Mon 24 Dec 07:32:33 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aam-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aam-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-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/2aam-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-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 07:32:37 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-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 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-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-3.4-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 3.400 Wilson plot Bfac: 59.77 75788 reflections ( 99.05 % complete ) and 0 restraints for refining 16592 atoms. Observations/parameters ratio is 1.14 ------------------------------------------------------ Starting model: R = 0.3520 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2877 (Rfree = 0.000) for 16592 atoms. Found 125 (125 requested) and removed 80 (62 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 1.96 Search for helices and strands: 0 residues in 0 chains, 17001 seeds are put forward NCS extension: 0 residues added, 17001 seeds are put forward Round 1: 1287 peptides, 155 chains. Longest chain 30 peptides. Score 0.421 Round 2: 1302 peptides, 152 chains. Longest chain 30 peptides. Score 0.430 Round 3: 1299 peptides, 151 chains. Longest chain 28 peptides. Score 0.430 Round 4: 1296 peptides, 141 chains. Longest chain 33 peptides. Score 0.444 Round 5: 1270 peptides, 145 chains. Longest chain 36 peptides. Score 0.431 Taking the results from Round 4 Chains 150, Residues 1155, Estimated correctness of the model 0.0 % 11 chains (125 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5025 restraints for refining 15970 atoms. Observations/parameters ratio is 1.19 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2527 (Rfree = 0.000) for 15970 atoms. Found 120 (120 requested) and removed 73 (60 requested) atoms. Cycle 2: After refmac, R = 0.2379 (Rfree = 0.000) for 16017 atoms. Found 120 (120 requested) and removed 77 (60 requested) atoms. Cycle 3: After refmac, R = 0.2282 (Rfree = 0.000) for 16060 atoms. Found 86 (121 requested) and removed 73 (60 requested) atoms. Cycle 4: After refmac, R = 0.2225 (Rfree = 0.000) for 16073 atoms. Found 71 (121 requested) and removed 66 (60 requested) atoms. Cycle 5: After refmac, R = 0.2183 (Rfree = 0.000) for 16078 atoms. Found 64 (121 requested) and removed 70 (60 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 1.94 Search for helices and strands: 0 residues in 0 chains, 16606 seeds are put forward NCS extension: 54 residues added (4 deleted due to clashes), 16660 seeds are put forward Round 1: 1301 peptides, 148 chains. Longest chain 38 peptides. Score 0.435 Round 2: 1324 peptides, 153 chains. Longest chain 25 peptides. Score 0.435 Round 3: 1301 peptides, 155 chains. Longest chain 33 peptides. Score 0.425 Round 4: 1307 peptides, 144 chains. Longest chain 32 peptides. Score 0.443 Round 5: 1317 peptides, 150 chains. Longest chain 26 peptides. Score 0.437 Taking the results from Round 4 Chains 152, Residues 1163, Estimated correctness of the model 0.0 % 10 chains (118 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5009 restraints for refining 16002 atoms. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2368 (Rfree = 0.000) for 16002 atoms. Found 120 (120 requested) and removed 71 (60 requested) atoms. Cycle 7: After refmac, R = 0.2248 (Rfree = 0.000) for 16051 atoms. Found 121 (121 requested) and removed 68 (60 requested) atoms. Cycle 8: After refmac, R = 0.2219 (Rfree = 0.000) for 16104 atoms. Found 117 (121 requested) and removed 66 (60 requested) atoms. Cycle 9: After refmac, R = 0.2052 (Rfree = 0.000) for 16155 atoms. Found 30 (121 requested) and removed 66 (60 requested) atoms. Cycle 10: After refmac, R = 0.2018 (Rfree = 0.000) for 16119 atoms. Found 27 (121 requested) and removed 65 (60 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 1.96 Search for helices and strands: 0 residues in 0 chains, 16630 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 16653 seeds are put forward Round 1: 1329 peptides, 155 chains. Longest chain 28 peptides. Score 0.433 Round 2: 1317 peptides, 162 chains. Longest chain 27 peptides. Score 0.420 Round 3: 1326 peptides, 161 chains. Longest chain 40 peptides. Score 0.424 Round 4: 1361 peptides, 155 chains. Longest chain 28 peptides. Score 0.443 Round 5: 1353 peptides, 157 chains. Longest chain 38 peptides. Score 0.438 Taking the results from Round 4 Chains 163, Residues 1206, Estimated correctness of the model 0.0 % 10 chains (159 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5369 restraints for refining 16093 atoms. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2324 (Rfree = 0.000) for 16093 atoms. Found 121 (121 requested) and removed 110 (60 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2189 (Rfree = 0.000) for 16104 atoms. Found 113 (121 requested) and removed 65 (60 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2154 (Rfree = 0.000) for 16152 atoms. Found 96 (121 requested) and removed 66 (60 requested) atoms. Cycle 14: After refmac, R = 0.2143 (Rfree = 0.000) for 16182 atoms. Found 98 (122 requested) and removed 64 (61 requested) atoms. Cycle 15: After refmac, R = 0.2039 (Rfree = 0.000) for 16216 atoms. Found 31 (122 requested) and removed 66 (61 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 1.97 Search for helices and strands: 0 residues in 0 chains, 16738 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 16761 seeds are put forward Round 1: 1334 peptides, 153 chains. Longest chain 28 peptides. Score 0.438 Round 2: 1356 peptides, 156 chains. Longest chain 27 peptides. Score 0.440 Round 3: 1370 peptides, 156 chains. Longest chain 36 peptides. Score 0.444 Round 4: 1348 peptides, 158 chains. Longest chain 28 peptides. Score 0.435 Round 5: 1324 peptides, 160 chains. Longest chain 33 peptides. Score 0.425 Taking the results from Round 3 Chains 164, Residues 1214, Estimated correctness of the model 0.0 % 8 chains (113 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5239 restraints for refining 15993 atoms. Observations/parameters ratio is 1.18 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2304 (Rfree = 0.000) for 15993 atoms. Found 120 (120 requested) and removed 84 (60 requested) atoms. Cycle 17: After refmac, R = 0.2173 (Rfree = 0.000) for 16029 atoms. Found 116 (121 requested) and removed 81 (60 requested) atoms. Cycle 18: After refmac, R = 0.2153 (Rfree = 0.000) for 16064 atoms. Found 86 (121 requested) and removed 70 (60 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2181 (Rfree = 0.000) for 16080 atoms. Found 107 (121 requested) and removed 66 (60 requested) atoms. Cycle 20: After refmac, R = 0.2180 (Rfree = 0.000) for 16121 atoms. Found 101 (121 requested) and removed 70 (60 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 1.96 Search for helices and strands: 0 residues in 0 chains, 16616 seeds are put forward NCS extension: 38 residues added (8 deleted due to clashes), 16654 seeds are put forward Round 1: 1278 peptides, 155 chains. Longest chain 34 peptides. Score 0.418 Round 2: 1375 peptides, 148 chains. Longest chain 41 peptides. Score 0.457 Round 3: 1348 peptides, 148 chains. Longest chain 30 peptides. Score 0.449 Round 4: 1350 peptides, 136 chains. Longest chain 37 peptides. Score 0.467 Round 5: 1351 peptides, 139 chains. Longest chain 36 peptides. Score 0.463 Taking the results from Round 4 Chains 146, Residues 1214, Estimated correctness of the model 0.0 % 13 chains (261 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5905 restraints for refining 16282 atoms. Observations/parameters ratio is 1.16 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2336 (Rfree = 0.000) for 16282 atoms. Found 122 (122 requested) and removed 85 (61 requested) atoms. Cycle 22: After refmac, R = 0.2186 (Rfree = 0.000) for 16319 atoms. Found 123 (123 requested) and removed 85 (61 requested) atoms. Cycle 23: After refmac, R = 0.2138 (Rfree = 0.000) for 16357 atoms. Found 105 (123 requested) and removed 90 (61 requested) atoms. Cycle 24: After refmac, R = 0.2095 (Rfree = 0.000) for 16372 atoms. Found 88 (123 requested) and removed 71 (61 requested) atoms. Cycle 25: After refmac, R = 0.2051 (Rfree = 0.000) for 16389 atoms. Found 70 (123 requested) and removed 71 (61 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 1.96 Search for helices and strands: 0 residues in 0 chains, 16903 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 16938 seeds are put forward Round 1: 1316 peptides, 158 chains. Longest chain 31 peptides. Score 0.425 Round 2: 1391 peptides, 159 chains. Longest chain 28 peptides. Score 0.446 Round 3: 1414 peptides, 159 chains. Longest chain 28 peptides. Score 0.453 Round 4: 1400 peptides, 149 chains. Longest chain 37 peptides. Score 0.463 Round 5: 1396 peptides, 151 chains. Longest chain 46 peptides. Score 0.459 Taking the results from Round 4 Chains 157, Residues 1251, Estimated correctness of the model 0.0 % 8 chains (113 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 75788 reflections ( 99.05 % complete ) and 5312 restraints for refining 15974 atoms. Observations/parameters ratio is 1.19 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2258 (Rfree = 0.000) for 15974 atoms. Found 120 (120 requested) and removed 68 (60 requested) atoms. Cycle 27: After refmac, R = 0.2121 (Rfree = 0.000) for 16026 atoms. Found 121 (121 requested) and removed 66 (60 requested) atoms. Cycle 28: After refmac, R = 0.2086 (Rfree = 0.000) for 16081 atoms. Found 94 (121 requested) and removed 67 (60 requested) atoms. Cycle 29: After refmac, R = 0.2049 (Rfree = 0.000) for 16108 atoms. Found 100 (121 requested) and removed 63 (60 requested) atoms. Cycle 30: After refmac, R = 0.2013 (Rfree = 0.000) for 16145 atoms. Found 94 (121 requested) and removed 71 (60 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 1.96 Search for helices and strands: 0 residues in 0 chains, 16668 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 16696 seeds are put forward Round 1: 1311 peptides, 175 chains. Longest chain 23 peptides. Score 0.399 Round 2: 1396 peptides, 158 chains. Longest chain 35 peptides. Score 0.449 Round 3: 1349 peptides, 149 chains. Longest chain 33 peptides. Score 0.448 Round 4: 1334 peptides, 146 chains. Longest chain 40 peptides. Score 0.448 Round 5: 1348 peptides, 153 chains. Longest chain 35 peptides. Score 0.442 Taking the results from Round 2 Chains 164, Residues 1238, Estimated correctness of the model 0.0 % 7 chains (92 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5157 restraints for refining 15771 atoms. Observations/parameters ratio is 1.20 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2234 (Rfree = 0.000) for 15771 atoms. Found 119 (119 requested) and removed 68 (59 requested) atoms. Cycle 32: After refmac, R = 0.2096 (Rfree = 0.000) for 15822 atoms. Found 86 (119 requested) and removed 60 (59 requested) atoms. Cycle 33: After refmac, R = 0.2070 (Rfree = 0.000) for 15848 atoms. Found 89 (119 requested) and removed 60 (59 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1959 (Rfree = 0.000) for 15877 atoms. Found 27 (119 requested) and removed 60 (59 requested) atoms. Cycle 35: After refmac, R = 0.1977 (Rfree = 0.000) for 15844 atoms. Found 41 (119 requested) and removed 60 (59 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 1.96 Search for helices and strands: 0 residues in 0 chains, 16280 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 16300 seeds are put forward Round 1: 1289 peptides, 160 chains. Longest chain 35 peptides. Score 0.414 Round 2: 1376 peptides, 164 chains. Longest chain 28 peptides. Score 0.434 Round 3: 1366 peptides, 156 chains. Longest chain 31 peptides. Score 0.443 Round 4: 1370 peptides, 146 chains. Longest chain 45 peptides. Score 0.458 Round 5: 1377 peptides, 149 chains. Longest chain 31 peptides. Score 0.456 Taking the results from Round 4 Chains 157, Residues 1224, Estimated correctness of the model 0.0 % 11 chains (177 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5598 restraints for refining 16260 atoms. Observations/parameters ratio is 1.17 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2273 (Rfree = 0.000) for 16260 atoms. Found 122 (122 requested) and removed 81 (61 requested) atoms. Cycle 37: After refmac, R = 0.2123 (Rfree = 0.000) for 16301 atoms. Found 119 (123 requested) and removed 82 (61 requested) atoms. Cycle 38: After refmac, R = 0.2107 (Rfree = 0.000) for 16338 atoms. Found 117 (123 requested) and removed 74 (61 requested) atoms. Cycle 39: After refmac, R = 0.2073 (Rfree = 0.000) for 16381 atoms. Found 88 (123 requested) and removed 75 (61 requested) atoms. Cycle 40: After refmac, R = 0.2065 (Rfree = 0.000) for 16394 atoms. Found 80 (123 requested) and removed 73 (61 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 1.96 Search for helices and strands: 0 residues in 0 chains, 16926 seeds are put forward NCS extension: 56 residues added (7 deleted due to clashes), 16982 seeds are put forward Round 1: 1265 peptides, 172 chains. Longest chain 25 peptides. Score 0.389 Round 2: 1337 peptides, 161 chains. Longest chain 36 peptides. Score 0.427 Round 3: 1360 peptides, 159 chains. Longest chain 27 peptides. Score 0.437 Round 4: 1379 peptides, 157 chains. Longest chain 37 peptides. Score 0.445 Round 5: 1385 peptides, 151 chains. Longest chain 47 peptides. Score 0.456 Taking the results from Round 5 Chains 157, Residues 1234, Estimated correctness of the model 0.0 % 12 chains (200 residues) have been docked in sequence ------------------------------------------------------ 75788 reflections ( 99.05 % complete ) and 5781 restraints for refining 15956 atoms. Observations/parameters ratio is 1.19 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2323 (Rfree = 0.000) for 15956 atoms. Found 120 (120 requested) and removed 72 (60 requested) atoms. Cycle 42: After refmac, R = 0.2192 (Rfree = 0.000) for 16004 atoms. Found 118 (120 requested) and removed 68 (60 requested) atoms. Cycle 43: After refmac, R = 0.2136 (Rfree = 0.000) for 16054 atoms. Found 87 (121 requested) and removed 68 (60 requested) atoms. Cycle 44: After refmac, R = 0.2109 (Rfree = 0.000) for 16073 atoms. Found 80 (121 requested) and removed 66 (60 requested) atoms. Cycle 45: After refmac, R = 0.2060 (Rfree = 0.000) for 16087 atoms. Found 70 (121 requested) and removed 66 (60 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 1.96 Search for helices and strands: 0 residues in 0 chains, 16594 seeds are put forward NCS extension: 21 residues added (14 deleted due to clashes), 16615 seeds are put forward Round 1: 1288 peptides, 166 chains. Longest chain 26 peptides. Score 0.405 Round 2: 1353 peptides, 152 chains. Longest chain 34 peptides. Score 0.445 Round 3: 1360 peptides, 157 chains. Longest chain 32 peptides. Score 0.440 Round 4: 1353 peptides, 159 chains. Longest chain 30 peptides. Score 0.435 Round 5: 1338 peptides, 156 chains. Longest chain 34 peptides. Score 0.435 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 158, Residues 1201, Estimated correctness of the model 0.0 % 7 chains (131 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2aam-3_warpNtrace.pdb as input Building loops using Loopy2018 158 chains (1201 residues) following loop building 7 chains (131 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 75788 reflections ( 99.05 % complete ) and 5247 restraints for refining 15936 atoms. Observations/parameters ratio is 1.19 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2198 (Rfree = 0.000) for 15936 atoms. Found 0 (120 requested) and removed 40 (60 requested) atoms. Cycle 47: After refmac, R = 0.2150 (Rfree = 0.000) for 15896 atoms. Found 0 (120 requested) and removed 23 (60 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2134 (Rfree = 0.000) for 15873 atoms. Found 0 (119 requested) and removed 31 (59 requested) atoms. Cycle 49: After refmac, R = 0.2091 (Rfree = 0.000) for 15842 atoms. TimeTaking 223.73