, Estimated correctness of the model 0.0 % 5 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6058 reflections ( 99.61 % complete ) and 3843 restraints for refining 1841 atoms. 3357 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3360 (Rfree = 0.000) for 1841 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 42: After refmac, R = 0.3085 (Rfree = 0.000) for 1839 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 43: After refmac, R = 0.3084 (Rfree = 0.000) for 1832 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.3142 (Rfree = 0.000) for 1832 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.2904 (Rfree = 0.000) for 1828 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 2.91 Search for helices and strands: 0 residues in 0 chains, 1873 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 7 peptides. Score 0.227 Round 2: 122 peptides, 23 chains. Longest chain 9 peptides. Score 0.332 Round 3: 120 peptides, 20 chains. Longest chain 11 peptides. Score 0.387 Round 4: 126 peptides, 21 chains. Longest chain 11 peptides. Score 0.395 Round 5: 118 peptides, 20 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 105, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2gpj-3_warpNtrace.pdb as input Building loops using Loopy2018 21 chains (105 residues) following loop building 2 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6058 reflections ( 99.61 % complete ) and 3822 restraints for refining 1841 atoms. 3345 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3103 (Rfree = 0.000) for 1841 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2918 (Rfree = 0.000) for 1813 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2707 (Rfree = 0.000) for 1797 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2697 (Rfree = 0.000) for 1783 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:42 GMT 2018 Job finished. TimeTaking 33.98 Used memory is bytes: 1427792