Sun 23 Dec 22:22:55 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 2ilb-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ilb-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ilb-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.6-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/2ilb-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.6-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 22:23:04 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/2ilb-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.6-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 69 and 0 Target number of residues in the AU: 69 Target solvent content: 0.6536 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 114 Adjusted target solvent content: 0.43 Input MTZ file: 2ilb-3.6-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: 5 Cell parameters: 48.900 72.000 32.740 90.000 110.754 90.000 Input sequence file: 2ilb-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 912 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 Loops will be built when appropriate and at the last cycle Resolution range: 38.600 3.600 Wilson plot Bfac: 79.58 1257 reflections ( 99.60 % complete ) and 0 restraints for refining 1016 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3403 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3000 (Rfree = 0.000) for 1016 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.82 Search for helices and strands: 0 residues in 0 chains, 1018 seeds are put forward Round 1: 26 peptides, 6 chains. Longest chain 5 peptides. Score 0.206 Round 2: 34 peptides, 8 chains. Longest chain 5 peptides. Score 0.203 Round 3: 37 peptides, 7 chains. Longest chain 8 peptides. Score 0.326 Round 4: 36 peptides, 7 chains. Longest chain 8 peptides. Score 0.309 Round 5: 38 peptides, 8 chains. Longest chain 6 peptides. Score 0.273 Taking the results from Round 3 Chains 7, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1257 reflections ( 99.60 % complete ) and 1969 restraints for refining 827 atoms. 1856 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2728 (Rfree = 0.000) for 827 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 2: After refmac, R = 0.2022 (Rfree = 0.000) for 821 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 3: After refmac, R = 0.2367 (Rfree = 0.000) for 816 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 4: After refmac, R = 0.2432 (Rfree = 0.000) for 809 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.2393 (Rfree = 0.000) for 803 atoms. Found 5 (5 requested) and removed 35 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.72 Search for helices and strands: 0 residues in 0 chains, 792 seeds are put forward Round 1: 22 peptides, 5 chains. Longest chain 5 peptides. Score 0.208 Round 2: 33 peptides, 7 chains. Longest chain 7 peptides. Score 0.258 Round 3: 39 peptides, 7 chains. Longest chain 8 peptides. Score 0.358 Round 4: 35 peptides, 6 chains. Longest chain 9 peptides. Score 0.363 Round 5: 38 peptides, 6 chains. Longest chain 10 peptides. Score 0.410 Taking the results from Round 5 Chains 6, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1257 reflections ( 99.60 % complete ) and 1390 restraints for refining 674 atoms. 1268 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2245 (Rfree = 0.000) for 674 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 7: After refmac, R = 0.1688 (Rfree = 0.000) for 670 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2149 (Rfree = 0.000) for 663 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 9: After refmac, R = 0.1599 (Rfree = 0.000) for 664 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.1985 (Rfree = 0.000) for 660 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 680 seeds are put forward Round 1: 31 peptides, 6 chains. Longest chain 8 peptides. Score 0.297 Round 2: 41 peptides, 7 chains. Longest chain 10 peptides. Score 0.389 Round 3: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.316 Round 4: 43 peptides, 8 chains. Longest chain 7 peptides. Score 0.354 Round 5: 46 peptides, 9 chains. Longest chain 8 peptides. Score 0.335 Taking the results from Round 2 Chains 7, Residues 34, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1257 reflections ( 99.60 % complete ) and 1226 restraints for refining 624 atoms. 1097 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1828 (Rfree = 0.000) for 624 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 12: After refmac, R = 0.1654 (Rfree = 0.000) for 614 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 13: After refmac, R = 0.1537 (Rfree = 0.000) for 612 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 14: After refmac, R = 0.1464 (Rfree = 0.000) for 611 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 15: After refmac, R = 0.1503 (Rfree = 0.000) for 609 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.88 Search for helices and strands: 0 residues in 0 chains, 627 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 7 peptides. Score 0.258 Round 2: 43 peptides, 8 chains. Longest chain 8 peptides. Score 0.354 Round 3: 41 peptides, 8 chains. Longest chain 9 peptides. Score 0.322 Round 4: 46 peptides, 8 chains. Longest chain 10 peptides. Score 0.399 Round 5: 47 peptides, 8 chains. Longest chain 10 peptides. Score 0.414 Taking the results from Round 5 Chains 8, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1257 reflections ( 99.60 % complete ) and 1364 restraints for refining 661 atoms. 1216 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2541 (Rfree = 0.000) for 661 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 17: After refmac, R = 0.1774 (Rfree = 0.000) for 655 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 18: After refmac, R = 0.1738 (Rfree = 0.000) for 652 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.1657 (Rfree = 0.000) for 650 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.1530 (Rfree = 0.000) for 650 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 670 seeds are put forward Round 1: 31 peptides, 6 chains. Longest chain 7 peptides. Score 0.297 Round 2: 38 peptides, 6 chains. Longest chain 9 peptides. Score 0.410 Round 3: 35 peptides, 5 chains. Longest chain 10 peptides. Score 0.432 Round 4: 42 peptides, 6 chains. Longest chain 9 peptides. Score 0.468 Round 5: 46 peptides, 6 chains. Longest chain 12 peptides. Score 0.522 Taking the results from Round 5 Chains 6, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1257 reflections ( 99.60 % complete ) and 1380 restraints for refining 681 atoms. 1226 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2106 (Rfree = 0.000) for 681 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 22: After refmac, R = 0.2013 (Rfree = 0.000) for 677 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 23: After refmac, R = 0.2224 (Rfree = 0.000) for 670 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.1870 (Rfree = 0.000) for 669 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 25: After refmac, R = 0.1684 (Rfree = 0.000) for 668 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.77 Search for helices and strands: 0 residues in 0 chains, 688 seeds are put forward Round 1: 34 peptides, 8 chains. Longest chain 6 peptides. Score 0.203 Round 2: 38 peptides, 8 chains. Longest chain 7 peptides. Score 0.273 Round 3: 34 peptides, 7 chains. Longest chain 7 peptides. Score 0.276 Round 4: 40 peptides, 7 chains. Longest chain 8 peptides. Score 0.374 Round 5: 39 peptides, 7 chains. Longest chain 8 peptides. Score 0.358 Taking the results from Round 4 Chains 7, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1257 reflections ( 99.60 % complete ) and 1352 restraints for refining 654 atoms. 1227 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1698 (Rfree = 0.000) for 654 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 27: After refmac, R = 0.1424 (Rfree = 0.000) for 653 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.1459 (Rfree = 0.000) for 649 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.1478 (Rfree = 0.000) for 644 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.1409 (Rfree = 0.000) for 641 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.83 Search for helices and strands: 0 residues in 0 chains, 650 seeds are put forward Round 1: 40 peptides, 8 chains. Longest chain 11 peptides. Score 0.306 Round 2: 38 peptides, 7 chains. Longest chain 9 peptides. Score 0.342 Round 3: 42 peptides, 6 chains. Longest chain 11 peptides. Score 0.468 Round 4: 40 peptides, 6 chains. Longest chain 11 peptides. Score 0.440 Round 5: 38 peptides, 6 chains. Longest chain 12 peptides. Score 0.410 Taking the results from Round 3 Chains 6, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1257 reflections ( 99.60 % complete ) and 1377 restraints for refining 657 atoms. 1239 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2002 (Rfree = 0.000) for 657 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 32: After refmac, R = 0.2230 (Rfree = 0.000) for 657 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 33: After refmac, R = 0.1690 (Rfree = 0.000) for 653 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.1601 (Rfree = 0.000) for 648 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.1589 (Rfree = 0.000) for 644 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 657 seeds are put forward Round 1: 34 peptides, 7 chains. Longest chain 7 peptides. Score 0.276 Round 2: 40 peptides, 7 chains. Longest chain 9 peptides. Score 0.374 Round 3: 40 peptides, 6 chains. Longest chain 13 peptides. Score 0.440 Round 4: 39 peptides, 6 chains. Longest chain 14 peptides. Score 0.425 Round 5: 38 peptides, 7 chains. Longest chain 11 peptides. Score 0.342 Taking the results from Round 3 Chains 6, Residues 34, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1257 reflections ( 99.60 % complete ) and 1318 restraints for refining 646 atoms. 1188 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2082 (Rfree = 0.000) for 646 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 37: After refmac, R = 0.1866 (Rfree = 0.000) for 641 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.1750 (Rfree = 0.000) for 643 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.1700 (Rfree = 0.000) for 645 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.1665 (Rfree = 0.000) for 643 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.80 Search for helices and strands: 0 residues in 0 chains, 655 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 8 peptides. Score 0.258 Round 2: 32 peptides, 7 chains. Longest chain 6 peptides. Score 0.241 Round 3: 33 peptides, 6 chains. Longest chain 9 peptides. Score 0.331 Round 4: 28 peptides, 4 chains. Longest chain 10 peptides. Score 0.395 Round 5: 31 peptides, 5 chains. Longest chain 9 peptides. Score 0.370 Taking the results from Round 4 Chains 4, Residues 24, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1257 reflections ( 99.60 % complete ) and 1446 restraints for refining 657 atoms. 1354 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2114 (Rfree = 0.000) for 657 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 42: After refmac, R = 0.1998 (Rfree = 0.000) for 656 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.1910 (Rfree = 0.000) for 655 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.1813 (Rfree = 0.000) for 652 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.1790 (Rfree = 0.000) for 651 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.81 Search for helices and strands: 0 residues in 0 chains, 661 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 7 peptides. Score 0.237 Round 2: 43 peptides, 8 chains. Longest chain 8 peptides. Score 0.354 Round 3: 44 peptides, 7 chains. Longest chain 8 peptides. Score 0.434 Round 4: 41 peptides, 7 chains. Longest chain 10 peptides. Score 0.389 Round 5: 46 peptides, 8 chains. Longest chain 9 peptides. Score 0.399 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 37, 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 2ilb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1257 reflections ( 99.60 % complete ) and 1491 restraints for refining 687 atoms. 1350 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2159 (Rfree = 0.000) for 687 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2003 (Rfree = 0.000) for 684 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1915 (Rfree = 0.000) for 681 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Cycle 49: After refmac, R = 0.1838 (Rfree = 0.000) for 680 atoms. TimeTaking 20