Mon 24 Dec 00:20:44 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1o6a-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1o6a-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-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/1o6a-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-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 00:20:49 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.6506 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-3.4-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: 92 Cell parameters: 61.652 61.652 113.295 90.000 90.000 90.000 Input sequence file: 1o6a-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 0.65 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 3.400 Wilson plot Bfac: 78.56 3317 reflections ( 99.88 % complete ) and 0 restraints for refining 1693 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.4210 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4372 (Rfree = 0.000) for 1693 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 1708 seeds are put forward NCS extension: 0 residues added, 1708 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.257 Round 2: 98 peptides, 13 chains. Longest chain 17 peptides. Score 0.532 Round 3: 93 peptides, 12 chains. Longest chain 13 peptides. Score 0.529 Round 4: 101 peptides, 11 chains. Longest chain 20 peptides. Score 0.604 Round 5: 105 peptides, 12 chains. Longest chain 16 peptides. Score 0.601 Taking the results from Round 4 Chains 11, Residues 90, Estimated correctness of the model 30.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3213 restraints for refining 1396 atoms. 2864 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3986 (Rfree = 0.000) for 1396 atoms. Found 6 (10 requested) and removed 37 (5 requested) atoms. Cycle 2: After refmac, R = 0.3817 (Rfree = 0.000) for 1337 atoms. Found 9 (10 requested) and removed 14 (5 requested) atoms. Cycle 3: After refmac, R = 0.3587 (Rfree = 0.000) for 1322 atoms. Found 2 (10 requested) and removed 14 (5 requested) atoms. Cycle 4: After refmac, R = 0.3497 (Rfree = 0.000) for 1304 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. Cycle 5: After refmac, R = 0.3307 (Rfree = 0.000) for 1289 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 1351 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1371 seeds are put forward Round 1: 88 peptides, 15 chains. Longest chain 12 peptides. Score 0.402 Round 2: 105 peptides, 16 chains. Longest chain 19 peptides. Score 0.491 Round 3: 109 peptides, 13 chains. Longest chain 20 peptides. Score 0.597 Round 4: 117 peptides, 15 chains. Longest chain 31 peptides. Score 0.591 Round 5: 114 peptides, 12 chains. Longest chain 35 peptides. Score 0.649 Taking the results from Round 5 Chains 12, Residues 102, Estimated correctness of the model 43.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 2877 restraints for refining 1326 atoms. 2481 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3510 (Rfree = 0.000) for 1326 atoms. Found 8 (10 requested) and removed 29 (5 requested) atoms. Cycle 7: After refmac, R = 0.3326 (Rfree = 0.000) for 1298 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 8: After refmac, R = 0.3305 (Rfree = 0.000) for 1287 atoms. Found 8 (9 requested) and removed 11 (4 requested) atoms. Cycle 9: After refmac, R = 0.3817 (Rfree = 0.000) for 1277 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 10: After refmac, R = 0.3208 (Rfree = 0.000) for 1265 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 1312 seeds are put forward NCS extension: 26 residues added (9 deleted due to clashes), 1338 seeds are put forward Round 1: 94 peptides, 13 chains. Longest chain 21 peptides. Score 0.506 Round 2: 109 peptides, 13 chains. Longest chain 17 peptides. Score 0.597 Round 3: 110 peptides, 13 chains. Longest chain 23 peptides. Score 0.603 Round 4: 113 peptides, 12 chains. Longest chain 23 peptides. Score 0.644 Round 5: 108 peptides, 13 chains. Longest chain 23 peptides. Score 0.592 Taking the results from Round 4 Chains 12, Residues 101, Estimated correctness of the model 42.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 2884 restraints for refining 1336 atoms. 2492 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3324 (Rfree = 0.000) for 1336 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 12: After refmac, R = 0.3349 (Rfree = 0.000) for 1320 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 13: After refmac, R = 0.3184 (Rfree = 0.000) for 1307 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.3326 (Rfree = 0.000) for 1302 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 15: After refmac, R = 0.3173 (Rfree = 0.000) for 1299 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 1349 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 1375 seeds are put forward Round 1: 98 peptides, 17 chains. Longest chain 22 peptides. Score 0.412 Round 2: 109 peptides, 16 chains. Longest chain 18 peptides. Score 0.517 Round 3: 100 peptides, 13 chains. Longest chain 15 peptides. Score 0.544 Round 4: 105 peptides, 14 chains. Longest chain 16 peptides. Score 0.547 Round 5: 107 peptides, 15 chains. Longest chain 17 peptides. Score 0.532 Taking the results from Round 4 Chains 14, Residues 91, Estimated correctness of the model 10.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3060 restraints for refining 1380 atoms. 2710 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3670 (Rfree = 0.000) for 1380 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 17: After refmac, R = 0.3493 (Rfree = 0.000) for 1360 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.3589 (Rfree = 0.000) for 1345 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 19: After refmac, R = 0.3357 (Rfree = 0.000) for 1334 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.3238 (Rfree = 0.000) for 1330 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 1369 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1386 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.369 Round 2: 112 peptides, 16 chains. Longest chain 13 peptides. Score 0.536 Round 3: 111 peptides, 15 chains. Longest chain 18 peptides. Score 0.556 Round 4: 108 peptides, 14 chains. Longest chain 22 peptides. Score 0.565 Round 5: 116 peptides, 17 chains. Longest chain 19 peptides. Score 0.533 Taking the results from Round 4 Chains 14, Residues 94, Estimated correctness of the model 16.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3033 restraints for refining 1384 atoms. 2671 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3408 (Rfree = 0.000) for 1384 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 22: After refmac, R = 0.3254 (Rfree = 0.000) for 1372 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 23: After refmac, R = 0.2954 (Rfree = 0.000) for 1360 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.2888 (Rfree = 0.000) for 1358 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2861 (Rfree = 0.000) for 1355 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 1390 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 1424 seeds are put forward Round 1: 93 peptides, 18 chains. Longest chain 10 peptides. Score 0.342 Round 2: 103 peptides, 17 chains. Longest chain 14 peptides. Score 0.448 Round 3: 110 peptides, 16 chains. Longest chain 17 peptides. Score 0.523 Round 4: 105 peptides, 14 chains. Longest chain 15 peptides. Score 0.547 Round 5: 111 peptides, 15 chains. Longest chain 16 peptides. Score 0.556 Taking the results from Round 5 Chains 15, Residues 96, Estimated correctness of the model 13.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3124 restraints for refining 1396 atoms. 2755 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3383 (Rfree = 0.000) for 1396 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 27: After refmac, R = 0.3287 (Rfree = 0.000) for 1384 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 28: After refmac, R = 0.3134 (Rfree = 0.000) for 1376 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.3081 (Rfree = 0.000) for 1375 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.3141 (Rfree = 0.000) for 1375 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 1431 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 1445 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 10 peptides. Score 0.324 Round 2: 89 peptides, 13 chains. Longest chain 16 peptides. Score 0.472 Round 3: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.389 Round 4: 87 peptides, 13 chains. Longest chain 14 peptides. Score 0.458 Round 5: 84 peptides, 14 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 2 Chains 13, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3174 restraints for refining 1395 atoms. 2883 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3274 (Rfree = 0.000) for 1395 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 32: After refmac, R = 0.3336 (Rfree = 0.000) for 1390 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 33: After refmac, R = 0.3199 (Rfree = 0.000) for 1383 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.3146 (Rfree = 0.000) for 1383 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.3176 (Rfree = 0.000) for 1382 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 1418 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1442 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 11 peptides. Score 0.324 Round 2: 80 peptides, 13 chains. Longest chain 17 peptides. Score 0.407 Round 3: 82 peptides, 12 chains. Longest chain 21 peptides. Score 0.454 Round 4: 81 peptides, 14 chains. Longest chain 12 peptides. Score 0.381 Round 5: 89 peptides, 13 chains. Longest chain 23 peptides. Score 0.472 Taking the results from Round 5 Chains 13, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3256 restraints for refining 1396 atoms. 2965 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3496 (Rfree = 0.000) for 1396 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.3364 (Rfree = 0.000) for 1390 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 38: After refmac, R = 0.3494 (Rfree = 0.000) for 1380 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 39: After refmac, R = 0.3194 (Rfree = 0.000) for 1374 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.3459 (Rfree = 0.000) for 1370 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 1401 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 1429 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.320 Round 2: 77 peptides, 12 chains. Longest chain 15 peptides. Score 0.417 Round 3: 72 peptides, 9 chains. Longest chain 19 peptides. Score 0.480 Round 4: 72 peptides, 9 chains. Longest chain 13 peptides. Score 0.480 Round 5: 71 peptides, 9 chains. Longest chain 19 peptides. Score 0.473 Taking the results from Round 4 Chains 9, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3317 reflections ( 99.88 % complete ) and 3283 restraints for refining 1386 atoms. 3040 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3346 (Rfree = 0.000) for 1386 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 42: After refmac, R = 0.3104 (Rfree = 0.000) for 1382 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 43: After refmac, R = 0.3172 (Rfree = 0.000) for 1373 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.3004 (Rfree = 0.000) for 1371 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.3176 (Rfree = 0.000) for 1369 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.26 Search for helices and strands: 0 residues in 0 chains, 1390 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1405 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 10 peptides. Score 0.295 Round 2: 71 peptides, 11 chains. Longest chain 13 peptides. Score 0.406 Round 3: 76 peptides, 12 chains. Longest chain 13 peptides. Score 0.410 Round 4: 73 peptides, 12 chains. Longest chain 13 peptides. Score 0.387 Round 5: 78 peptides, 11 chains. Longest chain 14 peptides. Score 0.458 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 67, 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 1o6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3317 reflections ( 99.88 % complete ) and 3228 restraints for refining 1392 atoms. 2971 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3120 (Rfree = 0.000) for 1392 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2911 (Rfree = 0.000) for 1381 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2957 (Rfree = 0.000) for 1372 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2858 (Rfree = 0.000) for 1364 atoms. TimeTaking 25.8