null Mon 24 Dec 07:52:11 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2owp-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2owp-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2owp-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-parrot-noncs ############### 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 07:52:15 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/noncs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2owp-3.2-parrot-noncs/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 321 and 0 Target number of residues in the AU: 321 Target solvent content: 0.6008 Checking the provided sequence file Detected sequence length: 129 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 258 Adjusted target solvent content: 0.68 Input MTZ file: 2owp-3.2-parrot-noncs.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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 2064 target number of atoms Had to go as low as 1.10 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: 29.899 3.200 Wilson plot Bfac: 52.66 7504 reflections ( 99.15 % complete ) and 0 restraints for refining 2289 atoms. Observations/parameters ratio is 0.82 ------------------------------------------------------ Starting model: R = 0.3701 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3871 (Rfree = 0.000) for 2289 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 2.51 Search for helices and strands: 0 residues in 0 chains, 2333 seeds are put forward NCS extension: 0 residues added, 2333 seeds are put forward Round 1: 136 peptides, 24 chains. Longest chain 12 peptides. Score 0.346 Round 2: 162 peptides, 26 chains. Longest chain 14 peptides. Score 0.412 Round 3: 185 peptides, 28 chains. Longest chain 16 peptides. Score 0.463 Round 4: 197 peptides, 27 chains. Longest chain 39 peptides. Score 0.517 Round 5: 186 peptides, 26 chains. Longest chain 17 peptides. Score 0.496 Taking the results from Round 4 Chains 31, Residues 170, Estimated correctness of the model 16.8 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3690 restraints for refining 1884 atoms. 2968 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3698 (Rfree = 0.000) for 1884 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 2: After refmac, R = 0.3622 (Rfree = 0.000) for 1845 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 3: After refmac, R = 0.3667 (Rfree = 0.000) for 1820 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 4: After refmac, R = 0.3367 (Rfree = 0.000) for 1817 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. Cycle 5: After refmac, R = 0.3315 (Rfree = 0.000) for 1811 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 2.74 Search for helices and strands: 0 residues in 0 chains, 1866 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 1894 seeds are put forward Round 1: 177 peptides, 28 chains. Longest chain 16 peptides. Score 0.435 Round 2: 189 peptides, 23 chains. Longest chain 21 peptides. Score 0.549 Round 3: 179 peptides, 24 chains. Longest chain 27 peptides. Score 0.503 Round 4: 183 peptides, 26 chains. Longest chain 19 peptides. Score 0.486 Round 5: 195 peptides, 28 chains. Longest chain 19 peptides. Score 0.497 Taking the results from Round 2 Chains 23, Residues 166, Estimated correctness of the model 26.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3919 restraints for refining 1884 atoms. 3278 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3716 (Rfree = 0.000) for 1884 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 7: After refmac, R = 0.3646 (Rfree = 0.000) for 1868 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 8: After refmac, R = 0.3523 (Rfree = 0.000) for 1851 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.3381 (Rfree = 0.000) for 1840 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.3396 (Rfree = 0.000) for 1839 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 2.50 Search for helices and strands: 0 residues in 0 chains, 1935 seeds are put forward NCS extension: 0 residues added, 1935 seeds are put forward Round 1: 158 peptides, 26 chains. Longest chain 14 peptides. Score 0.397 Round 2: 177 peptides, 25 chains. Longest chain 17 peptides. Score 0.481 Round 3: 170 peptides, 23 chains. Longest chain 20 peptides. Score 0.488 Round 4: 166 peptides, 23 chains. Longest chain 13 peptides. Score 0.474 Round 5: 177 peptides, 19 chains. Longest chain 18 peptides. Score 0.569 Taking the results from Round 5 Chains 19, Residues 158, Estimated correctness of the model 32.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3975 restraints for refining 1884 atoms. 3362 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3690 (Rfree = 0.000) for 1884 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 12: After refmac, R = 0.3407 (Rfree = 0.000) for 1872 atoms. Found 15 (16 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.3676 (Rfree = 0.000) for 1864 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 14: After refmac, R = 0.3298 (Rfree = 0.000) for 1857 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.3232 (Rfree = 0.000) for 1850 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 2.47 Search for helices and strands: 0 residues in 0 chains, 1918 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 1941 seeds are put forward Round 1: 175 peptides, 30 chains. Longest chain 12 peptides. Score 0.396 Round 2: 180 peptides, 25 chains. Longest chain 19 peptides. Score 0.491 Round 3: 188 peptides, 21 chains. Longest chain 17 peptides. Score 0.574 Round 4: 189 peptides, 24 chains. Longest chain 18 peptides. Score 0.535 Round 5: 194 peptides, 26 chains. Longest chain 23 peptides. Score 0.522 Taking the results from Round 3 Chains 25, Residues 167, Estimated correctness of the model 33.9 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3636 restraints for refining 1884 atoms. 2901 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3437 (Rfree = 0.000) for 1884 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 17: After refmac, R = 0.3386 (Rfree = 0.000) for 1879 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 18: After refmac, R = 0.3193 (Rfree = 0.000) for 1874 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.3186 (Rfree = 0.000) for 1863 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 20: After refmac, R = 0.3248 (Rfree = 0.000) for 1855 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 1912 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 1933 seeds are put forward Round 1: 173 peptides, 27 chains. Longest chain 19 peptides. Score 0.436 Round 2: 180 peptides, 27 chains. Longest chain 15 peptides. Score 0.461 Round 3: 173 peptides, 23 chains. Longest chain 24 peptides. Score 0.498 Round 4: 170 peptides, 22 chains. Longest chain 19 peptides. Score 0.503 Round 5: 169 peptides, 18 chains. Longest chain 38 peptides. Score 0.559 Taking the results from Round 5 Chains 18, Residues 151, Estimated correctness of the model 29.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 4040 restraints for refining 1884 atoms. 3454 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3165 (Rfree = 0.000) for 1884 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.3091 (Rfree = 0.000) for 1876 atoms. Found 13 (16 requested) and removed 9 (8 requested) atoms. Cycle 23: After refmac, R = 0.3099 (Rfree = 0.000) for 1877 atoms. Found 14 (16 requested) and removed 10 (8 requested) atoms. Cycle 24: After refmac, R = 0.2893 (Rfree = 0.000) for 1879 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2845 (Rfree = 0.000) for 1870 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.43 Search for helices and strands: 0 residues in 0 chains, 1936 seeds are put forward NCS extension: 67 residues added (2 deleted due to clashes), 2003 seeds are put forward Round 1: 135 peptides, 21 chains. Longest chain 16 peptides. Score 0.394 Round 2: 171 peptides, 23 chains. Longest chain 19 peptides. Score 0.491 Round 3: 168 peptides, 25 chains. Longest chain 15 peptides. Score 0.450 Round 4: 177 peptides, 23 chains. Longest chain 27 peptides. Score 0.511 Round 5: 151 peptides, 19 chains. Longest chain 15 peptides. Score 0.486 Taking the results from Round 4 Chains 23, Residues 154, Estimated correctness of the model 14.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 4027 restraints for refining 1884 atoms. 3434 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3076 (Rfree = 0.000) for 1884 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. Cycle 27: After refmac, R = 0.2992 (Rfree = 0.000) for 1875 atoms. Found 11 (16 requested) and removed 15 (8 requested) atoms. Cycle 28: After refmac, R = 0.2994 (Rfree = 0.000) for 1866 atoms. Found 11 (16 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.2994 (Rfree = 0.000) for 1863 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 30: After refmac, R = 0.2997 (Rfree = 0.000) for 1860 atoms. Found 13 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 2.45 Search for helices and strands: 0 residues in 0 chains, 1943 seeds are put forward NCS extension: 60 residues added (8 deleted due to clashes), 2003 seeds are put forward Round 1: 146 peptides, 24 chains. Longest chain 16 peptides. Score 0.385 Round 2: 158 peptides, 22 chains. Longest chain 16 peptides. Score 0.462 Round 3: 167 peptides, 24 chains. Longest chain 18 peptides. Score 0.462 Round 4: 173 peptides, 25 chains. Longest chain 18 peptides. Score 0.467 Round 5: 177 peptides, 24 chains. Longest chain 21 peptides. Score 0.496 Taking the results from Round 5 Chains 25, Residues 153, Estimated correctness of the model 10.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 3842 restraints for refining 1884 atoms. 3225 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3174 (Rfree = 0.000) for 1884 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 32: After refmac, R = 0.2972 (Rfree = 0.000) for 1881 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. Cycle 33: After refmac, R = 0.3046 (Rfree = 0.000) for 1869 atoms. Found 12 (16 requested) and removed 13 (8 requested) atoms. Cycle 34: After refmac, R = 0.3094 (Rfree = 0.000) for 1862 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 35: After refmac, R = 0.3086 (Rfree = 0.000) for 1863 atoms. Found 13 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 2.52 Search for helices and strands: 0 residues in 0 chains, 1949 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 1985 seeds are put forward Round 1: 156 peptides, 25 chains. Longest chain 12 peptides. Score 0.406 Round 2: 175 peptides, 28 chains. Longest chain 13 peptides. Score 0.428 Round 3: 173 peptides, 24 chains. Longest chain 20 peptides. Score 0.483 Round 4: 161 peptides, 23 chains. Longest chain 16 peptides. Score 0.457 Round 5: 168 peptides, 22 chains. Longest chain 24 peptides. Score 0.496 Taking the results from Round 5 Chains 22, Residues 146, Estimated correctness of the model 10.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 4110 restraints for refining 1884 atoms. 3548 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3074 (Rfree = 0.000) for 1884 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.3039 (Rfree = 0.000) for 1880 atoms. Found 2 (16 requested) and removed 12 (8 requested) atoms. Cycle 38: After refmac, R = 0.2962 (Rfree = 0.000) for 1867 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. Cycle 39: After refmac, R = 0.2908 (Rfree = 0.000) for 1857 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.2897 (Rfree = 0.000) for 1849 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 2.80 Search for helices and strands: 0 residues in 0 chains, 1925 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 1955 seeds are put forward Round 1: 138 peptides, 26 chains. Longest chain 14 peptides. Score 0.319 Round 2: 155 peptides, 23 chains. Longest chain 14 peptides. Score 0.435 Round 3: 164 peptides, 23 chains. Longest chain 25 peptides. Score 0.467 Round 4: 168 peptides, 22 chains. Longest chain 15 peptides. Score 0.496 Round 5: 165 peptides, 22 chains. Longest chain 18 peptides. Score 0.486 Taking the results from Round 4 Chains 22, Residues 146, Estimated correctness of the model 10.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7504 reflections ( 99.15 % complete ) and 4002 restraints for refining 1884 atoms. 3422 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3270 (Rfree = 0.000) for 1884 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 42: After refmac, R = 0.3210 (Rfree = 0.000) for 1883 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 43: After refmac, R = 0.3111 (Rfree = 0.000) for 1884 atoms. Found 12 (16 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.3127 (Rfree = 0.000) for 1885 atoms. Found 14 (16 requested) and removed 12 (8 requested) atoms. Cycle 45: After refmac, R = 0.3155 (Rfree = 0.000) for 1885 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 2.48 Search for helices and strands: 0 residues in 0 chains, 1933 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 1954 seeds are put forward Round 1: 168 peptides, 30 chains. Longest chain 24 peptides. Score 0.369 Round 2: 180 peptides, 29 chains. Longest chain 15 peptides. Score 0.430 Round 3: 177 peptides, 30 chains. Longest chain 11 peptides. Score 0.403 Round 4: 170 peptides, 25 chains. Longest chain 33 peptides. Score 0.457 Round 5: 168 peptides, 24 chains. Longest chain 22 peptides. Score 0.466 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 144, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 2owp-3_warpNtrace.pdb as input Building loops using Loopy2018 25 chains (144 residues) following loop building 3 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7504 reflections ( 99.15 % complete ) and 3863 restraints for refining 1884 atoms. 3208 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3132 (Rfree = 0.000) for 1884 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.3064 (Rfree = 0.000) for 1862 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2996 (Rfree = 0.000) for 1852 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2967 (Rfree = 0.000) for 1842 atoms. Found 0 (16 requested) and removed 7 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:21:10 GMT 2018 Job finished. TimeTaking 29 Used memory is bytes: 17579808