null Sun 23 Dec 22:22:42 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 2hh6-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-2.0-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/2hh6-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-2.0-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 22:22:51 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/2hh6-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-2.0-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 248 and 0 Target number of residues in the AU: 248 Target solvent content: 0.5392 Checking the provided sequence file Detected sequence length: 113 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 226 Adjusted target solvent content: 0.58 Input MTZ file: 2hh6-2.0-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: 179 Cell parameters: 93.536 93.536 115.318 90.000 90.000 120.000 Input sequence file: 2hh6-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1808 target number of atoms Had to go as low as 0.50 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 1 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: 81.005 2.040 Wilson plot Bfac: 32.34 19564 reflections ( 99.91 % complete ) and 0 restraints for refining 1999 atoms. Observations/parameters ratio is 2.45 ------------------------------------------------------ Starting model: R = 0.3310 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2723 (Rfree = 0.000) for 1999 atoms. Found 63 (64 requested) and removed 57 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.39 2.15 NCS extension: 0 residues added, 2005 seeds are put forward Round 1: 100 peptides, 10 chains. Longest chain 23 peptides. Score 0.544 Round 2: 115 peptides, 6 chains. Longest chain 41 peptides. Score 0.689 Round 3: 111 peptides, 5 chains. Longest chain 51 peptides. Score 0.694 Round 4: 111 peptides, 2 chains. Longest chain 88 peptides. Score 0.749 Round 5: 114 peptides, 4 chains. Longest chain 96 peptides. Score 0.723 Taking the results from Round 4 Chains 3, Residues 109, Estimated correctness of the model 94.0 % 2 chains (108 residues) have been docked in sequence Building loops using Loopy2018 3 chains (109 residues) following loop building 2 chains (108 residues) in sequence following loop building ------------------------------------------------------ 19564 reflections ( 99.91 % complete ) and 2256 restraints for refining 1677 atoms. 1358 conditional restraints added. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3147 (Rfree = 0.000) for 1677 atoms. Found 54 (54 requested) and removed 33 (27 requested) atoms. Cycle 2: After refmac, R = 0.2764 (Rfree = 0.000) for 1677 atoms. Found 53 (53 requested) and removed 30 (27 requested) atoms. Cycle 3: After refmac, R = 0.2569 (Rfree = 0.000) for 1659 atoms. Found 45 (53 requested) and removed 30 (27 requested) atoms. Cycle 4: After refmac, R = 0.2400 (Rfree = 0.000) for 1644 atoms. Found 51 (51 requested) and removed 27 (27 requested) atoms. Cycle 5: After refmac, R = 0.2276 (Rfree = 0.000) for 1646 atoms. Found 43 (49 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.28 2.05 NCS extension: 0 residues added, 1662 seeds are put forward Round 1: 110 peptides, 2 chains. Longest chain 89 peptides. Score 0.746 Round 2: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.766 Round 3: 104 peptides, 4 chains. Longest chain 64 peptides. Score 0.689 Round 4: 109 peptides, 3 chains. Longest chain 51 peptides. Score 0.725 Round 5: 108 peptides, 4 chains. Longest chain 32 peptides. Score 0.703 Taking the results from Round 2 Chains 1, Residues 110, Estimated correctness of the model 94.7 % 1 chains (110 residues) have been docked in sequence ------------------------------------------------------ 19564 reflections ( 99.91 % complete ) and 1843 restraints for refining 1511 atoms. 936 conditional restraints added. Observations/parameters ratio is 3.24 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2495 (Rfree = 0.000) for 1511 atoms. Found 43 (43 requested) and removed 24 (24 requested) atoms. Cycle 7: After refmac, R = 0.2366 (Rfree = 0.000) for 1516 atoms. Found 43 (43 requested) and removed 24 (24 requested) atoms. Cycle 8: After refmac, R = 0.2276 (Rfree = 0.000) for 1528 atoms. Found 42 (42 requested) and removed 24 (24 requested) atoms. Cycle 9: After refmac, R = 0.2202 (Rfree = 0.000) for 1534 atoms. Found 42 (42 requested) and removed 25 (25 requested) atoms. Cycle 10: After refmac, R = 0.2181 (Rfree = 0.000) for 1544 atoms. Found 41 (41 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.29 2.06 NCS extension: 0 residues added, 1560 seeds are put forward Round 1: 109 peptides, 2 chains. Longest chain 95 peptides. Score 0.743 Round 2: 108 peptides, 3 chains. Longest chain 52 peptides. Score 0.721 Round 3: 103 peptides, 4 chains. Longest chain 51 peptides. Score 0.685 Round 4: 109 peptides, 3 chains. Longest chain 67 peptides. Score 0.725 Round 5: 104 peptides, 5 chains. Longest chain 62 peptides. Score 0.669 Taking the results from Round 1 Chains 3, Residues 107, Estimated correctness of the model 93.7 % 3 chains (107 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A 2 chains (109 residues) following loop building 2 chains (109 residues) in sequence following loop building ------------------------------------------------------ 19564 reflections ( 99.91 % complete ) and 1744 restraints for refining 1470 atoms. 851 conditional restraints added. Observations/parameters ratio is 3.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2450 (Rfree = 0.000) for 1470 atoms. Found 38 (38 requested) and removed 26 (23 requested) atoms. Cycle 12: After refmac, R = 0.2338 (Rfree = 0.000) for 1479 atoms. Found 37 (37 requested) and removed 23 (23 requested) atoms. Cycle 13: After refmac, R = 0.2282 (Rfree = 0.000) for 1487 atoms. Found 36 (36 requested) and removed 25 (24 requested) atoms. Cycle 14: After refmac, R = 0.2294 (Rfree = 0.000) for 1476 atoms. Found 36 (36 requested) and removed 24 (24 requested) atoms. Cycle 15: After refmac, R = 0.2222 (Rfree = 0.000) for 1478 atoms. Found 35 (35 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.28 2.05 NCS extension: 0 residues added, 1489 seeds are put forward Round 1: 111 peptides, 1 chains. Longest chain 111 peptides. Score 0.766 Round 2: 109 peptides, 2 chains. Longest chain 60 peptides. Score 0.743 Round 3: 108 peptides, 4 chains. Longest chain 52 peptides. Score 0.703 Round 4: 110 peptides, 3 chains. Longest chain 67 peptides. Score 0.728 Round 5: 106 peptides, 6 chains. Longest chain 49 peptides. Score 0.656 Taking the results from Round 1 Chains 1, Residues 110, Estimated correctness of the model 94.7 % 1 chains (110 residues) have been docked in sequence ------------------------------------------------------ 19564 reflections ( 99.91 % complete ) and 1543 restraints for refining 1387 atoms. 636 conditional restraints added. Observations/parameters ratio is 3.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2412 (Rfree = 0.000) for 1387 atoms. Found 31 (31 requested) and removed 23 (22 requested) atoms. Cycle 17: After refmac, R = 0.2321 (Rfree = 0.000) for 1388 atoms. Found 31 (31 requested) and removed 22 (22 requested) atoms. Cycle 18: After refmac, R = 0.2257 (Rfree = 0.000) for 1391 atoms. Found 30 (30 requested) and removed 19 (22 requested) atoms. Cycle 19: After refmac, R = 0.2205 (Rfree = 0.000) for 1390 atoms. Found 29 (29 requested) and removed 21 (22 requested) atoms. Cycle 20: After refmac, R = 0.2205 (Rfree = 0.000) for 1386 atoms. Found 28 (28 requested) and removed 21 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.30 2.07 NCS extension: 0 residues added, 1393 seeds are put forward Round 1: 110 peptides, 2 chains. Longest chain 62 peptides. Score 0.746 Round 2: 110 peptides, 2 chains. Longest chain 65 peptides. Score 0.746 Round 3: 108 peptides, 4 chains. Longest chain 45 peptides. Score 0.703 Round 4: 106 peptides, 2 chains. Longest chain 79 peptides. Score 0.733 Round 5: 105 peptides, 3 chains. Longest chain 51 peptides. Score 0.711 Taking the results from Round 2 Chains 2, Residues 108, Estimated correctness of the model 93.9 % 2 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 49 A 1 chains (110 residues) following loop building 1 chains (110 residues) in sequence following loop building ------------------------------------------------------ 19564 reflections ( 99.91 % complete ) and 1456 restraints for refining 1334 atoms. 549 conditional restraints added. Observations/parameters ratio is 3.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2392 (Rfree = 0.000) for 1334 atoms. Found 26 (26 requested) and removed 23 (21 requested) atoms. Cycle 22: After refmac, R = 0.2274 (Rfree = 0.000) for 1330 atoms. Found 25 (25 requested) and removed 16 (21 requested) atoms. Cycle 23: After refmac, R = 0.2202 (Rfree = 0.000) for 1336 atoms. Found 24 (24 requested) and removed 13 (21 requested) atoms. Cycle 24: After refmac, R = 0.2164 (Rfree = 0.000) for 1342 atoms. Found 23 (23 requested) and removed 11 (21 requested) atoms. Cycle 25: After refmac, R = 0.2140 (Rfree = 0.000) for 1350 atoms. Found 23 (23 requested) and removed 15 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.28 2.05 NCS extension: 0 residues added, 1358 seeds are put forward Round 1: 110 peptides, 2 chains. Longest chain 104 peptides. Score 0.746 Round 2: 110 peptides, 2 chains. Longest chain 96 peptides. Score 0.746 Round 3: 109 peptides, 3 chains. Longest chain 60 peptides. Score 0.725 Round 4: 103 peptides, 5 chains. Longest chain 40 peptides. Score 0.665 Round 5: 109 peptides, 3 chains. Longest chain 60 peptides. Score 0.725 Taking the results from Round 2 Chains 2, Residues 108, Estimated correctness of the model 93.9 % 2 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A 1 chains (110 residues) following loop building 1 chains (110 residues) in sequence following loop building ------------------------------------------------------ 19564 reflections ( 99.91 % complete ) and 1408 restraints for refining 1313 atoms. 501 conditional restraints added. Observations/parameters ratio is 3.73 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2341 (Rfree = 0.000) for 1313 atoms. Found 22 (22 requested) and removed 21 (21 requested) atoms. Cycle 27: After refmac, R = 0.2242 (Rfree = 0.000) for 1305 atoms. Found 21 (21 requested) and removed 11 (21 requested) atoms. Cycle 28: After refmac, R = 0.2222 (Rfree = 0.000) for 1312 atoms. Found 21 (21 requested) and removed 17 (21 requested) atoms. Cycle 29: After refmac, R = 0.2189 (Rfree = 0.000) for 1311 atoms. Found 21 (21 requested) and removed 9 (21 requested) atoms. Cycle 30: After refmac, R = 0.2154 (Rfree = 0.000) for 1319 atoms. Found 21 (21 requested) and removed 9 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.28 2.05 NCS extension: 0 residues added, 1331 seeds are put forward Round 1: 110 peptides, 2 chains. Longest chain 97 peptides. Score 0.746 Round 2: 106 peptides, 2 chains. Longest chain 55 peptides. Score 0.733 Round 3: 109 peptides, 3 chains. Longest chain 81 peptides. Score 0.725 Round 4: 110 peptides, 2 chains. Longest chain 96 peptides. Score 0.746 Round 5: 105 peptides, 5 chains. Longest chain 47 peptides. Score 0.672 Taking the results from Round 4 Chains 2, Residues 108, Estimated correctness of the model 93.9 % 2 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A 1 chains (110 residues) following loop building 1 chains (110 residues) in sequence following loop building ------------------------------------------------------ 19564 reflections ( 99.91 % complete ) and 1429 restraints for refining 1308 atoms. 522 conditional restraints added. Observations/parameters ratio is 3.74 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2342 (Rfree = 0.000) for 1308 atoms. Found 21 (21 requested) and removed 22 (21 requested) atoms. Cycle 32: After refmac, R = 0.2225 (Rfree = 0.000) for 1301 atoms. Found 21 (21 requested) and removed 10 (21 requested) atoms. Cycle 33: After refmac, R = 0.2161 (Rfree = 0.000) for 1309 atoms. Found 21 (21 requested) and removed 4 (21 requested) atoms. Cycle 34: After refmac, R = 0.2107 (Rfree = 0.000) for 1325 atoms. Found 21 (21 requested) and removed 6 (21 requested) atoms. Cycle 35: After refmac, R = 0.2099 (Rfree = 0.000) for 1335 atoms. Found 21 (21 requested) and removed 9 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.29 2.06 NCS extension: 0 residues added, 1347 seeds are put forward Round 1: 110 peptides, 2 chains. Longest chain 96 peptides. Score 0.746 Round 2: 109 peptides, 3 chains. Longest chain 60 peptides. Score 0.725 Round 3: 107 peptides, 3 chains. Longest chain 81 peptides. Score 0.718 Round 4: 107 peptides, 3 chains. Longest chain 51 peptides. Score 0.718 Round 5: 109 peptides, 3 chains. Longest chain 61 peptides. Score 0.725 Taking the results from Round 1 Chains 2, Residues 108, Estimated correctness of the model 93.9 % 2 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A 1 chains (110 residues) following loop building 1 chains (110 residues) in sequence following loop building ------------------------------------------------------ 19564 reflections ( 99.91 % complete ) and 1403 restraints for refining 1309 atoms. 496 conditional restraints added. Observations/parameters ratio is 3.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2329 (Rfree = 0.000) for 1309 atoms. Found 21 (21 requested) and removed 21 (21 requested) atoms. Cycle 37: After refmac, R = 0.2207 (Rfree = 0.000) for 1302 atoms. Found 21 (21 requested) and removed 6 (21 requested) atoms. Cycle 38: After refmac, R = 0.2147 (Rfree = 0.000) for 1313 atoms. Found 21 (21 requested) and removed 13 (21 requested) atoms. Cycle 39: After refmac, R = 0.2111 (Rfree = 0.000) for 1317 atoms. Found 21 (21 requested) and removed 16 (21 requested) atoms. Cycle 40: After refmac, R = 0.2102 (Rfree = 0.000) for 1318 atoms. Found 21 (21 requested) and removed 17 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.29 2.06 NCS extension: 0 residues added, 1322 seeds are put forward Round 1: 110 peptides, 2 chains. Longest chain 96 peptides. Score 0.746 Round 2: 107 peptides, 3 chains. Longest chain 58 peptides. Score 0.718 Round 3: 105 peptides, 3 chains. Longest chain 51 peptides. Score 0.711 Round 4: 105 peptides, 3 chains. Longest chain 64 peptides. Score 0.711 Round 5: 109 peptides, 3 chains. Longest chain 51 peptides. Score 0.725 Taking the results from Round 1 Chains 2, Residues 108, Estimated correctness of the model 93.9 % 2 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A 1 chains (110 residues) following loop building 1 chains (110 residues) in sequence following loop building ------------------------------------------------------ 19564 reflections ( 99.91 % complete ) and 1375 restraints for refining 1307 atoms. 468 conditional restraints added. Observations/parameters ratio is 3.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2329 (Rfree = 0.000) for 1307 atoms. Found 21 (21 requested) and removed 22 (21 requested) atoms. Cycle 42: After refmac, R = 0.2210 (Rfree = 0.000) for 1297 atoms. Found 21 (21 requested) and removed 15 (21 requested) atoms. Cycle 43: After refmac, R = 0.2226 (Rfree = 0.000) for 1298 atoms. Found 21 (21 requested) and removed 14 (21 requested) atoms. Cycle 44: After refmac, R = 0.2162 (Rfree = 0.000) for 1304 atoms. Found 21 (21 requested) and removed 11 (21 requested) atoms. Cycle 45: After refmac, R = 0.2181 (Rfree = 0.000) for 1310 atoms. Found 21 (21 requested) and removed 18 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.31 2.07 NCS extension: 0 residues added, 1313 seeds are put forward Round 1: 109 peptides, 3 chains. Longest chain 88 peptides. Score 0.725 Round 2: 108 peptides, 4 chains. Longest chain 54 peptides. Score 0.703 Round 3: 108 peptides, 4 chains. Longest chain 40 peptides. Score 0.703 Round 4: 105 peptides, 3 chains. Longest chain 64 peptides. Score 0.711 Round 5: 109 peptides, 3 chains. Longest chain 60 peptides. Score 0.725 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 106, Estimated correctness of the model 92.9 % 3 chains (105 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 96 A and 100 A 1 chains (110 residues) following loop building 1 chains (110 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 19564 reflections ( 99.91 % complete ) and 907 restraints for refining 888 atoms. Observations/parameters ratio is 5.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2869 (Rfree = 0.000) for 888 atoms. Found 14 (14 requested) and removed 0 (14 requested) atoms. Cycle 47: After refmac, R = 0.2696 (Rfree = 0.000) for 888 atoms. Found 14 (14 requested) and removed 0 (14 requested) atoms. Cycle 48: After refmac, R = 0.2552 (Rfree = 0.000) for 888 atoms. Found 14 (14 requested) and removed 4 (14 requested) atoms. Cycle 49: After refmac, R = 0.2496 (Rfree = 0.000) for 888 atoms. Found 10 (14 requested) and removed 2 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:07:09 GMT 2018 Job finished. TimeTaking 44.45 Used memory is bytes: 16882536