Sun 23 Dec 22:22:44 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2isb-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2isb-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2isb-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:53 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/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.8-parrot-hancs/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 134 and 0 Target number of residues in the AU: 134 Target solvent content: 0.6555 Checking the provided sequence file Detected sequence length: 192 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 192 Adjusted target solvent content: 0.51 Input MTZ file: 2isb-3.8-parrot-hancs.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: 96 Cell parameters: 51.664 51.664 157.756 90.000 90.000 90.000 Input sequence file: 2isb-3.8-parrot-hancs.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 Loops will be built when appropriate and at the last cycle Resolution range: 49.098 3.800 Wilson plot Bfac: 80.75 2387 reflections ( 99.05 % complete ) and 0 restraints for refining 1692 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3427 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3463 (Rfree = 0.000) for 1692 atoms. Found 9 (9 requested) and removed 135 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.58 Search for helices and strands: 0 residues in 0 chains, 1599 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.312 Round 2: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.426 Round 3: 110 peptides, 14 chains. Longest chain 13 peptides. Score 0.583 Round 4: 111 peptides, 16 chains. Longest chain 13 peptides. Score 0.534 Round 5: 121 peptides, 15 chains. Longest chain 23 peptides. Score 0.619 Taking the results from Round 5 Chains 17, Residues 106, Estimated correctness of the model 7.5 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2387 reflections ( 99.05 % complete ) and 2987 restraints for refining 1389 atoms. 2547 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3026 (Rfree = 0.000) for 1389 atoms. Found 7 (7 requested) and removed 57 (3 requested) atoms. Cycle 2: After refmac, R = 0.3041 (Rfree = 0.000) for 1313 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 3: After refmac, R = 0.3027 (Rfree = 0.000) for 1291 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 4: After refmac, R = 0.3169 (Rfree = 0.000) for 1273 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 5: After refmac, R = 0.2956 (Rfree = 0.000) for 1256 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.61 Search for helices and strands: 0 residues in 0 chains, 1307 seeds are put forward Round 1: 87 peptides, 15 chains. Longest chain 9 peptides. Score 0.398 Round 2: 105 peptides, 15 chains. Longest chain 13 peptides. Score 0.524 Round 3: 113 peptides, 15 chains. Longest chain 21 peptides. Score 0.574 Round 4: 108 peptides, 14 chains. Longest chain 14 peptides. Score 0.571 Round 5: 110 peptides, 15 chains. Longest chain 14 peptides. Score 0.556 Taking the results from Round 3 Chains 16, Residues 98, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2387 reflections ( 99.05 % complete ) and 2920 restraints for refining 1373 atoms. 2475 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2979 (Rfree = 0.000) for 1373 atoms. Found 7 (7 requested) and removed 151 (3 requested) atoms. Cycle 7: After refmac, R = 0.3112 (Rfree = 0.000) for 1216 atoms. Found 6 (6 requested) and removed 39 (3 requested) atoms. Cycle 8: After refmac, R = 0.3002 (Rfree = 0.000) for 1179 atoms. Found 5 (6 requested) and removed 14 (3 requested) atoms. Cycle 9: After refmac, R = 0.3023 (Rfree = 0.000) for 1159 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 10: After refmac, R = 0.2876 (Rfree = 0.000) for 1142 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 1185 seeds are put forward Round 1: 83 peptides, 14 chains. Longest chain 9 peptides. Score 0.400 Round 2: 89 peptides, 13 chains. Longest chain 12 peptides. Score 0.476 Round 3: 102 peptides, 15 chains. Longest chain 13 peptides. Score 0.505 Round 4: 98 peptides, 12 chains. Longest chain 17 peptides. Score 0.565 Round 5: 96 peptides, 11 chains. Longest chain 22 peptides. Score 0.581 Taking the results from Round 5 Chains 11, Residues 85, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2387 reflections ( 99.05 % complete ) and 2753 restraints for refining 1282 atoms. 2394 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2767 (Rfree = 0.000) for 1282 atoms. Found 4 (7 requested) and removed 15 (3 requested) atoms. Cycle 12: After refmac, R = 0.2640 (Rfree = 0.000) for 1265 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 13: After refmac, R = 0.2613 (Rfree = 0.000) for 1257 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.2568 (Rfree = 0.000) for 1254 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2558 (Rfree = 0.000) for 1249 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 3.61 Search for helices and strands: 0 residues in 0 chains, 1266 seeds are put forward Round 1: 92 peptides, 16 chains. Longest chain 12 peptides. Score 0.403 Round 2: 94 peptides, 12 chains. Longest chain 17 peptides. Score 0.540 Round 3: 107 peptides, 18 chains. Longest chain 13 peptides. Score 0.450 Round 4: 102 peptides, 15 chains. Longest chain 20 peptides. Score 0.505 Round 5: 111 peptides, 18 chains. Longest chain 14 peptides. Score 0.477 Taking the results from Round 2 Chains 12, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2387 reflections ( 99.05 % complete ) and 2941 restraints for refining 1312 atoms. 2625 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3102 (Rfree = 0.000) for 1312 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.2997 (Rfree = 0.000) for 1305 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 18: After refmac, R = 0.3083 (Rfree = 0.000) for 1288 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 19: After refmac, R = 0.2479 (Rfree = 0.000) for 1277 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. Cycle 20: After refmac, R = 0.2381 (Rfree = 0.000) for 1272 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 1299 seeds are put forward Round 1: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.334 Round 2: 94 peptides, 16 chains. Longest chain 15 peptides. Score 0.418 Round 3: 100 peptides, 12 chains. Longest chain 18 peptides. Score 0.577 Round 4: 101 peptides, 16 chains. Longest chain 13 peptides. Score 0.468 Round 5: 101 peptides, 15 chains. Longest chain 19 peptides. Score 0.498 Taking the results from Round 3 Chains 14, Residues 88, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2387 reflections ( 99.05 % complete ) and 2991 restraints for refining 1370 atoms. 2606 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2915 (Rfree = 0.000) for 1370 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 22: After refmac, R = 0.2830 (Rfree = 0.000) for 1355 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2854 (Rfree = 0.000) for 1350 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 24: After refmac, R = 0.2586 (Rfree = 0.000) for 1341 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 25: After refmac, R = 0.2345 (Rfree = 0.000) for 1335 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.58 Search for helices and strands: 0 residues in 0 chains, 1364 seeds are put forward Round 1: 82 peptides, 16 chains. Longest chain 11 peptides. Score 0.324 Round 2: 83 peptides, 12 chains. Longest chain 13 peptides. Score 0.465 Round 3: 86 peptides, 13 chains. Longest chain 12 peptides. Score 0.455 Round 4: 83 peptides, 10 chains. Longest chain 18 peptides. Score 0.528 Round 5: 76 peptides, 12 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 4 Chains 10, Residues 73, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2387 reflections ( 99.05 % complete ) and 2991 restraints for refining 1389 atoms. 2629 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3183 (Rfree = 0.000) for 1389 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 27: After refmac, R = 0.3013 (Rfree = 0.000) for 1374 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.2439 (Rfree = 0.000) for 1370 atoms. Found 5 (7 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.2427 (Rfree = 0.000) for 1359 atoms. Found 6 (7 requested) and removed 8 (3 requested) atoms. Cycle 30: After refmac, R = 0.2415 (Rfree = 0.000) for 1355 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.57 Search for helices and strands: 0 residues in 0 chains, 1403 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.339 Round 2: 86 peptides, 15 chains. Longest chain 8 peptides. Score 0.390 Round 3: 89 peptides, 16 chains. Longest chain 12 peptides. Score 0.380 Round 4: 93 peptides, 15 chains. Longest chain 11 peptides. Score 0.442 Round 5: 93 peptides, 16 chains. Longest chain 12 peptides. Score 0.410 Taking the results from Round 4 Chains 15, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2387 reflections ( 99.05 % complete ) and 3222 restraints for refining 1389 atoms. 2925 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2625 (Rfree = 0.000) for 1389 atoms. Found 6 (7 requested) and removed 10 (3 requested) atoms. Cycle 32: After refmac, R = 0.2458 (Rfree = 0.000) for 1379 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 33: After refmac, R = 0.2371 (Rfree = 0.000) for 1375 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.2307 (Rfree = 0.000) for 1370 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.2288 (Rfree = 0.000) for 1367 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 1398 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 7 peptides. Score 0.293 Round 2: 90 peptides, 12 chains. Longest chain 17 peptides. Score 0.514 Round 3: 89 peptides, 14 chains. Longest chain 12 peptides. Score 0.445 Round 4: 97 peptides, 14 chains. Longest chain 14 peptides. Score 0.501 Round 5: 95 peptides, 14 chains. Longest chain 16 peptides. Score 0.487 Taking the results from Round 2 Chains 12, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2387 reflections ( 99.05 % complete ) and 3219 restraints for refining 1389 atoms. 2919 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2500 (Rfree = 0.000) for 1389 atoms. Found 2 (7 requested) and removed 57 (3 requested) atoms. Cycle 37: After refmac, R = 0.2453 (Rfree = 0.000) for 1332 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2395 (Rfree = 0.000) for 1330 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.2403 (Rfree = 0.000) for 1329 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.2350 (Rfree = 0.000) for 1325 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.58 Search for helices and strands: 0 residues in 0 chains, 1335 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 6 peptides. Score 0.242 Round 2: 71 peptides, 11 chains. Longest chain 15 peptides. Score 0.409 Round 3: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.363 Round 4: 77 peptides, 12 chains. Longest chain 15 peptides. Score 0.421 Round 5: 76 peptides, 14 chains. Longest chain 8 peptides. Score 0.345 Taking the results from Round 4 Chains 12, Residues 65, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2387 reflections ( 99.05 % complete ) and 3232 restraints for refining 1389 atoms. 2958 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2449 (Rfree = 0.000) for 1389 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 42: After refmac, R = 0.2313 (Rfree = 0.000) for 1381 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.2238 (Rfree = 0.000) for 1379 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2315 (Rfree = 0.000) for 1371 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.2304 (Rfree = 0.000) for 1370 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.61 Search for helices and strands: 0 residues in 0 chains, 1394 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 7 peptides. Score 0.267 Round 2: 76 peptides, 12 chains. Longest chain 12 peptides. Score 0.414 Round 3: 80 peptides, 14 chains. Longest chain 8 peptides. Score 0.377 Round 4: 75 peptides, 12 chains. Longest chain 12 peptides. Score 0.406 Round 5: 80 peptides, 13 chains. Longest chain 10 peptides. Score 0.410 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 64, 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 2isb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2387 reflections ( 99.05 % complete ) and 3321 restraints for refining 1389 atoms. 3077 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2574 (Rfree = 0.000) for 1389 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2522 (Rfree = 0.000) for 1383 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2492 (Rfree = 0.000) for 1379 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2478 (Rfree = 0.000) for 1376 atoms. TimeTaking 27