Sun 23 Dec 22:23:05 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 2hcf-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hcf-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hcf-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-4.0-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/2hcf-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-4.0-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 22:23:15 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/2hcf-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-4.0-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 141 and 0 Target number of residues in the AU: 141 Target solvent content: 0.6606 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 234 Adjusted target solvent content: 0.44 Input MTZ file: 2hcf-4.0-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: 37.750 71.590 83.200 90.000 90.000 90.000 Input sequence file: 2hcf-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.65 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: 54.266 4.001 Wilson plot Bfac: 84.82 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2097 reflections ( 99.10 % complete ) and 0 restraints for refining 2074 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3494 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2956 (Rfree = 0.000) for 2074 atoms. Found 9 (9 requested) and removed 37 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 4.06 Search for helices and strands: 0 residues in 0 chains, 2094 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 7 peptides. Score 0.276 Round 2: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.430 Round 3: 97 peptides, 15 chains. Longest chain 10 peptides. Score 0.457 Round 4: 91 peptides, 14 chains. Longest chain 12 peptides. Score 0.446 Round 5: 96 peptides, 15 chains. Longest chain 12 peptides. Score 0.450 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 ------------------------------------------------------ 2097 reflections ( 99.10 % complete ) and 4224 restraints for refining 1691 atoms. 3911 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2270 (Rfree = 0.000) for 1691 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 2: After refmac, R = 0.2174 (Rfree = 0.000) for 1665 atoms. Found 4 (8 requested) and removed 12 (4 requested) atoms. Cycle 3: After refmac, R = 0.2273 (Rfree = 0.000) for 1653 atoms. Found 3 (7 requested) and removed 11 (3 requested) atoms. Cycle 4: After refmac, R = 0.1957 (Rfree = 0.000) for 1639 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2232 (Rfree = 0.000) for 1635 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 4.02 Search for helices and strands: 0 residues in 0 chains, 1700 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.311 Round 2: 88 peptides, 15 chains. Longest chain 8 peptides. Score 0.394 Round 3: 95 peptides, 16 chains. Longest chain 8 peptides. Score 0.413 Round 4: 93 peptides, 13 chains. Longest chain 15 peptides. Score 0.489 Round 5: 107 peptides, 16 chains. Longest chain 21 peptides. Score 0.493 Taking the results from Round 5 Chains 16, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.10 % complete ) and 3946 restraints for refining 1667 atoms. 3598 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2128 (Rfree = 0.000) for 1667 atoms. Found 6 (7 requested) and removed 18 (3 requested) atoms. Cycle 7: After refmac, R = 0.1864 (Rfree = 0.000) for 1645 atoms. Found 0 (7 requested) and removed 10 (3 requested) atoms. Cycle 8: After refmac, R = 0.1831 (Rfree = 0.000) for 1633 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 9: After refmac, R = 0.1837 (Rfree = 0.000) for 1626 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 10: After refmac, R = 0.1762 (Rfree = 0.000) for 1622 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 4.03 Search for helices and strands: 0 residues in 0 chains, 1690 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.271 Round 2: 90 peptides, 15 chains. Longest chain 16 peptides. Score 0.408 Round 3: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.388 Round 4: 102 peptides, 14 chains. Longest chain 13 peptides. Score 0.518 Round 5: 101 peptides, 17 chains. Longest chain 10 peptides. Score 0.425 Taking the results from Round 4 Chains 14, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.10 % complete ) and 3990 restraints for refining 1670 atoms. 3652 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1907 (Rfree = 0.000) for 1670 atoms. Found 3 (7 requested) and removed 10 (3 requested) atoms. Cycle 12: After refmac, R = 0.1895 (Rfree = 0.000) for 1653 atoms. Found 5 (7 requested) and removed 9 (3 requested) atoms. Cycle 13: After refmac, R = 0.1802 (Rfree = 0.000) for 1645 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.1740 (Rfree = 0.000) for 1642 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 15: After refmac, R = 0.1810 (Rfree = 0.000) for 1634 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 4.12 Search for helices and strands: 0 residues in 0 chains, 1703 seeds are put forward Round 1: 77 peptides, 14 chains. Longest chain 8 peptides. Score 0.344 Round 2: 89 peptides, 15 chains. Longest chain 9 peptides. Score 0.401 Round 3: 87 peptides, 15 chains. Longest chain 9 peptides. Score 0.387 Round 4: 101 peptides, 15 chains. Longest chain 14 peptides. Score 0.483 Round 5: 100 peptides, 16 chains. Longest chain 11 peptides. Score 0.448 Taking the results from Round 4 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.10 % complete ) and 3830 restraints for refining 1691 atoms. 3441 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2091 (Rfree = 0.000) for 1691 atoms. Found 3 (8 requested) and removed 16 (4 requested) atoms. Cycle 17: After refmac, R = 0.1950 (Rfree = 0.000) for 1667 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 18: After refmac, R = 0.1934 (Rfree = 0.000) for 1661 atoms. Found 4 (7 requested) and removed 12 (3 requested) atoms. Cycle 19: After refmac, R = 0.1799 (Rfree = 0.000) for 1643 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.1846 (Rfree = 0.000) for 1636 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 4.05 Search for helices and strands: 0 residues in 0 chains, 1691 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 7 peptides. Score 0.262 Round 2: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.295 Round 3: 81 peptides, 14 chains. Longest chain 9 peptides. Score 0.375 Round 4: 85 peptides, 15 chains. Longest chain 13 peptides. Score 0.372 Round 5: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.382 Taking the results from Round 5 Chains 14, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.10 % complete ) and 4105 restraints for refining 1691 atoms. 3847 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1836 (Rfree = 0.000) for 1691 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.1864 (Rfree = 0.000) for 1684 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 23: After refmac, R = 0.1802 (Rfree = 0.000) for 1674 atoms. Found 4 (7 requested) and removed 10 (3 requested) atoms. Cycle 24: After refmac, R = 0.1474 (Rfree = 0.000) for 1664 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.1533 (Rfree = 0.000) for 1658 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 4.06 Search for helices and strands: 0 residues in 0 chains, 1737 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.301 Round 2: 73 peptides, 14 chains. Longest chain 13 peptides. Score 0.313 Round 3: 80 peptides, 15 chains. Longest chain 11 peptides. Score 0.334 Round 4: 66 peptides, 11 chains. Longest chain 15 peptides. Score 0.361 Round 5: 71 peptides, 14 chains. Longest chain 6 peptides. Score 0.297 Taking the results from Round 4 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.10 % complete ) and 4086 restraints for refining 1691 atoms. 3823 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1980 (Rfree = 0.000) for 1691 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 27: After refmac, R = 0.1765 (Rfree = 0.000) for 1674 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.1705 (Rfree = 0.000) for 1666 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.1620 (Rfree = 0.000) for 1659 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1697 (Rfree = 0.000) for 1656 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 4.06 Search for helices and strands: 0 residues in 0 chains, 1715 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 6 peptides. Score 0.244 Round 2: 81 peptides, 15 chains. Longest chain 7 peptides. Score 0.342 Round 3: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.317 Round 4: 89 peptides, 16 chains. Longest chain 8 peptides. Score 0.370 Round 5: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.311 Taking the results from Round 4 Chains 16, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.10 % complete ) and 4126 restraints for refining 1691 atoms. 3850 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1829 (Rfree = 0.000) for 1691 atoms. Found 3 (8 requested) and removed 12 (4 requested) atoms. Cycle 32: After refmac, R = 0.1819 (Rfree = 0.000) for 1671 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. Cycle 33: After refmac, R = 0.1658 (Rfree = 0.000) for 1661 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.1705 (Rfree = 0.000) for 1657 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1572 (Rfree = 0.000) for 1650 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 4.05 Search for helices and strands: 0 residues in 0 chains, 1714 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 7 peptides. Score 0.244 Round 2: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.363 Round 3: 82 peptides, 15 chains. Longest chain 8 peptides. Score 0.350 Round 4: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.313 Round 5: 66 peptides, 12 chains. Longest chain 8 peptides. Score 0.326 Taking the results from Round 2 Chains 16, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.10 % complete ) and 4063 restraints for refining 1682 atoms. 3791 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1736 (Rfree = 0.000) for 1682 atoms. Found 4 (7 requested) and removed 12 (3 requested) atoms. Cycle 37: After refmac, R = 0.1754 (Rfree = 0.000) for 1667 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.1729 (Rfree = 0.000) for 1661 atoms. Found 5 (7 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.2159 (Rfree = 0.000) for 1658 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.1726 (Rfree = 0.000) for 1655 atoms. Found 0 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 4.10 Search for helices and strands: 0 residues in 0 chains, 1712 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 6 peptides. Score 0.243 Round 2: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.340 Round 3: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.342 Round 4: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.372 Round 5: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.317 Taking the results from Round 4 Chains 15, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2097 reflections ( 99.10 % complete ) and 4083 restraints for refining 1691 atoms. 3818 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1993 (Rfree = 0.000) for 1691 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 42: After refmac, R = 0.1750 (Rfree = 0.000) for 1680 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.1748 (Rfree = 0.000) for 1669 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 44: After refmac, R = 0.1481 (Rfree = 0.000) for 1661 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.1637 (Rfree = 0.000) for 1654 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 4.04 Search for helices and strands: 0 residues in 0 chains, 1696 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 7 peptides. Score 0.205 Round 2: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.257 Round 3: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.279 Round 4: 61 peptides, 12 chains. Longest chain 7 peptides. Score 0.285 Round 5: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.296 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 47, 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 2hcf-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2097 reflections ( 99.10 % complete ) and 4147 restraints for refining 1652 atoms. 3970 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1785 (Rfree = 0.000) for 1652 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1783 (Rfree = 0.000) for 1643 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1720 (Rfree = 0.000) for 1637 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1536 (Rfree = 0.000) for 1633 atoms. TimeTaking 28.67