null Mon 24 Dec 00:40:17 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aam-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aam-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-parrot-mrncs ############### 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 00:40:21 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/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aam-3.6-parrot-mrncs/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-mrncs.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-mrncs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.45 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 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 16621 atoms. Observations/parameters ratio is 0.96 ------------------------------------------------------ Starting model: R = 0.3342 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2855 (Rfree = 0.000) for 16621 atoms. Found 106 (106 requested) and removed 79 (53 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 2.02 Search for helices and strands: 0 residues in 0 chains, 17009 seeds are put forward NCS extension: 0 residues added, 17009 seeds are put forward Round 1: 1291 peptides, 141 chains. Longest chain 47 peptides. Score 0.443 Round 2: 1267 peptides, 130 chains. Longest chain 27 peptides. Score 0.452 Round 3: 1277 peptides, 128 chains. Longest chain 38 peptides. Score 0.458 Round 4: 1275 peptides, 133 chains. Longest chain 31 peptides. Score 0.450 Round 5: 1274 peptides, 134 chains. Longest chain 26 peptides. Score 0.448 Taking the results from Round 3 Chains 139, Residues 1149, Estimated correctness of the model 0.0 % 8 chains (145 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5137 restraints for refining 15316 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2455 (Rfree = 0.000) for 15316 atoms. Found 98 (98 requested) and removed 59 (49 requested) atoms. Cycle 2: After refmac, R = 0.2326 (Rfree = 0.000) for 15355 atoms. Found 98 (98 requested) and removed 59 (49 requested) atoms. Cycle 3: After refmac, R = 0.2236 (Rfree = 0.000) for 15394 atoms. Found 98 (98 requested) and removed 67 (49 requested) atoms. Cycle 4: After refmac, R = 0.2197 (Rfree = 0.000) for 15425 atoms. Found 98 (98 requested) and removed 67 (49 requested) atoms. Cycle 5: After refmac, R = 0.2140 (Rfree = 0.000) for 15456 atoms. Found 99 (99 requested) and removed 68 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 1.99 Search for helices and strands: 0 residues in 0 chains, 15995 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 16025 seeds are put forward Round 1: 1303 peptides, 135 chains. Longest chain 35 peptides. Score 0.455 Round 2: 1313 peptides, 142 chains. Longest chain 33 peptides. Score 0.448 Round 3: 1263 peptides, 137 chains. Longest chain 35 peptides. Score 0.440 Round 4: 1274 peptides, 135 chains. Longest chain 33 peptides. Score 0.447 Round 5: 1310 peptides, 140 chains. Longest chain 34 peptides. Score 0.450 Taking the results from Round 1 Chains 142, Residues 1168, Estimated correctness of the model 0.0 % 8 chains (136 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5212 restraints for refining 14821 atoms. Observations/parameters ratio is 1.08 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2303 (Rfree = 0.000) for 14821 atoms. Found 95 (95 requested) and removed 54 (47 requested) atoms. Cycle 7: After refmac, R = 0.2196 (Rfree = 0.000) for 14862 atoms. Found 95 (95 requested) and removed 53 (47 requested) atoms. Cycle 8: After refmac, R = 0.2134 (Rfree = 0.000) for 14904 atoms. Found 95 (95 requested) and removed 57 (47 requested) atoms. Cycle 9: After refmac, R = 0.2079 (Rfree = 0.000) for 14942 atoms. Found 95 (95 requested) and removed 54 (47 requested) atoms. Cycle 10: After refmac, R = 0.2066 (Rfree = 0.000) for 14983 atoms. Found 96 (96 requested) and removed 71 (48 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 1.99 Search for helices and strands: 0 residues in 0 chains, 15502 seeds are put forward NCS extension: 10 residues added (11 deleted due to clashes), 15512 seeds are put forward Round 1: 1309 peptides, 135 chains. Longest chain 42 peptides. Score 0.457 Round 2: 1347 peptides, 129 chains. Longest chain 41 peptides. Score 0.476 Round 3: 1323 peptides, 127 chains. Longest chain 43 peptides. Score 0.472 Round 4: 1303 peptides, 123 chains. Longest chain 35 peptides. Score 0.472 Round 5: 1295 peptides, 122 chains. Longest chain 42 peptides. Score 0.472 Taking the results from Round 2 Chains 135, Residues 1218, Estimated correctness of the model 0.0 % 10 chains (108 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5175 restraints for refining 14600 atoms. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2208 (Rfree = 0.000) for 14600 atoms. Found 93 (93 requested) and removed 50 (46 requested) atoms. Cycle 12: After refmac, R = 0.2089 (Rfree = 0.000) for 14643 atoms. Found 93 (93 requested) and removed 53 (46 requested) atoms. Cycle 13: After refmac, R = 0.2051 (Rfree = 0.000) for 14683 atoms. Found 83 (94 requested) and removed 50 (47 requested) atoms. Cycle 14: After refmac, R = 0.2007 (Rfree = 0.000) for 14716 atoms. Found 72 (94 requested) and removed 50 (47 requested) atoms. Cycle 15: After refmac, R = 0.1989 (Rfree = 0.000) for 14738 atoms. Found 75 (94 requested) and removed 57 (47 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 2.00 Search for helices and strands: 0 residues in 0 chains, 15220 seeds are put forward NCS extension: 47 residues added (4 deleted due to clashes), 15267 seeds are put forward Round 1: 1296 peptides, 138 chains. Longest chain 47 peptides. Score 0.449 Round 2: 1274 peptides, 140 chains. Longest chain 32 peptides. Score 0.439 Round 3: 1314 peptides, 131 chains. Longest chain 39 peptides. Score 0.464 Round 4: 1292 peptides, 142 chains. Longest chain 35 peptides. Score 0.442 Round 5: 1311 peptides, 154 chains. Longest chain 28 peptides. Score 0.430 Taking the results from Round 3 Chains 136, Residues 1183, Estimated correctness of the model 0.0 % 9 chains (102 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5043 restraints for refining 15051 atoms. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2280 (Rfree = 0.000) for 15051 atoms. Found 96 (96 requested) and removed 53 (48 requested) atoms. Cycle 17: After refmac, R = 0.2128 (Rfree = 0.000) for 15094 atoms. Found 96 (96 requested) and removed 54 (48 requested) atoms. Cycle 18: After refmac, R = 0.2088 (Rfree = 0.000) for 15136 atoms. Found 97 (97 requested) and removed 62 (48 requested) atoms. Cycle 19: After refmac, R = 0.2043 (Rfree = 0.000) for 15171 atoms. Found 97 (97 requested) and removed 58 (48 requested) atoms. Cycle 20: After refmac, R = 0.2026 (Rfree = 0.000) for 15210 atoms. Found 97 (97 requested) and removed 62 (48 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 1.98 Search for helices and strands: 0 residues in 0 chains, 15762 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 15783 seeds are put forward Round 1: 1285 peptides, 150 chains. Longest chain 37 peptides. Score 0.428 Round 2: 1306 peptides, 138 chains. Longest chain 39 peptides. Score 0.451 Round 3: 1323 peptides, 143 chains. Longest chain 33 peptides. Score 0.449 Round 4: 1300 peptides, 138 chains. Longest chain 33 peptides. Score 0.450 Round 5: 1322 peptides, 132 chains. Longest chain 35 peptides. Score 0.465 Taking the results from Round 5 Chains 137, Residues 1190, Estimated correctness of the model 0.0 % 9 chains (143 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5329 restraints for refining 15661 atoms. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2223 (Rfree = 0.000) for 15661 atoms. Found 100 (100 requested) and removed 66 (50 requested) atoms. Cycle 22: After refmac, R = 0.2120 (Rfree = 0.000) for 15695 atoms. Found 100 (100 requested) and removed 62 (50 requested) atoms. Cycle 23: After refmac, R = 0.2077 (Rfree = 0.000) for 15733 atoms. Found 100 (100 requested) and removed 58 (50 requested) atoms. Cycle 24: After refmac, R = 0.2027 (Rfree = 0.000) for 15775 atoms. Found 101 (101 requested) and removed 57 (50 requested) atoms. Cycle 25: After refmac, R = 0.1858 (Rfree = 0.000) for 15819 atoms. Found 18 (101 requested) and removed 65 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 2.00 Search for helices and strands: 0 residues in 0 chains, 16236 seeds are put forward NCS extension: 24 residues added (10 deleted due to clashes), 16260 seeds are put forward Round 1: 1261 peptides, 157 chains. Longest chain 34 peptides. Score 0.410 Round 2: 1320 peptides, 144 chains. Longest chain 39 peptides. Score 0.447 Round 3: 1341 peptides, 156 chains. Longest chain 32 peptides. Score 0.436 Round 4: 1343 peptides, 147 chains. Longest chain 40 peptides. Score 0.449 Round 5: 1333 peptides, 144 chains. Longest chain 38 peptides. Score 0.451 Taking the results from Round 5 Chains 147, Residues 1189, Estimated correctness of the model 0.0 % 5 chains (61 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4901 restraints for refining 15704 atoms. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2252 (Rfree = 0.000) for 15704 atoms. Found 100 (100 requested) and removed 56 (50 requested) atoms. Cycle 27: After refmac, R = 0.2127 (Rfree = 0.000) for 15748 atoms. Found 101 (101 requested) and removed 56 (50 requested) atoms. Cycle 28: After refmac, R = 0.2106 (Rfree = 0.000) for 15793 atoms. Found 101 (101 requested) and removed 63 (50 requested) atoms. Cycle 29: After refmac, R = 0.2047 (Rfree = 0.000) for 15831 atoms. Found 101 (101 requested) and removed 59 (50 requested) atoms. Cycle 30: After refmac, R = 0.1847 (Rfree = 0.000) for 15873 atoms. Found 36 (101 requested) and removed 67 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 2.00 Search for helices and strands: 0 residues in 0 chains, 16370 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 16393 seeds are put forward Round 1: 1243 peptides, 150 chains. Longest chain 36 peptides. Score 0.415 Round 2: 1306 peptides, 146 chains. Longest chain 32 peptides. Score 0.440 Round 3: 1311 peptides, 140 chains. Longest chain 44 peptides. Score 0.450 Round 4: 1285 peptides, 140 chains. Longest chain 31 peptides. Score 0.442 Round 5: 1313 peptides, 149 chains. Longest chain 45 peptides. Score 0.437 Taking the results from Round 3 Chains 150, Residues 1171, Estimated correctness of the model 0.0 % 10 chains (167 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 5293 restraints for refining 15617 atoms. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2222 (Rfree = 0.000) for 15617 atoms. Found 100 (100 requested) and removed 64 (50 requested) atoms. Cycle 32: After refmac, R = 0.2109 (Rfree = 0.000) for 15653 atoms. Found 100 (100 requested) and removed 63 (50 requested) atoms. Cycle 33: After refmac, R = 0.2073 (Rfree = 0.000) for 15690 atoms. Found 100 (100 requested) and removed 72 (50 requested) atoms. Cycle 34: After refmac, R = 0.2057 (Rfree = 0.000) for 15718 atoms. Found 100 (100 requested) and removed 60 (50 requested) atoms. Cycle 35: After refmac, R = 0.2057 (Rfree = 0.000) for 15758 atoms. Found 101 (101 requested) and removed 64 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 1.99 Search for helices and strands: 0 residues in 0 chains, 16251 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 16276 seeds are put forward Round 1: 1239 peptides, 162 chains. Longest chain 26 peptides. Score 0.396 Round 2: 1314 peptides, 145 chains. Longest chain 33 peptides. Score 0.444 Round 3: 1321 peptides, 132 chains. Longest chain 38 peptides. Score 0.464 Round 4: 1310 peptides, 142 chains. Longest chain 34 peptides. Score 0.447 Round 5: 1335 peptides, 143 chains. Longest chain 43 peptides. Score 0.453 Taking the results from Round 3 Chains 136, Residues 1189, Estimated correctness of the model 0.0 % 5 chains (70 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4991 restraints for refining 15531 atoms. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2204 (Rfree = 0.000) for 15531 atoms. Found 99 (99 requested) and removed 55 (49 requested) atoms. Cycle 37: After refmac, R = 0.2139 (Rfree = 0.000) for 15575 atoms. Found 99 (99 requested) and removed 55 (49 requested) atoms. Cycle 38: After refmac, R = 0.2111 (Rfree = 0.000) for 15619 atoms. Found 100 (100 requested) and removed 57 (50 requested) atoms. Cycle 39: After refmac, R = 0.2101 (Rfree = 0.000) for 15662 atoms. Found 100 (100 requested) and removed 72 (50 requested) atoms. Cycle 40: After refmac, R = 0.2079 (Rfree = 0.000) for 15690 atoms. Found 100 (100 requested) and removed 71 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 1.99 Search for helices and strands: 0 residues in 0 chains, 16156 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 16171 seeds are put forward Round 1: 1199 peptides, 162 chains. Longest chain 22 peptides. Score 0.383 Round 2: 1291 peptides, 152 chains. Longest chain 30 peptides. Score 0.427 Round 3: 1289 peptides, 153 chains. Longest chain 26 peptides. Score 0.424 Round 4: 1288 peptides, 152 chains. Longest chain 31 peptides. Score 0.426 Round 5: 1290 peptides, 148 chains. Longest chain 42 peptides. Score 0.432 Taking the results from Round 5 Chains 152, Residues 1142, Estimated correctness of the model 0.0 % 8 chains (85 residues) have been docked in sequence ------------------------------------------------------ 63881 reflections ( 98.93 % complete ) and 4808 restraints for refining 15501 atoms. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2212 (Rfree = 0.000) for 15501 atoms. Found 99 (99 requested) and removed 57 (49 requested) atoms. Cycle 42: After refmac, R = 0.2066 (Rfree = 0.000) for 15543 atoms. Found 99 (99 requested) and removed 53 (49 requested) atoms. Cycle 43: After refmac, R = 0.2032 (Rfree = 0.000) for 15589 atoms. Found 100 (100 requested) and removed 57 (50 requested) atoms. Cycle 44: After refmac, R = 0.2017 (Rfree = 0.000) for 15632 atoms. Found 100 (100 requested) and removed 78 (50 requested) atoms. Cycle 45: After refmac, R = 0.1944 (Rfree = 0.000) for 15654 atoms. Found 79 (100 requested) and removed 63 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 1.99 Search for helices and strands: 0 residues in 0 chains, 16196 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 16221 seeds are put forward Round 1: 1194 peptides, 165 chains. Longest chain 25 peptides. Score 0.377 Round 2: 1272 peptides, 148 chains. Longest chain 32 peptides. Score 0.427 Round 3: 1282 peptides, 148 chains. Longest chain 37 peptides. Score 0.430 Round 4: 1278 peptides, 143 chains. Longest chain 33 peptides. Score 0.436 Round 5: 1280 peptides, 149 chains. Longest chain 29 peptides. Score 0.428 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 146, Residues 1135, Estimated correctness of the model 0.0 % 3 chains (35 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 146 chains (1135 residues) following loop building 3 chains (35 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 63881 reflections ( 98.93 % complete ) and 4565 restraints for refining 15456 atoms. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2158 (Rfree = 0.000) for 15456 atoms. Found 0 (99 requested) and removed 49 (49 requested) atoms. Cycle 47: After refmac, R = 0.2094 (Rfree = 0.000) for 15407 atoms. Found 0 (98 requested) and removed 43 (49 requested) atoms. Cycle 48: After refmac, R = 0.2081 (Rfree = 0.000) for 15364 atoms. Found 0 (98 requested) and removed 48 (49 requested) atoms. Cycle 49: After refmac, R = 0.2047 (Rfree = 0.000) for 15316 atoms. Found 0 (98 requested) and removed 49 (49 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 04:09:02 GMT 2018 Job finished. TimeTaking 208.76 Used memory is bytes: 17744584