Mon 24 Dec 00:35:34 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 2obp-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obp-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obp-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.4-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/2obp-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.4-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 00:35:39 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/2obp-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obp-3.4-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 156 and 0 Target number of residues in the AU: 156 Target solvent content: 0.6399 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.56 Input MTZ file: 2obp-3.4-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: 182 Cell parameters: 76.690 76.690 138.090 90.000 90.000 120.000 Input sequence file: 2obp-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1536 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: 29.462 3.400 Wilson plot Bfac: 71.63 3658 reflections ( 99.40 % complete ) and 0 restraints for refining 1693 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3555 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3329 (Rfree = 0.000) for 1693 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 1715 seeds are put forward NCS extension: 0 residues added, 1715 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.309 Round 2: 97 peptides, 15 chains. Longest chain 10 peptides. Score 0.448 Round 3: 98 peptides, 12 chains. Longest chain 11 peptides. Score 0.538 Round 4: 97 peptides, 15 chains. Longest chain 12 peptides. Score 0.448 Round 5: 102 peptides, 15 chains. Longest chain 11 peptides. Score 0.480 Taking the results from Round 3 Chains 12, Residues 86, Estimated correctness of the model 7.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 3207 restraints for refining 1385 atoms. 2875 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3027 (Rfree = 0.000) for 1385 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 2: After refmac, R = 0.2878 (Rfree = 0.000) for 1371 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 3: After refmac, R = 0.2775 (Rfree = 0.000) for 1369 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 4: After refmac, R = 0.2809 (Rfree = 0.000) for 1364 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2795 (Rfree = 0.000) for 1361 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.06 Search for helices and strands: 0 residues in 0 chains, 1398 seeds are put forward NCS extension: 0 residues added, 1398 seeds are put forward Round 1: 99 peptides, 17 chains. Longest chain 11 peptides. Score 0.404 Round 2: 105 peptides, 12 chains. Longest chain 13 peptides. Score 0.577 Round 3: 107 peptides, 13 chains. Longest chain 12 peptides. Score 0.563 Round 4: 105 peptides, 12 chains. Longest chain 17 peptides. Score 0.577 Round 5: 110 peptides, 15 chains. Longest chain 13 peptides. Score 0.528 Taking the results from Round 4 Chains 12, Residues 93, Estimated correctness of the model 21.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 3044 restraints for refining 1319 atoms. 2684 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2944 (Rfree = 0.000) for 1319 atoms. Found 8 (9 requested) and removed 13 (4 requested) atoms. Cycle 7: After refmac, R = 0.2877 (Rfree = 0.000) for 1298 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2828 (Rfree = 0.000) for 1291 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 9: After refmac, R = 0.2803 (Rfree = 0.000) for 1290 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.2818 (Rfree = 0.000) for 1282 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 1324 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1337 seeds are put forward Round 1: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.392 Round 2: 105 peptides, 14 chains. Longest chain 13 peptides. Score 0.525 Round 3: 110 peptides, 13 chains. Longest chain 21 peptides. Score 0.579 Round 4: 115 peptides, 16 chains. Longest chain 14 peptides. Score 0.532 Round 5: 103 peptides, 13 chains. Longest chain 19 peptides. Score 0.540 Taking the results from Round 3 Chains 13, Residues 97, Estimated correctness of the model 21.7 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 2657 restraints for refining 1303 atoms. 2209 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3014 (Rfree = 0.000) for 1303 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 12: After refmac, R = 0.2897 (Rfree = 0.000) for 1275 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2782 (Rfree = 0.000) for 1264 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2672 (Rfree = 0.000) for 1263 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.2643 (Rfree = 0.000) for 1254 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.21 Search for helices and strands: 0 residues in 0 chains, 1298 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 1322 seeds are put forward Round 1: 91 peptides, 17 chains. Longest chain 7 peptides. Score 0.347 Round 2: 92 peptides, 15 chains. Longest chain 11 peptides. Score 0.415 Round 3: 97 peptides, 14 chains. Longest chain 17 peptides. Score 0.477 Round 4: 105 peptides, 14 chains. Longest chain 21 peptides. Score 0.525 Round 5: 100 peptides, 11 chains. Longest chain 29 peptides. Score 0.575 Taking the results from Round 5 Chains 11, Residues 89, Estimated correctness of the model 20.3 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3658 reflections ( 99.40 % complete ) and 2892 restraints for refining 1350 atoms. 2495 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2977 (Rfree = 0.000) for 1350 atoms. Found 8 (10 requested) and removed 22 (5 requested) atoms. Cycle 17: After refmac, R = 0.2847 (Rfree = 0.000) for 1327 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.2806 (Rfree = 0.000) for 1321 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.2816 (Rfree = 0.000) for 1315 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2812 (Rfree = 0.000) for 1309 atoms. Found 5 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.19 Search for helices and strands: 0 residues in 0 chains, 1362 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 1387 seeds are put forward Round 1: 93 peptides, 14 chains. Longest chain 12 peptides. Score 0.451 Round 2: 104 peptides, 14 chains. Longest chain 16 peptides. Score 0.520 Round 3: 107 peptides, 15 chains. Longest chain 17 peptides. Score 0.511 Round 4: 106 peptides, 15 chains. Longest chain 17 peptides. Score 0.505 Round 5: 96 peptides, 13 chains. Longest chain 20 peptides. Score 0.498 Taking the results from Round 2 Chains 14, Residues 90, Estimated correctness of the model 0.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 3043 restraints for refining 1344 atoms. 2697 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3037 (Rfree = 0.000) for 1344 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 22: After refmac, R = 0.2926 (Rfree = 0.000) for 1346 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2886 (Rfree = 0.000) for 1344 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.2849 (Rfree = 0.000) for 1338 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2825 (Rfree = 0.000) for 1334 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 1381 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 1407 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 10 peptides. Score 0.311 Round 2: 92 peptides, 14 chains. Longest chain 15 peptides. Score 0.444 Round 3: 98 peptides, 16 chains. Longest chain 15 peptides. Score 0.426 Round 4: 95 peptides, 16 chains. Longest chain 15 peptides. Score 0.406 Round 5: 94 peptides, 14 chains. Longest chain 15 peptides. Score 0.458 Taking the results from Round 5 Chains 14, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 3185 restraints for refining 1368 atoms. 2879 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3008 (Rfree = 0.000) for 1368 atoms. Found 9 (10 requested) and removed 48 (5 requested) atoms. Cycle 27: After refmac, R = 0.2956 (Rfree = 0.000) for 1329 atoms. Found 3 (10 requested) and removed 13 (5 requested) atoms. Cycle 28: After refmac, R = 0.2915 (Rfree = 0.000) for 1317 atoms. Found 1 (9 requested) and removed 17 (4 requested) atoms. Cycle 29: After refmac, R = 0.2888 (Rfree = 0.000) for 1301 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2886 (Rfree = 0.000) for 1298 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 1356 seeds are put forward NCS extension: 0 residues added, 1356 seeds are put forward Round 1: 83 peptides, 14 chains. Longest chain 14 peptides. Score 0.383 Round 2: 87 peptides, 15 chains. Longest chain 12 peptides. Score 0.380 Round 3: 85 peptides, 14 chains. Longest chain 13 peptides. Score 0.397 Round 4: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.362 Round 5: 85 peptides, 14 chains. Longest chain 8 peptides. Score 0.397 Taking the results from Round 5 Chains 14, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 3146 restraints for refining 1345 atoms. 2876 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3126 (Rfree = 0.000) for 1345 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 32: After refmac, R = 0.3036 (Rfree = 0.000) for 1336 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2944 (Rfree = 0.000) for 1337 atoms. Found 3 (10 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.2914 (Rfree = 0.000) for 1328 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2870 (Rfree = 0.000) for 1322 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 1399 seeds are put forward NCS extension: 0 residues added, 1399 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 9 peptides. Score 0.257 Round 2: 77 peptides, 14 chains. Longest chain 10 peptides. Score 0.339 Round 3: 82 peptides, 14 chains. Longest chain 16 peptides. Score 0.376 Round 4: 86 peptides, 13 chains. Longest chain 14 peptides. Score 0.434 Round 5: 86 peptides, 12 chains. Longest chain 11 peptides. Score 0.464 Taking the results from Round 5 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 3232 restraints for refining 1380 atoms. 2948 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2907 (Rfree = 0.000) for 1380 atoms. Found 9 (10 requested) and removed 13 (5 requested) atoms. Cycle 37: After refmac, R = 0.2747 (Rfree = 0.000) for 1373 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.2704 (Rfree = 0.000) for 1367 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.2688 (Rfree = 0.000) for 1362 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2667 (Rfree = 0.000) for 1358 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.19 Search for helices and strands: 0 residues in 0 chains, 1401 seeds are put forward NCS extension: 0 residues added, 1401 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 9 peptides. Score 0.275 Round 2: 91 peptides, 16 chains. Longest chain 14 peptides. Score 0.378 Round 3: 88 peptides, 14 chains. Longest chain 15 peptides. Score 0.418 Round 4: 76 peptides, 10 chains. Longest chain 16 peptides. Score 0.458 Round 5: 83 peptides, 10 chains. Longest chain 15 peptides. Score 0.503 Taking the results from Round 5 Chains 12, Residues 73, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 3080 restraints for refining 1375 atoms. 2770 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3003 (Rfree = 0.000) for 1375 atoms. Found 8 (10 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.2868 (Rfree = 0.000) for 1369 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2785 (Rfree = 0.000) for 1365 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.2746 (Rfree = 0.000) for 1362 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2719 (Rfree = 0.000) for 1356 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.17 Search for helices and strands: 0 residues in 0 chains, 1402 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1423 seeds are put forward Round 1: 71 peptides, 14 chains. Longest chain 6 peptides. Score 0.293 Round 2: 91 peptides, 15 chains. Longest chain 10 peptides. Score 0.408 Round 3: 88 peptides, 14 chains. Longest chain 13 peptides. Score 0.418 Round 4: 83 peptides, 14 chains. Longest chain 10 peptides. Score 0.383 Round 5: 90 peptides, 13 chains. Longest chain 16 peptides. Score 0.460 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 77, 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 2obp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3658 reflections ( 99.40 % complete ) and 3068 restraints for refining 1343 atoms. 2773 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2896 (Rfree = 0.000) for 1343 atoms. Found 0 (10 requested) and removed 0 (5 requested) atoms. Cycle 47: After refmac, R = 0.2798 (Rfree = 0.000) for 1342 atoms. Found 0 (10 requested) and removed 1 (5 requested) atoms. Cycle 48: After refmac, R = 0.2768 (Rfree = 0.000) for 1339 atoms. Found 0 (10 requested) and removed 0 (5 requested) atoms. Cycle 49: After refmac, R = 0.2740 (Rfree = 0.000) for 1338 atoms. Found 0 (10 requested) and removed 0 (5 requested) atoms. Writing output files ... TimeTaking 30.6