Mon 24 Dec 00:50:21 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p1a-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p1a-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p1a-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:50:25 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.2-parrot-mrncs/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-mrncs.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-mrncs.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 2729 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3368 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3085 (Rfree = 0.000) for 2729 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.48 Search for helices and strands: 0 residues in 0 chains, 2818 seeds are put forward NCS extension: 0 residues added, 2818 seeds are put forward Round 1: 115 peptides, 27 chains. Longest chain 7 peptides. Score 0.209 Round 2: 144 peptides, 29 chains. Longest chain 10 peptides. Score 0.328 Round 3: 141 peptides, 27 chains. Longest chain 8 peptides. Score 0.357 Round 4: 150 peptides, 27 chains. Longest chain 12 peptides. Score 0.404 Round 5: 160 peptides, 26 chains. Longest chain 19 peptides. Score 0.473 Taking the results from Round 5 Chains 26, Residues 134, Estimated correctness of the model 2.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5375 restraints for refining 2249 atoms. 4865 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3010 (Rfree = 0.000) for 2249 atoms. Found 18 (20 requested) and removed 18 (10 requested) atoms. Cycle 2: After refmac, R = 0.2630 (Rfree = 0.000) for 2212 atoms. Found 12 (20 requested) and removed 13 (10 requested) atoms. Cycle 3: After refmac, R = 0.2590 (Rfree = 0.000) for 2199 atoms. Found 17 (19 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2248 (Rfree = 0.000) for 2193 atoms. Found 11 (19 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.2159 (Rfree = 0.000) for 2190 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.44 Search for helices and strands: 0 residues in 0 chains, 2315 seeds are put forward NCS extension: 32 residues added (6 deleted due to clashes), 2347 seeds are put forward Round 1: 134 peptides, 26 chains. Longest chain 10 peptides. Score 0.342 Round 2: 145 peptides, 21 chains. Longest chain 17 peptides. Score 0.505 Round 3: 156 peptides, 25 chains. Longest chain 18 peptides. Score 0.475 Round 4: 146 peptides, 23 chains. Longest chain 13 peptides. Score 0.469 Round 5: 157 peptides, 26 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 2 Chains 21, Residues 124, Estimated correctness of the model 12.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5160 restraints for refining 2179 atoms. 4685 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2354 (Rfree = 0.000) for 2179 atoms. Found 11 (19 requested) and removed 12 (9 requested) atoms. Cycle 7: After refmac, R = 0.2284 (Rfree = 0.000) for 2163 atoms. Found 10 (19 requested) and removed 18 (9 requested) atoms. Cycle 8: After refmac, R = 0.2791 (Rfree = 0.000) for 2142 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 9: After refmac, R = 0.2390 (Rfree = 0.000) for 2136 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 10: After refmac, R = 0.2170 (Rfree = 0.000) for 2135 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.38 Search for helices and strands: 0 residues in 0 chains, 2250 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 2278 seeds are put forward Round 1: 137 peptides, 28 chains. Longest chain 8 peptides. Score 0.312 Round 2: 147 peptides, 26 chains. Longest chain 10 peptides. Score 0.410 Round 3: 148 peptides, 22 chains. Longest chain 16 peptides. Score 0.499 Round 4: 149 peptides, 22 chains. Longest chain 12 peptides. Score 0.503 Round 5: 132 peptides, 17 chains. Longest chain 21 peptides. Score 0.527 Taking the results from Round 5 Chains 17, Residues 115, Estimated correctness of the model 19.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 4991 restraints for refining 2141 atoms. 4548 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2255 (Rfree = 0.000) for 2141 atoms. Found 10 (19 requested) and removed 15 (9 requested) atoms. Cycle 12: After refmac, R = 0.2876 (Rfree = 0.000) for 2125 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 13: After refmac, R = 0.2821 (Rfree = 0.000) for 2126 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 14: After refmac, R = 0.2333 (Rfree = 0.000) for 2124 atoms. Found 15 (19 requested) and removed 17 (9 requested) atoms. Cycle 15: After refmac, R = 0.2594 (Rfree = 0.000) for 2118 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.41 Search for helices and strands: 0 residues in 0 chains, 2239 seeds are put forward NCS extension: 43 residues added (3 deleted due to clashes), 2282 seeds are put forward Round 1: 103 peptides, 18 chains. Longest chain 13 peptides. Score 0.359 Round 2: 130 peptides, 21 chains. Longest chain 26 peptides. Score 0.433 Round 3: 128 peptides, 21 chains. Longest chain 14 peptides. Score 0.423 Round 4: 140 peptides, 24 chains. Longest chain 11 peptides. Score 0.418 Round 5: 133 peptides, 18 chains. Longest chain 18 peptides. Score 0.511 Taking the results from Round 5 Chains 18, Residues 115, Estimated correctness of the model 14.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5023 restraints for refining 2186 atoms. 4581 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2736 (Rfree = 0.000) for 2186 atoms. Found 19 (19 requested) and removed 38 (9 requested) atoms. Cycle 17: After refmac, R = 0.2313 (Rfree = 0.000) for 2162 atoms. Found 8 (19 requested) and removed 19 (9 requested) atoms. Cycle 18: After refmac, R = 0.2375 (Rfree = 0.000) for 2148 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 19: After refmac, R = 0.2124 (Rfree = 0.000) for 2143 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2030 (Rfree = 0.000) for 2139 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.40 Search for helices and strands: 0 residues in 0 chains, 2241 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 2271 seeds are put forward Round 1: 108 peptides, 21 chains. Longest chain 9 peptides. Score 0.315 Round 2: 136 peptides, 23 chains. Longest chain 11 peptides. Score 0.419 Round 3: 136 peptides, 23 chains. Longest chain 11 peptides. Score 0.419 Round 4: 138 peptides, 23 chains. Longest chain 12 peptides. Score 0.430 Round 5: 129 peptides, 21 chains. Longest chain 12 peptides. Score 0.428 Taking the results from Round 4 Chains 23, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 4900 restraints for refining 2196 atoms. 4463 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2084 (Rfree = 0.000) for 2196 atoms. Found 12 (19 requested) and removed 11 (9 requested) atoms. Cycle 22: After refmac, R = 0.2370 (Rfree = 0.000) for 2194 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 23: After refmac, R = 0.2019 (Rfree = 0.000) for 2193 atoms. Found 11 (19 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.2032 (Rfree = 0.000) for 2188 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. Cycle 25: After refmac, R = 0.2109 (Rfree = 0.000) for 2182 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.39 Search for helices and strands: 0 residues in 0 chains, 2293 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2309 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.293 Round 2: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.342 Round 3: 107 peptides, 18 chains. Longest chain 11 peptides. Score 0.381 Round 4: 108 peptides, 17 chains. Longest chain 10 peptides. Score 0.410 Round 5: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.401 Taking the results from Round 4 Chains 17, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5248 restraints for refining 2227 atoms. 4901 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2032 (Rfree = 0.000) for 2227 atoms. Found 15 (19 requested) and removed 12 (9 requested) atoms. Cycle 27: After refmac, R = 0.2023 (Rfree = 0.000) for 2226 atoms. Found 13 (20 requested) and removed 12 (10 requested) atoms. Cycle 28: After refmac, R = 0.1950 (Rfree = 0.000) for 2222 atoms. Found 13 (19 requested) and removed 12 (9 requested) atoms. Cycle 29: After refmac, R = 0.1859 (Rfree = 0.000) for 2223 atoms. Found 17 (19 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.1873 (Rfree = 0.000) for 2230 atoms. Found 12 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.39 Search for helices and strands: 0 residues in 0 chains, 2310 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2316 seeds are put forward Round 1: 116 peptides, 23 chains. Longest chain 9 peptides. Score 0.312 Round 2: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.409 Round 3: 121 peptides, 18 chains. Longest chain 14 peptides. Score 0.454 Round 4: 128 peptides, 20 chains. Longest chain 14 peptides. Score 0.445 Round 5: 122 peptides, 20 chains. Longest chain 11 peptides. Score 0.414 Taking the results from Round 3 Chains 18, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5252 restraints for refining 2250 atoms. 4858 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1962 (Rfree = 0.000) for 2250 atoms. Found 15 (20 requested) and removed 15 (10 requested) atoms. Cycle 32: After refmac, R = 0.2062 (Rfree = 0.000) for 2244 atoms. Found 14 (20 requested) and removed 15 (10 requested) atoms. Cycle 33: After refmac, R = 0.1955 (Rfree = 0.000) for 2241 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 34: After refmac, R = 0.1852 (Rfree = 0.000) for 2245 atoms. Found 14 (20 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1947 (Rfree = 0.000) for 2248 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.36 Search for helices and strands: 0 residues in 0 chains, 2342 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2359 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 9 peptides. Score 0.253 Round 2: 103 peptides, 20 chains. Longest chain 11 peptides. Score 0.310 Round 3: 84 peptides, 14 chains. Longest chain 17 peptides. Score 0.351 Round 4: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.342 Round 5: 94 peptides, 17 chains. Longest chain 12 peptides. Score 0.333 Taking the results from Round 3 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5461 restraints for refining 2250 atoms. 5195 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2094 (Rfree = 0.000) for 2250 atoms. Found 16 (20 requested) and removed 11 (10 requested) atoms. Cycle 37: After refmac, R = 0.1805 (Rfree = 0.000) for 2255 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 38: After refmac, R = 0.1925 (Rfree = 0.000) for 2248 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.2167 (Rfree = 0.000) for 2248 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 40: After refmac, R = 0.1964 (Rfree = 0.000) for 2254 atoms. Found 17 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.39 Search for helices and strands: 0 residues in 0 chains, 2337 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 2344 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 11 peptides. Score 0.273 Round 2: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.335 Round 3: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.361 Round 4: 82 peptides, 16 chains. Longest chain 10 peptides. Score 0.287 Round 5: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.301 Taking the results from Round 3 Chains 17, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5403 reflections ( 99.41 % complete ) and 5439 restraints for refining 2250 atoms. 5128 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2203 (Rfree = 0.000) for 2250 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 42: After refmac, R = 0.2308 (Rfree = 0.000) for 2256 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 43: After refmac, R = 0.2048 (Rfree = 0.000) for 2261 atoms. Found 16 (20 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.2035 (Rfree = 0.000) for 2264 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.1680 (Rfree = 0.000) for 2270 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.31 Search for helices and strands: 0 residues in 0 chains, 2335 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2338 seeds are put forward Round 1: 71 peptides, 16 chains. Longest chain 6 peptides. Score 0.216 Round 2: 81 peptides, 15 chains. Longest chain 11 peptides. Score 0.307 Round 3: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.282 Round 4: 82 peptides, 15 chains. Longest chain 11 peptides. Score 0.313 Round 5: 73 peptides, 12 chains. Longest chain 11 peptides. Score 0.339 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 61, 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 5545 restraints for refining 2249 atoms. 5313 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2005 (Rfree = 0.000) for 2249 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2015 (Rfree = 0.000) for 2236 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1994 (Rfree = 0.000) for 2223 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1879 (Rfree = 0.000) for 2214 atoms. TimeTaking 28.92