null Tue 25 Dec 19:27:55 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 2ghr-2.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-2.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-2.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-2.4-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/2ghr-2.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-2.4-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 ============================================================ Tue 25 Dec 19:28:04 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/2ghr-2.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-2.4-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 302 and 0 Target number of residues in the AU: 302 Target solvent content: 0.5275 Checking the provided sequence file Detected sequence length: 302 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 302 Adjusted target solvent content: 0.53 Input MTZ file: 2ghr-2.4-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: 91 Cell parameters: 95.828 95.828 75.339 90.000 90.000 90.000 Input sequence file: 2ghr-2.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2416 target number of atoms Had to go as low as 0.55 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: 95.828 2.400 Wilson plot Bfac: 29.52 14218 reflections ( 99.68 % complete ) and 0 restraints for refining 2691 atoms. Observations/parameters ratio is 1.32 ------------------------------------------------------ Starting model: R = 0.3470 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2792 (Rfree = 0.000) for 2691 atoms. Found 37 (54 requested) and removed 39 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.40 2.31 Round 1: 160 peptides, 29 chains. Longest chain 18 peptides. Score 0.390 Round 2: 192 peptides, 23 chains. Longest chain 30 peptides. Score 0.621 Round 3: 213 peptides, 21 chains. Longest chain 31 peptides. Score 0.711 Round 4: 218 peptides, 21 chains. Longest chain 61 peptides. Score 0.724 Round 5: 219 peptides, 17 chains. Longest chain 39 peptides. Score 0.771 Taking the results from Round 5 Chains 18, Residues 202, Estimated correctness of the model 91.5 % 3 chains (79 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 175 A and 180 A 16 chains (204 residues) following loop building 2 chains (83 residues) in sequence following loop building ------------------------------------------------------ 14218 reflections ( 99.68 % complete ) and 3738 restraints for refining 2276 atoms. 2547 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3354 (Rfree = 0.000) for 2276 atoms. Found 45 (46 requested) and removed 34 (23 requested) atoms. Cycle 2: After refmac, R = 0.3161 (Rfree = 0.000) for 2273 atoms. Found 38 (45 requested) and removed 27 (23 requested) atoms. Cycle 3: After refmac, R = 0.2983 (Rfree = 0.000) for 2277 atoms. Found 21 (44 requested) and removed 25 (23 requested) atoms. Cycle 4: After refmac, R = 0.2901 (Rfree = 0.000) for 2269 atoms. Found 22 (43 requested) and removed 23 (23 requested) atoms. Cycle 5: After refmac, R = 0.2888 (Rfree = 0.000) for 2263 atoms. Found 20 (42 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.35 2.26 Round 1: 223 peptides, 18 chains. Longest chain 28 peptides. Score 0.769 Round 2: 232 peptides, 15 chains. Longest chain 51 peptides. Score 0.816 Round 3: 232 peptides, 11 chains. Longest chain 47 peptides. Score 0.851 Round 4: 230 peptides, 13 chains. Longest chain 55 peptides. Score 0.831 Round 5: 220 peptides, 15 chains. Longest chain 40 peptides. Score 0.794 Taking the results from Round 3 Chains 12, Residues 221, Estimated correctness of the model 96.1 % 5 chains (159 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 265 A and 268 A 10 chains (222 residues) following loop building 4 chains (161 residues) in sequence following loop building ------------------------------------------------------ 14218 reflections ( 99.68 % complete ) and 2897 restraints for refining 2295 atoms. 1263 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3279 (Rfree = 0.000) for 2295 atoms. Found 41 (41 requested) and removed 47 (23 requested) atoms. Cycle 7: After refmac, R = 0.3074 (Rfree = 0.000) for 2281 atoms. Found 23 (40 requested) and removed 32 (23 requested) atoms. Cycle 8: After refmac, R = 0.2959 (Rfree = 0.000) for 2263 atoms. Found 24 (40 requested) and removed 27 (23 requested) atoms. Cycle 9: After refmac, R = 0.2892 (Rfree = 0.000) for 2251 atoms. Found 17 (39 requested) and removed 23 (23 requested) atoms. Cycle 10: After refmac, R = 0.2851 (Rfree = 0.000) for 2239 atoms. Found 21 (37 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.34 2.25 Round 1: 230 peptides, 14 chains. Longest chain 43 peptides. Score 0.822 Round 2: 227 peptides, 12 chains. Longest chain 51 peptides. Score 0.835 Round 3: 226 peptides, 12 chains. Longest chain 49 peptides. Score 0.833 Round 4: 223 peptides, 13 chains. Longest chain 32 peptides. Score 0.819 Round 5: 227 peptides, 10 chains. Longest chain 62 peptides. Score 0.852 Taking the results from Round 5 Chains 12, Residues 217, Estimated correctness of the model 96.2 % 4 chains (137 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 144 A and 153 A 11 chains (225 residues) following loop building 3 chains (145 residues) in sequence following loop building ------------------------------------------------------ 14218 reflections ( 99.68 % complete ) and 2995 restraints for refining 2277 atoms. 1434 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3225 (Rfree = 0.000) for 2277 atoms. Found 37 (37 requested) and removed 53 (23 requested) atoms. Cycle 12: After refmac, R = 0.3049 (Rfree = 0.000) for 2251 atoms. Found 22 (36 requested) and removed 27 (23 requested) atoms. Cycle 13: After refmac, R = 0.2880 (Rfree = 0.000) for 2236 atoms. Found 22 (34 requested) and removed 24 (22 requested) atoms. Cycle 14: After refmac, R = 0.2828 (Rfree = 0.000) for 2224 atoms. Found 27 (33 requested) and removed 23 (22 requested) atoms. Cycle 15: After refmac, R = 0.2792 (Rfree = 0.000) for 2221 atoms. Found 15 (32 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.34 2.25 Round 1: 237 peptides, 10 chains. Longest chain 72 peptides. Score 0.866 Round 2: 232 peptides, 8 chains. Longest chain 84 peptides. Score 0.874 Round 3: 231 peptides, 9 chains. Longest chain 75 peptides. Score 0.865 Round 4: 229 peptides, 13 chains. Longest chain 67 peptides. Score 0.829 Round 5: 232 peptides, 11 chains. Longest chain 63 peptides. Score 0.851 Taking the results from Round 2 Chains 9, Residues 224, Estimated correctness of the model 97.1 % 3 chains (165 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 206 A and 209 A Built loop between residues 266 A and 271 A 6 chains (229 residues) following loop building 1 chains (171 residues) in sequence following loop building ------------------------------------------------------ 14218 reflections ( 99.68 % complete ) and 2778 restraints for refining 2277 atoms. 1086 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2761 (Rfree = 0.000) for 2277 atoms. Found 31 (32 requested) and removed 24 (23 requested) atoms. Cycle 17: After refmac, R = 0.2647 (Rfree = 0.000) for 2273 atoms. Found 28 (31 requested) and removed 24 (23 requested) atoms. Cycle 18: After refmac, R = 0.2541 (Rfree = 0.000) for 2275 atoms. Found 18 (30 requested) and removed 23 (23 requested) atoms. Cycle 19: After refmac, R = 0.2498 (Rfree = 0.000) for 2265 atoms. Found 9 (29 requested) and removed 23 (23 requested) atoms. Cycle 20: After refmac, R = 0.2503 (Rfree = 0.000) for 2248 atoms. Found 10 (28 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.35 2.26 Round 1: 231 peptides, 8 chains. Longest chain 144 peptides. Score 0.873 Round 2: 238 peptides, 7 chains. Longest chain 120 peptides. Score 0.889 Round 3: 237 peptides, 11 chains. Longest chain 51 peptides. Score 0.858 Round 4: 237 peptides, 10 chains. Longest chain 110 peptides. Score 0.866 Round 5: 232 peptides, 11 chains. Longest chain 61 peptides. Score 0.851 Taking the results from Round 2 Chains 8, Residues 231, Estimated correctness of the model 97.7 % 4 chains (193 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 A and 122 A Built loop between residues 240 A and 243 A Built loop between residues 265 A and 269 A 4 chains (238 residues) following loop building 1 chains (202 residues) in sequence following loop building ------------------------------------------------------ 14218 reflections ( 99.68 % complete ) and 2474 restraints for refining 2278 atoms. 602 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2660 (Rfree = 0.000) for 2278 atoms. Found 28 (28 requested) and removed 28 (23 requested) atoms. Cycle 22: After refmac, R = 0.2525 (Rfree = 0.000) for 2274 atoms. Found 18 (27 requested) and removed 23 (23 requested) atoms. Cycle 23: After refmac, R = 0.2501 (Rfree = 0.000) for 2265 atoms. Found 26 (26 requested) and removed 23 (23 requested) atoms. Cycle 24: After refmac, R = 0.2492 (Rfree = 0.000) for 2264 atoms. Found 22 (25 requested) and removed 23 (23 requested) atoms. Cycle 25: After refmac, R = 0.2479 (Rfree = 0.000) for 2262 atoms. Found 21 (24 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.34 2.25 Round 1: 235 peptides, 9 chains. Longest chain 60 peptides. Score 0.871 Round 2: 237 peptides, 8 chains. Longest chain 118 peptides. Score 0.881 Round 3: 236 peptides, 11 chains. Longest chain 60 peptides. Score 0.857 Round 4: 232 peptides, 9 chains. Longest chain 88 peptides. Score 0.867 Round 5: 235 peptides, 10 chains. Longest chain 85 peptides. Score 0.863 Taking the results from Round 2 Chains 8, Residues 229, Estimated correctness of the model 97.4 % 4 chains (189 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 115 A and 123 A Built loop between residues 239 A and 242 A 5 chains (235 residues) following loop building 2 chains (198 residues) in sequence following loop building ------------------------------------------------------ 14218 reflections ( 99.68 % complete ) and 2542 restraints for refining 2277 atoms. 737 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2608 (Rfree = 0.000) for 2277 atoms. Found 23 (23 requested) and removed 33 (23 requested) atoms. Cycle 27: After refmac, R = 0.2488 (Rfree = 0.000) for 2264 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 28: After refmac, R = 0.2455 (Rfree = 0.000) for 2261 atoms. Found 18 (23 requested) and removed 23 (23 requested) atoms. Cycle 29: After refmac, R = 0.2413 (Rfree = 0.000) for 2255 atoms. Found 18 (22 requested) and removed 22 (22 requested) atoms. Cycle 30: After refmac, R = 0.2415 (Rfree = 0.000) for 2248 atoms. Found 18 (22 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.36 2.27 Round 1: 232 peptides, 7 chains. Longest chain 113 peptides. Score 0.882 Round 2: 240 peptides, 7 chains. Longest chain 87 peptides. Score 0.891 Round 3: 237 peptides, 7 chains. Longest chain 101 peptides. Score 0.888 Round 4: 238 peptides, 8 chains. Longest chain 90 peptides. Score 0.882 Round 5: 235 peptides, 12 chains. Longest chain 54 peptides. Score 0.847 Taking the results from Round 2 Chains 7, Residues 233, Estimated correctness of the model 97.8 % 3 chains (171 residues) have been docked in sequence Building loops using Loopy2018 7 chains (233 residues) following loop building 3 chains (171 residues) in sequence following loop building ------------------------------------------------------ 14218 reflections ( 99.68 % complete ) and 2820 restraints for refining 2306 atoms. 1082 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2723 (Rfree = 0.000) for 2306 atoms. Found 23 (23 requested) and removed 35 (23 requested) atoms. Cycle 32: After refmac, R = 0.2627 (Rfree = 0.000) for 2287 atoms. Found 21 (23 requested) and removed 25 (23 requested) atoms. Cycle 33: After refmac, R = 0.2561 (Rfree = 0.000) for 2279 atoms. Found 20 (23 requested) and removed 24 (23 requested) atoms. Cycle 34: After refmac, R = 0.2560 (Rfree = 0.000) for 2272 atoms. Found 16 (23 requested) and removed 24 (23 requested) atoms. Cycle 35: After refmac, R = 0.2490 (Rfree = 0.000) for 2255 atoms. Found 18 (23 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.32 2.23 Round 1: 240 peptides, 7 chains. Longest chain 143 peptides. Score 0.891 Round 2: 242 peptides, 7 chains. Longest chain 115 peptides. Score 0.893 Round 3: 240 peptides, 9 chains. Longest chain 49 peptides. Score 0.877 Round 4: 243 peptides, 10 chains. Longest chain 60 peptides. Score 0.873 Round 5: 241 peptides, 12 chains. Longest chain 60 peptides. Score 0.856 Taking the results from Round 2 Chains 7, Residues 235, Estimated correctness of the model 97.9 % 3 chains (199 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 206 A and 209 A Built loop between residues 265 A and 269 A 5 chains (240 residues) following loop building 1 chains (204 residues) in sequence following loop building ------------------------------------------------------ 14218 reflections ( 99.68 % complete ) and 2476 restraints for refining 2277 atoms. 583 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2501 (Rfree = 0.000) for 2277 atoms. Found 23 (23 requested) and removed 28 (23 requested) atoms. Cycle 37: After refmac, R = 0.2386 (Rfree = 0.000) for 2264 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 38: After refmac, R = 0.2349 (Rfree = 0.000) for 2263 atoms. Found 17 (23 requested) and removed 23 (23 requested) atoms. Cycle 39: After refmac, R = 0.2326 (Rfree = 0.000) for 2253 atoms. Found 19 (22 requested) and removed 23 (22 requested) atoms. Cycle 40: After refmac, R = 0.2315 (Rfree = 0.000) for 2247 atoms. Found 22 (22 requested) and removed 20 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.32 2.23 Round 1: 238 peptides, 7 chains. Longest chain 167 peptides. Score 0.889 Round 2: 243 peptides, 5 chains. Longest chain 173 peptides. Score 0.908 Round 3: 243 peptides, 9 chains. Longest chain 107 peptides. Score 0.881 Round 4: 239 peptides, 10 chains. Longest chain 51 peptides. Score 0.868 Round 5: 240 peptides, 9 chains. Longest chain 123 peptides. Score 0.877 Taking the results from Round 2 Chains 5, Residues 238, Estimated correctness of the model 98.4 % 3 chains (223 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 265 A and 269 A 4 chains (241 residues) following loop building 2 chains (226 residues) in sequence following loop building ------------------------------------------------------ 14218 reflections ( 99.68 % complete ) and 2368 restraints for refining 2287 atoms. 384 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2385 (Rfree = 0.000) for 2287 atoms. Found 23 (23 requested) and removed 29 (23 requested) atoms. Cycle 42: After refmac, R = 0.2294 (Rfree = 0.000) for 2279 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 43: After refmac, R = 0.2247 (Rfree = 0.000) for 2278 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 44: After refmac, R = 0.2217 (Rfree = 0.000) for 2277 atoms. Found 18 (23 requested) and removed 23 (23 requested) atoms. Cycle 45: After refmac, R = 0.2214 (Rfree = 0.000) for 2270 atoms. Found 22 (23 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.33 2.24 Round 1: 242 peptides, 6 chains. Longest chain 114 peptides. Score 0.900 Round 2: 245 peptides, 8 chains. Longest chain 85 peptides. Score 0.890 Round 3: 246 peptides, 6 chains. Longest chain 114 peptides. Score 0.904 Round 4: 244 peptides, 7 chains. Longest chain 86 peptides. Score 0.896 Round 5: 238 peptides, 11 chains. Longest chain 63 peptides. Score 0.859 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 240, Estimated correctness of the model 98.3 % 4 chains (221 residues) have been docked in sequence Sequence coverage is 91 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 205 A and 208 A Built loop between residues 265 A and 270 A 4 chains (244 residues) following loop building 2 chains (227 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 14218 reflections ( 99.68 % complete ) and 2004 restraints for refining 1958 atoms. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2948 (Rfree = 0.000) for 1958 atoms. Found 9 (19 requested) and removed 0 (19 requested) atoms. Cycle 47: After refmac, R = 0.2825 (Rfree = 0.000) for 1958 atoms. Found 1 (20 requested) and removed 0 (20 requested) atoms. Cycle 48: After refmac, R = 0.2804 (Rfree = 0.000) for 1958 atoms. Found 3 (20 requested) and removed 4 (20 requested) atoms. Cycle 49: After refmac, R = 0.2750 (Rfree = 0.000) for 1958 atoms. Found 1 (20 requested) and removed 1 (20 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:20:16 GMT 2018 Job finished. TimeTaking 52.35 Used memory is bytes: 1981336