null Sun 23 Dec 22:22:49 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 2huh-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2huh-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2huh-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huh-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/2huh-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huh-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 22:22:59 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/2huh-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huh-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 97 and 0 Target number of residues in the AU: 97 Target solvent content: 0.6607 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 147 Adjusted target solvent content: 0.49 Input MTZ file: 2huh-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: 96 Cell parameters: 43.026 43.026 167.168 90.000 90.000 90.000 Input sequence file: 2huh-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1176 target number of atoms Had to go as low as 0.80 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: 41.792 4.000 Wilson plot Bfac: 83.66 1564 reflections ( 99.55 % complete ) and 0 restraints for refining 1300 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3674 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2889 (Rfree = 0.000) for 1300 atoms. Found 6 (6 requested) and removed 67 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 1239 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.292 Round 2: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.343 Round 3: 75 peptides, 12 chains. Longest chain 19 peptides. Score 0.466 Round 4: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.411 Round 5: 71 peptides, 12 chains. Longest chain 13 peptides. Score 0.427 Taking the results from Round 3 Chains 12, Residues 63, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.55 % complete ) and 2420 restraints for refining 1062 atoms. 2165 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2864 (Rfree = 0.000) for 1062 atoms. Found 5 (5 requested) and removed 25 (2 requested) atoms. Cycle 2: After refmac, R = 0.2352 (Rfree = 0.000) for 1039 atoms. Found 1 (4 requested) and removed 12 (2 requested) atoms. Cycle 3: After refmac, R = 0.2229 (Rfree = 0.000) for 1028 atoms. Found 1 (4 requested) and removed 10 (2 requested) atoms. Cycle 4: After refmac, R = 0.2075 (Rfree = 0.000) for 1018 atoms. Found 1 (4 requested) and removed 7 (2 requested) atoms. Cycle 5: After refmac, R = 0.2017 (Rfree = 0.000) for 1012 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.87 Search for helices and strands: 0 residues in 0 chains, 1062 seeds are put forward Round 1: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.357 Round 2: 76 peptides, 9 chains. Longest chain 17 peptides. Score 0.591 Round 3: 71 peptides, 11 chains. Longest chain 15 peptides. Score 0.469 Round 4: 73 peptides, 9 chains. Longest chain 15 peptides. Score 0.566 Round 5: 73 peptides, 8 chains. Longest chain 17 peptides. Score 0.604 Taking the results from Round 5 Chains 9, Residues 65, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.55 % complete ) and 2403 restraints for refining 1062 atoms. 2120 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2523 (Rfree = 0.000) for 1062 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 7: After refmac, R = 0.2202 (Rfree = 0.000) for 1055 atoms. Found 2 (5 requested) and removed 11 (2 requested) atoms. Cycle 8: After refmac, R = 0.2149 (Rfree = 0.000) for 1045 atoms. Found 1 (4 requested) and removed 9 (2 requested) atoms. Cycle 9: After refmac, R = 0.2110 (Rfree = 0.000) for 1037 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2069 (Rfree = 0.000) for 1035 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 1061 seeds are put forward Round 1: 62 peptides, 10 chains. Longest chain 13 peptides. Score 0.423 Round 2: 66 peptides, 9 chains. Longest chain 14 peptides. Score 0.505 Round 3: 63 peptides, 8 chains. Longest chain 13 peptides. Score 0.519 Round 4: 63 peptides, 8 chains. Longest chain 10 peptides. Score 0.519 Round 5: 68 peptides, 8 chains. Longest chain 12 peptides. Score 0.563 Taking the results from Round 5 Chains 8, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.55 % complete ) and 2519 restraints for refining 1062 atoms. 2287 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2360 (Rfree = 0.000) for 1062 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 12: After refmac, R = 0.2198 (Rfree = 0.000) for 1055 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.2081 (Rfree = 0.000) for 1051 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2000 (Rfree = 0.000) for 1048 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.1963 (Rfree = 0.000) for 1046 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.77 Search for helices and strands: 0 residues in 0 chains, 1075 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.286 Round 2: 75 peptides, 13 chains. Longest chain 11 peptides. Score 0.424 Round 3: 90 peptides, 13 chains. Longest chain 12 peptides. Score 0.559 Round 4: 87 peptides, 15 chains. Longest chain 12 peptides. Score 0.457 Round 5: 75 peptides, 13 chains. Longest chain 8 peptides. Score 0.424 Taking the results from Round 3 Chains 13, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.55 % complete ) and 2324 restraints for refining 1062 atoms. 2029 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2339 (Rfree = 0.000) for 1062 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 17: After refmac, R = 0.2137 (Rfree = 0.000) for 1054 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.2065 (Rfree = 0.000) for 1049 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. Cycle 19: After refmac, R = 0.2030 (Rfree = 0.000) for 1045 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.1998 (Rfree = 0.000) for 1041 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 1072 seeds are put forward Round 1: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.378 Round 2: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.382 Round 3: 66 peptides, 11 chains. Longest chain 11 peptides. Score 0.420 Round 4: 61 peptides, 10 chains. Longest chain 11 peptides. Score 0.413 Round 5: 64 peptides, 10 chains. Longest chain 11 peptides. Score 0.444 Taking the results from Round 5 Chains 10, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.55 % complete ) and 2523 restraints for refining 1062 atoms. 2317 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2254 (Rfree = 0.000) for 1062 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 22: After refmac, R = 0.2034 (Rfree = 0.000) for 1060 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 23: After refmac, R = 0.2011 (Rfree = 0.000) for 1055 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 24: After refmac, R = 0.1935 (Rfree = 0.000) for 1049 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 25: After refmac, R = 0.2135 (Rfree = 0.000) for 1046 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.82 Search for helices and strands: 0 residues in 0 chains, 1077 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 7 peptides. Score 0.242 Round 2: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.328 Round 3: 72 peptides, 14 chains. Longest chain 10 peptides. Score 0.349 Round 4: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.373 Round 5: 64 peptides, 11 chains. Longest chain 8 peptides. Score 0.399 Taking the results from Round 5 Chains 11, Residues 53, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.55 % complete ) and 2449 restraints for refining 1062 atoms. 2229 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2258 (Rfree = 0.000) for 1062 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 27: After refmac, R = 0.2183 (Rfree = 0.000) for 1054 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 28: After refmac, R = 0.2198 (Rfree = 0.000) for 1044 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Cycle 29: After refmac, R = 0.2578 (Rfree = 0.000) for 1039 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2601 (Rfree = 0.000) for 1037 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 1066 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 6 peptides. Score 0.256 Round 2: 58 peptides, 9 chains. Longest chain 11 peptides. Score 0.427 Round 3: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.378 Round 4: 70 peptides, 10 chains. Longest chain 12 peptides. Score 0.501 Round 5: 66 peptides, 10 chains. Longest chain 12 peptides. Score 0.463 Taking the results from Round 4 Chains 10, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.55 % complete ) and 2495 restraints for refining 1062 atoms. 2265 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2376 (Rfree = 0.000) for 1062 atoms. Found 3 (5 requested) and removed 8 (2 requested) atoms. Cycle 32: After refmac, R = 0.2432 (Rfree = 0.000) for 1055 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 33: After refmac, R = 0.2207 (Rfree = 0.000) for 1055 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 34: After refmac, R = 0.2192 (Rfree = 0.000) for 1054 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2555 (Rfree = 0.000) for 1056 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.87 Search for helices and strands: 0 residues in 0 chains, 1083 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.261 Round 2: 53 peptides, 10 chains. Longest chain 9 peptides. Score 0.327 Round 3: 54 peptides, 9 chains. Longest chain 9 peptides. Score 0.385 Round 4: 58 peptides, 9 chains. Longest chain 12 peptides. Score 0.427 Round 5: 60 peptides, 9 chains. Longest chain 12 peptides. Score 0.448 Taking the results from Round 5 Chains 9, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.55 % complete ) and 2559 restraints for refining 1062 atoms. 2364 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2405 (Rfree = 0.000) for 1062 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 37: After refmac, R = 0.2230 (Rfree = 0.000) for 1055 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 38: After refmac, R = 0.1976 (Rfree = 0.000) for 1056 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 39: After refmac, R = 0.2016 (Rfree = 0.000) for 1051 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.2049 (Rfree = 0.000) for 1047 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 1078 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 5 peptides. Score 0.231 Round 2: 56 peptides, 9 chains. Longest chain 9 peptides. Score 0.407 Round 3: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.295 Round 4: 47 peptides, 8 chains. Longest chain 11 peptides. Score 0.357 Round 5: 47 peptides, 8 chains. Longest chain 8 peptides. Score 0.357 Taking the results from Round 2 Chains 9, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1564 reflections ( 99.55 % complete ) and 2528 restraints for refining 1062 atoms. 2349 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1972 (Rfree = 0.000) for 1062 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 42: After refmac, R = 0.1917 (Rfree = 0.000) for 1059 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 43: After refmac, R = 0.1847 (Rfree = 0.000) for 1057 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.1827 (Rfree = 0.000) for 1058 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.1765 (Rfree = 0.000) for 1056 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 3.88 Search for helices and strands: 0 residues in 0 chains, 1079 seeds are put forward Round 1: 38 peptides, 9 chains. Longest chain 5 peptides. Score 0.194 Round 2: 51 peptides, 10 chains. Longest chain 6 peptides. Score 0.304 Round 3: 58 peptides, 11 chains. Longest chain 7 peptides. Score 0.335 Round 4: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.324 Round 5: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 53, 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 2huh-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1564 reflections ( 99.55 % complete ) and 2556 restraints for refining 1062 atoms. 2355 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2444 (Rfree = 0.000) for 1062 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2238 (Rfree = 0.000) for 1057 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2487 (Rfree = 0.000) for 1055 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2519 (Rfree = 0.000) for 1053 atoms. Found 0 (5 requested) and removed 0 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:29 GMT 2018 Job finished. TimeTaking 24.66 Used memory is bytes: 19929320