Sun 23 Dec 22:23:08 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 2ia7-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.6-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/2ia7-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.6-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 22:23:18 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/2ia7-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.6-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 78 and 0 Target number of residues in the AU: 78 Target solvent content: 0.6257 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 134 Adjusted target solvent content: 0.36 Input MTZ file: 2ia7-3.6-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: 19 Cell parameters: 40.240 43.350 64.660 90.000 90.000 90.000 Input sequence file: 2ia7-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1072 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: 26.833 3.600 Wilson plot Bfac: 63.65 1433 reflections ( 97.48 % complete ) and 0 restraints for refining 1182 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3513 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3410 (Rfree = 0.000) for 1182 atoms. Found 7 (7 requested) and removed 24 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 4.00 Search for helices and strands: 0 residues in 0 chains, 1188 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 5 peptides. Score 0.221 Round 2: 37 peptides, 7 chains. Longest chain 9 peptides. Score 0.320 Round 3: 38 peptides, 7 chains. Longest chain 9 peptides. Score 0.336 Round 4: 44 peptides, 6 chains. Longest chain 14 peptides. Score 0.485 Round 5: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.362 Taking the results from Round 4 Chains 6, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1433 reflections ( 97.48 % complete ) and 2353 restraints for refining 972 atoms. 2207 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3077 (Rfree = 0.000) for 972 atoms. Found 1 (6 requested) and removed 12 (3 requested) atoms. Cycle 2: After refmac, R = 0.3654 (Rfree = 0.000) for 938 atoms. Found 4 (6 requested) and removed 18 (3 requested) atoms. Cycle 3: After refmac, R = 0.3156 (Rfree = 0.000) for 911 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 4: After refmac, R = 0.3598 (Rfree = 0.000) for 903 atoms. Found 4 (5 requested) and removed 10 (2 requested) atoms. Cycle 5: After refmac, R = 0.3408 (Rfree = 0.000) for 891 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 4.49 Search for helices and strands: 0 residues in 0 chains, 912 seeds are put forward Round 1: 37 peptides, 9 chains. Longest chain 5 peptides. Score 0.184 Round 2: 45 peptides, 9 chains. Longest chain 8 peptides. Score 0.313 Round 3: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.415 Round 4: 48 peptides, 8 chains. Longest chain 10 peptides. Score 0.419 Round 5: 49 peptides, 8 chains. Longest chain 10 peptides. Score 0.433 Taking the results from Round 5 Chains 8, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1433 reflections ( 97.48 % complete ) and 1730 restraints for refining 769 atoms. 1574 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2712 (Rfree = 0.000) for 769 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 7: After refmac, R = 0.2350 (Rfree = 0.000) for 764 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 8: After refmac, R = 0.2183 (Rfree = 0.000) for 757 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 9: After refmac, R = 0.2154 (Rfree = 0.000) for 754 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.2141 (Rfree = 0.000) for 750 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 4.15 Search for helices and strands: 0 residues in 0 chains, 765 seeds are put forward Round 1: 34 peptides, 6 chains. Longest chain 8 peptides. Score 0.341 Round 2: 41 peptides, 7 chains. Longest chain 8 peptides. Score 0.381 Round 3: 47 peptides, 8 chains. Longest chain 14 peptides. Score 0.405 Round 4: 49 peptides, 8 chains. Longest chain 12 peptides. Score 0.433 Round 5: 48 peptides, 8 chains. Longest chain 13 peptides. Score 0.419 Taking the results from Round 4 Chains 8, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1433 reflections ( 97.48 % complete ) and 1743 restraints for refining 776 atoms. 1587 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2489 (Rfree = 0.000) for 776 atoms. Found 3 (4 requested) and removed 10 (2 requested) atoms. Cycle 12: After refmac, R = 0.2375 (Rfree = 0.000) for 767 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 13: After refmac, R = 0.2171 (Rfree = 0.000) for 768 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Cycle 14: After refmac, R = 0.2633 (Rfree = 0.000) for 763 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 15: After refmac, R = 0.2269 (Rfree = 0.000) for 760 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 4.13 Search for helices and strands: 0 residues in 0 chains, 786 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.285 Round 2: 39 peptides, 7 chains. Longest chain 11 peptides. Score 0.351 Round 3: 47 peptides, 7 chains. Longest chain 11 peptides. Score 0.465 Round 4: 52 peptides, 7 chains. Longest chain 11 peptides. Score 0.529 Round 5: 50 peptides, 7 chains. Longest chain 11 peptides. Score 0.504 Taking the results from Round 4 Chains 8, Residues 45, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1433 reflections ( 97.48 % complete ) and 1799 restraints for refining 835 atoms. 1589 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3714 (Rfree = 0.000) for 835 atoms. Found 5 (5 requested) and removed 30 (2 requested) atoms. Cycle 17: After refmac, R = 0.2857 (Rfree = 0.000) for 800 atoms. Found 0 (5 requested) and removed 7 (2 requested) atoms. Cycle 18: After refmac, R = 0.2680 (Rfree = 0.000) for 788 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.2577 (Rfree = 0.000) for 785 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2459 (Rfree = 0.000) for 785 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 4.07 Search for helices and strands: 0 residues in 0 chains, 797 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.236 Round 2: 43 peptides, 9 chains. Longest chain 7 peptides. Score 0.282 Round 3: 55 peptides, 10 chains. Longest chain 8 peptides. Score 0.398 Round 4: 49 peptides, 7 chains. Longest chain 11 peptides. Score 0.491 Round 5: 51 peptides, 8 chains. Longest chain 7 peptides. Score 0.460 Taking the results from Round 4 Chains 7, Residues 42, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1433 reflections ( 97.48 % complete ) and 1803 restraints for refining 775 atoms. 1642 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2534 (Rfree = 0.000) for 775 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 22: After refmac, R = 0.2240 (Rfree = 0.000) for 770 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 23: After refmac, R = 0.2100 (Rfree = 0.000) for 770 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.2021 (Rfree = 0.000) for 768 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 25: After refmac, R = 0.1967 (Rfree = 0.000) for 762 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 4.03 Search for helices and strands: 0 residues in 0 chains, 786 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 7 peptides. Score 0.236 Round 2: 48 peptides, 9 chains. Longest chain 11 peptides. Score 0.358 Round 3: 51 peptides, 8 chains. Longest chain 12 peptides. Score 0.460 Round 4: 52 peptides, 9 chains. Longest chain 12 peptides. Score 0.415 Round 5: 53 peptides, 9 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 3 Chains 8, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1433 reflections ( 97.48 % complete ) and 1700 restraints for refining 774 atoms. 1536 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2141 (Rfree = 0.000) for 774 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 27: After refmac, R = 0.2249 (Rfree = 0.000) for 771 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.1988 (Rfree = 0.000) for 769 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.1918 (Rfree = 0.000) for 766 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.1756 (Rfree = 0.000) for 767 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.94 Search for helices and strands: 0 residues in 0 chains, 786 seeds are put forward Round 1: 39 peptides, 9 chains. Longest chain 6 peptides. Score 0.218 Round 2: 43 peptides, 6 chains. Longest chain 12 peptides. Score 0.472 Round 3: 45 peptides, 8 chains. Longest chain 9 peptides. Score 0.377 Round 4: 48 peptides, 8 chains. Longest chain 12 peptides. Score 0.419 Round 5: 41 peptides, 7 chains. Longest chain 8 peptides. Score 0.381 Taking the results from Round 2 Chains 6, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1433 reflections ( 97.48 % complete ) and 1696 restraints for refining 776 atoms. 1554 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2071 (Rfree = 0.000) for 776 atoms. Found 4 (4 requested) and removed 14 (2 requested) atoms. Cycle 32: After refmac, R = 0.2208 (Rfree = 0.000) for 764 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. Cycle 33: After refmac, R = 0.1922 (Rfree = 0.000) for 758 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.1855 (Rfree = 0.000) for 755 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.1728 (Rfree = 0.000) for 755 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 4.00 Search for helices and strands: 0 residues in 0 chains, 775 seeds are put forward Round 1: 33 peptides, 8 chains. Longest chain 5 peptides. Score 0.184 Round 2: 42 peptides, 7 chains. Longest chain 8 peptides. Score 0.396 Round 3: 46 peptides, 8 chains. Longest chain 10 peptides. Score 0.391 Round 4: 45 peptides, 7 chains. Longest chain 11 peptides. Score 0.438 Round 5: 45 peptides, 5 chains. Longest chain 15 peptides. Score 0.555 Taking the results from Round 5 Chains 5, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1433 reflections ( 97.48 % complete ) and 1661 restraints for refining 794 atoms. 1506 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1956 (Rfree = 0.000) for 794 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 37: After refmac, R = 0.1824 (Rfree = 0.000) for 790 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.1832 (Rfree = 0.000) for 787 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.1674 (Rfree = 0.000) for 786 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.1545 (Rfree = 0.000) for 783 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.91 Search for helices and strands: 0 residues in 0 chains, 790 seeds are put forward Round 1: 43 peptides, 9 chains. Longest chain 7 peptides. Score 0.282 Round 2: 53 peptides, 9 chains. Longest chain 9 peptides. Score 0.429 Round 3: 50 peptides, 7 chains. Longest chain 16 peptides. Score 0.504 Round 4: 52 peptides, 8 chains. Longest chain 9 peptides. Score 0.473 Round 5: 50 peptides, 7 chains. Longest chain 16 peptides. Score 0.504 Taking the results from Round 5 Chains 7, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1433 reflections ( 97.48 % complete ) and 1601 restraints for refining 776 atoms. 1436 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2097 (Rfree = 0.000) for 776 atoms. Found 3 (4 requested) and removed 30 (2 requested) atoms. Cycle 42: After refmac, R = 0.3051 (Rfree = 0.000) for 743 atoms. Found 2 (4 requested) and removed 10 (2 requested) atoms. Cycle 43: After refmac, R = 0.2361 (Rfree = 0.000) for 726 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.2114 (Rfree = 0.000) for 724 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.1986 (Rfree = 0.000) for 723 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.98 Search for helices and strands: 0 residues in 0 chains, 756 seeds are put forward Round 1: 37 peptides, 9 chains. Longest chain 5 peptides. Score 0.184 Round 2: 36 peptides, 7 chains. Longest chain 8 peptides. Score 0.304 Round 3: 34 peptides, 6 chains. Longest chain 8 peptides. Score 0.341 Round 4: 35 peptides, 6 chains. Longest chain 8 peptides. Score 0.357 Round 5: 32 peptides, 5 chains. Longest chain 11 peptides. Score 0.379 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 27, 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 2ia7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1433 reflections ( 97.48 % complete ) and 1606 restraints for refining 753 atoms. 1503 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1939 (Rfree = 0.000) for 753 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1715 (Rfree = 0.000) for 748 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1777 (Rfree = 0.000) for 746 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1646 (Rfree = 0.000) for 744 atoms. TimeTaking 21.08