null Sun 23 Dec 22:22:41 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 2ou6-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.8-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/2ou6-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.8-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 22:22:50 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/2ou6-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-3.8-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 155 and 0 Target number of residues in the AU: 155 Target solvent content: 0.6547 Checking the provided sequence file Detected sequence length: 190 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 190 Adjusted target solvent content: 0.58 Input MTZ file: 2ou6-3.8-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: 179 Cell parameters: 57.933 57.933 250.773 90.000 90.000 120.000 Input sequence file: 2ou6-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.85 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: 50.171 3.801 Wilson plot Bfac: 79.84 2854 reflections ( 99.72 % complete ) and 0 restraints for refining 1675 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3787 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3763 (Rfree = 0.000) for 1675 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.38 Search for helices and strands: 0 residues in 0 chains, 1707 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 7 peptides. Score 0.281 Round 2: 87 peptides, 13 chains. Longest chain 14 peptides. Score 0.434 Round 3: 84 peptides, 12 chains. Longest chain 13 peptides. Score 0.444 Round 4: 95 peptides, 14 chains. Longest chain 16 peptides. Score 0.456 Round 5: 102 peptides, 12 chains. Longest chain 15 peptides. Score 0.551 Taking the results from Round 5 Chains 15, Residues 90, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2854 reflections ( 99.72 % complete ) and 2810 restraints for refining 1341 atoms. 2382 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3222 (Rfree = 0.000) for 1341 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 2: After refmac, R = 0.2942 (Rfree = 0.000) for 1301 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2823 (Rfree = 0.000) for 1283 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 4: After refmac, R = 0.2670 (Rfree = 0.000) for 1269 atoms. Found 6 (7 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2573 (Rfree = 0.000) for 1264 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.25 Search for helices and strands: 0 residues in 0 chains, 1326 seeds are put forward Round 1: 101 peptides, 15 chains. Longest chain 12 peptides. Score 0.466 Round 2: 105 peptides, 12 chains. Longest chain 19 peptides. Score 0.568 Round 3: 111 peptides, 13 chains. Longest chain 18 peptides. Score 0.575 Round 4: 112 peptides, 13 chains. Longest chain 19 peptides. Score 0.580 Round 5: 99 peptides, 9 chains. Longest chain 27 peptides. Score 0.610 Taking the results from Round 5 Chains 9, Residues 90, Estimated correctness of the model 3.4 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2854 reflections ( 99.72 % complete ) and 2972 restraints for refining 1343 atoms. 2583 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2965 (Rfree = 0.000) for 1343 atoms. Found 3 (7 requested) and removed 9 (3 requested) atoms. Cycle 7: After refmac, R = 0.2761 (Rfree = 0.000) for 1329 atoms. Found 2 (7 requested) and removed 8 (3 requested) atoms. Cycle 8: After refmac, R = 0.2673 (Rfree = 0.000) for 1321 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 9: After refmac, R = 0.2630 (Rfree = 0.000) for 1316 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2632 (Rfree = 0.000) for 1311 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 3.29 Search for helices and strands: 0 residues in 0 chains, 1373 seeds are put forward Round 1: 97 peptides, 14 chains. Longest chain 13 peptides. Score 0.469 Round 2: 106 peptides, 11 chains. Longest chain 17 peptides. Score 0.597 Round 3: 103 peptides, 13 chains. Longest chain 14 peptides. Score 0.531 Round 4: 105 peptides, 14 chains. Longest chain 13 peptides. Score 0.517 Round 5: 113 peptides, 14 chains. Longest chain 20 peptides. Score 0.561 Taking the results from Round 2 Chains 11, Residues 95, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2854 reflections ( 99.72 % complete ) and 2986 restraints for refining 1375 atoms. 2599 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2794 (Rfree = 0.000) for 1375 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 12: After refmac, R = 0.2622 (Rfree = 0.000) for 1355 atoms. Found 3 (7 requested) and removed 10 (3 requested) atoms. Cycle 13: After refmac, R = 0.2596 (Rfree = 0.000) for 1344 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.2558 (Rfree = 0.000) for 1337 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2573 (Rfree = 0.000) for 1329 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 3.29 Search for helices and strands: 0 residues in 0 chains, 1367 seeds are put forward Round 1: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.382 Round 2: 113 peptides, 16 chains. Longest chain 20 peptides. Score 0.511 Round 3: 107 peptides, 15 chains. Longest chain 18 peptides. Score 0.502 Round 4: 111 peptides, 15 chains. Longest chain 24 peptides. Score 0.525 Round 5: 112 peptides, 13 chains. Longest chain 24 peptides. Score 0.580 Taking the results from Round 5 Chains 13, Residues 99, Estimated correctness of the model 0.0 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 2854 reflections ( 99.72 % complete ) and 2864 restraints for refining 1375 atoms. 2377 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2923 (Rfree = 0.000) for 1375 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 17: After refmac, R = 0.2669 (Rfree = 0.000) for 1359 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2588 (Rfree = 0.000) for 1350 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2483 (Rfree = 0.000) for 1347 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.2450 (Rfree = 0.000) for 1342 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.25 Search for helices and strands: 0 residues in 0 chains, 1386 seeds are put forward Round 1: 94 peptides, 16 chains. Longest chain 13 peptides. Score 0.393 Round 2: 103 peptides, 15 chains. Longest chain 15 peptides. Score 0.478 Round 3: 100 peptides, 13 chains. Longest chain 13 peptides. Score 0.514 Round 4: 99 peptides, 15 chains. Longest chain 14 peptides. Score 0.454 Round 5: 103 peptides, 13 chains. Longest chain 17 peptides. Score 0.531 Taking the results from Round 5 Chains 13, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2854 reflections ( 99.72 % complete ) and 3164 restraints for refining 1375 atoms. 2817 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2751 (Rfree = 0.000) for 1375 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 22: After refmac, R = 0.2505 (Rfree = 0.000) for 1364 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 23: After refmac, R = 0.2341 (Rfree = 0.000) for 1359 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.2271 (Rfree = 0.000) for 1355 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.2237 (Rfree = 0.000) for 1351 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.25 Search for helices and strands: 0 residues in 0 chains, 1400 seeds are put forward Round 1: 78 peptides, 13 chains. Longest chain 13 peptides. Score 0.373 Round 2: 103 peptides, 15 chains. Longest chain 21 peptides. Score 0.478 Round 3: 109 peptides, 16 chains. Longest chain 22 peptides. Score 0.488 Round 4: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.436 Round 5: 99 peptides, 12 chains. Longest chain 22 peptides. Score 0.535 Taking the results from Round 5 Chains 12, Residues 87, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2854 reflections ( 99.72 % complete ) and 3051 restraints for refining 1375 atoms. 2693 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2796 (Rfree = 0.000) for 1375 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.2565 (Rfree = 0.000) for 1364 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 28: After refmac, R = 0.2468 (Rfree = 0.000) for 1358 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.2414 (Rfree = 0.000) for 1359 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2060 (Rfree = 0.000) for 1357 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.22 Search for helices and strands: 0 residues in 0 chains, 1404 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 11 peptides. Score 0.307 Round 2: 104 peptides, 15 chains. Longest chain 15 peptides. Score 0.484 Round 3: 97 peptides, 14 chains. Longest chain 19 peptides. Score 0.469 Round 4: 99 peptides, 13 chains. Longest chain 19 peptides. Score 0.508 Round 5: 108 peptides, 16 chains. Longest chain 20 peptides. Score 0.482 Taking the results from Round 4 Chains 13, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2854 reflections ( 99.72 % complete ) and 3108 restraints for refining 1375 atoms. 2777 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2500 (Rfree = 0.000) for 1375 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 32: After refmac, R = 0.2511 (Rfree = 0.000) for 1363 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 33: After refmac, R = 0.2122 (Rfree = 0.000) for 1359 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.2332 (Rfree = 0.000) for 1357 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 35: After refmac, R = 0.2663 (Rfree = 0.000) for 1356 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.22 Search for helices and strands: 0 residues in 0 chains, 1395 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 16 peptides. Score 0.352 Round 2: 99 peptides, 16 chains. Longest chain 11 peptides. Score 0.426 Round 3: 100 peptides, 15 chains. Longest chain 25 peptides. Score 0.460 Round 4: 91 peptides, 14 chains. Longest chain 15 peptides. Score 0.431 Round 5: 98 peptides, 14 chains. Longest chain 27 peptides. Score 0.475 Taking the results from Round 5 Chains 15, Residues 84, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2854 reflections ( 99.72 % complete ) and 3143 restraints for refining 1375 atoms. 2787 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2821 (Rfree = 0.000) for 1375 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 37: After refmac, R = 0.2701 (Rfree = 0.000) for 1361 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 38: After refmac, R = 0.2489 (Rfree = 0.000) for 1354 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.2478 (Rfree = 0.000) for 1352 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.2436 (Rfree = 0.000) for 1347 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.23 Search for helices and strands: 0 residues in 0 chains, 1405 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 9 peptides. Score 0.274 Round 2: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.318 Round 3: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.368 Round 4: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.391 Round 5: 83 peptides, 14 chains. Longest chain 13 peptides. Score 0.377 Taking the results from Round 4 Chains 14, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2854 reflections ( 99.72 % complete ) and 3033 restraints for refining 1346 atoms. 2763 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2480 (Rfree = 0.000) for 1346 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.2342 (Rfree = 0.000) for 1340 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. Cycle 43: After refmac, R = 0.2348 (Rfree = 0.000) for 1323 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.2392 (Rfree = 0.000) for 1322 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.2464 (Rfree = 0.000) for 1314 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.22 Search for helices and strands: 0 residues in 0 chains, 1385 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.209 Round 2: 82 peptides, 15 chains. Longest chain 10 peptides. Score 0.340 Round 3: 74 peptides, 12 chains. Longest chain 13 peptides. Score 0.376 Round 4: 70 peptides, 12 chains. Longest chain 9 peptides. Score 0.347 Round 5: 78 peptides, 12 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 66, 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 2ou6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2854 reflections ( 99.72 % complete ) and 2984 restraints for refining 1334 atoms. 2732 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2385 (Rfree = 0.000) for 1334 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2421 (Rfree = 0.000) for 1326 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2414 (Rfree = 0.000) for 1319 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2326 (Rfree = 0.000) for 1311 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:27 GMT 2018 Job finished. TimeTaking 28.78 Used memory is bytes: 11978184