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 2i9w-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i9w-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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/2i9w-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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 22:22:51 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/2i9w-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i9w-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 132 and 0 Target number of residues in the AU: 132 Target solvent content: 0.6236 Checking the provided sequence file Detected sequence length: 184 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 184 Adjusted target solvent content: 0.48 Input MTZ file: 2i9w-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: 19 Cell parameters: 41.450 54.640 83.800 90.000 90.000 90.000 Input sequence file: 2i9w-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1472 target number of atoms Had to go as low as 0.75 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: 45.770 3.200 Wilson plot Bfac: 62.80 3394 reflections ( 99.59 % complete ) and 0 restraints for refining 1644 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3480 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2825 (Rfree = 0.000) for 1644 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 1667 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.312 Round 2: 99 peptides, 14 chains. Longest chain 20 peptides. Score 0.540 Round 3: 108 peptides, 14 chains. Longest chain 15 peptides. Score 0.599 Round 4: 110 peptides, 14 chains. Longest chain 21 peptides. Score 0.611 Round 5: 115 peptides, 14 chains. Longest chain 20 peptides. Score 0.641 Taking the results from Round 5 Chains 14, Residues 101, Estimated correctness of the model 51.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3394 reflections ( 99.59 % complete ) and 2977 restraints for refining 1344 atoms. 2587 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2714 (Rfree = 0.000) for 1344 atoms. Found 11 (12 requested) and removed 10 (6 requested) atoms. Cycle 2: After refmac, R = 0.2628 (Rfree = 0.000) for 1333 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.2547 (Rfree = 0.000) for 1326 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2463 (Rfree = 0.000) for 1321 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2464 (Rfree = 0.000) for 1321 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 1360 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 11 peptides. Score 0.434 Round 2: 103 peptides, 12 chains. Longest chain 22 peptides. Score 0.624 Round 3: 100 peptides, 11 chains. Longest chain 15 peptides. Score 0.633 Round 4: 118 peptides, 11 chains. Longest chain 25 peptides. Score 0.727 Round 5: 119 peptides, 11 chains. Longest chain 25 peptides. Score 0.732 Taking the results from Round 5 Chains 12, Residues 108, Estimated correctness of the model 71.7 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3394 reflections ( 99.59 % complete ) and 2835 restraints for refining 1344 atoms. 2371 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2910 (Rfree = 0.000) for 1344 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 7: After refmac, R = 0.2636 (Rfree = 0.000) for 1340 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. Cycle 8: After refmac, R = 0.2326 (Rfree = 0.000) for 1335 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.2191 (Rfree = 0.000) for 1332 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.2368 (Rfree = 0.000) for 1329 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.31 Search for helices and strands: 0 residues in 0 chains, 1370 seeds are put forward Round 1: 110 peptides, 16 chains. Longest chain 18 peptides. Score 0.555 Round 2: 120 peptides, 14 chains. Longest chain 25 peptides. Score 0.668 Round 3: 118 peptides, 14 chains. Longest chain 30 peptides. Score 0.657 Round 4: 120 peptides, 11 chains. Longest chain 32 peptides. Score 0.736 Round 5: 106 peptides, 12 chains. Longest chain 22 peptides. Score 0.641 Taking the results from Round 4 Chains 12, Residues 109, Estimated correctness of the model 72.4 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3394 reflections ( 99.59 % complete ) and 2830 restraints for refining 1344 atoms. 2360 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2684 (Rfree = 0.000) for 1344 atoms. Found 11 (11 requested) and removed 8 (6 requested) atoms. Cycle 12: After refmac, R = 0.2433 (Rfree = 0.000) for 1345 atoms. Found 4 (11 requested) and removed 6 (6 requested) atoms. Cycle 13: After refmac, R = 0.2341 (Rfree = 0.000) for 1341 atoms. Found 4 (10 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.2251 (Rfree = 0.000) for 1336 atoms. Found 2 (10 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2230 (Rfree = 0.000) for 1331 atoms. Found 5 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 1380 seeds are put forward Round 1: 104 peptides, 15 chains. Longest chain 15 peptides. Score 0.544 Round 2: 112 peptides, 12 chains. Longest chain 20 peptides. Score 0.674 Round 3: 114 peptides, 12 chains. Longest chain 20 peptides. Score 0.685 Round 4: 115 peptides, 13 chains. Longest chain 24 peptides. Score 0.666 Round 5: 109 peptides, 11 chains. Longest chain 27 peptides. Score 0.683 Taking the results from Round 3 Chains 12, Residues 102, Estimated correctness of the model 61.9 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3394 reflections ( 99.59 % complete ) and 2787 restraints for refining 1344 atoms. 2309 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2559 (Rfree = 0.000) for 1344 atoms. Found 9 (10 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.2354 (Rfree = 0.000) for 1335 atoms. Found 7 (10 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2237 (Rfree = 0.000) for 1334 atoms. Found 6 (9 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.2212 (Rfree = 0.000) for 1330 atoms. Found 6 (9 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2133 (Rfree = 0.000) for 1331 atoms. Found 1 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 1359 seeds are put forward Round 1: 94 peptides, 14 chains. Longest chain 11 peptides. Score 0.504 Round 2: 107 peptides, 14 chains. Longest chain 14 peptides. Score 0.593 Round 3: 114 peptides, 14 chains. Longest chain 14 peptides. Score 0.635 Round 4: 107 peptides, 14 chains. Longest chain 18 peptides. Score 0.593 Round 5: 114 peptides, 15 chains. Longest chain 13 peptides. Score 0.608 Taking the results from Round 3 Chains 14, Residues 100, Estimated correctness of the model 50.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3394 reflections ( 99.59 % complete ) and 2965 restraints for refining 1337 atoms. 2579 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2404 (Rfree = 0.000) for 1337 atoms. Found 7 (9 requested) and removed 5 (5 requested) atoms. Cycle 22: After refmac, R = 0.2573 (Rfree = 0.000) for 1338 atoms. Found 8 (10 requested) and removed 11 (6 requested) atoms. Cycle 23: After refmac, R = 0.3123 (Rfree = 0.000) for 1331 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.2320 (Rfree = 0.000) for 1328 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2608 (Rfree = 0.000) for 1331 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 1353 seeds are put forward Round 1: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.440 Round 2: 88 peptides, 12 chains. Longest chain 14 peptides. Score 0.525 Round 3: 95 peptides, 14 chains. Longest chain 12 peptides. Score 0.511 Round 4: 98 peptides, 13 chains. Longest chain 19 peptides. Score 0.563 Round 5: 92 peptides, 10 chains. Longest chain 17 peptides. Score 0.613 Taking the results from Round 5 Chains 10, Residues 82, Estimated correctness of the model 44.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3394 reflections ( 99.59 % complete ) and 3103 restraints for refining 1344 atoms. 2785 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3680 (Rfree = 0.000) for 1344 atoms. Found 10 (10 requested) and removed 16 (6 requested) atoms. Cycle 27: After refmac, R = 0.2564 (Rfree = 0.000) for 1331 atoms. Found 6 (10 requested) and removed 10 (6 requested) atoms. Cycle 28: After refmac, R = 0.2456 (Rfree = 0.000) for 1326 atoms. Found 9 (9 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2303 (Rfree = 0.000) for 1329 atoms. Found 5 (9 requested) and removed 7 (5 requested) atoms. Cycle 30: After refmac, R = 0.2151 (Rfree = 0.000) for 1327 atoms. Found 4 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 1357 seeds are put forward Round 1: 83 peptides, 14 chains. Longest chain 12 peptides. Score 0.418 Round 2: 90 peptides, 16 chains. Longest chain 12 peptides. Score 0.405 Round 3: 104 peptides, 13 chains. Longest chain 22 peptides. Score 0.602 Round 4: 95 peptides, 13 chains. Longest chain 16 peptides. Score 0.543 Round 5: 98 peptides, 14 chains. Longest chain 17 peptides. Score 0.533 Taking the results from Round 3 Chains 13, Residues 91, Estimated correctness of the model 41.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3394 reflections ( 99.59 % complete ) and 2888 restraints for refining 1311 atoms. 2537 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2970 (Rfree = 0.000) for 1311 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2212 (Rfree = 0.000) for 1306 atoms. Found 9 (9 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.2123 (Rfree = 0.000) for 1303 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.2016 (Rfree = 0.000) for 1306 atoms. Found 5 (9 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2048 (Rfree = 0.000) for 1304 atoms. Found 1 (9 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 1338 seeds are put forward Round 1: 85 peptides, 13 chains. Longest chain 16 peptides. Score 0.469 Round 2: 89 peptides, 12 chains. Longest chain 16 peptides. Score 0.532 Round 3: 88 peptides, 11 chains. Longest chain 16 peptides. Score 0.557 Round 4: 87 peptides, 12 chains. Longest chain 19 peptides. Score 0.517 Round 5: 96 peptides, 12 chains. Longest chain 16 peptides. Score 0.580 Taking the results from Round 5 Chains 12, Residues 84, Estimated correctness of the model 35.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3394 reflections ( 99.59 % complete ) and 3012 restraints for refining 1344 atoms. 2688 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2466 (Rfree = 0.000) for 1344 atoms. Found 10 (10 requested) and removed 8 (6 requested) atoms. Cycle 37: After refmac, R = 0.2223 (Rfree = 0.000) for 1341 atoms. Found 10 (10 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.2194 (Rfree = 0.000) for 1340 atoms. Found 10 (10 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.2104 (Rfree = 0.000) for 1342 atoms. Found 8 (10 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1964 (Rfree = 0.000) for 1342 atoms. Found 6 (10 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 1378 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.434 Round 2: 90 peptides, 12 chains. Longest chain 11 peptides. Score 0.539 Round 3: 83 peptides, 12 chains. Longest chain 12 peptides. Score 0.488 Round 4: 86 peptides, 12 chains. Longest chain 11 peptides. Score 0.510 Round 5: 92 peptides, 10 chains. Longest chain 21 peptides. Score 0.613 Taking the results from Round 5 Chains 10, Residues 82, Estimated correctness of the model 44.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3394 reflections ( 99.59 % complete ) and 3101 restraints for refining 1344 atoms. 2783 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2392 (Rfree = 0.000) for 1344 atoms. Found 10 (10 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.2145 (Rfree = 0.000) for 1348 atoms. Found 10 (10 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.2182 (Rfree = 0.000) for 1347 atoms. Found 9 (10 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.2054 (Rfree = 0.000) for 1349 atoms. Found 9 (10 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2072 (Rfree = 0.000) for 1350 atoms. Found 8 (10 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.30 Search for helices and strands: 0 residues in 0 chains, 1374 seeds are put forward Round 1: 83 peptides, 12 chains. Longest chain 12 peptides. Score 0.488 Round 2: 87 peptides, 11 chains. Longest chain 17 peptides. Score 0.550 Round 3: 89 peptides, 11 chains. Longest chain 18 peptides. Score 0.563 Round 4: 91 peptides, 13 chains. Longest chain 12 peptides. Score 0.514 Round 5: 84 peptides, 11 chains. Longest chain 17 peptides. Score 0.528 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 78, Estimated correctness of the model 30.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2i9w-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3394 reflections ( 99.59 % complete ) and 3115 restraints for refining 1344 atoms. 2814 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2284 (Rfree = 0.000) for 1344 atoms. Found 0 (10 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2105 (Rfree = 0.000) for 1338 atoms. Found 0 (10 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1998 (Rfree = 0.000) for 1331 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2015 (Rfree = 0.000) for 1325 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:49:44 GMT 2018 Job finished. TimeTaking 27.03 Used memory is bytes: 8437880