Sun 23 Dec 22:23:14 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 2huj-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2huj-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2huj-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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/2huj-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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 22:23:22 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/2huj-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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 131 and 0 Target number of residues in the AU: 131 Target solvent content: 0.6319 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 140 Adjusted target solvent content: 0.61 Input MTZ file: 2huj-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: 182 Cell parameters: 100.110 100.110 66.570 90.000 90.000 120.000 Input sequence file: 2huj-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 target number of atoms Had to go as low as 0.85 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: 86.698 3.601 Wilson plot Bfac: 66.98 2526 reflections ( 99.64 % complete ) and 0 restraints for refining 1246 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3442 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2575 (Rfree = 0.000) for 1246 atoms. Found 5 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 2.92 Search for helices and strands: 0 residues in 0 chains, 1275 seeds are put forward Round 1: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.356 Round 2: 66 peptides, 8 chains. Longest chain 13 peptides. Score 0.494 Round 3: 75 peptides, 9 chains. Longest chain 13 peptides. Score 0.527 Round 4: 72 peptides, 7 chains. Longest chain 15 peptides. Score 0.572 Round 5: 69 peptides, 9 chains. Longest chain 14 peptides. Score 0.482 Taking the results from Round 4 Chains 7, Residues 65, Estimated correctness of the model 3.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2526 reflections ( 99.64 % complete ) and 2342 restraints for refining 1014 atoms. 2089 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2723 (Rfree = 0.000) for 1014 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 2: After refmac, R = 0.2647 (Rfree = 0.000) for 998 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2613 (Rfree = 0.000) for 985 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 4: After refmac, R = 0.2642 (Rfree = 0.000) for 979 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2559 (Rfree = 0.000) for 975 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 2.90 Search for helices and strands: 0 residues in 0 chains, 1036 seeds are put forward Round 1: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.409 Round 2: 83 peptides, 11 chains. Longest chain 14 peptides. Score 0.518 Round 3: 79 peptides, 11 chains. Longest chain 15 peptides. Score 0.489 Round 4: 73 peptides, 10 chains. Longest chain 16 peptides. Score 0.477 Round 5: 75 peptides, 11 chains. Longest chain 15 peptides. Score 0.458 Taking the results from Round 2 Chains 12, Residues 72, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2526 reflections ( 99.64 % complete ) and 2023 restraints for refining 960 atoms. 1699 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2707 (Rfree = 0.000) for 960 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 7: After refmac, R = 0.2495 (Rfree = 0.000) for 945 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 8: After refmac, R = 0.2492 (Rfree = 0.000) for 938 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2464 (Rfree = 0.000) for 937 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.2459 (Rfree = 0.000) for 932 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 2.96 Search for helices and strands: 0 residues in 0 chains, 981 seeds are put forward Round 1: 74 peptides, 12 chains. Longest chain 13 peptides. Score 0.414 Round 2: 83 peptides, 11 chains. Longest chain 13 peptides. Score 0.518 Round 3: 82 peptides, 11 chains. Longest chain 21 peptides. Score 0.511 Round 4: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.446 Round 5: 83 peptides, 11 chains. Longest chain 10 peptides. Score 0.518 Taking the results from Round 5 Chains 11, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2526 reflections ( 99.64 % complete ) and 2227 restraints for refining 1012 atoms. 1950 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2814 (Rfree = 0.000) for 1012 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 12: After refmac, R = 0.2586 (Rfree = 0.000) for 995 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 13: After refmac, R = 0.2462 (Rfree = 0.000) for 990 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 14: After refmac, R = 0.2452 (Rfree = 0.000) for 989 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2292 (Rfree = 0.000) for 987 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.02 Search for helices and strands: 0 residues in 0 chains, 1058 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.285 Round 2: 76 peptides, 10 chains. Longest chain 13 peptides. Score 0.500 Round 3: 71 peptides, 12 chains. Longest chain 11 peptides. Score 0.388 Round 4: 74 peptides, 11 chains. Longest chain 10 peptides. Score 0.450 Round 5: 66 peptides, 10 chains. Longest chain 9 peptides. Score 0.421 Taking the results from Round 2 Chains 10, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2526 reflections ( 99.64 % complete ) and 2320 restraints for refining 1011 atoms. 2066 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2701 (Rfree = 0.000) for 1011 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 17: After refmac, R = 0.2405 (Rfree = 0.000) for 1004 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2305 (Rfree = 0.000) for 1001 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.2272 (Rfree = 0.000) for 995 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.2117 (Rfree = 0.000) for 995 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 1050 seeds are put forward Round 1: 77 peptides, 13 chains. Longest chain 16 peptides. Score 0.402 Round 2: 85 peptides, 15 chains. Longest chain 8 peptides. Score 0.397 Round 3: 85 peptides, 13 chains. Longest chain 9 peptides. Score 0.467 Round 4: 82 peptides, 11 chains. Longest chain 13 peptides. Score 0.511 Round 5: 73 peptides, 12 chains. Longest chain 11 peptides. Score 0.405 Taking the results from Round 4 Chains 11, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2526 reflections ( 99.64 % complete ) and 2241 restraints for refining 1016 atoms. 1968 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2487 (Rfree = 0.000) for 1016 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 22: After refmac, R = 0.2344 (Rfree = 0.000) for 1001 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 23: After refmac, R = 0.2285 (Rfree = 0.000) for 996 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.2255 (Rfree = 0.000) for 991 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2259 (Rfree = 0.000) for 985 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 2.85 Search for helices and strands: 0 residues in 0 chains, 1021 seeds are put forward Round 1: 73 peptides, 13 chains. Longest chain 16 peptides. Score 0.368 Round 2: 79 peptides, 13 chains. Longest chain 12 peptides. Score 0.419 Round 3: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.419 Round 4: 75 peptides, 11 chains. Longest chain 12 peptides. Score 0.458 Round 5: 67 peptides, 11 chains. Longest chain 9 peptides. Score 0.392 Taking the results from Round 4 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2526 reflections ( 99.64 % complete ) and 2357 restraints for refining 1016 atoms. 2112 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2613 (Rfree = 0.000) for 1016 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.2392 (Rfree = 0.000) for 1008 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.2329 (Rfree = 0.000) for 1001 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.2261 (Rfree = 0.000) for 999 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.2210 (Rfree = 0.000) for 994 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 2.91 Search for helices and strands: 0 residues in 0 chains, 1056 seeds are put forward Round 1: 61 peptides, 11 chains. Longest chain 10 peptides. Score 0.338 Round 2: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.385 Round 3: 76 peptides, 11 chains. Longest chain 15 peptides. Score 0.466 Round 4: 76 peptides, 12 chains. Longest chain 13 peptides. Score 0.430 Round 5: 70 peptides, 11 chains. Longest chain 15 peptides. Score 0.417 Taking the results from Round 3 Chains 11, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2526 reflections ( 99.64 % complete ) and 2308 restraints for refining 1016 atoms. 2059 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2387 (Rfree = 0.000) for 1016 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 32: After refmac, R = 0.2108 (Rfree = 0.000) for 1010 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2120 (Rfree = 0.000) for 1007 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.2030 (Rfree = 0.000) for 1004 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1923 (Rfree = 0.000) for 1004 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 2.85 Search for helices and strands: 0 residues in 0 chains, 1058 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 8 peptides. Score 0.250 Round 2: 69 peptides, 11 chains. Longest chain 14 peptides. Score 0.409 Round 3: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.458 Round 4: 76 peptides, 12 chains. Longest chain 10 peptides. Score 0.430 Round 5: 77 peptides, 10 chains. Longest chain 15 peptides. Score 0.508 Taking the results from Round 5 Chains 10, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2526 reflections ( 99.64 % complete ) and 2292 restraints for refining 1012 atoms. 2034 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2276 (Rfree = 0.000) for 1012 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2099 (Rfree = 0.000) for 1010 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.2002 (Rfree = 0.000) for 1011 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.1977 (Rfree = 0.000) for 1007 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1967 (Rfree = 0.000) for 1006 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 2.93 Search for helices and strands: 0 residues in 0 chains, 1057 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 10 peptides. Score 0.326 Round 2: 73 peptides, 10 chains. Longest chain 15 peptides. Score 0.477 Round 3: 80 peptides, 11 chains. Longest chain 16 peptides. Score 0.496 Round 4: 82 peptides, 11 chains. Longest chain 15 peptides. Score 0.511 Round 5: 76 peptides, 11 chains. Longest chain 15 peptides. Score 0.466 Taking the results from Round 4 Chains 11, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2526 reflections ( 99.64 % complete ) and 2236 restraints for refining 1015 atoms. 1963 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2249 (Rfree = 0.000) for 1015 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.2198 (Rfree = 0.000) for 1008 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.2176 (Rfree = 0.000) for 1003 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.2121 (Rfree = 0.000) for 1001 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.2111 (Rfree = 0.000) for 999 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 1067 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.276 Round 2: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.411 Round 3: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.394 Round 4: 76 peptides, 11 chains. Longest chain 14 peptides. Score 0.466 Round 5: 81 peptides, 12 chains. Longest chain 14 peptides. Score 0.470 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 69, 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 2huj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2526 reflections ( 99.64 % complete ) and 2271 restraints for refining 1015 atoms. 2007 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2548 (Rfree = 0.000) for 1015 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2314 (Rfree = 0.000) for 1003 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2370 (Rfree = 0.000) for 997 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2167 (Rfree = 0.000) for 990 atoms. TimeTaking 28.03