null Sun 23 Dec 22:22:43 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2isb-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2isb-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.4-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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2isb-3.4-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 142 and 0 Target number of residues in the AU: 142 Target solvent content: 0.6350 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-3.4-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-3.4-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 3.401 Wilson plot Bfac: 67.85 3273 reflections ( 99.30 % complete ) and 0 restraints for refining 1721 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3251 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3091 (Rfree = 0.000) for 1721 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 1746 seeds are put forward Round 1: 109 peptides, 20 chains. Longest chain 10 peptides. Score 0.403 Round 2: 131 peptides, 15 chains. Longest chain 25 peptides. Score 0.670 Round 3: 129 peptides, 12 chains. Longest chain 36 peptides. Score 0.724 Round 4: 134 peptides, 12 chains. Longest chain 23 peptides. Score 0.744 Round 5: 139 peptides, 15 chains. Longest chain 23 peptides. Score 0.706 Taking the results from Round 4 Chains 15, Residues 122, Estimated correctness of the model 68.5 % 3 chains (42 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 86 A 13 chains (131 residues) following loop building 2 chains (52 residues) in sequence following loop building ------------------------------------------------------ 3273 reflections ( 99.30 % complete ) and 2397 restraints for refining 1396 atoms. 1693 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3204 (Rfree = 0.000) for 1396 atoms. Found 10 (10 requested) and removed 39 (5 requested) atoms. Cycle 2: After refmac, R = 0.2728 (Rfree = 0.000) for 1338 atoms. Found 9 (10 requested) and removed 17 (5 requested) atoms. Cycle 3: After refmac, R = 0.2708 (Rfree = 0.000) for 1316 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.3079 (Rfree = 0.000) for 1310 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 5: After refmac, R = 0.2588 (Rfree = 0.000) for 1296 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 1336 seeds are put forward Round 1: 127 peptides, 14 chains. Longest chain 21 peptides. Score 0.673 Round 2: 132 peptides, 12 chains. Longest chain 30 peptides. Score 0.736 Round 3: 138 peptides, 12 chains. Longest chain 25 peptides. Score 0.759 Round 4: 141 peptides, 14 chains. Longest chain 22 peptides. Score 0.734 Round 5: 140 peptides, 13 chains. Longest chain 21 peptides. Score 0.748 Taking the results from Round 3 Chains 14, Residues 126, Estimated correctness of the model 71.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3273 reflections ( 99.30 % complete ) and 2734 restraints for refining 1353 atoms. 2202 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2792 (Rfree = 0.000) for 1353 atoms. Found 6 (9 requested) and removed 10 (5 requested) atoms. Cycle 7: After refmac, R = 0.2617 (Rfree = 0.000) for 1341 atoms. Found 5 (9 requested) and removed 5 (5 requested) atoms. Cycle 8: After refmac, R = 0.2656 (Rfree = 0.000) for 1338 atoms. Found 8 (9 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2463 (Rfree = 0.000) for 1336 atoms. Found 4 (8 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.2458 (Rfree = 0.000) for 1329 atoms. Found 7 (8 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 1375 seeds are put forward Round 1: 120 peptides, 16 chains. Longest chain 16 peptides. Score 0.589 Round 2: 127 peptides, 13 chains. Longest chain 20 peptides. Score 0.695 Round 3: 134 peptides, 14 chains. Longest chain 17 peptides. Score 0.705 Round 4: 119 peptides, 11 chains. Longest chain 33 peptides. Score 0.701 Round 5: 127 peptides, 16 chains. Longest chain 18 peptides. Score 0.627 Taking the results from Round 3 Chains 15, Residues 120, Estimated correctness of the model 59.1 % 2 chains (17 residues) have been docked in sequence Building loops using Loopy2018 15 chains (120 residues) following loop building 2 chains (17 residues) in sequence following loop building ------------------------------------------------------ 3273 reflections ( 99.30 % complete ) and 2854 restraints for refining 1396 atoms. 2324 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2722 (Rfree = 0.000) for 1396 atoms. Found 8 (8 requested) and removed 76 (5 requested) atoms. Cycle 12: After refmac, R = 0.2594 (Rfree = 0.000) for 1323 atoms. Found 6 (8 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.2525 (Rfree = 0.000) for 1320 atoms. Found 7 (7 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2463 (Rfree = 0.000) for 1316 atoms. Found 7 (7 requested) and removed 10 (4 requested) atoms. Cycle 15: After refmac, R = 0.2501 (Rfree = 0.000) for 1310 atoms. Found 6 (6 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 1344 seeds are put forward Round 1: 111 peptides, 15 chains. Longest chain 16 peptides. Score 0.562 Round 2: 121 peptides, 15 chains. Longest chain 20 peptides. Score 0.619 Round 3: 126 peptides, 12 chains. Longest chain 21 peptides. Score 0.711 Round 4: 132 peptides, 13 chains. Longest chain 21 peptides. Score 0.716 Round 5: 137 peptides, 12 chains. Longest chain 39 peptides. Score 0.755 Taking the results from Round 5 Chains 13, Residues 125, Estimated correctness of the model 70.9 % 2 chains (22 residues) have been docked in sequence Building loops using Loopy2018 13 chains (125 residues) following loop building 2 chains (22 residues) in sequence following loop building ------------------------------------------------------ 3273 reflections ( 99.30 % complete ) and 2727 restraints for refining 1396 atoms. 2159 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2723 (Rfree = 0.000) for 1396 atoms. Found 7 (7 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.2549 (Rfree = 0.000) for 1381 atoms. Found 6 (7 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.2548 (Rfree = 0.000) for 1369 atoms. Found 7 (7 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2387 (Rfree = 0.000) for 1366 atoms. Found 3 (6 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.2467 (Rfree = 0.000) for 1361 atoms. Found 6 (6 requested) and removed 43 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 1353 seeds are put forward Round 1: 102 peptides, 13 chains. Longest chain 18 peptides. Score 0.562 Round 2: 114 peptides, 13 chains. Longest chain 19 peptides. Score 0.631 Round 3: 117 peptides, 12 chains. Longest chain 20 peptides. Score 0.670 Round 4: 118 peptides, 13 chains. Longest chain 19 peptides. Score 0.651 Round 5: 110 peptides, 14 chains. Longest chain 17 peptides. Score 0.583 Taking the results from Round 3 Chains 12, Residues 105, Estimated correctness of the model 49.8 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3273 reflections ( 99.30 % complete ) and 2894 restraints for refining 1373 atoms. 2472 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2556 (Rfree = 0.000) for 1373 atoms. Found 6 (6 requested) and removed 8 (5 requested) atoms. Cycle 22: After refmac, R = 0.2681 (Rfree = 0.000) for 1368 atoms. Found 6 (6 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.2327 (Rfree = 0.000) for 1363 atoms. Found 4 (6 requested) and removed 24 (5 requested) atoms. Cycle 24: After refmac, R = 0.2261 (Rfree = 0.000) for 1342 atoms. Found 2 (6 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2243 (Rfree = 0.000) for 1338 atoms. Found 3 (6 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 1381 seeds are put forward Round 1: 107 peptides, 16 chains. Longest chain 15 peptides. Score 0.509 Round 2: 112 peptides, 12 chains. Longest chain 18 peptides. Score 0.644 Round 3: 124 peptides, 16 chains. Longest chain 14 peptides. Score 0.611 Round 4: 117 peptides, 13 chains. Longest chain 21 peptides. Score 0.646 Round 5: 125 peptides, 11 chains. Longest chain 22 peptides. Score 0.727 Taking the results from Round 5 Chains 12, Residues 114, Estimated correctness of the model 64.5 % 2 chains (30 residues) have been docked in sequence Building loops using Loopy2018 12 chains (114 residues) following loop building 2 chains (30 residues) in sequence following loop building ------------------------------------------------------ 3273 reflections ( 99.30 % complete ) and 2720 restraints for refining 1396 atoms. 2161 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2834 (Rfree = 0.000) for 1396 atoms. Found 6 (6 requested) and removed 21 (5 requested) atoms. Cycle 27: After refmac, R = 0.2622 (Rfree = 0.000) for 1375 atoms. Found 6 (6 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2482 (Rfree = 0.000) for 1364 atoms. Found 5 (6 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2490 (Rfree = 0.000) for 1360 atoms. Found 5 (5 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.2414 (Rfree = 0.000) for 1359 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.31 Search for helices and strands: 0 residues in 0 chains, 1387 seeds are put forward Round 1: 103 peptides, 16 chains. Longest chain 13 peptides. Score 0.482 Round 2: 118 peptides, 14 chains. Longest chain 22 peptides. Score 0.627 Round 3: 109 peptides, 13 chains. Longest chain 28 peptides. Score 0.603 Round 4: 122 peptides, 14 chains. Longest chain 21 peptides. Score 0.648 Round 5: 120 peptides, 16 chains. Longest chain 21 peptides. Score 0.589 Taking the results from Round 4 Chains 15, Residues 108, Estimated correctness of the model 43.5 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3273 reflections ( 99.30 % complete ) and 2791 restraints for refining 1396 atoms. 2288 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2629 (Rfree = 0.000) for 1396 atoms. Found 5 (5 requested) and removed 13 (5 requested) atoms. Cycle 32: After refmac, R = 0.2566 (Rfree = 0.000) for 1384 atoms. Found 5 (5 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.2767 (Rfree = 0.000) for 1383 atoms. Found 5 (5 requested) and removed 11 (5 requested) atoms. Cycle 34: After refmac, R = 0.2583 (Rfree = 0.000) for 1371 atoms. Found 5 (5 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2440 (Rfree = 0.000) for 1371 atoms. Found 4 (5 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 1402 seeds are put forward Round 1: 106 peptides, 13 chains. Longest chain 16 peptides. Score 0.586 Round 2: 116 peptides, 14 chains. Longest chain 23 peptides. Score 0.617 Round 3: 119 peptides, 15 chains. Longest chain 18 peptides. Score 0.608 Round 4: 120 peptides, 13 chains. Longest chain 16 peptides. Score 0.661 Round 5: 131 peptides, 14 chains. Longest chain 28 peptides. Score 0.692 Taking the results from Round 5 Chains 15, Residues 117, Estimated correctness of the model 55.7 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3273 reflections ( 99.30 % complete ) and 2857 restraints for refining 1396 atoms. 2358 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2646 (Rfree = 0.000) for 1396 atoms. Found 5 (5 requested) and removed 6 (5 requested) atoms. Cycle 37: After refmac, R = 0.2610 (Rfree = 0.000) for 1387 atoms. Found 5 (5 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2659 (Rfree = 0.000) for 1377 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2814 (Rfree = 0.000) for 1372 atoms. Found 5 (5 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2583 (Rfree = 0.000) for 1366 atoms. Found 5 (5 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 1392 seeds are put forward Round 1: 112 peptides, 15 chains. Longest chain 20 peptides. Score 0.568 Round 2: 119 peptides, 13 chains. Longest chain 21 peptides. Score 0.656 Round 3: 121 peptides, 15 chains. Longest chain 21 peptides. Score 0.619 Round 4: 121 peptides, 14 chains. Longest chain 21 peptides. Score 0.643 Round 5: 129 peptides, 13 chains. Longest chain 21 peptides. Score 0.703 Taking the results from Round 5 Chains 14, Residues 116, Estimated correctness of the model 58.6 % 3 chains (33 residues) have been docked in sequence Building loops using Loopy2018 14 chains (116 residues) following loop building 3 chains (33 residues) in sequence following loop building ------------------------------------------------------ 3273 reflections ( 99.30 % complete ) and 2668 restraints for refining 1396 atoms. 2121 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2816 (Rfree = 0.000) for 1396 atoms. Found 5 (5 requested) and removed 11 (5 requested) atoms. Cycle 42: After refmac, R = 0.2851 (Rfree = 0.000) for 1375 atoms. Found 5 (5 requested) and removed 12 (5 requested) atoms. Cycle 43: After refmac, R = 0.2818 (Rfree = 0.000) for 1366 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.2622 (Rfree = 0.000) for 1364 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.2587 (Rfree = 0.000) for 1361 atoms. Found 5 (5 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 1391 seeds are put forward Round 1: 96 peptides, 15 chains. Longest chain 16 peptides. Score 0.464 Round 2: 108 peptides, 15 chains. Longest chain 18 peptides. Score 0.543 Round 3: 111 peptides, 15 chains. Longest chain 19 peptides. Score 0.562 Round 4: 111 peptides, 14 chains. Longest chain 14 peptides. Score 0.589 Round 5: 107 peptides, 15 chains. Longest chain 18 peptides. Score 0.537 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 97, Estimated correctness of the model 25.0 % 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. 3273 reflections ( 99.30 % complete ) and 3101 restraints for refining 1396 atoms. 2727 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3247 (Rfree = 0.000) for 1396 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2937 (Rfree = 0.000) for 1383 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.3339 (Rfree = 0.000) for 1373 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3035 (Rfree = 0.000) for 1356 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:31 GMT 2018 Job finished. TimeTaking 29.8 Used memory is bytes: 4741280