null 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 2pn1-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-4.0-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/2pn1-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-4.0-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 22:23:18 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/2pn1-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-4.0-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 232 and 0 Target number of residues in the AU: 232 Target solvent content: 0.6471 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 331 Adjusted target solvent content: 0.50 Input MTZ file: 2pn1-4.0-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: 5 Cell parameters: 91.460 61.130 76.770 90.000 124.022 90.000 Input sequence file: 2pn1-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2648 target number of atoms Had to go as low as 0.70 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: 63.629 4.000 Wilson plot Bfac: 76.19 2924 reflections ( 95.34 % complete ) and 0 restraints for refining 2926 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3335 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3145 (Rfree = 0.000) for 2926 atoms. Found 13 (13 requested) and removed 61 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.61 Search for helices and strands: 0 residues in 0 chains, 2917 seeds are put forward Round 1: 80 peptides, 19 chains. Longest chain 5 peptides. Score 0.191 Round 2: 119 peptides, 23 chains. Longest chain 9 peptides. Score 0.312 Round 3: 130 peptides, 27 chains. Longest chain 12 peptides. Score 0.283 Round 4: 127 peptides, 22 chains. Longest chain 10 peptides. Score 0.372 Round 5: 136 peptides, 23 chains. Longest chain 17 peptides. Score 0.394 Taking the results from Round 5 Chains 25, Residues 113, Estimated correctness of the model 0.0 % 5 chains (26 residues) have been docked in sequence ------------------------------------------------------ 2924 reflections ( 95.34 % complete ) and 5564 restraints for refining 2391 atoms. 5058 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2434 (Rfree = 0.000) for 2391 atoms. Found 5 (11 requested) and removed 22 (5 requested) atoms. Cycle 2: After refmac, R = 0.2247 (Rfree = 0.000) for 2334 atoms. Found 1 (11 requested) and removed 10 (5 requested) atoms. Cycle 3: After refmac, R = 0.2023 (Rfree = 0.000) for 2311 atoms. Found 3 (11 requested) and removed 13 (5 requested) atoms. Cycle 4: After refmac, R = 0.1883 (Rfree = 0.000) for 2285 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.1822 (Rfree = 0.000) for 2266 atoms. Found 4 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 2333 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 8 peptides. Score 0.241 Round 2: 129 peptides, 22 chains. Longest chain 11 peptides. Score 0.382 Round 3: 115 peptides, 19 chains. Longest chain 10 peptides. Score 0.377 Round 4: 139 peptides, 22 chains. Longest chain 12 peptides. Score 0.427 Round 5: 146 peptides, 21 chains. Longest chain 12 peptides. Score 0.476 Taking the results from Round 5 Chains 21, Residues 125, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2924 reflections ( 95.34 % complete ) and 5214 restraints for refining 2264 atoms. 4705 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2162 (Rfree = 0.000) for 2264 atoms. Found 6 (10 requested) and removed 22 (5 requested) atoms. Cycle 7: After refmac, R = 0.2107 (Rfree = 0.000) for 2222 atoms. Found 1 (10 requested) and removed 16 (5 requested) atoms. Cycle 8: After refmac, R = 0.1935 (Rfree = 0.000) for 2194 atoms. Found 2 (10 requested) and removed 14 (5 requested) atoms. Cycle 9: After refmac, R = 0.1993 (Rfree = 0.000) for 2174 atoms. Found 7 (10 requested) and removed 19 (5 requested) atoms. Cycle 10: After refmac, R = 0.1909 (Rfree = 0.000) for 2157 atoms. Found 6 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.63 Search for helices and strands: 0 residues in 0 chains, 2224 seeds are put forward Round 1: 115 peptides, 21 chains. Longest chain 10 peptides. Score 0.335 Round 2: 126 peptides, 19 chains. Longest chain 18 peptides. Score 0.428 Round 3: 137 peptides, 20 chains. Longest chain 15 peptides. Score 0.457 Round 4: 140 peptides, 21 chains. Longest chain 18 peptides. Score 0.451 Round 5: 135 peptides, 21 chains. Longest chain 14 peptides. Score 0.429 Taking the results from Round 3 Chains 20, Residues 117, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2924 reflections ( 95.34 % complete ) and 5200 restraints for refining 2276 atoms. 4719 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2159 (Rfree = 0.000) for 2276 atoms. Found 3 (10 requested) and removed 31 (5 requested) atoms. Cycle 12: After refmac, R = 0.2103 (Rfree = 0.000) for 2237 atoms. Found 3 (10 requested) and removed 29 (5 requested) atoms. Cycle 13: After refmac, R = 0.1869 (Rfree = 0.000) for 2203 atoms. Found 6 (10 requested) and removed 21 (5 requested) atoms. Cycle 14: After refmac, R = 0.1629 (Rfree = 0.000) for 2183 atoms. Found 4 (10 requested) and removed 12 (5 requested) atoms. Cycle 15: After refmac, R = 0.1328 (Rfree = 0.000) for 2170 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 2249 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 9 peptides. Score 0.240 Round 2: 127 peptides, 23 chains. Longest chain 13 peptides. Score 0.352 Round 3: 131 peptides, 23 chains. Longest chain 17 peptides. Score 0.371 Round 4: 128 peptides, 22 chains. Longest chain 14 peptides. Score 0.377 Round 5: 124 peptides, 18 chains. Longest chain 22 peptides. Score 0.439 Taking the results from Round 5 Chains 18, Residues 106, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2924 reflections ( 95.34 % complete ) and 5430 restraints for refining 2364 atoms. 4994 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1914 (Rfree = 0.000) for 2364 atoms. Found 11 (11 requested) and removed 25 (5 requested) atoms. Cycle 17: After refmac, R = 0.1997 (Rfree = 0.000) for 2327 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 18: After refmac, R = 0.1843 (Rfree = 0.000) for 2309 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 19: After refmac, R = 0.1822 (Rfree = 0.000) for 2283 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 20: After refmac, R = 0.1883 (Rfree = 0.000) for 2259 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 2343 seeds are put forward Round 1: 102 peptides, 22 chains. Longest chain 9 peptides. Score 0.246 Round 2: 116 peptides, 23 chains. Longest chain 10 peptides. Score 0.297 Round 3: 127 peptides, 24 chains. Longest chain 10 peptides. Score 0.331 Round 4: 130 peptides, 23 chains. Longest chain 9 peptides. Score 0.366 Round 5: 127 peptides, 22 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 5 Chains 22, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2924 reflections ( 95.34 % complete ) and 5446 restraints for refining 2337 atoms. 5048 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1771 (Rfree = 0.000) for 2337 atoms. Found 11 (11 requested) and removed 32 (5 requested) atoms. Cycle 22: After refmac, R = 0.2077 (Rfree = 0.000) for 2305 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 23: After refmac, R = 0.1656 (Rfree = 0.000) for 2285 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.1675 (Rfree = 0.000) for 2278 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 25: After refmac, R = 0.1762 (Rfree = 0.000) for 2271 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.52 Search for helices and strands: 0 residues in 0 chains, 2346 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 8 peptides. Score 0.229 Round 2: 136 peptides, 25 chains. Longest chain 14 peptides. Score 0.354 Round 3: 134 peptides, 24 chains. Longest chain 10 peptides. Score 0.364 Round 4: 138 peptides, 26 chains. Longest chain 11 peptides. Score 0.343 Round 5: 135 peptides, 23 chains. Longest chain 11 peptides. Score 0.389 Taking the results from Round 5 Chains 23, Residues 112, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2924 reflections ( 95.34 % complete ) and 5459 restraints for refining 2392 atoms. 5014 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2060 (Rfree = 0.000) for 2392 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Cycle 27: After refmac, R = 0.1852 (Rfree = 0.000) for 2352 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 28: After refmac, R = 0.1858 (Rfree = 0.000) for 2326 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 29: After refmac, R = 0.1793 (Rfree = 0.000) for 2312 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.1732 (Rfree = 0.000) for 2304 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.56 Search for helices and strands: 0 residues in 0 chains, 2389 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 9 peptides. Score 0.248 Round 2: 107 peptides, 23 chains. Longest chain 7 peptides. Score 0.250 Round 3: 122 peptides, 22 chains. Longest chain 9 peptides. Score 0.348 Round 4: 123 peptides, 24 chains. Longest chain 9 peptides. Score 0.311 Round 5: 120 peptides, 21 chains. Longest chain 13 peptides. Score 0.359 Taking the results from Round 5 Chains 21, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2924 reflections ( 95.34 % complete ) and 5652 restraints for refining 2392 atoms. 5277 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1821 (Rfree = 0.000) for 2392 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 32: After refmac, R = 0.2006 (Rfree = 0.000) for 2366 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 33: After refmac, R = 0.1665 (Rfree = 0.000) for 2349 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 34: After refmac, R = 0.1575 (Rfree = 0.000) for 2348 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 35: After refmac, R = 0.1493 (Rfree = 0.000) for 2338 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 2415 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 6 peptides. Score 0.231 Round 2: 106 peptides, 21 chains. Longest chain 11 peptides. Score 0.289 Round 3: 115 peptides, 21 chains. Longest chain 10 peptides. Score 0.335 Round 4: 126 peptides, 23 chains. Longest chain 11 peptides. Score 0.347 Round 5: 129 peptides, 22 chains. Longest chain 12 peptides. Score 0.382 Taking the results from Round 5 Chains 23, Residues 107, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2924 reflections ( 95.34 % complete ) and 5500 restraints for refining 2392 atoms. 5064 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1826 (Rfree = 0.000) for 2392 atoms. Found 11 (11 requested) and removed 25 (5 requested) atoms. Cycle 37: After refmac, R = 0.1878 (Rfree = 0.000) for 2365 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 38: After refmac, R = 0.1696 (Rfree = 0.000) for 2355 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 39: After refmac, R = 0.1588 (Rfree = 0.000) for 2347 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 40: After refmac, R = 0.1380 (Rfree = 0.000) for 2343 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 2419 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 7 peptides. Score 0.232 Round 2: 109 peptides, 20 chains. Longest chain 11 peptides. Score 0.327 Round 3: 108 peptides, 17 chains. Longest chain 9 peptides. Score 0.386 Round 4: 93 peptides, 17 chains. Longest chain 9 peptides. Score 0.311 Round 5: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.367 Taking the results from Round 3 Chains 17, Residues 91, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2924 reflections ( 95.34 % complete ) and 5578 restraints for refining 2392 atoms. 5194 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1505 (Rfree = 0.000) for 2392 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Cycle 42: After refmac, R = 0.1241 (Rfree = 0.000) for 2380 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.1159 (Rfree = 0.000) for 2370 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.1071 (Rfree = 0.000) for 2363 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.0956 (Rfree = 0.000) for 2356 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.57 Search for helices and strands: 0 residues in 0 chains, 2424 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 5 peptides. Score 0.193 Round 2: 78 peptides, 16 chains. Longest chain 7 peptides. Score 0.253 Round 3: 87 peptides, 18 chains. Longest chain 6 peptides. Score 0.256 Round 4: 87 peptides, 17 chains. Longest chain 8 peptides. Score 0.279 Round 5: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.301 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 74, 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 2pn1-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2924 reflections ( 95.34 % complete ) and 5739 restraints for refining 2392 atoms. 5460 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1766 (Rfree = 0.000) for 2392 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2088 (Rfree = 0.000) for 2372 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1747 (Rfree = 0.000) for 2358 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1941 (Rfree = 0.000) for 2346 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:09:09 GMT 2018 Job finished. TimeTaking 46.02 Used memory is bytes: 18712984