null Tue 25 Dec 19:27:57 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 2aam-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aam-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aam-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.4-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/2aam-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.4-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 19:28:07 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/2aam-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.4-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 3952 and 0 Target number of residues in the AU: 3952 Target solvent content: 0.6164 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-3.4-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: 4 Cell parameters: 195.000 84.610 194.910 90.000 119.891 90.000 Input sequence file: 2aam-3.4-parrot-hancs.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 3.400 Wilson plot Bfac: 59.77 75788 reflections ( 99.05 % complete ) and 0 restraints for refining 16342 atoms. Observations/parameters ratio is 1.16 ------------------------------------------------------ Starting model: R = 0.3397 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2742 (Rfree = 0.000) for 16342 atoms. Found 123 (123 requested) and removed 79 (61 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 1.94 Search for helices and strands: 0 residues in 0 chains, 16767 seeds are put forward NCS extension: 0 residues added, 16767 seeds are put forward Round 1: 1325 peptides, 142 chains. Longest chain 33 peptides. Score 0.451 Round 2: 1348 peptides, 150 chains. Longest chain 25 peptides. Score 0.446 Round 3: 1328 peptides, 148 chains. Longest chain 27 peptides. Score 0.443 Round 4: 1353 peptides, 146 chains. Longest chain 34 peptides. Score 0.454 Round 5: 1362 peptides, 142 chains. Longest chain 37 peptides. Score 0.462 Taking the results from Round 5 Chains 151, Residues 1220, Estimated correctness of the model 0.0 % 10 chains (148 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5388 restraints for refining 15359 atoms. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2468 (Rfree = 0.000) for 15359 atoms. Found 115 (115 requested) and removed 61 (57 requested) atoms. Cycle 2: After refmac, R = 0.2321 (Rfree = 0.000) for 15413 atoms. Found 116 (116 requested) and removed 63 (58 requested) atoms. Cycle 3: After refmac, R = 0.2246 (Rfree = 0.000) for 15466 atoms. Found 97 (116 requested) and removed 66 (58 requested) atoms. Cycle 4: After refmac, R = 0.2176 (Rfree = 0.000) for 15497 atoms. Found 83 (117 requested) and removed 74 (58 requested) atoms. Cycle 5: After refmac, R = 0.2146 (Rfree = 0.000) for 15506 atoms. Found 67 (117 requested) and removed 73 (58 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 1.94 Search for helices and strands: 0 residues in 0 chains, 16065 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 16075 seeds are put forward Round 1: 1388 peptides, 138 chains. Longest chain 37 peptides. Score 0.475 Round 2: 1338 peptides, 147 chains. Longest chain 32 peptides. Score 0.448 Round 3: 1392 peptides, 151 chains. Longest chain 40 peptides. Score 0.458 Round 4: 1367 peptides, 148 chains. Longest chain 34 peptides. Score 0.455 Round 5: 1374 peptides, 149 chains. Longest chain 38 peptides. Score 0.455 Taking the results from Round 1 Chains 147, Residues 1250, Estimated correctness of the model 0.0 % 13 chains (186 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5671 restraints for refining 15108 atoms. Observations/parameters ratio is 1.25 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2256 (Rfree = 0.000) for 15108 atoms. Found 114 (114 requested) and removed 84 (57 requested) atoms. Cycle 7: After refmac, R = 0.2129 (Rfree = 0.000) for 15138 atoms. Found 114 (114 requested) and removed 71 (57 requested) atoms. Cycle 8: After refmac, R = 0.2073 (Rfree = 0.000) for 15181 atoms. Found 70 (114 requested) and removed 64 (57 requested) atoms. Cycle 9: After refmac, R = 0.2049 (Rfree = 0.000) for 15187 atoms. Found 66 (114 requested) and removed 60 (57 requested) atoms. Cycle 10: After refmac, R = 0.1995 (Rfree = 0.000) for 15193 atoms. Found 58 (114 requested) and removed 64 (57 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 1.94 Search for helices and strands: 0 residues in 0 chains, 15693 seeds are put forward NCS extension: 23 residues added (22 deleted due to clashes), 15716 seeds are put forward Round 1: 1397 peptides, 142 chains. Longest chain 37 peptides. Score 0.472 Round 2: 1369 peptides, 141 chains. Longest chain 28 peptides. Score 0.465 Round 3: 1371 peptides, 143 chains. Longest chain 54 peptides. Score 0.463 Round 4: 1379 peptides, 138 chains. Longest chain 33 peptides. Score 0.472 Round 5: 1361 peptides, 142 chains. Longest chain 41 peptides. Score 0.462 Taking the results from Round 4 Chains 148, Residues 1241, Estimated correctness of the model 0.0 % 14 chains (240 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5936 restraints for refining 15484 atoms. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2332 (Rfree = 0.000) for 15484 atoms. Found 116 (116 requested) and removed 82 (58 requested) atoms. Cycle 12: After refmac, R = 0.2186 (Rfree = 0.000) for 15518 atoms. Found 117 (117 requested) and removed 64 (58 requested) atoms. Cycle 13: After refmac, R = 0.2139 (Rfree = 0.000) for 15571 atoms. Found 110 (117 requested) and removed 70 (58 requested) atoms. Cycle 14: After refmac, R = 0.2080 (Rfree = 0.000) for 15611 atoms. Found 73 (117 requested) and removed 63 (58 requested) atoms. Cycle 15: After refmac, R = 0.2049 (Rfree = 0.000) for 15621 atoms. Found 67 (117 requested) and removed 69 (58 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 1.94 Search for helices and strands: 0 residues in 0 chains, 16138 seeds are put forward NCS extension: 13 residues added (9 deleted due to clashes), 16151 seeds are put forward Round 1: 1355 peptides, 133 chains. Longest chain 51 peptides. Score 0.473 Round 2: 1402 peptides, 138 chains. Longest chain 51 peptides. Score 0.479 Round 3: 1403 peptides, 135 chains. Longest chain 35 peptides. Score 0.483 Round 4: 1381 peptides, 132 chains. Longest chain 49 peptides. Score 0.481 Round 5: 1381 peptides, 140 chains. Longest chain 38 peptides. Score 0.470 Taking the results from Round 3 Chains 150, Residues 1268, Estimated correctness of the model 0.0 % 18 chains (323 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 6437 restraints for refining 15977 atoms. Observations/parameters ratio is 1.19 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2311 (Rfree = 0.000) for 15977 atoms. Found 120 (120 requested) and removed 88 (60 requested) atoms. Cycle 17: After refmac, R = 0.2176 (Rfree = 0.000) for 16009 atoms. Found 118 (120 requested) and removed 72 (60 requested) atoms. Cycle 18: After refmac, R = 0.2121 (Rfree = 0.000) for 16055 atoms. Found 109 (121 requested) and removed 71 (60 requested) atoms. Cycle 19: After refmac, R = 0.2093 (Rfree = 0.000) for 16093 atoms. Found 67 (121 requested) and removed 66 (60 requested) atoms. Cycle 20: After refmac, R = 0.2060 (Rfree = 0.000) for 16094 atoms. Found 61 (121 requested) and removed 65 (60 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 1.94 Search for helices and strands: 0 residues in 0 chains, 16625 seeds are put forward NCS extension: 17 residues added (9 deleted due to clashes), 16642 seeds are put forward Round 1: 1349 peptides, 134 chains. Longest chain 41 peptides. Score 0.470 Round 2: 1403 peptides, 139 chains. Longest chain 34 peptides. Score 0.478 Round 3: 1382 peptides, 138 chains. Longest chain 36 peptides. Score 0.473 Round 4: 1408 peptides, 151 chains. Longest chain 51 peptides. Score 0.462 Round 5: 1407 peptides, 148 chains. Longest chain 38 peptides. Score 0.466 Taking the results from Round 2 Chains 149, Residues 1264, Estimated correctness of the model 0.0 % 10 chains (168 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5630 restraints for refining 15627 atoms. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2252 (Rfree = 0.000) for 15627 atoms. Found 117 (117 requested) and removed 65 (58 requested) atoms. Cycle 22: After refmac, R = 0.2115 (Rfree = 0.000) for 15679 atoms. Found 96 (118 requested) and removed 61 (59 requested) atoms. Cycle 23: After refmac, R = 0.2056 (Rfree = 0.000) for 15714 atoms. Found 63 (118 requested) and removed 66 (59 requested) atoms. Cycle 24: After refmac, R = 0.2030 (Rfree = 0.000) for 15711 atoms. Found 65 (118 requested) and removed 64 (59 requested) atoms. Cycle 25: After refmac, R = 0.1984 (Rfree = 0.000) for 15712 atoms. Found 52 (118 requested) and removed 62 (59 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 1.94 Search for helices and strands: 0 residues in 0 chains, 16180 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 16197 seeds are put forward Round 1: 1324 peptides, 152 chains. Longest chain 30 peptides. Score 0.436 Round 2: 1378 peptides, 144 chains. Longest chain 40 peptides. Score 0.464 Round 3: 1402 peptides, 143 chains. Longest chain 35 peptides. Score 0.472 Round 4: 1402 peptides, 143 chains. Longest chain 35 peptides. Score 0.472 Round 5: 1441 peptides, 145 chains. Longest chain 39 peptides. Score 0.480 Taking the results from Round 5 Chains 154, Residues 1296, Estimated correctness of the model 0.0 % 14 chains (242 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 6122 restraints for refining 16249 atoms. Observations/parameters ratio is 1.17 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2306 (Rfree = 0.000) for 16249 atoms. Found 122 (122 requested) and removed 75 (61 requested) atoms. Cycle 27: After refmac, R = 0.2164 (Rfree = 0.000) for 16296 atoms. Found 123 (123 requested) and removed 81 (61 requested) atoms. Cycle 28: After refmac, R = 0.2120 (Rfree = 0.000) for 16338 atoms. Found 95 (123 requested) and removed 66 (61 requested) atoms. Cycle 29: After refmac, R = 0.2073 (Rfree = 0.000) for 16367 atoms. Found 74 (123 requested) and removed 69 (61 requested) atoms. Cycle 30: After refmac, R = 0.2043 (Rfree = 0.000) for 16372 atoms. Found 73 (123 requested) and removed 64 (61 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 1.94 Search for helices and strands: 0 residues in 0 chains, 16864 seeds are put forward NCS extension: 20 residues added (8 deleted due to clashes), 16884 seeds are put forward Round 1: 1349 peptides, 156 chains. Longest chain 28 peptides. Score 0.438 Round 2: 1367 peptides, 129 chains. Longest chain 41 peptides. Score 0.482 Round 3: 1373 peptides, 146 chains. Longest chain 37 peptides. Score 0.459 Round 4: 1391 peptides, 142 chains. Longest chain 36 peptides. Score 0.470 Round 5: 1384 peptides, 141 chains. Longest chain 42 peptides. Score 0.469 Taking the results from Round 2 Chains 137, Residues 1238, Estimated correctness of the model 0.0 % 10 chains (111 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5294 restraints for refining 16001 atoms. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2217 (Rfree = 0.000) for 16001 atoms. Found 120 (120 requested) and removed 68 (60 requested) atoms. Cycle 32: After refmac, R = 0.2097 (Rfree = 0.000) for 16053 atoms. Found 91 (121 requested) and removed 62 (60 requested) atoms. Cycle 33: After refmac, R = 0.2055 (Rfree = 0.000) for 16082 atoms. Found 82 (121 requested) and removed 65 (60 requested) atoms. Cycle 34: After refmac, R = 0.2021 (Rfree = 0.000) for 16099 atoms. Found 90 (121 requested) and removed 65 (60 requested) atoms. Cycle 35: After refmac, R = 0.1988 (Rfree = 0.000) for 16124 atoms. Found 64 (121 requested) and removed 64 (60 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 1.94 Search for helices and strands: 0 residues in 0 chains, 16623 seeds are put forward NCS extension: 30 residues added (17 deleted due to clashes), 16653 seeds are put forward Round 1: 1371 peptides, 158 chains. Longest chain 44 peptides. Score 0.442 Round 2: 1389 peptides, 149 chains. Longest chain 46 peptides. Score 0.460 Round 3: 1410 peptides, 149 chains. Longest chain 41 peptides. Score 0.466 Round 4: 1411 peptides, 142 chains. Longest chain 38 peptides. Score 0.476 Round 5: 1362 peptides, 143 chains. Longest chain 51 peptides. Score 0.460 Taking the results from Round 4 Chains 148, Residues 1269, Estimated correctness of the model 0.0 % 6 chains (83 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5308 restraints for refining 16177 atoms. Observations/parameters ratio is 1.17 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2201 (Rfree = 0.000) for 16177 atoms. Found 122 (122 requested) and removed 65 (61 requested) atoms. Cycle 37: After refmac, R = 0.2090 (Rfree = 0.000) for 16234 atoms. Found 122 (122 requested) and removed 65 (61 requested) atoms. Cycle 38: After refmac, R = 0.2065 (Rfree = 0.000) for 16291 atoms. Found 110 (123 requested) and removed 65 (61 requested) atoms. Cycle 39: After refmac, R = 0.2018 (Rfree = 0.000) for 16336 atoms. Found 84 (123 requested) and removed 64 (61 requested) atoms. Cycle 40: After refmac, R = 0.1993 (Rfree = 0.000) for 16356 atoms. Found 64 (123 requested) and removed 65 (61 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 1.94 Search for helices and strands: 0 residues in 0 chains, 16856 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 16868 seeds are put forward Round 1: 1318 peptides, 163 chains. Longest chain 26 peptides. Score 0.418 Round 2: 1359 peptides, 137 chains. Longest chain 43 peptides. Score 0.468 Round 3: 1384 peptides, 151 chains. Longest chain 34 peptides. Score 0.455 Round 4: 1375 peptides, 139 chains. Longest chain 38 peptides. Score 0.470 Round 5: 1355 peptides, 147 chains. Longest chain 36 peptides. Score 0.453 Taking the results from Round 4 Chains 149, Residues 1236, Estimated correctness of the model 0.0 % 11 chains (168 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5529 restraints for refining 16178 atoms. Observations/parameters ratio is 1.17 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2203 (Rfree = 0.000) for 16178 atoms. Found 122 (122 requested) and removed 63 (61 requested) atoms. Cycle 42: After refmac, R = 0.2076 (Rfree = 0.000) for 16237 atoms. Found 102 (122 requested) and removed 66 (61 requested) atoms. Cycle 43: After refmac, R = 0.2056 (Rfree = 0.000) for 16273 atoms. Found 89 (122 requested) and removed 66 (61 requested) atoms. Cycle 44: After refmac, R = 0.2044 (Rfree = 0.000) for 16296 atoms. Found 109 (123 requested) and removed 65 (61 requested) atoms. Cycle 45: After refmac, R = 0.1992 (Rfree = 0.000) for 16340 atoms. Found 79 (123 requested) and removed 66 (61 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 1.93 Search for helices and strands: 0 residues in 0 chains, 16849 seeds are put forward NCS extension: 32 residues added (8 deleted due to clashes), 16881 seeds are put forward Round 1: 1287 peptides, 165 chains. Longest chain 32 peptides. Score 0.406 Round 2: 1350 peptides, 142 chains. Longest chain 60 peptides. Score 0.458 Round 3: 1358 peptides, 145 chains. Longest chain 36 peptides. Score 0.456 Round 4: 1350 peptides, 143 chains. Longest chain 48 peptides. Score 0.457 Round 5: 1350 peptides, 134 chains. Longest chain 45 peptides. Score 0.470 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 141, Residues 1216, Estimated correctness of the model 0.0 % 6 chains (104 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2aam-3_warpNtrace.pdb as input Building loops using Loopy2018 141 chains (1216 residues) following loop building 6 chains (104 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 75788 reflections ( 99.05 % complete ) and 5154 restraints for refining 16341 atoms. Observations/parameters ratio is 1.16 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2221 (Rfree = 0.000) for 16341 atoms. Found 0 (123 requested) and removed 46 (61 requested) atoms. Cycle 47: After refmac, R = 0.2167 (Rfree = 0.000) for 16295 atoms. Found 0 (123 requested) and removed 29 (61 requested) atoms. Cycle 48: After refmac, R = 0.2113 (Rfree = 0.000) for 16266 atoms. Found 0 (122 requested) and removed 45 (61 requested) atoms. Cycle 49: After refmac, R = 0.2071 (Rfree = 0.000) for 16221 atoms. Found 0 (122 requested) and removed 30 (61 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 23:51:19 GMT 2018 Job finished. TimeTaking 263.36 Used memory is bytes: 21828880