Mon 24 Dec 00:20:37 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pg4-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.4-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:20:42 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-3.4-parrot-mrncs/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 146 and 0 Target number of residues in the AU: 146 Target solvent content: 0.6437 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 190 Adjusted target solvent content: 0.54 Input MTZ file: 2pg4-3.4-parrot-mrncs.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: 90 Cell parameters: 109.840 109.840 36.760 90.000 90.000 90.000 Input sequence file: 2pg4-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1520 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: 77.669 3.400 Wilson plot Bfac: 73.96 3374 reflections ( 99.59 % complete ) and 0 restraints for refining 1680 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3741 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3487 (Rfree = 0.000) for 1680 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 1723 seeds are put forward NCS extension: 0 residues added, 1723 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 8 peptides. Score 0.253 Round 2: 100 peptides, 16 chains. Longest chain 13 peptides. Score 0.451 Round 3: 109 peptides, 15 chains. Longest chain 21 peptides. Score 0.537 Round 4: 104 peptides, 13 chains. Longest chain 26 peptides. Score 0.561 Round 5: 113 peptides, 13 chains. Longest chain 27 peptides. Score 0.611 Taking the results from Round 5 Chains 13, Residues 100, Estimated correctness of the model 32.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3095 restraints for refining 1382 atoms. 2708 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3031 (Rfree = 0.000) for 1382 atoms. Found 3 (10 requested) and removed 16 (5 requested) atoms. Cycle 2: After refmac, R = 0.2972 (Rfree = 0.000) for 1347 atoms. Found 6 (10 requested) and removed 14 (5 requested) atoms. Cycle 3: After refmac, R = 0.2874 (Rfree = 0.000) for 1327 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2768 (Rfree = 0.000) for 1314 atoms. Found 3 (9 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2367 (Rfree = 0.000) for 1306 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1369 seeds are put forward NCS extension: 54 residues added (3 deleted due to clashes), 1423 seeds are put forward Round 1: 91 peptides, 15 chains. Longest chain 11 peptides. Score 0.418 Round 2: 112 peptides, 13 chains. Longest chain 16 peptides. Score 0.606 Round 3: 115 peptides, 12 chains. Longest chain 20 peptides. Score 0.645 Round 4: 110 peptides, 10 chains. Longest chain 24 peptides. Score 0.667 Round 5: 115 peptides, 13 chains. Longest chain 22 peptides. Score 0.622 Taking the results from Round 4 Chains 10, Residues 100, Estimated correctness of the model 49.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 2874 restraints for refining 1334 atoms. 2484 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2905 (Rfree = 0.000) for 1334 atoms. Found 1 (10 requested) and removed 8 (5 requested) atoms. Cycle 7: After refmac, R = 0.2758 (Rfree = 0.000) for 1318 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.2593 (Rfree = 0.000) for 1309 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 9: After refmac, R = 0.2546 (Rfree = 0.000) for 1306 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2645 (Rfree = 0.000) for 1303 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 1368 seeds are put forward NCS extension: 40 residues added (4 deleted due to clashes), 1408 seeds are put forward Round 1: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.412 Round 2: 110 peptides, 13 chains. Longest chain 21 peptides. Score 0.595 Round 3: 119 peptides, 15 chains. Longest chain 20 peptides. Score 0.594 Round 4: 109 peptides, 14 chains. Longest chain 17 peptides. Score 0.563 Round 5: 108 peptides, 10 chains. Longest chain 19 peptides. Score 0.657 Taking the results from Round 5 Chains 11, Residues 98, Estimated correctness of the model 46.2 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 2960 restraints for refining 1368 atoms. 2553 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3119 (Rfree = 0.000) for 1368 atoms. Found 6 (10 requested) and removed 14 (5 requested) atoms. Cycle 12: After refmac, R = 0.2690 (Rfree = 0.000) for 1339 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2460 (Rfree = 0.000) for 1335 atoms. Found 0 (10 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.2472 (Rfree = 0.000) for 1328 atoms. Found 1 (10 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.2368 (Rfree = 0.000) for 1318 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 1377 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1399 seeds are put forward Round 1: 88 peptides, 15 chains. Longest chain 9 peptides. Score 0.397 Round 2: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.397 Round 3: 100 peptides, 15 chains. Longest chain 18 peptides. Score 0.480 Round 4: 97 peptides, 15 chains. Longest chain 13 peptides. Score 0.460 Round 5: 93 peptides, 14 chains. Longest chain 15 peptides. Score 0.463 Taking the results from Round 3 Chains 15, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3046 restraints for refining 1371 atoms. 2721 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2529 (Rfree = 0.000) for 1371 atoms. Found 0 (10 requested) and removed 10 (5 requested) atoms. Cycle 17: After refmac, R = 0.2672 (Rfree = 0.000) for 1359 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.2551 (Rfree = 0.000) for 1356 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.2621 (Rfree = 0.000) for 1353 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2547 (Rfree = 0.000) for 1345 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1397 seeds are put forward NCS extension: 40 residues added (3 deleted due to clashes), 1437 seeds are put forward Round 1: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.370 Round 2: 92 peptides, 14 chains. Longest chain 13 peptides. Score 0.456 Round 3: 101 peptides, 15 chains. Longest chain 14 peptides. Score 0.487 Round 4: 104 peptides, 15 chains. Longest chain 14 peptides. Score 0.506 Round 5: 106 peptides, 15 chains. Longest chain 15 peptides. Score 0.518 Taking the results from Round 5 Chains 15, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3105 restraints for refining 1382 atoms. 2756 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2743 (Rfree = 0.000) for 1382 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 22: After refmac, R = 0.2771 (Rfree = 0.000) for 1377 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2680 (Rfree = 0.000) for 1372 atoms. Found 0 (10 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2665 (Rfree = 0.000) for 1361 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2747 (Rfree = 0.000) for 1358 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 1419 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1436 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.309 Round 2: 100 peptides, 14 chains. Longest chain 13 peptides. Score 0.509 Round 3: 89 peptides, 13 chains. Longest chain 9 peptides. Score 0.466 Round 4: 92 peptides, 14 chains. Longest chain 9 peptides. Score 0.456 Round 5: 97 peptides, 14 chains. Longest chain 14 peptides. Score 0.489 Taking the results from Round 2 Chains 14, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3088 restraints for refining 1381 atoms. 2758 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2661 (Rfree = 0.000) for 1381 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 27: After refmac, R = 0.2476 (Rfree = 0.000) for 1372 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.2529 (Rfree = 0.000) for 1365 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2641 (Rfree = 0.000) for 1360 atoms. Found 3 (10 requested) and removed 11 (5 requested) atoms. Cycle 30: After refmac, R = 0.2462 (Rfree = 0.000) for 1348 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1402 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 1410 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.320 Round 2: 90 peptides, 14 chains. Longest chain 10 peptides. Score 0.442 Round 3: 97 peptides, 15 chains. Longest chain 12 peptides. Score 0.460 Round 4: 88 peptides, 14 chains. Longest chain 10 peptides. Score 0.428 Round 5: 87 peptides, 16 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 3 Chains 15, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3070 restraints for refining 1378 atoms. 2757 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2897 (Rfree = 0.000) for 1378 atoms. Found 5 (10 requested) and removed 9 (5 requested) atoms. Cycle 32: After refmac, R = 0.2795 (Rfree = 0.000) for 1367 atoms. Found 1 (10 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.2779 (Rfree = 0.000) for 1359 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.2655 (Rfree = 0.000) for 1356 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2639 (Rfree = 0.000) for 1352 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 1389 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 1402 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 8 peptides. Score 0.295 Round 2: 91 peptides, 17 chains. Longest chain 8 peptides. Score 0.355 Round 3: 89 peptides, 14 chains. Longest chain 14 peptides. Score 0.435 Round 4: 88 peptides, 14 chains. Longest chain 11 peptides. Score 0.428 Round 5: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.387 Taking the results from Round 3 Chains 14, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3148 restraints for refining 1382 atoms. 2862 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2434 (Rfree = 0.000) for 1382 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.2648 (Rfree = 0.000) for 1379 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.2237 (Rfree = 0.000) for 1381 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2545 (Rfree = 0.000) for 1379 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2322 (Rfree = 0.000) for 1375 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1426 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1435 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 9 peptides. Score 0.295 Round 2: 81 peptides, 15 chains. Longest chain 10 peptides. Score 0.344 Round 3: 80 peptides, 14 chains. Longest chain 11 peptides. Score 0.369 Round 4: 82 peptides, 14 chains. Longest chain 11 peptides. Score 0.384 Round 5: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.402 Taking the results from Round 5 Chains 13, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3374 reflections ( 99.59 % complete ) and 3155 restraints for refining 1382 atoms. 2900 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2639 (Rfree = 0.000) for 1382 atoms. Found 7 (10 requested) and removed 17 (5 requested) atoms. Cycle 42: After refmac, R = 0.2193 (Rfree = 0.000) for 1369 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2191 (Rfree = 0.000) for 1366 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2226 (Rfree = 0.000) for 1360 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2113 (Rfree = 0.000) for 1358 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 1416 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 6 peptides. Score 0.221 Round 2: 72 peptides, 13 chains. Longest chain 9 peptides. Score 0.341 Round 3: 68 peptides, 11 chains. Longest chain 8 peptides. Score 0.378 Round 4: 68 peptides, 12 chains. Longest chain 8 peptides. Score 0.344 Round 5: 69 peptides, 10 chains. Longest chain 13 peptides. Score 0.420 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 59, 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 2pg4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3374 reflections ( 99.59 % complete ) and 3286 restraints for refining 1382 atoms. 3060 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2478 (Rfree = 0.000) for 1382 atoms. Found 0 (10 requested) and removed 4 (5 requested) atoms. Cycle 47: After refmac, R = 0.2316 (Rfree = 0.000) for 1376 atoms. Found 0 (10 requested) and removed 4 (5 requested) atoms. Cycle 48: After refmac, R = 0.2160 (Rfree = 0.000) for 1371 atoms. Found 0 (10 requested) and removed 3 (5 requested) atoms. Cycle 49: After refmac, R = 0.2238 (Rfree = 0.000) for 1368 atoms. TimeTaking 26.97