Mon 24 Dec 07:44:01 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p1a-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-parrot-noncs ############### 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 07:44:05 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/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-parrot-noncs/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 201 and 0 Target number of residues in the AU: 201 Target solvent content: 0.6456 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-3.4-parrot-noncs.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-3.4-parrot-noncs.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 3.400 Wilson plot Bfac: 75.28 4531 reflections ( 99.47 % complete ) and 0 restraints for refining 2754 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3499 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3206 (Rfree = 0.000) for 2754 atoms. Found 13 (20 requested) and removed 26 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.65 Search for helices and strands: 0 residues in 0 chains, 2829 seeds are put forward NCS extension: 0 residues added, 2829 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 6 peptides. Score 0.213 Round 2: 96 peptides, 20 chains. Longest chain 6 peptides. Score 0.269 Round 3: 91 peptides, 17 chains. Longest chain 8 peptides. Score 0.315 Round 4: 94 peptides, 17 chains. Longest chain 13 peptides. Score 0.333 Round 5: 104 peptides, 20 chains. Longest chain 8 peptides. Score 0.316 Taking the results from Round 4 Chains 17, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5593 restraints for refining 2241 atoms. 5302 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2550 (Rfree = 0.000) for 2241 atoms. Found 12 (16 requested) and removed 14 (8 requested) atoms. Cycle 2: After refmac, R = 0.2569 (Rfree = 0.000) for 2223 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 3: After refmac, R = 0.2455 (Rfree = 0.000) for 2218 atoms. Found 15 (16 requested) and removed 14 (8 requested) atoms. Cycle 4: After refmac, R = 0.2106 (Rfree = 0.000) for 2214 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. Cycle 5: After refmac, R = 0.2266 (Rfree = 0.000) for 2202 atoms. Found 9 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 2321 seeds are put forward NCS extension: 0 residues added, 2321 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 6 peptides. Score 0.244 Round 2: 121 peptides, 21 chains. Longest chain 11 peptides. Score 0.386 Round 3: 119 peptides, 19 chains. Longest chain 14 peptides. Score 0.422 Round 4: 131 peptides, 22 chains. Longest chain 11 peptides. Score 0.416 Round 5: 134 peptides, 21 chains. Longest chain 14 peptides. Score 0.453 Taking the results from Round 5 Chains 21, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5398 restraints for refining 2241 atoms. 4967 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2466 (Rfree = 0.000) for 2241 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 7: After refmac, R = 0.2367 (Rfree = 0.000) for 2223 atoms. Found 9 (16 requested) and removed 15 (8 requested) atoms. Cycle 8: After refmac, R = 0.2440 (Rfree = 0.000) for 2211 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. Cycle 9: After refmac, R = 0.2417 (Rfree = 0.000) for 2204 atoms. Found 14 (16 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2132 (Rfree = 0.000) for 2206 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 2333 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 2351 seeds are put forward Round 1: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.299 Round 2: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.358 Round 3: 129 peptides, 23 chains. Longest chain 9 peptides. Score 0.383 Round 4: 131 peptides, 24 chains. Longest chain 10 peptides. Score 0.371 Round 5: 141 peptides, 23 chains. Longest chain 11 peptides. Score 0.444 Taking the results from Round 5 Chains 23, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5262 restraints for refining 2238 atoms. 4813 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2425 (Rfree = 0.000) for 2238 atoms. Found 8 (16 requested) and removed 14 (8 requested) atoms. Cycle 12: After refmac, R = 0.2315 (Rfree = 0.000) for 2221 atoms. Found 5 (16 requested) and removed 16 (8 requested) atoms. Cycle 13: After refmac, R = 0.2323 (Rfree = 0.000) for 2204 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2364 (Rfree = 0.000) for 2204 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.2270 (Rfree = 0.000) for 2201 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 2316 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2325 seeds are put forward Round 1: 111 peptides, 23 chains. Longest chain 8 peptides. Score 0.283 Round 2: 131 peptides, 23 chains. Longest chain 12 peptides. Score 0.394 Round 3: 135 peptides, 19 chains. Longest chain 16 peptides. Score 0.500 Round 4: 132 peptides, 22 chains. Longest chain 16 peptides. Score 0.421 Round 5: 135 peptides, 20 chains. Longest chain 14 peptides. Score 0.479 Taking the results from Round 3 Chains 19, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5199 restraints for refining 2239 atoms. 4754 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2295 (Rfree = 0.000) for 2239 atoms. Found 8 (16 requested) and removed 14 (8 requested) atoms. Cycle 17: After refmac, R = 0.2445 (Rfree = 0.000) for 2224 atoms. Found 8 (16 requested) and removed 16 (8 requested) atoms. Cycle 18: After refmac, R = 0.2374 (Rfree = 0.000) for 2206 atoms. Found 14 (16 requested) and removed 15 (8 requested) atoms. Cycle 19: After refmac, R = 0.2478 (Rfree = 0.000) for 2193 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 20: After refmac, R = 0.2524 (Rfree = 0.000) for 2183 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.57 Search for helices and strands: 0 residues in 0 chains, 2296 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2317 seeds are put forward Round 1: 104 peptides, 20 chains. Longest chain 12 peptides. Score 0.316 Round 2: 118 peptides, 19 chains. Longest chain 15 peptides. Score 0.416 Round 3: 118 peptides, 22 chains. Longest chain 14 peptides. Score 0.347 Round 4: 119 peptides, 20 chains. Longest chain 14 peptides. Score 0.399 Round 5: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.409 Taking the results from Round 2 Chains 19, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5164 restraints for refining 2195 atoms. 4787 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2373 (Rfree = 0.000) for 2195 atoms. Found 5 (16 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.2736 (Rfree = 0.000) for 2182 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 23: After refmac, R = 0.3043 (Rfree = 0.000) for 2172 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 24: After refmac, R = 0.2612 (Rfree = 0.000) for 2160 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.2917 (Rfree = 0.000) for 2159 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 2253 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2274 seeds are put forward Round 1: 103 peptides, 23 chains. Longest chain 8 peptides. Score 0.236 Round 2: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.337 Round 3: 120 peptides, 21 chains. Longest chain 10 peptides. Score 0.381 Round 4: 110 peptides, 19 chains. Longest chain 12 peptides. Score 0.374 Round 5: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 5 Chains 20, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5337 restraints for refining 2206 atoms. 4973 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2351 (Rfree = 0.000) for 2206 atoms. Found 13 (16 requested) and removed 22 (8 requested) atoms. Cycle 27: After refmac, R = 0.2390 (Rfree = 0.000) for 2186 atoms. Found 15 (16 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.2390 (Rfree = 0.000) for 2183 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.2657 (Rfree = 0.000) for 2187 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 30: After refmac, R = 0.2321 (Rfree = 0.000) for 2177 atoms. Found 9 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.53 Search for helices and strands: 0 residues in 0 chains, 2279 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2285 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 10 peptides. Score 0.280 Round 2: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.358 Round 3: 123 peptides, 22 chains. Longest chain 10 peptides. Score 0.374 Round 4: 118 peptides, 18 chains. Longest chain 14 peptides. Score 0.439 Round 5: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.388 Taking the results from Round 4 Chains 18, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5332 restraints for refining 2237 atoms. 4950 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2365 (Rfree = 0.000) for 2237 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 32: After refmac, R = 0.2302 (Rfree = 0.000) for 2233 atoms. Found 14 (16 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2485 (Rfree = 0.000) for 2233 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 34: After refmac, R = 0.2289 (Rfree = 0.000) for 2227 atoms. Found 14 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.2361 (Rfree = 0.000) for 2229 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.50 Search for helices and strands: 0 residues in 0 chains, 2324 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2339 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 7 peptides. Score 0.245 Round 2: 102 peptides, 17 chains. Longest chain 9 peptides. Score 0.378 Round 3: 97 peptides, 17 chains. Longest chain 8 peptides. Score 0.350 Round 4: 95 peptides, 16 chains. Longest chain 8 peptides. Score 0.363 Round 5: 99 peptides, 16 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 5 Chains 16, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5360 restraints for refining 2241 atoms. 5044 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2263 (Rfree = 0.000) for 2241 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 37: After refmac, R = 0.2155 (Rfree = 0.000) for 2240 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 38: After refmac, R = 0.2320 (Rfree = 0.000) for 2244 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.2201 (Rfree = 0.000) for 2245 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 40: After refmac, R = 0.2283 (Rfree = 0.000) for 2246 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.60 Search for helices and strands: 0 residues in 0 chains, 2322 seeds are put forward NCS extension: 3 residues added (1 deleted due to clashes), 2325 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 7 peptides. Score 0.282 Round 2: 92 peptides, 17 chains. Longest chain 7 peptides. Score 0.321 Round 3: 103 peptides, 20 chains. Longest chain 7 peptides. Score 0.310 Round 4: 100 peptides, 16 chains. Longest chain 9 peptides. Score 0.391 Round 5: 105 peptides, 18 chains. Longest chain 10 peptides. Score 0.370 Taking the results from Round 4 Chains 16, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5423 restraints for refining 2241 atoms. 5103 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2257 (Rfree = 0.000) for 2241 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 42: After refmac, R = 0.2217 (Rfree = 0.000) for 2234 atoms. Found 11 (16 requested) and removed 11 (8 requested) atoms. Cycle 43: After refmac, R = 0.2382 (Rfree = 0.000) for 2231 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 44: After refmac, R = 0.2150 (Rfree = 0.000) for 2233 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2254 (Rfree = 0.000) for 2228 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 2327 seeds are put forward NCS extension: 0 residues added, 2327 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 6 peptides. Score 0.221 Round 2: 104 peptides, 23 chains. Longest chain 6 peptides. Score 0.242 Round 3: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.312 Round 4: 97 peptides, 16 chains. Longest chain 10 peptides. Score 0.375 Round 5: 92 peptides, 17 chains. Longest chain 9 peptides. Score 0.321 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 81, 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. 4531 reflections ( 99.47 % complete ) and 5445 restraints for refining 2241 atoms. 5137 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2260 (Rfree = 0.000) for 2241 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2592 (Rfree = 0.000) for 2226 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2321 (Rfree = 0.000) for 2214 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2268 (Rfree = 0.000) for 2202 atoms. TimeTaking 26.93