Sun 23 Dec 22:22:40 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 2p1a-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p1a-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p1a-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-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/2p1a-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-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 22:22:49 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/2p1a-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-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 207 and 0 Target number of residues in the AU: 207 Target solvent content: 0.6351 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.46 Input MTZ file: 2p1a-3.2-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: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.60 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.570 3.200 Wilson plot Bfac: 69.16 5403 reflections ( 99.41 % complete ) and 0 restraints for refining 2751 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3391 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3084 (Rfree = 0.000) for 2751 atoms. Found 17 (24 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.45 Search for helices and strands: 0 residues in 0 chains, 2820 seeds are put forward NCS extension: 0 residues added, 2820 seeds are put forward Round 1: 109 peptides, 22 chains. Longest chain 12 peptides. Score 0.296 Round 2: 144 peptides, 26 chains. Longest chain 9 peptides. Score 0.395 Round 3: 141 peptides, 23 chains. Longest chain 20 peptides. Score 0.444 Round 4: 131 peptides, 21 chains. Longest chain 17 peptides. Score 0.438 Round 5: 156 peptides, 24 chains. Longest chain 19 peptides. Score 0.495 Taking the results from Round 5 Chains 24, Residues 132, Estimated correctness of the model 9.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5270 restraints for refining 2250 atoms. 4766 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2688 (Rfree = 0.000) for 2250 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 2: After refmac, R = 0.3136 (Rfree = 0.000) for 2231 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2540 (Rfree = 0.000) for 2223 atoms. Found 17 (20 requested) and removed 12 (10 requested) atoms. Cycle 4: After refmac, R = 0.2556 (Rfree = 0.000) for 2221 atoms. Found 12 (19 requested) and removed 15 (9 requested) atoms. Cycle 5: After refmac, R = 0.2419 (Rfree = 0.000) for 2214 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.40 Search for helices and strands: 0 residues in 0 chains, 2329 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2348 seeds are put forward Round 1: 130 peptides, 25 chains. Longest chain 14 peptides. Score 0.343 Round 2: 139 peptides, 22 chains. Longest chain 14 peptides. Score 0.456 Round 3: 146 peptides, 24 chains. Longest chain 12 peptides. Score 0.448 Round 4: 137 peptides, 24 chains. Longest chain 14 peptides. Score 0.403 Round 5: 141 peptides, 21 chains. Longest chain 18 peptides. Score 0.487 Taking the results from Round 5 Chains 21, Residues 120, Estimated correctness of the model 7.1 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5138 restraints for refining 2248 atoms. 4604 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2910 (Rfree = 0.000) for 2248 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 7: After refmac, R = 0.2568 (Rfree = 0.000) for 2236 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 8: After refmac, R = 0.2316 (Rfree = 0.000) for 2229 atoms. Found 9 (20 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.2315 (Rfree = 0.000) for 2224 atoms. Found 13 (19 requested) and removed 15 (9 requested) atoms. Cycle 10: After refmac, R = 0.2204 (Rfree = 0.000) for 2215 atoms. Found 13 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.42 Search for helices and strands: 0 residues in 0 chains, 2314 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 2336 seeds are put forward Round 1: 132 peptides, 24 chains. Longest chain 13 peptides. Score 0.377 Round 2: 148 peptides, 24 chains. Longest chain 14 peptides. Score 0.458 Round 3: 141 peptides, 22 chains. Longest chain 15 peptides. Score 0.466 Round 4: 144 peptides, 23 chains. Longest chain 15 peptides. Score 0.459 Round 5: 146 peptides, 25 chains. Longest chain 12 peptides. Score 0.427 Taking the results from Round 3 Chains 22, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5215 restraints for refining 2236 atoms. 4761 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2363 (Rfree = 0.000) for 2236 atoms. Found 18 (20 requested) and removed 20 (10 requested) atoms. Cycle 12: After refmac, R = 0.2218 (Rfree = 0.000) for 2231 atoms. Found 15 (20 requested) and removed 14 (10 requested) atoms. Cycle 13: After refmac, R = 0.2139 (Rfree = 0.000) for 2227 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. Cycle 14: After refmac, R = 0.2100 (Rfree = 0.000) for 2224 atoms. Found 13 (19 requested) and removed 10 (9 requested) atoms. Cycle 15: After refmac, R = 0.2098 (Rfree = 0.000) for 2224 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.42 Search for helices and strands: 0 residues in 0 chains, 2318 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 2346 seeds are put forward Round 1: 135 peptides, 24 chains. Longest chain 14 peptides. Score 0.392 Round 2: 146 peptides, 26 chains. Longest chain 20 peptides. Score 0.405 Round 3: 145 peptides, 24 chains. Longest chain 12 peptides. Score 0.443 Round 4: 145 peptides, 23 chains. Longest chain 17 peptides. Score 0.464 Round 5: 150 peptides, 26 chains. Longest chain 12 peptides. Score 0.425 Taking the results from Round 4 Chains 23, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5237 restraints for refining 2233 atoms. 4772 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2105 (Rfree = 0.000) for 2233 atoms. Found 9 (20 requested) and removed 13 (10 requested) atoms. Cycle 17: After refmac, R = 0.2076 (Rfree = 0.000) for 2226 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. Cycle 18: After refmac, R = 0.2189 (Rfree = 0.000) for 2219 atoms. Found 18 (19 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.2066 (Rfree = 0.000) for 2221 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. Cycle 20: After refmac, R = 0.2006 (Rfree = 0.000) for 2218 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.38 Search for helices and strands: 0 residues in 0 chains, 2322 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2338 seeds are put forward Round 1: 132 peptides, 25 chains. Longest chain 12 peptides. Score 0.354 Round 2: 163 peptides, 30 chains. Longest chain 12 peptides. Score 0.405 Round 3: 157 peptides, 27 chains. Longest chain 12 peptides. Score 0.439 Round 4: 153 peptides, 26 chains. Longest chain 14 peptides. Score 0.440 Round 5: 140 peptides, 22 chains. Longest chain 14 peptides. Score 0.461 Taking the results from Round 5 Chains 22, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5244 restraints for refining 2250 atoms. 4794 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2267 (Rfree = 0.000) for 2250 atoms. Found 6 (20 requested) and removed 13 (10 requested) atoms. Cycle 22: After refmac, R = 0.2410 (Rfree = 0.000) for 2238 atoms. Found 18 (20 requested) and removed 13 (10 requested) atoms. Cycle 23: After refmac, R = 0.2161 (Rfree = 0.000) for 2238 atoms. Found 10 (20 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.2160 (Rfree = 0.000) for 2235 atoms. Found 13 (20 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.2072 (Rfree = 0.000) for 2236 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.38 Search for helices and strands: 0 residues in 0 chains, 2331 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2348 seeds are put forward Round 1: 113 peptides, 25 chains. Longest chain 8 peptides. Score 0.246 Round 2: 131 peptides, 24 chains. Longest chain 10 peptides. Score 0.371 Round 3: 126 peptides, 23 chains. Longest chain 11 peptides. Score 0.367 Round 4: 127 peptides, 24 chains. Longest chain 11 peptides. Score 0.350 Round 5: 132 peptides, 24 chains. Longest chain 9 peptides. Score 0.377 Taking the results from Round 5 Chains 24, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5356 restraints for refining 2250 atoms. 4948 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2193 (Rfree = 0.000) for 2250 atoms. Found 15 (20 requested) and removed 10 (10 requested) atoms. Cycle 27: After refmac, R = 0.2055 (Rfree = 0.000) for 2249 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.2025 (Rfree = 0.000) for 2242 atoms. Found 13 (20 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.1986 (Rfree = 0.000) for 2243 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.1927 (Rfree = 0.000) for 2241 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.39 Search for helices and strands: 0 residues in 0 chains, 2336 seeds are put forward NCS extension: 0 residues added, 2336 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 7 peptides. Score 0.303 Round 2: 122 peptides, 22 chains. Longest chain 11 peptides. Score 0.369 Round 3: 129 peptides, 23 chains. Longest chain 10 peptides. Score 0.383 Round 4: 130 peptides, 22 chains. Longest chain 11 peptides. Score 0.411 Round 5: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.402 Taking the results from Round 4 Chains 23, Residues 108, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5147 restraints for refining 2250 atoms. 4687 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2129 (Rfree = 0.000) for 2250 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 32: After refmac, R = 0.1996 (Rfree = 0.000) for 2244 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.1970 (Rfree = 0.000) for 2239 atoms. Found 5 (20 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.2005 (Rfree = 0.000) for 2231 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.1939 (Rfree = 0.000) for 2223 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.39 Search for helices and strands: 0 residues in 0 chains, 2304 seeds are put forward NCS extension: 0 residues added, 2304 seeds are put forward Round 1: 110 peptides, 22 chains. Longest chain 9 peptides. Score 0.302 Round 2: 110 peptides, 19 chains. Longest chain 12 peptides. Score 0.374 Round 3: 123 peptides, 21 chains. Longest chain 14 peptides. Score 0.397 Round 4: 103 peptides, 18 chains. Longest chain 14 peptides. Score 0.359 Round 5: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.367 Taking the results from Round 3 Chains 21, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5229 restraints for refining 2249 atoms. 4842 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2012 (Rfree = 0.000) for 2249 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. Cycle 37: After refmac, R = 0.1997 (Rfree = 0.000) for 2241 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.1812 (Rfree = 0.000) for 2239 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.1820 (Rfree = 0.000) for 2232 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1736 (Rfree = 0.000) for 2228 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.42 Search for helices and strands: 0 residues in 0 chains, 2318 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2338 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.300 Round 2: 107 peptides, 19 chains. Longest chain 13 peptides. Score 0.357 Round 3: 106 peptides, 19 chains. Longest chain 10 peptides. Score 0.352 Round 4: 111 peptides, 21 chains. Longest chain 10 peptides. Score 0.332 Round 5: 114 peptides, 20 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 5 Chains 20, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5214 restraints for refining 2238 atoms. 4858 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1875 (Rfree = 0.000) for 2238 atoms. Found 15 (20 requested) and removed 10 (10 requested) atoms. Cycle 42: After refmac, R = 0.1798 (Rfree = 0.000) for 2239 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.1687 (Rfree = 0.000) for 2237 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.1712 (Rfree = 0.000) for 2230 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1685 (Rfree = 0.000) for 2227 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.40 Search for helices and strands: 0 residues in 0 chains, 2291 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2313 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 8 peptides. Score 0.261 Round 2: 124 peptides, 22 chains. Longest chain 16 peptides. Score 0.379 Round 3: 113 peptides, 20 chains. Longest chain 14 peptides. Score 0.367 Round 4: 112 peptides, 19 chains. Longest chain 13 peptides. Score 0.385 Round 5: 98 peptides, 17 chains. Longest chain 12 peptides. Score 0.356 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 93, 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 2p1a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5403 reflections ( 99.41 % complete ) and 5354 restraints for refining 2250 atoms. 5001 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2019 (Rfree = 0.000) for 2250 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1949 (Rfree = 0.000) for 2235 atoms. Found 0 (20 requested) and removed 6 (10 requested) atoms. Cycle 48: After refmac, R = 0.1955 (Rfree = 0.000) for 2223 atoms. Found 0 (20 requested) and removed 6 (10 requested) atoms. Cycle 49: After refmac, R = 0.1886 (Rfree = 0.000) for 2216 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:05:34 GMT 2018 Job finished. TimeTaking 42.91