null Sun 23 Dec 22:22:49 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 1o6a-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.2-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/1o6a-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.2-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 22:22:59 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/1o6a-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.2-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 144 and 0 Target number of residues in the AU: 144 Target solvent content: 0.6380 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-3.2-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: 92 Cell parameters: 61.652 61.652 113.295 90.000 90.000 90.000 Input sequence file: 1o6a-3.2-parrot-hancs.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 3.201 Wilson plot Bfac: 70.40 3949 reflections ( 99.90 % complete ) and 0 restraints for refining 1703 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.4258 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3394 (Rfree = 0.000) for 1703 atoms. Found 9 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.15 Search for helices and strands: 0 residues in 0 chains, 1727 seeds are put forward NCS extension: 0 residues added, 1727 seeds are put forward Round 1: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.382 Round 2: 117 peptides, 11 chains. Longest chain 17 peptides. Score 0.686 Round 3: 126 peptides, 16 chains. Longest chain 15 peptides. Score 0.616 Round 4: 114 peptides, 12 chains. Longest chain 16 peptides. Score 0.649 Round 5: 119 peptides, 13 chains. Longest chain 18 peptides. Score 0.650 Taking the results from Round 2 Chains 11, Residues 106, Estimated correctness of the model 62.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3098 restraints for refining 1403 atoms. 2685 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3747 (Rfree = 0.000) for 1403 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. Cycle 2: After refmac, R = 0.3655 (Rfree = 0.000) for 1387 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.3596 (Rfree = 0.000) for 1376 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.3569 (Rfree = 0.000) for 1364 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.3536 (Rfree = 0.000) for 1356 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 1389 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1403 seeds are put forward Round 1: 110 peptides, 16 chains. Longest chain 21 peptides. Score 0.523 Round 2: 121 peptides, 14 chains. Longest chain 15 peptides. Score 0.637 Round 3: 117 peptides, 16 chains. Longest chain 22 peptides. Score 0.566 Round 4: 125 peptides, 15 chains. Longest chain 23 peptides. Score 0.634 Round 5: 129 peptides, 13 chains. Longest chain 29 peptides. Score 0.697 Taking the results from Round 5 Chains 13, Residues 116, Estimated correctness of the model 64.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3016 restraints for refining 1370 atoms. 2565 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.4000 (Rfree = 0.000) for 1370 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 7: After refmac, R = 0.3741 (Rfree = 0.000) for 1359 atoms. Found 8 (12 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.3647 (Rfree = 0.000) for 1352 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.3568 (Rfree = 0.000) for 1347 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.3520 (Rfree = 0.000) for 1340 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 1360 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 1393 seeds are put forward Round 1: 114 peptides, 14 chains. Longest chain 29 peptides. Score 0.600 Round 2: 119 peptides, 13 chains. Longest chain 21 peptides. Score 0.650 Round 3: 121 peptides, 9 chains. Longest chain 31 peptides. Score 0.744 Round 4: 114 peptides, 13 chains. Longest chain 18 peptides. Score 0.625 Round 5: 115 peptides, 13 chains. Longest chain 24 peptides. Score 0.630 Taking the results from Round 3 Chains 11, Residues 112, Estimated correctness of the model 73.9 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 2776 restraints for refining 1370 atoms. 2274 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3830 (Rfree = 0.000) for 1370 atoms. Found 4 (12 requested) and removed 20 (6 requested) atoms. Cycle 12: After refmac, R = 0.3693 (Rfree = 0.000) for 1353 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.3642 (Rfree = 0.000) for 1349 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.3570 (Rfree = 0.000) for 1345 atoms. Found 1 (11 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.3522 (Rfree = 0.000) for 1339 atoms. Found 1 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.23 Search for helices and strands: 0 residues in 0 chains, 1363 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 1393 seeds are put forward Round 1: 117 peptides, 13 chains. Longest chain 24 peptides. Score 0.640 Round 2: 125 peptides, 13 chains. Longest chain 44 peptides. Score 0.679 Round 3: 132 peptides, 12 chains. Longest chain 29 peptides. Score 0.730 Round 4: 112 peptides, 10 chains. Longest chain 26 peptides. Score 0.685 Round 5: 111 peptides, 13 chains. Longest chain 20 peptides. Score 0.609 Taking the results from Round 3 Chains 12, Residues 120, Estimated correctness of the model 71.3 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 2798 restraints for refining 1362 atoms. 2297 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3814 (Rfree = 0.000) for 1362 atoms. Found 5 (11 requested) and removed 15 (6 requested) atoms. Cycle 17: After refmac, R = 0.3636 (Rfree = 0.000) for 1348 atoms. Found 4 (11 requested) and removed 14 (6 requested) atoms. Cycle 18: After refmac, R = 0.3569 (Rfree = 0.000) for 1337 atoms. Found 3 (9 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.3482 (Rfree = 0.000) for 1333 atoms. Found 1 (9 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.3439 (Rfree = 0.000) for 1324 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 1356 seeds are put forward NCS extension: 22 residues added (11 deleted due to clashes), 1378 seeds are put forward Round 1: 120 peptides, 13 chains. Longest chain 42 peptides. Score 0.655 Round 2: 128 peptides, 12 chains. Longest chain 31 peptides. Score 0.714 Round 3: 127 peptides, 15 chains. Longest chain 31 peptides. Score 0.645 Round 4: 114 peptides, 13 chains. Longest chain 18 peptides. Score 0.625 Round 5: 125 peptides, 14 chains. Longest chain 21 peptides. Score 0.657 Taking the results from Round 2 Chains 12, Residues 116, Estimated correctness of the model 68.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 2947 restraints for refining 1358 atoms. 2495 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3653 (Rfree = 0.000) for 1358 atoms. Found 3 (10 requested) and removed 10 (6 requested) atoms. Cycle 22: After refmac, R = 0.3549 (Rfree = 0.000) for 1351 atoms. Found 1 (9 requested) and removed 8 (6 requested) atoms. Cycle 23: After refmac, R = 0.3483 (Rfree = 0.000) for 1343 atoms. Found 1 (9 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.3441 (Rfree = 0.000) for 1336 atoms. Found 1 (8 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.3399 (Rfree = 0.000) for 1331 atoms. Found 0 (8 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.25 Search for helices and strands: 0 residues in 0 chains, 1355 seeds are put forward NCS extension: 48 residues added (4 deleted due to clashes), 1403 seeds are put forward Round 1: 107 peptides, 15 chains. Longest chain 19 peptides. Score 0.532 Round 2: 112 peptides, 13 chains. Longest chain 27 peptides. Score 0.614 Round 3: 116 peptides, 12 chains. Longest chain 43 peptides. Score 0.659 Round 4: 114 peptides, 14 chains. Longest chain 18 peptides. Score 0.600 Round 5: 105 peptides, 13 chains. Longest chain 20 peptides. Score 0.574 Taking the results from Round 3 Chains 12, Residues 104, Estimated correctness of the model 55.9 % 1 chains (42 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 2705 restraints for refining 1403 atoms. 2146 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3814 (Rfree = 0.000) for 1403 atoms. Found 8 (8 requested) and removed 30 (6 requested) atoms. Cycle 27: After refmac, R = 0.3623 (Rfree = 0.000) for 1378 atoms. Found 7 (8 requested) and removed 8 (6 requested) atoms. Cycle 28: After refmac, R = 0.3413 (Rfree = 0.000) for 1377 atoms. Found 4 (8 requested) and removed 10 (6 requested) atoms. Cycle 29: After refmac, R = 0.3341 (Rfree = 0.000) for 1371 atoms. Found 0 (8 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.3301 (Rfree = 0.000) for 1362 atoms. Found 1 (8 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.23 Search for helices and strands: 0 residues in 0 chains, 1390 seeds are put forward NCS extension: 94 residues added (2 deleted due to clashes), 1484 seeds are put forward Round 1: 88 peptides, 12 chains. Longest chain 16 peptides. Score 0.496 Round 2: 104 peptides, 13 chains. Longest chain 17 peptides. Score 0.568 Round 3: 96 peptides, 12 chains. Longest chain 17 peptides. Score 0.547 Round 4: 97 peptides, 12 chains. Longest chain 17 peptides. Score 0.554 Round 5: 101 peptides, 12 chains. Longest chain 17 peptides. Score 0.578 Taking the results from Round 5 Chains 12, Residues 89, Estimated correctness of the model 34.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3219 restraints for refining 1399 atoms. 2875 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3577 (Rfree = 0.000) for 1399 atoms. Found 8 (8 requested) and removed 15 (6 requested) atoms. Cycle 32: After refmac, R = 0.3337 (Rfree = 0.000) for 1391 atoms. Found 4 (8 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.3190 (Rfree = 0.000) for 1385 atoms. Found 2 (8 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.3107 (Rfree = 0.000) for 1379 atoms. Found 2 (8 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.3040 (Rfree = 0.000) for 1375 atoms. Found 0 (8 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.21 Search for helices and strands: 0 residues in 0 chains, 1406 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 1435 seeds are put forward Round 1: 97 peptides, 16 chains. Longest chain 13 peptides. Score 0.436 Round 2: 114 peptides, 16 chains. Longest chain 20 peptides. Score 0.548 Round 3: 109 peptides, 15 chains. Longest chain 17 peptides. Score 0.544 Round 4: 107 peptides, 15 chains. Longest chain 17 peptides. Score 0.532 Round 5: 106 peptides, 16 chains. Longest chain 17 peptides. Score 0.497 Taking the results from Round 2 Chains 16, Residues 98, Estimated correctness of the model 26.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3087 restraints for refining 1403 atoms. 2711 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3551 (Rfree = 0.000) for 1403 atoms. Found 8 (8 requested) and removed 7 (6 requested) atoms. Cycle 37: After refmac, R = 0.3164 (Rfree = 0.000) for 1403 atoms. Found 1 (8 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.3080 (Rfree = 0.000) for 1396 atoms. Found 2 (8 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.3075 (Rfree = 0.000) for 1390 atoms. Found 5 (8 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.3043 (Rfree = 0.000) for 1389 atoms. Found 1 (8 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 1418 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 1451 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.412 Round 2: 88 peptides, 12 chains. Longest chain 18 peptides. Score 0.496 Round 3: 92 peptides, 10 chains. Longest chain 18 peptides. Score 0.579 Round 4: 92 peptides, 12 chains. Longest chain 13 peptides. Score 0.522 Round 5: 94 peptides, 11 chains. Longest chain 18 peptides. Score 0.563 Taking the results from Round 3 Chains 10, Residues 82, Estimated correctness of the model 35.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3949 reflections ( 99.90 % complete ) and 3248 restraints for refining 1403 atoms. 2930 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3418 (Rfree = 0.000) for 1403 atoms. Found 8 (8 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.3243 (Rfree = 0.000) for 1402 atoms. Found 4 (8 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.3116 (Rfree = 0.000) for 1398 atoms. Found 2 (8 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.3014 (Rfree = 0.000) for 1393 atoms. Found 0 (8 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2969 (Rfree = 0.000) for 1387 atoms. Found 1 (8 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.21 Search for helices and strands: 0 residues in 0 chains, 1419 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 1445 seeds are put forward Round 1: 81 peptides, 15 chains. Longest chain 9 peptides. Score 0.348 Round 2: 78 peptides, 12 chains. Longest chain 20 peptides. Score 0.425 Round 3: 94 peptides, 12 chains. Longest chain 18 peptides. Score 0.535 Round 4: 93 peptides, 15 chains. Longest chain 10 peptides. Score 0.438 Round 5: 89 peptides, 13 chains. Longest chain 17 peptides. Score 0.472 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 82, Estimated correctness of the model 22.3 % 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. 3949 reflections ( 99.90 % complete ) and 3281 restraints for refining 1398 atoms. 2965 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3399 (Rfree = 0.000) for 1398 atoms. Found 0 (8 requested) and removed 1 (6 requested) atoms. Cycle 47: After refmac, R = 0.3295 (Rfree = 0.000) for 1397 atoms. Found 0 (8 requested) and removed 0 (6 requested) atoms. Cycle 48: After refmac, R = 0.3218 (Rfree = 0.000) for 1397 atoms. Found 0 (8 requested) and removed 1 (6 requested) atoms. Cycle 49: After refmac, R = 0.3146 (Rfree = 0.000) for 1396 atoms. Found 0 (8 requested) and removed 1 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:54 GMT 2018 Job finished. TimeTaking 29.08 Used memory is bytes: 187216