null Mon 24 Dec 00:04:20 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 2o62-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o62-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o62-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-3.8-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/2o62-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-3.8-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 00:04:24 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/2o62-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-3.8-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 397 and 0 Target number of residues in the AU: 397 Target solvent content: 0.6318 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.50 Input MTZ file: 2o62-3.8-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: 61.210 71.880 132.610 90.000 90.000 90.000 Input sequence file: 2o62-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4320 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 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: 66.305 3.800 Wilson plot Bfac: 67.27 6019 reflections ( 97.97 % complete ) and 0 restraints for refining 4793 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3788 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3631 (Rfree = 0.000) for 4793 atoms. Found 26 (26 requested) and removed 137 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 4708 seeds are put forward NCS extension: 0 residues added, 4708 seeds are put forward Round 1: 147 peptides, 32 chains. Longest chain 9 peptides. Score 0.235 Round 2: 180 peptides, 36 chains. Longest chain 11 peptides. Score 0.288 Round 3: 211 peptides, 44 chains. Longest chain 8 peptides. Score 0.280 Round 4: 220 peptides, 40 chains. Longest chain 15 peptides. Score 0.357 Round 5: 223 peptides, 38 chains. Longest chain 14 peptides. Score 0.390 Taking the results from Round 5 Chains 38, Residues 185, Estimated correctness of the model 0.0 % 5 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 9159 restraints for refining 3904 atoms. 8427 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3148 (Rfree = 0.000) for 3904 atoms. Found 21 (21 requested) and removed 89 (10 requested) atoms. Cycle 2: After refmac, R = 0.2962 (Rfree = 0.000) for 3788 atoms. Found 21 (21 requested) and removed 45 (10 requested) atoms. Cycle 3: After refmac, R = 0.2914 (Rfree = 0.000) for 3738 atoms. Found 20 (20 requested) and removed 37 (10 requested) atoms. Cycle 4: After refmac, R = 0.2387 (Rfree = 0.000) for 3696 atoms. Found 8 (20 requested) and removed 18 (10 requested) atoms. Cycle 5: After refmac, R = 0.2417 (Rfree = 0.000) for 3663 atoms. Found 8 (20 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.37 Search for helices and strands: 0 residues in 0 chains, 3724 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3745 seeds are put forward Round 1: 175 peptides, 38 chains. Longest chain 9 peptides. Score 0.245 Round 2: 216 peptides, 41 chains. Longest chain 13 peptides. Score 0.333 Round 3: 221 peptides, 40 chains. Longest chain 15 peptides. Score 0.360 Round 4: 213 peptides, 38 chains. Longest chain 12 peptides. Score 0.362 Round 5: 216 peptides, 38 chains. Longest chain 12 peptides. Score 0.370 Taking the results from Round 5 Chains 38, Residues 178, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8900 restraints for refining 3753 atoms. 8206 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2646 (Rfree = 0.000) for 3753 atoms. Found 20 (20 requested) and removed 56 (10 requested) atoms. Cycle 7: After refmac, R = 0.2563 (Rfree = 0.000) for 3671 atoms. Found 20 (20 requested) and removed 51 (10 requested) atoms. Cycle 8: After refmac, R = 0.2494 (Rfree = 0.000) for 3610 atoms. Found 14 (20 requested) and removed 31 (10 requested) atoms. Cycle 9: After refmac, R = 0.2403 (Rfree = 0.000) for 3570 atoms. Found 18 (19 requested) and removed 36 (9 requested) atoms. Cycle 10: After refmac, R = 0.2376 (Rfree = 0.000) for 3543 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.37 Search for helices and strands: 0 residues in 0 chains, 3604 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3618 seeds are put forward Round 1: 205 peptides, 44 chains. Longest chain 7 peptides. Score 0.261 Round 2: 227 peptides, 45 chains. Longest chain 12 peptides. Score 0.315 Round 3: 234 peptides, 44 chains. Longest chain 12 peptides. Score 0.348 Round 4: 224 peptides, 42 chains. Longest chain 10 peptides. Score 0.344 Round 5: 226 peptides, 40 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 5 Chains 40, Residues 186, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8488 restraints for refining 3711 atoms. 7756 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2492 (Rfree = 0.000) for 3711 atoms. Found 20 (20 requested) and removed 59 (10 requested) atoms. Cycle 12: After refmac, R = 0.2497 (Rfree = 0.000) for 3651 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 13: After refmac, R = 0.2432 (Rfree = 0.000) for 3632 atoms. Found 20 (20 requested) and removed 36 (10 requested) atoms. Cycle 14: After refmac, R = 0.2057 (Rfree = 0.000) for 3609 atoms. Found 5 (19 requested) and removed 19 (9 requested) atoms. Cycle 15: After refmac, R = 0.1944 (Rfree = 0.000) for 3585 atoms. Found 4 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.43 Search for helices and strands: 0 residues in 0 chains, 3615 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3626 seeds are put forward Round 1: 198 peptides, 44 chains. Longest chain 8 peptides. Score 0.239 Round 2: 233 peptides, 45 chains. Longest chain 11 peptides. Score 0.333 Round 3: 252 peptides, 45 chains. Longest chain 11 peptides. Score 0.387 Round 4: 254 peptides, 47 chains. Longest chain 12 peptides. Score 0.369 Round 5: 253 peptides, 41 chains. Longest chain 16 peptides. Score 0.436 Taking the results from Round 5 Chains 41, Residues 212, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8481 restraints for refining 3881 atoms. 7577 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2541 (Rfree = 0.000) for 3881 atoms. Found 21 (21 requested) and removed 43 (10 requested) atoms. Cycle 17: After refmac, R = 0.2454 (Rfree = 0.000) for 3829 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 18: After refmac, R = 0.2377 (Rfree = 0.000) for 3802 atoms. Found 18 (21 requested) and removed 31 (10 requested) atoms. Cycle 19: After refmac, R = 0.2050 (Rfree = 0.000) for 3779 atoms. Found 6 (20 requested) and removed 15 (10 requested) atoms. Cycle 20: After refmac, R = 0.1981 (Rfree = 0.000) for 3765 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.35 Search for helices and strands: 0 residues in 0 chains, 3814 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3828 seeds are put forward Round 1: 180 peptides, 40 chains. Longest chain 7 peptides. Score 0.234 Round 2: 205 peptides, 41 chains. Longest chain 10 peptides. Score 0.300 Round 3: 216 peptides, 40 chains. Longest chain 8 peptides. Score 0.345 Round 4: 214 peptides, 36 chains. Longest chain 10 peptides. Score 0.389 Round 5: 215 peptides, 36 chains. Longest chain 9 peptides. Score 0.392 Taking the results from Round 5 Chains 36, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 9097 restraints for refining 3907 atoms. 8417 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2651 (Rfree = 0.000) for 3907 atoms. Found 21 (21 requested) and removed 35 (10 requested) atoms. Cycle 22: After refmac, R = 0.2651 (Rfree = 0.000) for 3873 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 23: After refmac, R = 0.2224 (Rfree = 0.000) for 3850 atoms. Found 10 (21 requested) and removed 17 (10 requested) atoms. Cycle 24: After refmac, R = 0.2135 (Rfree = 0.000) for 3828 atoms. Found 11 (21 requested) and removed 13 (10 requested) atoms. Cycle 25: After refmac, R = 0.2013 (Rfree = 0.000) for 3818 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.38 Search for helices and strands: 0 residues in 0 chains, 3857 seeds are put forward NCS extension: 0 residues added, 3857 seeds are put forward Round 1: 149 peptides, 31 chains. Longest chain 8 peptides. Score 0.256 Round 2: 175 peptides, 35 chains. Longest chain 11 peptides. Score 0.285 Round 3: 208 peptides, 39 chains. Longest chain 11 peptides. Score 0.334 Round 4: 185 peptides, 33 chains. Longest chain 14 peptides. Score 0.343 Round 5: 180 peptides, 30 chains. Longest chain 17 peptides. Score 0.367 Taking the results from Round 5 Chains 31, Residues 150, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8946 restraints for refining 3907 atoms. 8319 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2497 (Rfree = 0.000) for 3907 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 27: After refmac, R = 0.2607 (Rfree = 0.000) for 3875 atoms. Found 21 (21 requested) and removed 28 (10 requested) atoms. Cycle 28: After refmac, R = 0.2630 (Rfree = 0.000) for 3856 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 29: After refmac, R = 0.2532 (Rfree = 0.000) for 3832 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 30: After refmac, R = 0.2491 (Rfree = 0.000) for 3833 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.36 Search for helices and strands: 0 residues in 0 chains, 3886 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3898 seeds are put forward Round 1: 157 peptides, 36 chains. Longest chain 7 peptides. Score 0.212 Round 2: 187 peptides, 38 chains. Longest chain 9 peptides. Score 0.283 Round 3: 194 peptides, 36 chains. Longest chain 10 peptides. Score 0.331 Round 4: 188 peptides, 33 chains. Longest chain 12 peptides. Score 0.352 Round 5: 186 peptides, 31 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 5 Chains 31, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8455 restraints for refining 3747 atoms. 7866 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2663 (Rfree = 0.000) for 3747 atoms. Found 20 (20 requested) and removed 33 (10 requested) atoms. Cycle 32: After refmac, R = 0.2764 (Rfree = 0.000) for 3717 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 33: After refmac, R = 0.2611 (Rfree = 0.000) for 3700 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 34: After refmac, R = 0.2661 (Rfree = 0.000) for 3688 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 35: After refmac, R = 0.2581 (Rfree = 0.000) for 3680 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 3723 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3735 seeds are put forward Round 1: 171 peptides, 38 chains. Longest chain 7 peptides. Score 0.232 Round 2: 209 peptides, 43 chains. Longest chain 9 peptides. Score 0.286 Round 3: 210 peptides, 42 chains. Longest chain 10 peptides. Score 0.302 Round 4: 206 peptides, 37 chains. Longest chain 9 peptides. Score 0.354 Round 5: 220 peptides, 40 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 5 Chains 40, Residues 180, Estimated correctness of the model 0.0 % 7 chains (29 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8282 restraints for refining 3800 atoms. 7531 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2574 (Rfree = 0.000) for 3800 atoms. Found 20 (20 requested) and removed 41 (10 requested) atoms. Cycle 37: After refmac, R = 0.2731 (Rfree = 0.000) for 3750 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 38: After refmac, R = 0.2553 (Rfree = 0.000) for 3722 atoms. Found 20 (20 requested) and removed 29 (10 requested) atoms. Cycle 39: After refmac, R = 0.2087 (Rfree = 0.000) for 3691 atoms. Found 15 (20 requested) and removed 14 (10 requested) atoms. Cycle 40: After refmac, R = 0.1949 (Rfree = 0.000) for 3684 atoms. Found 13 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.41 Search for helices and strands: 0 residues in 0 chains, 3704 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3713 seeds are put forward Round 1: 149 peptides, 34 chains. Longest chain 8 peptides. Score 0.213 Round 2: 186 peptides, 37 chains. Longest chain 10 peptides. Score 0.293 Round 3: 200 peptides, 35 chains. Longest chain 10 peptides. Score 0.362 Round 4: 184 peptides, 33 chains. Longest chain 9 peptides. Score 0.340 Round 5: 191 peptides, 34 chains. Longest chain 9 peptides. Score 0.348 Taking the results from Round 3 Chains 35, Residues 165, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8091 restraints for refining 3664 atoms. 7458 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2558 (Rfree = 0.000) for 3664 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 42: After refmac, R = 0.2201 (Rfree = 0.000) for 3641 atoms. Found 14 (20 requested) and removed 16 (10 requested) atoms. Cycle 43: After refmac, R = 0.2020 (Rfree = 0.000) for 3632 atoms. Found 12 (20 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.2031 (Rfree = 0.000) for 3627 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 45: After refmac, R = 0.1944 (Rfree = 0.000) for 3613 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.37 Search for helices and strands: 0 residues in 0 chains, 3658 seeds are put forward NCS extension: 0 residues added, 3658 seeds are put forward Round 1: 160 peptides, 34 chains. Longest chain 9 peptides. Score 0.250 Round 2: 192 peptides, 38 chains. Longest chain 13 peptides. Score 0.299 Round 3: 181 peptides, 33 chains. Longest chain 14 peptides. Score 0.331 Round 4: 171 peptides, 30 chains. Longest chain 14 peptides. Score 0.340 Round 5: 170 peptides, 28 chains. Longest chain 14 peptides. Score 0.364 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 142, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2o62-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6019 reflections ( 97.97 % complete ) and 8707 restraints for refining 3776 atoms. 8155 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2424 (Rfree = 0.000) for 3776 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2653 (Rfree = 0.000) for 3754 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2026 (Rfree = 0.000) for 3733 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1945 (Rfree = 0.000) for 3716 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:43:18 GMT 2018 Job finished. TimeTaking 38.97 Used memory is bytes: 6482464