Sun 23 Dec 22:22:52 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 2aj6-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aj6-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aj6-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-4.0-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/2aj6-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-4.0-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 22:23:00 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/2aj6-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-4.0-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 85 and 0 Target number of residues in the AU: 85 Target solvent content: 0.6616 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 159 Adjusted target solvent content: 0.37 Input MTZ file: 2aj6-4.0-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: 23 Cell parameters: 40.044 74.871 90.673 90.000 90.000 90.000 Input sequence file: 2aj6-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1272 target number of atoms Had to go as low as 0.40 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: 28.866 4.001 Wilson plot Bfac: 85.17 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1255 reflections ( 97.97 % complete ) and 0 restraints for refining 1413 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3286 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2705 (Rfree = 0.000) for 1413 atoms. Found 5 (6 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 4.50 Search for helices and strands: 0 residues in 0 chains, 1422 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.279 Round 2: 61 peptides, 9 chains. Longest chain 12 peptides. Score 0.486 Round 3: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.374 Round 4: 74 peptides, 10 chains. Longest chain 12 peptides. Score 0.572 Round 5: 75 peptides, 9 chains. Longest chain 15 peptides. Score 0.620 Taking the results from Round 5 Chains 9, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 97.97 % complete ) and 2677 restraints for refining 1106 atoms. 2422 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2230 (Rfree = 0.000) for 1106 atoms. Found 1 (5 requested) and removed 11 (2 requested) atoms. Cycle 2: After refmac, R = 0.2062 (Rfree = 0.000) for 1078 atoms. Found 0 (5 requested) and removed 9 (2 requested) atoms. Cycle 3: After refmac, R = 0.1973 (Rfree = 0.000) for 1063 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.1806 (Rfree = 0.000) for 1055 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 5: After refmac, R = 0.1728 (Rfree = 0.000) for 1050 atoms. Found 0 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 4.45 Search for helices and strands: 0 residues in 0 chains, 1079 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 11 peptides. Score 0.350 Round 2: 70 peptides, 12 chains. Longest chain 12 peptides. Score 0.443 Round 3: 73 peptides, 10 chains. Longest chain 18 peptides. Score 0.562 Round 4: 76 peptides, 10 chains. Longest chain 18 peptides. Score 0.590 Round 5: 82 peptides, 11 chains. Longest chain 19 peptides. Score 0.603 Taking the results from Round 5 Chains 11, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 97.97 % complete ) and 2432 restraints for refining 1039 atoms. 2159 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2358 (Rfree = 0.000) for 1039 atoms. Found 1 (4 requested) and removed 10 (2 requested) atoms. Cycle 7: After refmac, R = 0.2185 (Rfree = 0.000) for 1020 atoms. Found 1 (4 requested) and removed 7 (2 requested) atoms. Cycle 8: After refmac, R = 0.1959 (Rfree = 0.000) for 1012 atoms. Found 0 (4 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.1866 (Rfree = 0.000) for 1006 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.1783 (Rfree = 0.000) for 1003 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 4.41 Search for helices and strands: 0 residues in 0 chains, 1020 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 9 peptides. Score 0.297 Round 2: 73 peptides, 11 chains. Longest chain 13 peptides. Score 0.520 Round 3: 79 peptides, 11 chains. Longest chain 12 peptides. Score 0.577 Round 4: 78 peptides, 11 chains. Longest chain 12 peptides. Score 0.568 Round 5: 76 peptides, 10 chains. Longest chain 12 peptides. Score 0.590 Taking the results from Round 5 Chains 10, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 97.97 % complete ) and 2513 restraints for refining 1060 atoms. 2259 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2085 (Rfree = 0.000) for 1060 atoms. Found 3 (5 requested) and removed 14 (2 requested) atoms. Cycle 12: After refmac, R = 0.1998 (Rfree = 0.000) for 1037 atoms. Found 0 (4 requested) and removed 7 (2 requested) atoms. Cycle 13: After refmac, R = 0.2270 (Rfree = 0.000) for 1029 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.1797 (Rfree = 0.000) for 1028 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.1795 (Rfree = 0.000) for 1026 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 4.49 Search for helices and strands: 0 residues in 0 chains, 1064 seeds are put forward Round 1: 46 peptides, 9 chains. Longest chain 8 peptides. Score 0.308 Round 2: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.404 Round 3: 61 peptides, 11 chains. Longest chain 10 peptides. Score 0.389 Round 4: 60 peptides, 10 chains. Longest chain 11 peptides. Score 0.427 Round 5: 62 peptides, 10 chains. Longest chain 12 peptides. Score 0.450 Taking the results from Round 5 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 97.97 % complete ) and 2477 restraints for refining 1032 atoms. 2279 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2120 (Rfree = 0.000) for 1032 atoms. Found 2 (4 requested) and removed 9 (2 requested) atoms. Cycle 17: After refmac, R = 0.1792 (Rfree = 0.000) for 1021 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.1758 (Rfree = 0.000) for 1012 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.1821 (Rfree = 0.000) for 1010 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.1932 (Rfree = 0.000) for 1005 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 4.39 Search for helices and strands: 0 residues in 0 chains, 1032 seeds are put forward Round 1: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.311 Round 2: 56 peptides, 8 chains. Longest chain 12 peptides. Score 0.480 Round 3: 57 peptides, 8 chains. Longest chain 13 peptides. Score 0.491 Round 4: 59 peptides, 8 chains. Longest chain 13 peptides. Score 0.512 Round 5: 53 peptides, 9 chains. Longest chain 11 peptides. Score 0.396 Taking the results from Round 4 Chains 8, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 97.97 % complete ) and 2524 restraints for refining 1053 atoms. 2328 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1824 (Rfree = 0.000) for 1053 atoms. Found 3 (4 requested) and removed 9 (2 requested) atoms. Cycle 22: After refmac, R = 0.1629 (Rfree = 0.000) for 1043 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 23: After refmac, R = 0.1682 (Rfree = 0.000) for 1036 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.1683 (Rfree = 0.000) for 1035 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 25: After refmac, R = 0.1611 (Rfree = 0.000) for 1030 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 4.51 Search for helices and strands: 0 residues in 0 chains, 1061 seeds are put forward Round 1: 48 peptides, 9 chains. Longest chain 8 peptides. Score 0.334 Round 2: 50 peptides, 8 chains. Longest chain 9 peptides. Score 0.412 Round 3: 54 peptides, 8 chains. Longest chain 10 peptides. Score 0.458 Round 4: 51 peptides, 8 chains. Longest chain 11 peptides. Score 0.424 Round 5: 56 peptides, 9 chains. Longest chain 11 peptides. Score 0.431 Taking the results from Round 3 Chains 8, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 97.97 % complete ) and 2578 restraints for refining 1055 atoms. 2402 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1779 (Rfree = 0.000) for 1055 atoms. Found 3 (5 requested) and removed 8 (2 requested) atoms. Cycle 27: After refmac, R = 0.1575 (Rfree = 0.000) for 1046 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.1610 (Rfree = 0.000) for 1043 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 29: After refmac, R = 0.1829 (Rfree = 0.000) for 1038 atoms. Found 0 (4 requested) and removed 6 (2 requested) atoms. Cycle 30: After refmac, R = 0.1753 (Rfree = 0.000) for 1032 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 4.37 Search for helices and strands: 0 residues in 0 chains, 1089 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.270 Round 2: 53 peptides, 9 chains. Longest chain 11 peptides. Score 0.396 Round 3: 51 peptides, 9 chains. Longest chain 9 peptides. Score 0.371 Round 4: 53 peptides, 8 chains. Longest chain 12 peptides. Score 0.447 Round 5: 56 peptides, 9 chains. Longest chain 9 peptides. Score 0.431 Taking the results from Round 4 Chains 8, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 97.97 % complete ) and 2488 restraints for refining 1047 atoms. 2316 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1878 (Rfree = 0.000) for 1047 atoms. Found 2 (4 requested) and removed 11 (2 requested) atoms. Cycle 32: After refmac, R = 0.1679 (Rfree = 0.000) for 1035 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Cycle 33: After refmac, R = 0.1619 (Rfree = 0.000) for 1031 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 34: After refmac, R = 0.1737 (Rfree = 0.000) for 1028 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 35: After refmac, R = 0.2105 (Rfree = 0.000) for 1023 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 4.38 Search for helices and strands: 0 residues in 0 chains, 1051 seeds are put forward Round 1: 37 peptides, 7 chains. Longest chain 10 peptides. Score 0.302 Round 2: 35 peptides, 6 chains. Longest chain 8 peptides. Score 0.334 Round 3: 39 peptides, 7 chains. Longest chain 9 peptides. Score 0.329 Round 4: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.311 Round 5: 39 peptides, 7 chains. Longest chain 7 peptides. Score 0.329 Taking the results from Round 2 Chains 6, Residues 29, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 97.97 % complete ) and 2605 restraints for refining 1045 atoms. 2495 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1819 (Rfree = 0.000) for 1045 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 37: After refmac, R = 0.1659 (Rfree = 0.000) for 1042 atoms. Found 1 (4 requested) and removed 7 (2 requested) atoms. Cycle 38: After refmac, R = 0.1603 (Rfree = 0.000) for 1035 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 39: After refmac, R = 0.1529 (Rfree = 0.000) for 1030 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.1455 (Rfree = 0.000) for 1027 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 4.44 Search for helices and strands: 0 residues in 0 chains, 1057 seeds are put forward Round 1: 30 peptides, 5 chains. Longest chain 8 peptides. Score 0.327 Round 2: 32 peptides, 5 chains. Longest chain 9 peptides. Score 0.355 Round 3: 35 peptides, 5 chains. Longest chain 10 peptides. Score 0.394 Round 4: 37 peptides, 5 chains. Longest chain 11 peptides. Score 0.419 Round 5: 37 peptides, 6 chains. Longest chain 9 peptides. Score 0.361 Taking the results from Round 4 Chains 5, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1255 reflections ( 97.97 % complete ) and 2578 restraints for refining 1043 atoms. 2455 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1702 (Rfree = 0.000) for 1043 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 42: After refmac, R = 0.1581 (Rfree = 0.000) for 1041 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.1461 (Rfree = 0.000) for 1039 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.1403 (Rfree = 0.000) for 1038 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.1455 (Rfree = 0.000) for 1034 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 4.45 Search for helices and strands: 0 residues in 0 chains, 1059 seeds are put forward Round 1: 33 peptides, 6 chains. Longest chain 10 peptides. Score 0.307 Round 2: 34 peptides, 6 chains. Longest chain 10 peptides. Score 0.321 Round 3: 33 peptides, 5 chains. Longest chain 10 peptides. Score 0.368 Round 4: 35 peptides, 5 chains. Longest chain 10 peptides. Score 0.394 Round 5: 39 peptides, 6 chains. Longest chain 10 peptides. Score 0.387 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 30, 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 2aj6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1255 reflections ( 97.97 % complete ) and 2531 restraints for refining 1049 atoms. 2416 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1631 (Rfree = 0.000) for 1049 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1724 (Rfree = 0.000) for 1046 atoms. Found 0 (4 requested) and removed 0 (2 requested) atoms. Cycle 48: After refmac, R = 0.1580 (Rfree = 0.000) for 1046 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1609 (Rfree = 0.000) for 1044 atoms. TimeTaking 23.98