null Mon 24 Dec 01:13:35 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1o6a-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1o6a-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-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 01:13:39 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/1o6a-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-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 136 and 0 Target number of residues in the AU: 136 Target solvent content: 0.6582 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-3.6-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-3.6-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 3.601 Wilson plot Bfac: 83.20 2821 reflections ( 99.86 % complete ) and 0 restraints for refining 1705 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.4273 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4140 (Rfree = 0.000) for 1705 atoms. Found 10 (10 requested) and removed 31 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 1699 seeds are put forward NCS extension: 0 residues added, 1699 seeds are put forward Round 1: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.328 Round 2: 92 peptides, 12 chains. Longest chain 14 peptides. Score 0.522 Round 3: 99 peptides, 14 chains. Longest chain 16 peptides. Score 0.509 Round 4: 110 peptides, 12 chains. Longest chain 18 peptides. Score 0.628 Round 5: 108 peptides, 14 chains. Longest chain 15 peptides. Score 0.565 Taking the results from Round 4 Chains 12, Residues 98, Estimated correctness of the model 25.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3153 restraints for refining 1388 atoms. 2773 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3885 (Rfree = 0.000) for 1388 atoms. Found 6 (8 requested) and removed 25 (4 requested) atoms. Cycle 2: After refmac, R = 0.3370 (Rfree = 0.000) for 1345 atoms. Found 3 (8 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.3200 (Rfree = 0.000) for 1328 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.3451 (Rfree = 0.000) for 1322 atoms. Found 3 (8 requested) and removed 13 (4 requested) atoms. Cycle 5: After refmac, R = 0.3075 (Rfree = 0.000) for 1298 atoms. Found 0 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.40 Search for helices and strands: 0 residues in 0 chains, 1332 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1354 seeds are put forward Round 1: 112 peptides, 18 chains. Longest chain 13 peptides. Score 0.479 Round 2: 112 peptides, 15 chains. Longest chain 14 peptides. Score 0.562 Round 3: 104 peptides, 12 chains. Longest chain 16 peptides. Score 0.595 Round 4: 105 peptides, 9 chains. Longest chain 31 peptides. Score 0.675 Round 5: 100 peptides, 10 chains. Longest chain 25 peptides. Score 0.625 Taking the results from Round 4 Chains 9, Residues 96, Estimated correctness of the model 41.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3004 restraints for refining 1339 atoms. 2629 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3227 (Rfree = 0.000) for 1339 atoms. Found 4 (8 requested) and removed 25 (4 requested) atoms. Cycle 7: After refmac, R = 0.3060 (Rfree = 0.000) for 1312 atoms. Found 5 (8 requested) and removed 11 (4 requested) atoms. Cycle 8: After refmac, R = 0.2962 (Rfree = 0.000) for 1302 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2897 (Rfree = 0.000) for 1299 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.2841 (Rfree = 0.000) for 1293 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 1318 seeds are put forward NCS extension: 28 residues added (12 deleted due to clashes), 1346 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 16 peptides. Score 0.412 Round 2: 106 peptides, 16 chains. Longest chain 23 peptides. Score 0.497 Round 3: 100 peptides, 13 chains. Longest chain 20 peptides. Score 0.544 Round 4: 111 peptides, 13 chains. Longest chain 23 peptides. Score 0.609 Round 5: 106 peptides, 14 chains. Longest chain 16 peptides. Score 0.553 Taking the results from Round 4 Chains 13, Residues 98, Estimated correctness of the model 18.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 2962 restraints for refining 1343 atoms. 2583 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3113 (Rfree = 0.000) for 1343 atoms. Found 5 (8 requested) and removed 13 (4 requested) atoms. Cycle 12: After refmac, R = 0.3021 (Rfree = 0.000) for 1324 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.2947 (Rfree = 0.000) for 1311 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2807 (Rfree = 0.000) for 1301 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.2841 (Rfree = 0.000) for 1290 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 1313 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 1343 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 8 peptides. Score 0.412 Round 2: 99 peptides, 11 chains. Longest chain 17 peptides. Score 0.593 Round 3: 105 peptides, 16 chains. Longest chain 16 peptides. Score 0.491 Round 4: 107 peptides, 16 chains. Longest chain 15 peptides. Score 0.504 Round 5: 104 peptides, 15 chains. Longest chain 19 peptides. Score 0.513 Taking the results from Round 2 Chains 11, Residues 88, Estimated correctness of the model 11.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 2902 restraints for refining 1293 atoms. 2561 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3370 (Rfree = 0.000) for 1293 atoms. Found 4 (8 requested) and removed 18 (4 requested) atoms. Cycle 17: After refmac, R = 0.2869 (Rfree = 0.000) for 1274 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 18: After refmac, R = 0.2765 (Rfree = 0.000) for 1267 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.2802 (Rfree = 0.000) for 1261 atoms. Found 1 (8 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.2628 (Rfree = 0.000) for 1250 atoms. Found 0 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 1274 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 1300 seeds are put forward Round 1: 77 peptides, 12 chains. Longest chain 9 peptides. Score 0.417 Round 2: 87 peptides, 12 chains. Longest chain 15 peptides. Score 0.489 Round 3: 90 peptides, 13 chains. Longest chain 13 peptides. Score 0.479 Round 4: 92 peptides, 13 chains. Longest chain 13 peptides. Score 0.492 Round 5: 89 peptides, 13 chains. Longest chain 13 peptides. Score 0.472 Taking the results from Round 4 Chains 13, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3097 restraints for refining 1326 atoms. 2794 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3084 (Rfree = 0.000) for 1326 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 22: After refmac, R = 0.3107 (Rfree = 0.000) for 1295 atoms. Found 7 (8 requested) and removed 22 (4 requested) atoms. Cycle 23: After refmac, R = 0.3232 (Rfree = 0.000) for 1278 atoms. Found 7 (8 requested) and removed 12 (4 requested) atoms. Cycle 24: After refmac, R = 0.3157 (Rfree = 0.000) for 1268 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 25: After refmac, R = 0.3065 (Rfree = 0.000) for 1257 atoms. Found 3 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.39 Search for helices and strands: 0 residues in 0 chains, 1291 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1308 seeds are put forward Round 1: 82 peptides, 15 chains. Longest chain 14 peptides. Score 0.356 Round 2: 93 peptides, 16 chains. Longest chain 18 peptides. Score 0.407 Round 3: 89 peptides, 13 chains. Longest chain 19 peptides. Score 0.472 Round 4: 87 peptides, 15 chains. Longest chain 14 peptides. Score 0.394 Round 5: 93 peptides, 15 chains. Longest chain 14 peptides. Score 0.438 Taking the results from Round 3 Chains 13, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 2985 restraints for refining 1307 atoms. 2694 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3448 (Rfree = 0.000) for 1307 atoms. Found 5 (8 requested) and removed 17 (4 requested) atoms. Cycle 27: After refmac, R = 0.3160 (Rfree = 0.000) for 1288 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.3046 (Rfree = 0.000) for 1277 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.3205 (Rfree = 0.000) for 1268 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 30: After refmac, R = 0.3061 (Rfree = 0.000) for 1260 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 1306 seeds are put forward NCS extension: 0 residues added, 1306 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 6 peptides. Score 0.266 Round 2: 83 peptides, 16 chains. Longest chain 7 peptides. Score 0.330 Round 3: 79 peptides, 14 chains. Longest chain 8 peptides. Score 0.366 Round 4: 84 peptides, 14 chains. Longest chain 9 peptides. Score 0.404 Round 5: 73 peptides, 13 chains. Longest chain 11 peptides. Score 0.353 Taking the results from Round 4 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3017 restraints for refining 1318 atoms. 2751 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3182 (Rfree = 0.000) for 1318 atoms. Found 3 (8 requested) and removed 15 (4 requested) atoms. Cycle 32: After refmac, R = 0.3181 (Rfree = 0.000) for 1300 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 33: After refmac, R = 0.3240 (Rfree = 0.000) for 1292 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.3107 (Rfree = 0.000) for 1292 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 35: After refmac, R = 0.3281 (Rfree = 0.000) for 1287 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 1325 seeds are put forward NCS extension: 0 residues added, 1325 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.274 Round 2: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.299 Round 3: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.359 Round 4: 80 peptides, 14 chains. Longest chain 10 peptides. Score 0.374 Round 5: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.412 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 ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3023 restraints for refining 1326 atoms. 2753 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3198 (Rfree = 0.000) for 1326 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. Cycle 37: After refmac, R = 0.3206 (Rfree = 0.000) for 1305 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 38: After refmac, R = 0.3088 (Rfree = 0.000) for 1291 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 39: After refmac, R = 0.3274 (Rfree = 0.000) for 1286 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 40: After refmac, R = 0.3004 (Rfree = 0.000) for 1277 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 1316 seeds are put forward NCS extension: 4 residues added (2 deleted due to clashes), 1320 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 5 peptides. Score 0.204 Round 2: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.361 Round 3: 69 peptides, 12 chains. Longest chain 11 peptides. Score 0.355 Round 4: 72 peptides, 11 chains. Longest chain 12 peptides. Score 0.413 Round 5: 73 peptides, 12 chains. Longest chain 12 peptides. Score 0.387 Taking the results from Round 4 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 2954 restraints for refining 1294 atoms. 2721 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3131 (Rfree = 0.000) for 1294 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 42: After refmac, R = 0.3108 (Rfree = 0.000) for 1280 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 43: After refmac, R = 0.3036 (Rfree = 0.000) for 1266 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.3018 (Rfree = 0.000) for 1262 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 45: After refmac, R = 0.2865 (Rfree = 0.000) for 1256 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 1301 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 1309 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.225 Round 2: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.278 Round 3: 70 peptides, 12 chains. Longest chain 12 peptides. Score 0.363 Round 4: 74 peptides, 12 chains. Longest chain 13 peptides. Score 0.395 Round 5: 77 peptides, 13 chains. Longest chain 13 peptides. Score 0.384 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 62, 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. 2821 reflections ( 99.86 % complete ) and 2808 restraints for refining 1270 atoms. 2572 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3360 (Rfree = 0.000) for 1270 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3163 (Rfree = 0.000) for 1259 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3219 (Rfree = 0.000) for 1252 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3195 (Rfree = 0.000) for 1247 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:35:01 GMT 2018 Job finished. TimeTaking 21.44 Used memory is bytes: 19290648