null Sun 23 Dec 22:23:07 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 2pc1-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pc1-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.4-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/2pc1-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.4-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 22:23:17 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/2pc1-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pc1-3.4-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 130 and 0 Target number of residues in the AU: 130 Target solvent content: 0.6238 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 201 Adjusted target solvent content: 0.42 Input MTZ file: 2pc1-3.4-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: 1 Cell parameters: 35.480 37.650 41.500 94.220 109.420 113.080 Input sequence file: 2pc1-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1608 target number of atoms Had to go as low as 0.60 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: 25.956 3.401 Wilson plot Bfac: 62.19 2368 reflections ( 95.22 % complete ) and 0 restraints for refining 1772 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.2933 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2574 (Rfree = 0.000) for 1772 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.63 Search for helices and strands: 0 residues in 0 chains, 1794 seeds are put forward Round 1: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.323 Round 2: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.361 Round 3: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.385 Round 4: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.438 Round 5: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.423 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 ------------------------------------------------------ 2368 reflections ( 95.22 % complete ) and 3386 restraints for refining 1460 atoms. 3116 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2191 (Rfree = 0.000) for 1460 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 2: After refmac, R = 0.1948 (Rfree = 0.000) for 1444 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.1738 (Rfree = 0.000) for 1431 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.1577 (Rfree = 0.000) for 1427 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.1540 (Rfree = 0.000) for 1418 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.67 Search for helices and strands: 0 residues in 0 chains, 1476 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 8 peptides. Score 0.264 Round 2: 84 peptides, 15 chains. Longest chain 15 peptides. Score 0.394 Round 3: 87 peptides, 16 chains. Longest chain 9 peptides. Score 0.383 Round 4: 104 peptides, 19 chains. Longest chain 16 peptides. Score 0.419 Round 5: 98 peptides, 16 chains. Longest chain 11 peptides. Score 0.473 Taking the results from Round 5 Chains 16, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2368 reflections ( 95.22 % complete ) and 3330 restraints for refining 1415 atoms. 3018 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1925 (Rfree = 0.000) for 1415 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 7: After refmac, R = 0.1794 (Rfree = 0.000) for 1408 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 8: After refmac, R = 0.1683 (Rfree = 0.000) for 1408 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 9: After refmac, R = 0.1623 (Rfree = 0.000) for 1405 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.1593 (Rfree = 0.000) for 1401 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.67 Search for helices and strands: 0 residues in 0 chains, 1443 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 9 peptides. Score 0.303 Round 2: 90 peptides, 13 chains. Longest chain 14 peptides. Score 0.511 Round 3: 89 peptides, 13 chains. Longest chain 14 peptides. Score 0.504 Round 4: 92 peptides, 13 chains. Longest chain 13 peptides. Score 0.526 Round 5: 97 peptides, 14 chains. Longest chain 15 peptides. Score 0.530 Taking the results from Round 5 Chains 14, Residues 83, Estimated correctness of the model 4.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2368 reflections ( 95.22 % complete ) and 3299 restraints for refining 1425 atoms. 2981 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1928 (Rfree = 0.000) for 1425 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 12: After refmac, R = 0.1757 (Rfree = 0.000) for 1419 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 13: After refmac, R = 0.1677 (Rfree = 0.000) for 1418 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.1587 (Rfree = 0.000) for 1416 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.1537 (Rfree = 0.000) for 1408 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.66 Search for helices and strands: 0 residues in 0 chains, 1451 seeds are put forward Round 1: 68 peptides, 13 chains. Longest chain 9 peptides. Score 0.327 Round 2: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.444 Round 3: 77 peptides, 13 chains. Longest chain 13 peptides. Score 0.407 Round 4: 71 peptides, 10 chains. Longest chain 13 peptides. Score 0.467 Round 5: 76 peptides, 11 chains. Longest chain 16 peptides. Score 0.472 Taking the results from Round 5 Chains 11, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2368 reflections ( 95.22 % complete ) and 3341 restraints for refining 1401 atoms. 3092 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1771 (Rfree = 0.000) for 1401 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 17: After refmac, R = 0.1662 (Rfree = 0.000) for 1398 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.1496 (Rfree = 0.000) for 1399 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.1570 (Rfree = 0.000) for 1391 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.1498 (Rfree = 0.000) for 1388 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.63 Search for helices and strands: 0 residues in 0 chains, 1446 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 9 peptides. Score 0.267 Round 2: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.352 Round 3: 96 peptides, 14 chains. Longest chain 24 peptides. Score 0.523 Round 4: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.386 Round 5: 95 peptides, 15 chains. Longest chain 13 peptides. Score 0.483 Taking the results from Round 3 Chains 16, Residues 82, Estimated correctness of the model 1.5 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 2368 reflections ( 95.22 % complete ) and 3112 restraints for refining 1462 atoms. 2694 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1776 (Rfree = 0.000) for 1462 atoms. Found 9 (11 requested) and removed 15 (5 requested) atoms. Cycle 22: After refmac, R = 0.1516 (Rfree = 0.000) for 1451 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.1434 (Rfree = 0.000) for 1449 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.1446 (Rfree = 0.000) for 1441 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.1336 (Rfree = 0.000) for 1437 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.66 Search for helices and strands: 0 residues in 0 chains, 1476 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 10 peptides. Score 0.314 Round 2: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.419 Round 3: 100 peptides, 16 chains. Longest chain 10 peptides. Score 0.488 Round 4: 95 peptides, 15 chains. Longest chain 13 peptides. Score 0.483 Round 5: 91 peptides, 14 chains. Longest chain 14 peptides. Score 0.485 Taking the results from Round 3 Chains 16, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2368 reflections ( 95.22 % complete ) and 3294 restraints for refining 1443 atoms. 2974 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1663 (Rfree = 0.000) for 1443 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 27: After refmac, R = 0.1441 (Rfree = 0.000) for 1442 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.1464 (Rfree = 0.000) for 1435 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.1395 (Rfree = 0.000) for 1434 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.1352 (Rfree = 0.000) for 1430 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.64 Search for helices and strands: 0 residues in 0 chains, 1465 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.301 Round 2: 95 peptides, 16 chains. Longest chain 14 peptides. Score 0.449 Round 3: 96 peptides, 13 chains. Longest chain 14 peptides. Score 0.554 Round 4: 98 peptides, 16 chains. Longest chain 14 peptides. Score 0.473 Round 5: 85 peptides, 14 chains. Longest chain 13 peptides. Score 0.438 Taking the results from Round 3 Chains 13, Residues 83, Estimated correctness of the model 12.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2368 reflections ( 95.22 % complete ) and 3300 restraints for refining 1422 atoms. 2981 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1737 (Rfree = 0.000) for 1422 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.1431 (Rfree = 0.000) for 1425 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.1394 (Rfree = 0.000) for 1420 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1373 (Rfree = 0.000) for 1416 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1377 (Rfree = 0.000) for 1412 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.63 Search for helices and strands: 0 residues in 0 chains, 1451 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 9 peptides. Score 0.299 Round 2: 81 peptides, 12 chains. Longest chain 14 peptides. Score 0.476 Round 3: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.361 Round 4: 81 peptides, 13 chains. Longest chain 14 peptides. Score 0.441 Round 5: 89 peptides, 14 chains. Longest chain 14 peptides. Score 0.470 Taking the results from Round 2 Chains 12, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2368 reflections ( 95.22 % complete ) and 3317 restraints for refining 1415 atoms. 3053 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1553 (Rfree = 0.000) for 1415 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 37: After refmac, R = 0.1472 (Rfree = 0.000) for 1415 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.1430 (Rfree = 0.000) for 1412 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1391 (Rfree = 0.000) for 1410 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1412 (Rfree = 0.000) for 1403 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.66 Search for helices and strands: 0 residues in 0 chains, 1453 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 7 peptides. Score 0.249 Round 2: 85 peptides, 15 chains. Longest chain 14 peptides. Score 0.402 Round 3: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.396 Round 4: 73 peptides, 13 chains. Longest chain 13 peptides. Score 0.372 Round 5: 73 peptides, 14 chains. Longest chain 11 peptides. Score 0.334 Taking the results from Round 2 Chains 15, Residues 70, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2368 reflections ( 95.22 % complete ) and 3220 restraints for refining 1414 atoms. 2916 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1559 (Rfree = 0.000) for 1414 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.1430 (Rfree = 0.000) for 1414 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.1393 (Rfree = 0.000) for 1411 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1378 (Rfree = 0.000) for 1406 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.1475 (Rfree = 0.000) for 1402 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.71 Search for helices and strands: 0 residues in 0 chains, 1446 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.284 Round 2: 82 peptides, 16 chains. Longest chain 11 peptides. Score 0.339 Round 3: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.294 Round 4: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.314 Round 5: 78 peptides, 14 chains. Longest chain 13 peptides. Score 0.379 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 64, 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 2pc1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2368 reflections ( 95.22 % complete ) and 3526 restraints for refining 1454 atoms. 3284 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1604 (Rfree = 0.000) for 1454 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1537 (Rfree = 0.000) for 1446 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1518 (Rfree = 0.000) for 1439 atoms. Found 0 (10 requested) and removed 4 (5 requested) atoms. Cycle 49: After refmac, R = 0.1474 (Rfree = 0.000) for 1434 atoms. Found 0 (10 requested) and removed 2 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:57 GMT 2018 Job finished. TimeTaking 27.83 Used memory is bytes: 14033184