null Mon 24 Dec 00:56:07 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 1o6a-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1o6a-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1o6a-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.2-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/1o6a-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.2-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 00:56:12 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/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.2-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 144 and 0 Target number of residues in the AU: 144 Target solvent content: 0.6380 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: 0.52 Input MTZ file: 1o6a-3.2-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: 92 Cell parameters: 61.652 61.652 113.295 90.000 90.000 90.000 Input sequence file: 1o6a-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.65 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: 41.713 3.201 Wilson plot Bfac: 70.40 3949 reflections ( 99.90 % complete ) and 0 restraints for refining 1699 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.4219 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3328 (Rfree = 0.000) for 1699 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.18 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: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.397 Round 2: 116 peptides, 15 chains. Longest chain 14 peptides. Score 0.586 Round 3: 103 peptides, 11 chains. Longest chain 20 peptides. Score 0.615 Round 4: 118 peptides, 14 chains. Longest chain 18 peptides. Score 0.622 Round 5: 113 peptides, 11 chains. Longest chain 22 peptides. Score 0.667 Taking the results from Round 5 Chains 11, Residues 102, Estimated correctness of the model 57.8 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3008 restraints for refining 1403 atoms. 2554 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3861 (Rfree = 0.000) for 1403 atoms. Found 11 (12 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.3811 (Rfree = 0.000) for 1391 atoms. Found 8 (12 requested) and removed 6 (6 requested) atoms. Cycle 3: After refmac, R = 0.3696 (Rfree = 0.000) for 1391 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 4: After refmac, R = 0.3613 (Rfree = 0.000) for 1387 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.3555 (Rfree = 0.000) for 1383 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 1433 seeds are put forward Round 1: 103 peptides, 15 chains. Longest chain 18 peptides. Score 0.506 Round 2: 122 peptides, 14 chains. Longest chain 19 peptides. Score 0.642 Round 3: 115 peptides, 11 chains. Longest chain 23 peptides. Score 0.677 Round 4: 102 peptides, 10 chains. Longest chain 27 peptides. Score 0.635 Round 5: 111 peptides, 10 chains. Longest chain 32 peptides. Score 0.680 Taking the results from Round 5 Chains 12, Residues 101, Estimated correctness of the model 60.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3050 restraints for refining 1403 atoms. 2625 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3995 (Rfree = 0.000) for 1403 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.3746 (Rfree = 0.000) for 1397 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.3637 (Rfree = 0.000) for 1392 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.3541 (Rfree = 0.000) for 1389 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.3467 (Rfree = 0.000) for 1384 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 1430 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1451 seeds are put forward Round 1: 110 peptides, 16 chains. Longest chain 19 peptides. Score 0.523 Round 2: 118 peptides, 13 chains. Longest chain 23 peptides. Score 0.646 Round 3: 117 peptides, 13 chains. Longest chain 25 peptides. Score 0.640 Round 4: 113 peptides, 12 chains. Longest chain 31 peptides. Score 0.644 Round 5: 118 peptides, 13 chains. Longest chain 26 peptides. Score 0.646 Taking the results from Round 5 Chains 13, Residues 105, Estimated correctness of the model 52.8 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 2872 restraints for refining 1403 atoms. 2372 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3785 (Rfree = 0.000) for 1403 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 12: After refmac, R = 0.3398 (Rfree = 0.000) for 1398 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 13: After refmac, R = 0.3337 (Rfree = 0.000) for 1388 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.3239 (Rfree = 0.000) for 1380 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.3181 (Rfree = 0.000) for 1372 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 1404 seeds are put forward NCS extension: 26 residues added (8 deleted due to clashes), 1430 seeds are put forward Round 1: 105 peptides, 14 chains. Longest chain 21 peptides. Score 0.547 Round 2: 112 peptides, 12 chains. Longest chain 23 peptides. Score 0.638 Round 3: 108 peptides, 10 chains. Longest chain 25 peptides. Score 0.666 Round 4: 107 peptides, 14 chains. Longest chain 22 peptides. Score 0.559 Round 5: 105 peptides, 12 chains. Longest chain 23 peptides. Score 0.601 Taking the results from Round 3 Chains 10, Residues 98, Estimated correctness of the model 57.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3222 restraints for refining 1403 atoms. 2840 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3478 (Rfree = 0.000) for 1403 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 17: After refmac, R = 0.3232 (Rfree = 0.000) for 1399 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.3105 (Rfree = 0.000) for 1391 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.3066 (Rfree = 0.000) for 1382 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.3018 (Rfree = 0.000) for 1376 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 1397 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 1434 seeds are put forward Round 1: 103 peptides, 15 chains. Longest chain 14 peptides. Score 0.506 Round 2: 112 peptides, 12 chains. Longest chain 24 peptides. Score 0.638 Round 3: 106 peptides, 12 chains. Longest chain 15 peptides. Score 0.606 Round 4: 110 peptides, 9 chains. Longest chain 37 peptides. Score 0.698 Round 5: 103 peptides, 10 chains. Longest chain 33 peptides. Score 0.641 Taking the results from Round 4 Chains 9, Residues 101, Estimated correctness of the model 64.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3121 restraints for refining 1403 atoms. 2726 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3199 (Rfree = 0.000) for 1403 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.3123 (Rfree = 0.000) for 1391 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.2977 (Rfree = 0.000) for 1381 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.2896 (Rfree = 0.000) for 1374 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2969 (Rfree = 0.000) for 1366 atoms. Found 3 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 1395 seeds are put forward NCS extension: 39 residues added (4 deleted due to clashes), 1434 seeds are put forward Round 1: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.392 Round 2: 97 peptides, 14 chains. Longest chain 14 peptides. Score 0.496 Round 3: 87 peptides, 10 chains. Longest chain 28 peptides. Score 0.549 Round 4: 90 peptides, 10 chains. Longest chain 19 peptides. Score 0.567 Round 5: 88 peptides, 10 chains. Longest chain 21 peptides. Score 0.555 Taking the results from Round 4 Chains 10, Residues 80, Estimated correctness of the model 31.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3168 restraints for refining 1398 atoms. 2858 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3279 (Rfree = 0.000) for 1398 atoms. Found 7 (12 requested) and removed 14 (6 requested) atoms. Cycle 27: After refmac, R = 0.3040 (Rfree = 0.000) for 1389 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.2917 (Rfree = 0.000) for 1384 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.2873 (Rfree = 0.000) for 1377 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.2868 (Rfree = 0.000) for 1368 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.22 Search for helices and strands: 0 residues in 0 chains, 1385 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 1418 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 17 peptides. Score 0.412 Round 2: 95 peptides, 11 chains. Longest chain 17 peptides. Score 0.569 Round 3: 98 peptides, 13 chains. Longest chain 16 peptides. Score 0.532 Round 4: 104 peptides, 12 chains. Longest chain 31 peptides. Score 0.595 Round 5: 103 peptides, 12 chains. Longest chain 23 peptides. Score 0.589 Taking the results from Round 4 Chains 12, Residues 92, Estimated correctness of the model 39.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3044 restraints for refining 1381 atoms. 2688 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3346 (Rfree = 0.000) for 1381 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.3194 (Rfree = 0.000) for 1378 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.3090 (Rfree = 0.000) for 1373 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.3033 (Rfree = 0.000) for 1366 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2991 (Rfree = 0.000) for 1361 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 1381 seeds are put forward NCS extension: 44 residues added (5 deleted due to clashes), 1425 seeds are put forward Round 1: 84 peptides, 13 chains. Longest chain 14 peptides. Score 0.436 Round 2: 90 peptides, 11 chains. Longest chain 15 peptides. Score 0.539 Round 3: 98 peptides, 13 chains. Longest chain 15 peptides. Score 0.532 Round 4: 100 peptides, 11 chains. Longest chain 30 peptides. Score 0.599 Round 5: 104 peptides, 13 chains. Longest chain 18 peptides. Score 0.568 Taking the results from Round 4 Chains 13, Residues 89, Estimated correctness of the model 40.7 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 2929 restraints for refining 1403 atoms. 2511 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3496 (Rfree = 0.000) for 1403 atoms. Found 8 (12 requested) and removed 15 (6 requested) atoms. Cycle 37: After refmac, R = 0.3097 (Rfree = 0.000) for 1394 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 38: After refmac, R = 0.3033 (Rfree = 0.000) for 1382 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.2884 (Rfree = 0.000) for 1374 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2925 (Rfree = 0.000) for 1366 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 1409 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1429 seeds are put forward Round 1: 69 peptides, 12 chains. Longest chain 15 peptides. Score 0.355 Round 2: 93 peptides, 12 chains. Longest chain 19 peptides. Score 0.529 Round 3: 84 peptides, 11 chains. Longest chain 22 peptides. Score 0.499 Round 4: 85 peptides, 10 chains. Longest chain 20 peptides. Score 0.536 Round 5: 91 peptides, 12 chains. Longest chain 22 peptides. Score 0.516 Taking the results from Round 4 Chains 10, Residues 75, Estimated correctness of the model 22.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3205 restraints for refining 1385 atoms. 2915 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2969 (Rfree = 0.000) for 1385 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.2766 (Rfree = 0.000) for 1381 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.2732 (Rfree = 0.000) for 1371 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2750 (Rfree = 0.000) for 1367 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.2941 (Rfree = 0.000) for 1361 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.21 Search for helices and strands: 0 residues in 0 chains, 1385 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 1414 seeds are put forward Round 1: 73 peptides, 12 chains. Longest chain 9 peptides. Score 0.387 Round 2: 80 peptides, 7 chains. Longest chain 27 peptides. Score 0.593 Round 3: 81 peptides, 10 chains. Longest chain 31 peptides. Score 0.510 Round 4: 96 peptides, 11 chains. Longest chain 30 peptides. Score 0.575 Round 5: 91 peptides, 11 chains. Longest chain 25 peptides. Score 0.545 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 73, Estimated correctness of the model 39.1 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1o6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3949 reflections ( 99.90 % complete ) and 3003 restraints for refining 1367 atoms. 2718 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2959 (Rfree = 0.000) for 1367 atoms. Found 0 (12 requested) and removed 4 (6 requested) atoms. Cycle 47: After refmac, R = 0.2812 (Rfree = 0.000) for 1363 atoms. Found 0 (12 requested) and removed 0 (6 requested) atoms. Cycle 48: After refmac, R = 0.2857 (Rfree = 0.000) for 1363 atoms. Found 0 (12 requested) and removed 2 (6 requested) atoms. Cycle 49: After refmac, R = 0.2834 (Rfree = 0.000) for 1361 atoms. Found 0 (12 requested) and removed 2 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:19:37 GMT 2018 Job finished. TimeTaking 23.51 Used memory is bytes: 14856456