Sun 23 Dec 22:23:01 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 2oh3-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oh3-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oh3-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-2.0-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/2oh3-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-2.0-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 22:23:10 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/2oh3-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oh3-2.0-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 190 and 0 Target number of residues in the AU: 190 Target solvent content: 0.5273 Checking the provided sequence file Detected sequence length: 167 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 167 Adjusted target solvent content: 0.58 Input MTZ file: 2oh3-2.0-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: 23 Cell parameters: 64.360 75.280 89.790 90.000 90.000 90.000 Input sequence file: 2oh3-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1336 target number of atoms Had to go as low as 0.45 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 1 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: 57.688 2.000 Wilson plot Bfac: 29.24 14774 reflections ( 97.77 % complete ) and 0 restraints for refining 1483 atoms. Observations/parameters ratio is 2.49 ------------------------------------------------------ Starting model: R = 0.3231 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2790 (Rfree = 0.000) for 1483 atoms. Found 50 (50 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.21 1.98 Round 1: 119 peptides, 17 chains. Longest chain 22 peptides. Score 0.549 Round 2: 125 peptides, 5 chains. Longest chain 51 peptides. Score 0.825 Round 3: 132 peptides, 5 chains. Longest chain 43 peptides. Score 0.844 Round 4: 136 peptides, 4 chains. Longest chain 51 peptides. Score 0.867 Round 5: 138 peptides, 3 chains. Longest chain 75 peptides. Score 0.884 Taking the results from Round 5 Chains 3, Residues 135, Estimated correctness of the model 98.6 % 2 chains (128 residues) have been docked in sequence Building loops using Loopy2018 3 chains (135 residues) following loop building 2 chains (128 residues) in sequence following loop building ------------------------------------------------------ 14774 reflections ( 97.77 % complete ) and 1412 restraints for refining 1318 atoms. 327 conditional restraints added. Observations/parameters ratio is 2.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2741 (Rfree = 0.000) for 1318 atoms. Found 45 (45 requested) and removed 25 (22 requested) atoms. Cycle 2: After refmac, R = 0.2512 (Rfree = 0.000) for 1331 atoms. Found 43 (44 requested) and removed 17 (22 requested) atoms. Cycle 3: After refmac, R = 0.2511 (Rfree = 0.000) for 1351 atoms. Found 41 (45 requested) and removed 25 (23 requested) atoms. Cycle 4: After refmac, R = 0.2399 (Rfree = 0.000) for 1359 atoms. Found 44 (44 requested) and removed 13 (23 requested) atoms. Cycle 5: After refmac, R = 0.2397 (Rfree = 0.000) for 1380 atoms. Found 45 (45 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.15 1.93 Round 1: 138 peptides, 2 chains. Longest chain 74 peptides. Score 0.896 Round 2: 139 peptides, 2 chains. Longest chain 74 peptides. Score 0.898 Round 3: 139 peptides, 2 chains. Longest chain 74 peptides. Score 0.898 Round 4: 139 peptides, 2 chains. Longest chain 74 peptides. Score 0.898 Round 5: 138 peptides, 4 chains. Longest chain 47 peptides. Score 0.871 Taking the results from Round 4 Chains 2, Residues 137, Estimated correctness of the model 98.9 % 2 chains (137 residues) have been docked in sequence Building loops using Loopy2018 2 chains (137 residues) following loop building 2 chains (137 residues) in sequence following loop building ------------------------------------------------------ 14774 reflections ( 97.77 % complete ) and 1374 restraints for refining 1342 atoms. 232 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2387 (Rfree = 0.000) for 1342 atoms. Found 42 (42 requested) and removed 24 (22 requested) atoms. Cycle 7: After refmac, R = 0.2302 (Rfree = 0.000) for 1355 atoms. Found 39 (42 requested) and removed 21 (23 requested) atoms. Cycle 8: After refmac, R = 0.2219 (Rfree = 0.000) for 1371 atoms. Found 37 (42 requested) and removed 18 (23 requested) atoms. Cycle 9: After refmac, R = 0.2227 (Rfree = 0.000) for 1390 atoms. Found 40 (42 requested) and removed 24 (23 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2267 (Rfree = 0.000) for 1404 atoms. Found 38 (42 requested) and removed 30 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.13 1.91 Round 1: 141 peptides, 2 chains. Longest chain 76 peptides. Score 0.901 Round 2: 141 peptides, 2 chains. Longest chain 76 peptides. Score 0.901 Round 3: 139 peptides, 4 chains. Longest chain 55 peptides. Score 0.873 Round 4: 141 peptides, 2 chains. Longest chain 76 peptides. Score 0.901 Round 5: 141 peptides, 2 chains. Longest chain 76 peptides. Score 0.901 Taking the results from Round 5 Chains 2, Residues 139, Estimated correctness of the model 99.0 % 2 chains (139 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 90 A 1 chains (149 residues) following loop building 1 chains (149 residues) in sequence following loop building ------------------------------------------------------ 14774 reflections ( 97.77 % complete ) and 1410 restraints for refining 1415 atoms. 172 conditional restraints added. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2584 (Rfree = 0.000) for 1415 atoms. Found 41 (41 requested) and removed 31 (24 requested) atoms. Cycle 12: After refmac, R = 0.2377 (Rfree = 0.000) for 1420 atoms. Found 40 (40 requested) and removed 24 (24 requested) atoms. Cycle 13: After refmac, R = 0.2294 (Rfree = 0.000) for 1435 atoms. Found 40 (40 requested) and removed 24 (24 requested) atoms. Cycle 14: After refmac, R = 0.2274 (Rfree = 0.000) for 1448 atoms. Found 39 (39 requested) and removed 25 (24 requested) atoms. Cycle 15: After refmac, R = 0.2234 (Rfree = 0.000) for 1462 atoms. Found 39 (39 requested) and removed 27 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.14 1.92 Round 1: 140 peptides, 2 chains. Longest chain 76 peptides. Score 0.899 Round 2: 140 peptides, 2 chains. Longest chain 76 peptides. Score 0.899 Round 3: 137 peptides, 4 chains. Longest chain 57 peptides. Score 0.869 Round 4: 139 peptides, 3 chains. Longest chain 64 peptides. Score 0.886 Round 5: 139 peptides, 4 chains. Longest chain 77 peptides. Score 0.873 Taking the results from Round 2 Chains 2, Residues 138, Estimated correctness of the model 98.9 % 2 chains (138 residues) have been docked in sequence Building loops using Loopy2018 2 chains (138 residues) following loop building 2 chains (138 residues) in sequence following loop building ------------------------------------------------------ 14774 reflections ( 97.77 % complete ) and 1435 restraints for refining 1382 atoms. 291 conditional restraints added. Observations/parameters ratio is 2.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2270 (Rfree = 0.000) for 1382 atoms. Found 36 (36 requested) and removed 21 (23 requested) atoms. Cycle 17: After refmac, R = 0.2166 (Rfree = 0.000) for 1395 atoms. Found 35 (35 requested) and removed 14 (23 requested) atoms. Cycle 18: After refmac, R = 0.2140 (Rfree = 0.000) for 1413 atoms. Found 36 (36 requested) and removed 19 (24 requested) atoms. Cycle 19: After refmac, R = 0.2143 (Rfree = 0.000) for 1428 atoms. Found 35 (35 requested) and removed 23 (24 requested) atoms. Cycle 20: After refmac, R = 0.2134 (Rfree = 0.000) for 1439 atoms. Found 34 (34 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.13 1.91 Round 1: 140 peptides, 2 chains. Longest chain 76 peptides. Score 0.899 Round 2: 139 peptides, 3 chains. Longest chain 64 peptides. Score 0.886 Round 3: 137 peptides, 4 chains. Longest chain 56 peptides. Score 0.869 Round 4: 141 peptides, 2 chains. Longest chain 77 peptides. Score 0.901 Round 5: 137 peptides, 5 chains. Longest chain 56 peptides. Score 0.856 Taking the results from Round 4 Chains 2, Residues 139, Estimated correctness of the model 99.0 % 2 chains (139 residues) have been docked in sequence Building loops using Loopy2018 2 chains (139 residues) following loop building 2 chains (139 residues) in sequence following loop building ------------------------------------------------------ 14774 reflections ( 97.77 % complete ) and 1410 restraints for refining 1373 atoms. 253 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2273 (Rfree = 0.000) for 1373 atoms. Found 32 (32 requested) and removed 25 (23 requested) atoms. Cycle 22: After refmac, R = 0.2224 (Rfree = 0.000) for 1377 atoms. Found 31 (31 requested) and removed 14 (23 requested) atoms. Cycle 23: After refmac, R = 0.2161 (Rfree = 0.000) for 1392 atoms. Found 31 (31 requested) and removed 16 (23 requested) atoms. Cycle 24: After refmac, R = 0.2173 (Rfree = 0.000) for 1404 atoms. Found 31 (31 requested) and removed 20 (24 requested) atoms. Cycle 25: After refmac, R = 0.2130 (Rfree = 0.000) for 1413 atoms. Found 30 (30 requested) and removed 16 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.13 1.91 Round 1: 139 peptides, 3 chains. Longest chain 70 peptides. Score 0.886 Round 2: 139 peptides, 3 chains. Longest chain 76 peptides. Score 0.886 Round 3: 140 peptides, 2 chains. Longest chain 76 peptides. Score 0.899 Round 4: 138 peptides, 4 chains. Longest chain 56 peptides. Score 0.871 Round 5: 139 peptides, 3 chains. Longest chain 75 peptides. Score 0.886 Taking the results from Round 3 Chains 2, Residues 138, Estimated correctness of the model 98.9 % 2 chains (138 residues) have been docked in sequence Building loops using Loopy2018 2 chains (138 residues) following loop building 2 chains (138 residues) in sequence following loop building ------------------------------------------------------ 14774 reflections ( 97.77 % complete ) and 1402 restraints for refining 1358 atoms. 258 conditional restraints added. Observations/parameters ratio is 2.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2256 (Rfree = 0.000) for 1358 atoms. Found 28 (28 requested) and removed 16 (23 requested) atoms. Cycle 27: After refmac, R = 0.2174 (Rfree = 0.000) for 1365 atoms. Found 27 (27 requested) and removed 10 (23 requested) atoms. Cycle 28: After refmac, R = 0.2145 (Rfree = 0.000) for 1382 atoms. Found 27 (27 requested) and removed 14 (23 requested) atoms. Cycle 29: After refmac, R = 0.2154 (Rfree = 0.000) for 1392 atoms. Found 26 (26 requested) and removed 21 (23 requested) atoms. Cycle 30: After refmac, R = 0.2142 (Rfree = 0.000) for 1395 atoms. Found 25 (25 requested) and removed 20 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.14 1.92 Round 1: 139 peptides, 3 chains. Longest chain 70 peptides. Score 0.886 Round 2: 140 peptides, 2 chains. Longest chain 76 peptides. Score 0.899 Round 3: 140 peptides, 2 chains. Longest chain 76 peptides. Score 0.899 Round 4: 139 peptides, 4 chains. Longest chain 55 peptides. Score 0.873 Round 5: 139 peptides, 4 chains. Longest chain 57 peptides. Score 0.873 Taking the results from Round 3 Chains 2, Residues 138, Estimated correctness of the model 98.9 % 2 chains (138 residues) have been docked in sequence Building loops using Loopy2018 2 chains (138 residues) following loop building 2 chains (138 residues) in sequence following loop building ------------------------------------------------------ 14774 reflections ( 97.77 % complete ) and 1367 restraints for refining 1344 atoms. 223 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2261 (Rfree = 0.000) for 1344 atoms. Found 24 (24 requested) and removed 22 (23 requested) atoms. Cycle 32: After refmac, R = 0.2185 (Rfree = 0.000) for 1345 atoms. Found 23 (23 requested) and removed 2 (23 requested) atoms. Cycle 33: After refmac, R = 0.2162 (Rfree = 0.000) for 1365 atoms. Found 23 (23 requested) and removed 13 (23 requested) atoms. Cycle 34: After refmac, R = 0.2157 (Rfree = 0.000) for 1373 atoms. Found 23 (23 requested) and removed 13 (23 requested) atoms. Cycle 35: After refmac, R = 0.2171 (Rfree = 0.000) for 1383 atoms. Found 23 (23 requested) and removed 17 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.16 1.94 Round 1: 139 peptides, 3 chains. Longest chain 70 peptides. Score 0.886 Round 2: 139 peptides, 2 chains. Longest chain 75 peptides. Score 0.898 Round 3: 139 peptides, 2 chains. Longest chain 75 peptides. Score 0.898 Round 4: 138 peptides, 3 chains. Longest chain 75 peptides. Score 0.884 Round 5: 139 peptides, 3 chains. Longest chain 75 peptides. Score 0.886 Taking the results from Round 3 Chains 2, Residues 137, Estimated correctness of the model 98.9 % 2 chains (137 residues) have been docked in sequence Building loops using Loopy2018 2 chains (137 residues) following loop building 2 chains (137 residues) in sequence following loop building ------------------------------------------------------ 14774 reflections ( 97.77 % complete ) and 1383 restraints for refining 1344 atoms. 247 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2249 (Rfree = 0.000) for 1344 atoms. Found 23 (23 requested) and removed 22 (23 requested) atoms. Cycle 37: After refmac, R = 0.2218 (Rfree = 0.000) for 1342 atoms. Found 23 (23 requested) and removed 6 (23 requested) atoms. Cycle 38: After refmac, R = 0.2185 (Rfree = 0.000) for 1357 atoms. Found 23 (23 requested) and removed 7 (23 requested) atoms. Cycle 39: After refmac, R = 0.2205 (Rfree = 0.000) for 1369 atoms. Found 23 (23 requested) and removed 19 (23 requested) atoms. Cycle 40: After refmac, R = 0.2123 (Rfree = 0.000) for 1371 atoms. Found 23 (23 requested) and removed 16 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.13 1.91 Round 1: 139 peptides, 2 chains. Longest chain 75 peptides. Score 0.898 Round 2: 140 peptides, 2 chains. Longest chain 75 peptides. Score 0.899 Round 3: 140 peptides, 2 chains. Longest chain 75 peptides. Score 0.899 Round 4: 139 peptides, 3 chains. Longest chain 65 peptides. Score 0.886 Round 5: 137 peptides, 4 chains. Longest chain 57 peptides. Score 0.869 Taking the results from Round 3 Chains 2, Residues 138, Estimated correctness of the model 98.9 % 2 chains (138 residues) have been docked in sequence Building loops using Loopy2018 2 chains (138 residues) following loop building 2 chains (138 residues) in sequence following loop building ------------------------------------------------------ 14774 reflections ( 97.77 % complete ) and 1354 restraints for refining 1343 atoms. 205 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2239 (Rfree = 0.000) for 1343 atoms. Found 23 (23 requested) and removed 21 (23 requested) atoms. Cycle 42: After refmac, R = 0.2194 (Rfree = 0.000) for 1343 atoms. Found 23 (23 requested) and removed 12 (23 requested) atoms. Cycle 43: After refmac, R = 0.2194 (Rfree = 0.000) for 1352 atoms. Found 23 (23 requested) and removed 14 (23 requested) atoms. Cycle 44: After refmac, R = 0.2200 (Rfree = 0.000) for 1360 atoms. Found 23 (23 requested) and removed 15 (23 requested) atoms. Cycle 45: After refmac, R = 0.2201 (Rfree = 0.000) for 1366 atoms. Found 23 (23 requested) and removed 20 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.15 1.93 Round 1: 140 peptides, 2 chains. Longest chain 75 peptides. Score 0.899 Round 2: 139 peptides, 3 chains. Longest chain 65 peptides. Score 0.886 Round 3: 140 peptides, 2 chains. Longest chain 75 peptides. Score 0.899 Round 4: 136 peptides, 5 chains. Longest chain 56 peptides. Score 0.854 Round 5: 139 peptides, 2 chains. Longest chain 74 peptides. Score 0.898 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 138, Estimated correctness of the model 98.9 % 2 chains (138 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 78 A and 90 A 1 chains (149 residues) following loop building 1 chains (149 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 14774 reflections ( 97.77 % complete ) and 1238 restraints for refining 1209 atoms. Observations/parameters ratio is 3.06 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2889 (Rfree = 0.000) for 1209 atoms. Found 8 (20 requested) and removed 0 (20 requested) atoms. Cycle 47: After refmac, R = 0.2672 (Rfree = 0.000) for 1209 atoms. Found 5 (20 requested) and removed 0 (20 requested) atoms. Cycle 48: After refmac, R = 0.2548 (Rfree = 0.000) for 1209 atoms. Found 1 (20 requested) and removed 1 (20 requested) atoms. Cycle 49: After refmac, R = 0.2481 (Rfree = 0.000) for 1209 atoms. Found 4 (20 requested) and removed 0 (20 requested) atoms. Writing output files ... TimeTaking 32.7