null Sun 23 Dec 22:23:02 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 2obp-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obp-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obp-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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/2obp-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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 22:23:12 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/2obp-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obp-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 156 and 0 Target number of residues in the AU: 156 Target solvent content: 0.6399 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: 0.56 Input MTZ file: 2obp-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: 182 Cell parameters: 76.690 76.690 138.090 90.000 90.000 120.000 Input sequence file: 2obp-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 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: 29.462 3.400 Wilson plot Bfac: 71.63 3658 reflections ( 99.40 % complete ) and 0 restraints for refining 1691 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3583 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3250 (Rfree = 0.000) for 1691 atoms. Found 11 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.09 Search for helices and strands: 0 residues in 0 chains, 1721 seeds are put forward NCS extension: 0 residues added, 1721 seeds are put forward Round 1: 82 peptides, 14 chains. Longest chain 11 peptides. Score 0.376 Round 2: 110 peptides, 16 chains. Longest chain 16 peptides. Score 0.502 Round 3: 112 peptides, 12 chains. Longest chain 18 peptides. Score 0.614 Round 4: 111 peptides, 12 chains. Longest chain 29 peptides. Score 0.609 Round 5: 114 peptides, 8 chains. Longest chain 30 peptides. Score 0.711 Taking the results from Round 5 Chains 8, Residues 106, Estimated correctness of the model 60.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 2913 restraints for refining 1372 atoms. 2473 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2885 (Rfree = 0.000) for 1372 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 2: After refmac, R = 0.2735 (Rfree = 0.000) for 1346 atoms. Found 5 (10 requested) and removed 15 (5 requested) atoms. Cycle 3: After refmac, R = 0.2718 (Rfree = 0.000) for 1329 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 4: After refmac, R = 0.2697 (Rfree = 0.000) for 1326 atoms. Found 4 (9 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2710 (Rfree = 0.000) for 1320 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.15 Search for helices and strands: 0 residues in 0 chains, 1385 seeds are put forward NCS extension: 45 residues added (8 deleted due to clashes), 1430 seeds are put forward Round 1: 103 peptides, 18 chains. Longest chain 9 peptides. Score 0.401 Round 2: 112 peptides, 15 chains. Longest chain 15 peptides. Score 0.540 Round 3: 111 peptides, 15 chains. Longest chain 16 peptides. Score 0.534 Round 4: 110 peptides, 14 chains. Longest chain 19 peptides. Score 0.554 Round 5: 115 peptides, 16 chains. Longest chain 12 peptides. Score 0.532 Taking the results from Round 4 Chains 15, Residues 96, Estimated correctness of the model 13.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 2797 restraints for refining 1311 atoms. 2386 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2991 (Rfree = 0.000) for 1311 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 7: After refmac, R = 0.2882 (Rfree = 0.000) for 1293 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2798 (Rfree = 0.000) for 1286 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2786 (Rfree = 0.000) for 1280 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2752 (Rfree = 0.000) for 1278 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.17 Search for helices and strands: 0 residues in 0 chains, 1332 seeds are put forward NCS extension: 0 residues added, 1332 seeds are put forward Round 1: 117 peptides, 15 chains. Longest chain 17 peptides. Score 0.568 Round 2: 115 peptides, 16 chains. Longest chain 13 peptides. Score 0.532 Round 3: 117 peptides, 15 chains. Longest chain 17 peptides. Score 0.568 Round 4: 114 peptides, 13 chains. Longest chain 22 peptides. Score 0.600 Round 5: 98 peptides, 11 chains. Longest chain 16 peptides. Score 0.564 Taking the results from Round 4 Chains 13, Residues 101, Estimated correctness of the model 28.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 2934 restraints for refining 1316 atoms. 2543 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3114 (Rfree = 0.000) for 1316 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 12: After refmac, R = 0.2987 (Rfree = 0.000) for 1311 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 13: After refmac, R = 0.2917 (Rfree = 0.000) for 1304 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.2870 (Rfree = 0.000) for 1301 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2826 (Rfree = 0.000) for 1299 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.24 Search for helices and strands: 0 residues in 0 chains, 1340 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 1350 seeds are put forward Round 1: 98 peptides, 16 chains. Longest chain 13 peptides. Score 0.426 Round 2: 118 peptides, 17 chains. Longest chain 12 peptides. Score 0.523 Round 3: 111 peptides, 13 chains. Longest chain 18 peptides. Score 0.585 Round 4: 116 peptides, 14 chains. Longest chain 18 peptides. Score 0.587 Round 5: 112 peptides, 15 chains. Longest chain 14 peptides. Score 0.540 Taking the results from Round 4 Chains 14, Residues 102, Estimated correctness of the model 24.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 2970 restraints for refining 1328 atoms. 2576 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3076 (Rfree = 0.000) for 1328 atoms. Found 9 (9 requested) and removed 12 (5 requested) atoms. Cycle 17: After refmac, R = 0.2930 (Rfree = 0.000) for 1315 atoms. Found 4 (9 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.2870 (Rfree = 0.000) for 1304 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.2808 (Rfree = 0.000) for 1306 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2775 (Rfree = 0.000) for 1302 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.09 Search for helices and strands: 0 residues in 0 chains, 1338 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 1360 seeds are put forward Round 1: 96 peptides, 16 chains. Longest chain 14 peptides. Score 0.412 Round 2: 99 peptides, 15 chains. Longest chain 15 peptides. Score 0.461 Round 3: 110 peptides, 16 chains. Longest chain 15 peptides. Score 0.502 Round 4: 117 peptides, 12 chains. Longest chain 33 peptides. Score 0.638 Round 5: 110 peptides, 11 chains. Longest chain 24 peptides. Score 0.627 Taking the results from Round 4 Chains 12, Residues 105, Estimated correctness of the model 40.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 2875 restraints for refining 1326 atoms. 2467 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3105 (Rfree = 0.000) for 1326 atoms. Found 4 (9 requested) and removed 19 (5 requested) atoms. Cycle 22: After refmac, R = 0.3057 (Rfree = 0.000) for 1301 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 23: After refmac, R = 0.2920 (Rfree = 0.000) for 1296 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.2886 (Rfree = 0.000) for 1292 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2793 (Rfree = 0.000) for 1288 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 1351 seeds are put forward NCS extension: 28 residues added (5 deleted due to clashes), 1379 seeds are put forward Round 1: 98 peptides, 19 chains. Longest chain 10 peptides. Score 0.337 Round 2: 98 peptides, 15 chains. Longest chain 11 peptides. Score 0.455 Round 3: 105 peptides, 15 chains. Longest chain 12 peptides. Score 0.499 Round 4: 102 peptides, 14 chains. Longest chain 13 peptides. Score 0.508 Round 5: 110 peptides, 15 chains. Longest chain 15 peptides. Score 0.528 Taking the results from Round 5 Chains 16, Residues 95, Estimated correctness of the model 3.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 3144 restraints for refining 1394 atoms. 2752 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3039 (Rfree = 0.000) for 1394 atoms. Found 9 (9 requested) and removed 20 (5 requested) atoms. Cycle 27: After refmac, R = 0.2852 (Rfree = 0.000) for 1374 atoms. Found 8 (9 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.2737 (Rfree = 0.000) for 1371 atoms. Found 3 (9 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2728 (Rfree = 0.000) for 1364 atoms. Found 6 (9 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2645 (Rfree = 0.000) for 1361 atoms. Found 6 (9 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 3.01 Search for helices and strands: 0 residues in 0 chains, 1416 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1434 seeds are put forward Round 1: 74 peptides, 12 chains. Longest chain 11 peptides. Score 0.381 Round 2: 83 peptides, 12 chains. Longest chain 14 peptides. Score 0.444 Round 3: 81 peptides, 11 chains. Longest chain 15 peptides. Score 0.461 Round 4: 86 peptides, 12 chains. Longest chain 12 peptides. Score 0.464 Round 5: 88 peptides, 13 chains. Longest chain 15 peptides. Score 0.447 Taking the results from Round 4 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 3101 restraints for refining 1359 atoms. 2817 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2714 (Rfree = 0.000) for 1359 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2837 (Rfree = 0.000) for 1359 atoms. Found 9 (9 requested) and removed 15 (5 requested) atoms. Cycle 33: After refmac, R = 0.2744 (Rfree = 0.000) for 1348 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2385 (Rfree = 0.000) for 1345 atoms. Found 8 (9 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2362 (Rfree = 0.000) for 1347 atoms. Found 1 (9 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.03 Search for helices and strands: 0 residues in 0 chains, 1404 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1420 seeds are put forward Round 1: 86 peptides, 14 chains. Longest chain 10 peptides. Score 0.404 Round 2: 96 peptides, 16 chains. Longest chain 9 peptides. Score 0.412 Round 3: 98 peptides, 14 chains. Longest chain 16 peptides. Score 0.483 Round 4: 90 peptides, 13 chains. Longest chain 14 peptides. Score 0.460 Round 5: 96 peptides, 15 chains. Longest chain 12 peptides. Score 0.442 Taking the results from Round 3 Chains 14, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 2992 restraints for refining 1346 atoms. 2670 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2711 (Rfree = 0.000) for 1346 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.2647 (Rfree = 0.000) for 1344 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.2587 (Rfree = 0.000) for 1345 atoms. Found 3 (9 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2534 (Rfree = 0.000) for 1342 atoms. Found 5 (9 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.2783 (Rfree = 0.000) for 1335 atoms. Found 7 (9 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.00 Search for helices and strands: 0 residues in 0 chains, 1396 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1414 seeds are put forward Round 1: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.371 Round 2: 97 peptides, 15 chains. Longest chain 13 peptides. Score 0.448 Round 3: 93 peptides, 14 chains. Longest chain 13 peptides. Score 0.451 Round 4: 98 peptides, 13 chains. Longest chain 13 peptides. Score 0.511 Round 5: 104 peptides, 15 chains. Longest chain 12 peptides. Score 0.493 Taking the results from Round 4 Chains 15, Residues 85, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 3658 reflections ( 99.40 % complete ) and 2945 restraints for refining 1396 atoms. 2549 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2678 (Rfree = 0.000) for 1396 atoms. Found 6 (9 requested) and removed 9 (5 requested) atoms. Cycle 42: After refmac, R = 0.2525 (Rfree = 0.000) for 1383 atoms. Found 3 (9 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2449 (Rfree = 0.000) for 1378 atoms. Found 3 (9 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2411 (Rfree = 0.000) for 1372 atoms. Found 2 (9 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2388 (Rfree = 0.000) for 1368 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.07 Search for helices and strands: 0 residues in 0 chains, 1418 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 1430 seeds are put forward Round 1: 95 peptides, 16 chains. Longest chain 9 peptides. Score 0.406 Round 2: 86 peptides, 14 chains. Longest chain 11 peptides. Score 0.404 Round 3: 96 peptides, 14 chains. Longest chain 10 peptides. Score 0.470 Round 4: 98 peptides, 13 chains. Longest chain 12 peptides. Score 0.511 Round 5: 98 peptides, 16 chains. Longest chain 11 peptides. Score 0.426 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 85, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2obp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3658 reflections ( 99.40 % complete ) and 3011 restraints for refining 1396 atoms. 2654 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2847 (Rfree = 0.000) for 1396 atoms. Found 0 (9 requested) and removed 3 (5 requested) atoms. Cycle 47: After refmac, R = 0.2776 (Rfree = 0.000) for 1392 atoms. Found 0 (9 requested) and removed 0 (5 requested) atoms. Cycle 48: After refmac, R = 0.2718 (Rfree = 0.000) for 1391 atoms. Found 0 (9 requested) and removed 0 (5 requested) atoms. Cycle 49: After refmac, R = 0.2670 (Rfree = 0.000) for 1391 atoms. Found 0 (9 requested) and removed 0 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:05:37 GMT 2018 Job finished. TimeTaking 42.6 Used memory is bytes: 21630464