Mon 24 Dec 07:39:55 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 2aam-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aam-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aam-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-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/2aam-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-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 07:40:00 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/2aam-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-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 3850 and 0 Target number of residues in the AU: 3850 Target solvent content: 0.6263 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 309 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1854 Adjusted target solvent content: 0.82 Input MTZ file: 2aam-3.6-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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.50 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. 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: 169.060 3.600 Wilson plot Bfac: 64.60 63881 reflections ( 98.93 % complete ) and 0 restraints for refining 16552 atoms. Observations/parameters ratio is 0.96 ------------------------------------------------------ Starting model: R = 0.3548 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2967 (Rfree = 0.000) for 16552 atoms. Found 106 (106 requested) and removed 78 (53 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 2.05 Search for helices and strands: 0 residues in 0 chains, 16933 seeds are put forward NCS extension: 0 residues added, 16933 seeds are put forward Round 1: 1207 peptides, 149 chains. Longest chain 27 peptides. Score 0.405 Round 2: 1260 peptides, 151 chains. Longest chain 27 peptides. Score 0.419 Round 3: 1268 peptides, 144 chains. Longest chain 25 peptides. Score 0.431 Round 4: 1258 peptides, 141 chains. Longest chain 26 peptides. Score 0.433 Round 5: 1287 peptides, 141 chains. Longest chain 39 peptides. Score 0.442 Taking the results from Round 5 Chains 147, Residues 1146, Estimated correctness of the model 0.0 % 6 chains (71 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4703 restraints for refining 15444 atoms. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2461 (Rfree = 0.000) for 15444 atoms. Found 99 (99 requested) and removed 55 (49 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2341 (Rfree = 0.000) for 15488 atoms. Found 99 (99 requested) and removed 62 (49 requested) atoms. Cycle 3: After refmac, R = 0.2272 (Rfree = 0.000) for 15525 atoms. Found 99 (99 requested) and removed 80 (49 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2176 (Rfree = 0.000) for 15544 atoms. Found 99 (99 requested) and removed 68 (49 requested) atoms. Cycle 5: After refmac, R = 0.2152 (Rfree = 0.000) for 15575 atoms. Found 99 (99 requested) and removed 67 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 2.02 Search for helices and strands: 0 residues in 0 chains, 16160 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 16192 seeds are put forward Round 1: 1286 peptides, 137 chains. Longest chain 43 peptides. Score 0.447 Round 2: 1296 peptides, 123 chains. Longest chain 38 peptides. Score 0.470 Round 3: 1272 peptides, 142 chains. Longest chain 30 peptides. Score 0.436 Round 4: 1290 peptides, 150 chains. Longest chain 28 peptides. Score 0.429 Round 5: 1284 peptides, 146 chains. Longest chain 31 peptides. Score 0.433 Taking the results from Round 2 Chains 131, Residues 1173, Estimated correctness of the model 0.0 % 10 chains (146 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5258 restraints for refining 15294 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2223 (Rfree = 0.000) for 15294 atoms. Found 98 (98 requested) and removed 56 (49 requested) atoms. Cycle 7: After refmac, R = 0.2104 (Rfree = 0.000) for 15336 atoms. Found 98 (98 requested) and removed 64 (49 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2089 (Rfree = 0.000) for 15370 atoms. Found 98 (98 requested) and removed 69 (49 requested) atoms. Cycle 9: After refmac, R = 0.2035 (Rfree = 0.000) for 15399 atoms. Found 63 (98 requested) and removed 60 (49 requested) atoms. Cycle 10: After refmac, R = 0.2022 (Rfree = 0.000) for 15402 atoms. Found 98 (98 requested) and removed 66 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 2.02 Search for helices and strands: 0 residues in 0 chains, 15985 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 16019 seeds are put forward Round 1: 1295 peptides, 150 chains. Longest chain 51 peptides. Score 0.431 Round 2: 1302 peptides, 132 chains. Longest chain 42 peptides. Score 0.459 Round 3: 1301 peptides, 125 chains. Longest chain 36 peptides. Score 0.469 Round 4: 1308 peptides, 136 chains. Longest chain 32 peptides. Score 0.455 Round 5: 1339 peptides, 135 chains. Longest chain 37 peptides. Score 0.465 Taking the results from Round 3 Chains 129, Residues 1176, Estimated correctness of the model 0.0 % 6 chains (115 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5084 restraints for refining 15855 atoms. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2221 (Rfree = 0.000) for 15855 atoms. Found 101 (101 requested) and removed 54 (50 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2165 (Rfree = 0.000) for 15902 atoms. Found 102 (102 requested) and removed 58 (51 requested) atoms. Cycle 13: After refmac, R = 0.2086 (Rfree = 0.000) for 15946 atoms. Found 102 (102 requested) and removed 62 (51 requested) atoms. Cycle 14: After refmac, R = 0.2091 (Rfree = 0.000) for 15986 atoms. Found 102 (102 requested) and removed 77 (51 requested) atoms. Cycle 15: After refmac, R = 0.2088 (Rfree = 0.000) for 16011 atoms. Found 102 (102 requested) and removed 75 (51 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 1.99 Search for helices and strands: 0 residues in 0 chains, 16571 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 16597 seeds are put forward Round 1: 1287 peptides, 166 chains. Longest chain 35 peptides. Score 0.404 Round 2: 1319 peptides, 157 chains. Longest chain 38 peptides. Score 0.428 Round 3: 1348 peptides, 159 chains. Longest chain 33 peptides. Score 0.433 Round 4: 1335 peptides, 163 chains. Longest chain 32 peptides. Score 0.424 Round 5: 1330 peptides, 148 chains. Longest chain 36 peptides. Score 0.444 Taking the results from Round 5 Chains 152, Residues 1182, Estimated correctness of the model 0.0 % 6 chains (57 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4828 restraints for refining 16390 atoms. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2362 (Rfree = 0.000) for 16390 atoms. Found 105 (105 requested) and removed 59 (52 requested) atoms. Cycle 17: After refmac, R = 0.2349 (Rfree = 0.000) for 16436 atoms. Found 105 (105 requested) and removed 60 (52 requested) atoms. Cycle 18: After refmac, R = 0.2333 (Rfree = 0.000) for 16481 atoms. Found 105 (105 requested) and removed 65 (52 requested) atoms. Cycle 19: After refmac, R = 0.2344 (Rfree = 0.000) for 16521 atoms. Found 105 (105 requested) and removed 77 (52 requested) atoms. Cycle 20: After refmac, R = 0.2338 (Rfree = 0.000) for 16549 atoms. Found 106 (106 requested) and removed 72 (53 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 1.96 Search for helices and strands: 0 residues in 0 chains, 17176 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 17204 seeds are put forward Round 1: 1259 peptides, 184 chains. Longest chain 22 peptides. Score 0.369 Round 2: 1386 peptides, 178 chains. Longest chain 37 peptides. Score 0.417 Round 3: 1313 peptides, 167 chains. Longest chain 34 peptides. Score 0.411 Round 4: 1347 peptides, 165 chains. Longest chain 28 peptides. Score 0.424 Round 5: 1324 peptides, 168 chains. Longest chain 26 peptides. Score 0.413 Taking the results from Round 4 Chains 169, Residues 1182, Estimated correctness of the model 0.0 % 5 chains (69 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4869 restraints for refining 16442 atoms. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2431 (Rfree = 0.000) for 16442 atoms. Found 105 (105 requested) and removed 63 (52 requested) atoms. Cycle 22: After refmac, R = 0.2403 (Rfree = 0.000) for 16484 atoms. Found 105 (105 requested) and removed 71 (52 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2378 (Rfree = 0.000) for 16518 atoms. Found 105 (105 requested) and removed 66 (52 requested) atoms. Cycle 24: After refmac, R = 0.2373 (Rfree = 0.000) for 16557 atoms. Found 106 (106 requested) and removed 62 (53 requested) atoms. Cycle 25: After refmac, R = 0.2422 (Rfree = 0.000) for 16601 atoms. Found 106 (106 requested) and removed 72 (53 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 1.94 Search for helices and strands: 0 residues in 0 chains, 17221 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 17236 seeds are put forward Round 1: 1212 peptides, 188 chains. Longest chain 20 peptides. Score 0.347 Round 2: 1323 peptides, 168 chains. Longest chain 28 peptides. Score 0.413 Round 3: 1334 peptides, 170 chains. Longest chain 26 peptides. Score 0.413 Round 4: 1322 peptides, 160 chains. Longest chain 27 peptides. Score 0.424 Round 5: 1342 peptides, 166 chains. Longest chain 23 peptides. Score 0.421 Taking the results from Round 4 Chains 163, Residues 1162, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4610 restraints for refining 16279 atoms. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2503 (Rfree = 0.000) for 16279 atoms. Found 104 (104 requested) and removed 55 (52 requested) atoms. Cycle 27: After refmac, R = 0.2471 (Rfree = 0.000) for 16328 atoms. Found 104 (104 requested) and removed 61 (52 requested) atoms. Cycle 28: After refmac, R = 0.2462 (Rfree = 0.000) for 16371 atoms. Found 105 (105 requested) and removed 64 (52 requested) atoms. Cycle 29: After refmac, R = 0.2470 (Rfree = 0.000) for 16412 atoms. Found 105 (105 requested) and removed 73 (52 requested) atoms. Cycle 30: After refmac, R = 0.2436 (Rfree = 0.000) for 16444 atoms. Found 105 (105 requested) and removed 65 (52 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 1.94 Search for helices and strands: 0 residues in 0 chains, 17038 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 17058 seeds are put forward Round 1: 1231 peptides, 187 chains. Longest chain 22 peptides. Score 0.355 Round 2: 1321 peptides, 180 chains. Longest chain 33 peptides. Score 0.394 Round 3: 1339 peptides, 182 chains. Longest chain 21 peptides. Score 0.397 Round 4: 1323 peptides, 178 chains. Longest chain 23 peptides. Score 0.398 Round 5: 1307 peptides, 175 chains. Longest chain 24 peptides. Score 0.397 Taking the results from Round 4 Chains 180, Residues 1145, Estimated correctness of the model 0.0 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 63881 reflections ( 98.93 % complete ) and 4602 restraints for refining 16295 atoms. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2527 (Rfree = 0.000) for 16295 atoms. Found 104 (104 requested) and removed 60 (52 requested) atoms. Cycle 32: After refmac, R = 0.2555 (Rfree = 0.000) for 16339 atoms. Found 104 (104 requested) and removed 67 (52 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2519 (Rfree = 0.000) for 16376 atoms. Found 105 (105 requested) and removed 68 (52 requested) atoms. Cycle 34: After refmac, R = 0.2552 (Rfree = 0.000) for 16413 atoms. Found 105 (105 requested) and removed 75 (52 requested) atoms. Cycle 35: After refmac, R = 0.2539 (Rfree = 0.000) for 16443 atoms. Found 105 (105 requested) and removed 75 (52 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 1.94 Search for helices and strands: 0 residues in 0 chains, 17048 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 17061 seeds are put forward Round 1: 1211 peptides, 201 chains. Longest chain 22 peptides. Score 0.326 Round 2: 1324 peptides, 181 chains. Longest chain 30 peptides. Score 0.394 Round 3: 1327 peptides, 185 chains. Longest chain 27 peptides. Score 0.389 Round 4: 1330 peptides, 184 chains. Longest chain 25 peptides. Score 0.391 Round 5: 1330 peptides, 186 chains. Longest chain 25 peptides. Score 0.388 Taking the results from Round 2 Chains 181, Residues 1143, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4463 restraints for refining 15752 atoms. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2445 (Rfree = 0.000) for 15752 atoms. Found 101 (101 requested) and removed 56 (50 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2449 (Rfree = 0.000) for 15797 atoms. Found 101 (101 requested) and removed 55 (50 requested) atoms. Cycle 38: After refmac, R = 0.2469 (Rfree = 0.000) for 15843 atoms. Found 101 (101 requested) and removed 69 (50 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2504 (Rfree = 0.000) for 15875 atoms. Found 101 (101 requested) and removed 74 (50 requested) atoms. Cycle 40: After refmac, R = 0.2458 (Rfree = 0.000) for 15902 atoms. Found 102 (102 requested) and removed 69 (51 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 1.93 Search for helices and strands: 0 residues in 0 chains, 16449 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 16468 seeds are put forward Round 1: 1164 peptides, 193 chains. Longest chain 21 peptides. Score 0.323 Round 2: 1266 peptides, 185 chains. Longest chain 23 peptides. Score 0.369 Round 3: 1307 peptides, 188 chains. Longest chain 25 peptides. Score 0.378 Round 4: 1290 peptides, 179 chains. Longest chain 30 peptides. Score 0.386 Round 5: 1302 peptides, 185 chains. Longest chain 25 peptides. Score 0.381 Taking the results from Round 4 Chains 180, Residues 1111, Estimated correctness of the model 0.0 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4413 restraints for refining 16017 atoms. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2492 (Rfree = 0.000) for 16017 atoms. Found 102 (102 requested) and removed 58 (51 requested) atoms. Cycle 42: After refmac, R = 0.2456 (Rfree = 0.000) for 16061 atoms. Found 103 (103 requested) and removed 60 (51 requested) atoms. Cycle 43: After refmac, R = 0.2453 (Rfree = 0.000) for 16104 atoms. Found 103 (103 requested) and removed 58 (51 requested) atoms. Cycle 44: After refmac, R = 0.2413 (Rfree = 0.000) for 16149 atoms. Found 103 (103 requested) and removed 62 (51 requested) atoms. Cycle 45: After refmac, R = 0.2449 (Rfree = 0.000) for 16190 atoms. Found 103 (103 requested) and removed 68 (51 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 1.92 Search for helices and strands: 0 residues in 0 chains, 16706 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 16726 seeds are put forward Round 1: 1136 peptides, 189 chains. Longest chain 27 peptides. Score 0.319 Round 2: 1247 peptides, 181 chains. Longest chain 22 peptides. Score 0.369 Round 3: 1281 peptides, 183 chains. Longest chain 30 peptides. Score 0.377 Round 4: 1277 peptides, 181 chains. Longest chain 20 peptides. Score 0.379 Round 5: 1226 peptides, 175 chains. Longest chain 17 peptides. Score 0.372 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 183, Residues 1096, Estimated correctness of the model 0.0 % 3 chains (34 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2aam-3_warpNtrace.pdb as input Building loops using Loopy2018 183 chains (1096 residues) following loop building 3 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 63881 reflections ( 98.93 % complete ) and 4377 restraints for refining 15736 atoms. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2463 (Rfree = 0.000) for 15736 atoms. Found 0 (100 requested) and removed 50 (50 requested) atoms. Cycle 47: After refmac, R = 0.2475 (Rfree = 0.000) for 15686 atoms. Found 0 (100 requested) and removed 50 (50 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2511 (Rfree = 0.000) for 15636 atoms. Found 0 (100 requested) and removed 50 (50 requested) atoms. Cycle 49: After refmac, R = 0.2496 (Rfree = 0.000) for 15586 atoms. TimeTaking 226.7