null Mon 24 Dec 07:30:24 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aam-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aam-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-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 07:30:28 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-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 3732 and 0 Target number of residues in the AU: 3732 Target solvent content: 0.6378 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-3.8-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-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 14832 target number of atoms Had to go as low as 1.55 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 3.800 Wilson plot Bfac: 70.79 54333 reflections ( 98.81 % complete ) and 0 restraints for refining 18179 atoms. Observations/parameters ratio is 0.75 ------------------------------------------------------ Starting model: R = 0.3518 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2952 (Rfree = 0.000) for 18179 atoms. Found 99 (99 requested) and removed 98 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 2.16 Search for helices and strands: 0 residues in 0 chains, 18535 seeds are put forward NCS extension: 0 residues added, 18535 seeds are put forward Round 1: 1166 peptides, 141 chains. Longest chain 25 peptides. Score 0.405 Round 2: 1221 peptides, 120 chains. Longest chain 46 peptides. Score 0.453 Round 3: 1232 peptides, 121 chains. Longest chain 41 peptides. Score 0.455 Round 4: 1235 peptides, 117 chains. Longest chain 44 peptides. Score 0.462 Round 5: 1171 peptides, 128 chains. Longest chain 31 peptides. Score 0.426 Taking the results from Round 4 Chains 124, Residues 1118, Estimated correctness of the model 0.0 % 6 chains (118 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4913 restraints for refining 16144 atoms. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2451 (Rfree = 0.000) for 16144 atoms. Found 88 (88 requested) and removed 59 (44 requested) atoms. Cycle 2: After refmac, R = 0.2317 (Rfree = 0.000) for 16173 atoms. Found 88 (88 requested) and removed 64 (44 requested) atoms. Cycle 3: After refmac, R = 0.2237 (Rfree = 0.000) for 16197 atoms. Found 89 (89 requested) and removed 70 (44 requested) atoms. Cycle 4: After refmac, R = 0.2180 (Rfree = 0.000) for 16216 atoms. Found 75 (89 requested) and removed 76 (44 requested) atoms. Cycle 5: After refmac, R = 0.2137 (Rfree = 0.000) for 16215 atoms. Found 89 (89 requested) and removed 59 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 2.13 Search for helices and strands: 0 residues in 0 chains, 16743 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 16772 seeds are put forward Round 1: 1200 peptides, 131 chains. Longest chain 43 peptides. Score 0.431 Round 2: 1246 peptides, 131 chains. Longest chain 38 peptides. Score 0.444 Round 3: 1230 peptides, 144 chains. Longest chain 28 peptides. Score 0.420 Round 4: 1238 peptides, 143 chains. Longest chain 33 peptides. Score 0.424 Round 5: 1206 peptides, 132 chains. Longest chain 27 peptides. Score 0.431 Taking the results from Round 2 Chains 134, Residues 1115, Estimated correctness of the model 0.0 % 4 chains (80 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4701 restraints for refining 15509 atoms. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2252 (Rfree = 0.000) for 15509 atoms. Found 85 (85 requested) and removed 56 (42 requested) atoms. Cycle 7: After refmac, R = 0.2105 (Rfree = 0.000) for 15538 atoms. Found 85 (85 requested) and removed 48 (42 requested) atoms. Cycle 8: After refmac, R = 0.2099 (Rfree = 0.000) for 15575 atoms. Found 85 (85 requested) and removed 55 (42 requested) atoms. Cycle 9: After refmac, R = 0.2055 (Rfree = 0.000) for 15605 atoms. Found 85 (85 requested) and removed 59 (42 requested) atoms. Cycle 10: After refmac, R = 0.2045 (Rfree = 0.000) for 15631 atoms. Found 85 (85 requested) and removed 66 (42 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 2.10 Search for helices and strands: 0 residues in 0 chains, 16205 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 16221 seeds are put forward Round 1: 1249 peptides, 141 chains. Longest chain 29 peptides. Score 0.430 Round 2: 1267 peptides, 128 chains. Longest chain 35 peptides. Score 0.455 Round 3: 1251 peptides, 133 chains. Longest chain 35 peptides. Score 0.443 Round 4: 1198 peptides, 131 chains. Longest chain 28 peptides. Score 0.430 Round 5: 1268 peptides, 134 chains. Longest chain 32 peptides. Score 0.446 Taking the results from Round 2 Chains 135, Residues 1139, Estimated correctness of the model 0.0 % 7 chains (132 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 5056 restraints for refining 15620 atoms. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2220 (Rfree = 0.000) for 15620 atoms. Found 85 (85 requested) and removed 58 (42 requested) atoms. Cycle 12: After refmac, R = 0.2132 (Rfree = 0.000) for 15647 atoms. Found 86 (86 requested) and removed 55 (43 requested) atoms. Cycle 13: After refmac, R = 0.2114 (Rfree = 0.000) for 15678 atoms. Found 86 (86 requested) and removed 72 (43 requested) atoms. Cycle 14: After refmac, R = 0.2054 (Rfree = 0.000) for 15692 atoms. Found 86 (86 requested) and removed 65 (43 requested) atoms. Cycle 15: After refmac, R = 0.2070 (Rfree = 0.000) for 15713 atoms. Found 86 (86 requested) and removed 75 (43 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 2.03 Search for helices and strands: 0 residues in 0 chains, 16284 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 16305 seeds are put forward Round 1: 1234 peptides, 153 chains. Longest chain 32 peptides. Score 0.408 Round 2: 1263 peptides, 143 chains. Longest chain 37 peptides. Score 0.431 Round 3: 1266 peptides, 138 chains. Longest chain 34 peptides. Score 0.440 Round 4: 1276 peptides, 136 chains. Longest chain 39 peptides. Score 0.446 Round 5: 1289 peptides, 143 chains. Longest chain 31 peptides. Score 0.439 Taking the results from Round 4 Chains 141, Residues 1140, Estimated correctness of the model 0.0 % 6 chains (102 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4962 restraints for refining 16021 atoms. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2341 (Rfree = 0.000) for 16021 atoms. Found 88 (88 requested) and removed 55 (44 requested) atoms. Cycle 17: After refmac, R = 0.2246 (Rfree = 0.000) for 16054 atoms. Found 88 (88 requested) and removed 57 (44 requested) atoms. Cycle 18: After refmac, R = 0.2223 (Rfree = 0.000) for 16085 atoms. Found 88 (88 requested) and removed 58 (44 requested) atoms. Cycle 19: After refmac, R = 0.2229 (Rfree = 0.000) for 16115 atoms. Found 88 (88 requested) and removed 73 (44 requested) atoms. Cycle 20: After refmac, R = 0.2255 (Rfree = 0.000) for 16130 atoms. Found 88 (88 requested) and removed 69 (44 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 2.04 Search for helices and strands: 0 residues in 0 chains, 16689 seeds are put forward NCS extension: 42 residues added (1 deleted due to clashes), 16731 seeds are put forward Round 1: 1201 peptides, 160 chains. Longest chain 22 peptides. Score 0.387 Round 2: 1268 peptides, 143 chains. Longest chain 29 peptides. Score 0.433 Round 3: 1271 peptides, 147 chains. Longest chain 35 peptides. Score 0.428 Round 4: 1265 peptides, 143 chains. Longest chain 46 peptides. Score 0.432 Round 5: 1274 peptides, 148 chains. Longest chain 30 peptides. Score 0.427 Taking the results from Round 2 Chains 146, Residues 1125, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4448 restraints for refining 15374 atoms. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2365 (Rfree = 0.000) for 15374 atoms. Found 84 (84 requested) and removed 48 (42 requested) atoms. Cycle 22: After refmac, R = 0.2417 (Rfree = 0.000) for 15410 atoms. Found 84 (84 requested) and removed 49 (42 requested) atoms. Cycle 23: After refmac, R = 0.2441 (Rfree = 0.000) for 15445 atoms. Found 84 (84 requested) and removed 60 (42 requested) atoms. Cycle 24: After refmac, R = 0.2096 (Rfree = 0.000) for 15469 atoms. Found 52 (85 requested) and removed 47 (42 requested) atoms. Cycle 25: After refmac, R = 0.2025 (Rfree = 0.000) for 15474 atoms. Found 20 (85 requested) and removed 55 (42 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 1.99 Search for helices and strands: 0 residues in 0 chains, 16032 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 16055 seeds are put forward Round 1: 1210 peptides, 178 chains. Longest chain 21 peptides. Score 0.362 Round 2: 1263 peptides, 159 chains. Longest chain 29 peptides. Score 0.408 Round 3: 1292 peptides, 165 chains. Longest chain 37 peptides. Score 0.408 Round 4: 1289 peptides, 161 chains. Longest chain 29 peptides. Score 0.413 Round 5: 1261 peptides, 146 chains. Longest chain 38 peptides. Score 0.426 Taking the results from Round 5 Chains 151, Residues 1115, Estimated correctness of the model 0.0 % 8 chains (81 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4655 restraints for refining 16228 atoms. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2495 (Rfree = 0.000) for 16228 atoms. Found 89 (89 requested) and removed 60 (44 requested) atoms. Cycle 27: After refmac, R = 0.2527 (Rfree = 0.000) for 16257 atoms. Found 89 (89 requested) and removed 57 (44 requested) atoms. Cycle 28: After refmac, R = 0.2508 (Rfree = 0.000) for 16289 atoms. Found 89 (89 requested) and removed 61 (44 requested) atoms. Cycle 29: After refmac, R = 0.2160 (Rfree = 0.000) for 16317 atoms. Found 49 (89 requested) and removed 57 (44 requested) atoms. Cycle 30: After refmac, R = 0.2106 (Rfree = 0.000) for 16309 atoms. Found 22 (89 requested) and removed 65 (44 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 1.96 Search for helices and strands: 0 residues in 0 chains, 16788 seeds are put forward NCS extension: 38 residues added (4 deleted due to clashes), 16826 seeds are put forward Round 1: 1173 peptides, 178 chains. Longest chain 30 peptides. Score 0.349 Round 2: 1313 peptides, 175 chains. Longest chain 30 peptides. Score 0.399 Round 3: 1268 peptides, 171 chains. Longest chain 27 peptides. Score 0.391 Round 4: 1289 peptides, 166 chains. Longest chain 27 peptides. Score 0.405 Round 5: 1289 peptides, 163 chains. Longest chain 24 peptides. Score 0.410 Taking the results from Round 5 Chains 170, Residues 1126, Estimated correctness of the model 0.0 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4490 restraints for refining 15942 atoms. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2573 (Rfree = 0.000) for 15942 atoms. Found 87 (87 requested) and removed 53 (43 requested) atoms. Cycle 32: After refmac, R = 0.2611 (Rfree = 0.000) for 15976 atoms. Found 87 (87 requested) and removed 68 (43 requested) atoms. Cycle 33: After refmac, R = 0.2625 (Rfree = 0.000) for 15995 atoms. Found 87 (87 requested) and removed 61 (43 requested) atoms. Cycle 34: After refmac, R = 0.2263 (Rfree = 0.000) for 16021 atoms. Found 68 (88 requested) and removed 63 (44 requested) atoms. Cycle 35: After refmac, R = 0.2193 (Rfree = 0.000) for 16026 atoms. Found 25 (88 requested) and removed 56 (44 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 1.94 Search for helices and strands: 0 residues in 0 chains, 16509 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 16526 seeds are put forward Round 1: 1138 peptides, 189 chains. Longest chain 17 peptides. Score 0.320 Round 2: 1255 peptides, 179 chains. Longest chain 20 peptides. Score 0.375 Round 3: 1275 peptides, 176 chains. Longest chain 25 peptides. Score 0.386 Round 4: 1277 peptides, 171 chains. Longest chain 25 peptides. Score 0.394 Round 5: 1227 peptides, 165 chains. Longest chain 34 peptides. Score 0.387 Taking the results from Round 4 Chains 173, Residues 1106, Estimated correctness of the model 0.0 % 6 chains (50 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4442 restraints for refining 15776 atoms. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2746 (Rfree = 0.000) for 15776 atoms. Found 86 (86 requested) and removed 64 (43 requested) atoms. Cycle 37: After refmac, R = 0.2709 (Rfree = 0.000) for 15798 atoms. Found 86 (86 requested) and removed 58 (43 requested) atoms. Cycle 38: After refmac, R = 0.2696 (Rfree = 0.000) for 15826 atoms. Found 87 (87 requested) and removed 65 (43 requested) atoms. Cycle 39: After refmac, R = 0.2198 (Rfree = 0.000) for 15848 atoms. Found 52 (87 requested) and removed 54 (43 requested) atoms. Cycle 40: After refmac, R = 0.2212 (Rfree = 0.000) for 15846 atoms. Found 22 (87 requested) and removed 52 (43 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 1.95 Search for helices and strands: 0 residues in 0 chains, 16527 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 16542 seeds are put forward Round 1: 1120 peptides, 189 chains. Longest chain 15 peptides. Score 0.314 Round 2: 1264 peptides, 183 chains. Longest chain 30 peptides. Score 0.372 Round 3: 1263 peptides, 172 chains. Longest chain 30 peptides. Score 0.388 Round 4: 1272 peptides, 186 chains. Longest chain 24 peptides. Score 0.370 Round 5: 1266 peptides, 175 chains. Longest chain 29 peptides. Score 0.384 Taking the results from Round 3 Chains 173, Residues 1091, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4329 restraints for refining 15587 atoms. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2652 (Rfree = 0.000) for 15587 atoms. Found 85 (85 requested) and removed 51 (42 requested) atoms. Cycle 42: After refmac, R = 0.2721 (Rfree = 0.000) for 15621 atoms. Found 85 (85 requested) and removed 55 (42 requested) atoms. Cycle 43: After refmac, R = 0.2577 (Rfree = 0.000) for 15651 atoms. Found 86 (86 requested) and removed 65 (43 requested) atoms. Cycle 44: After refmac, R = 0.2625 (Rfree = 0.000) for 15672 atoms. Found 86 (86 requested) and removed 72 (43 requested) atoms. Cycle 45: After refmac, R = 0.2575 (Rfree = 0.000) for 15686 atoms. Found 86 (86 requested) and removed 64 (43 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 2.03 Search for helices and strands: 0 residues in 0 chains, 16496 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 16530 seeds are put forward Round 1: 1136 peptides, 201 chains. Longest chain 17 peptides. Score 0.300 Round 2: 1196 peptides, 174 chains. Longest chain 22 peptides. Score 0.363 Round 3: 1238 peptides, 172 chains. Longest chain 24 peptides. Score 0.380 Round 4: 1225 peptides, 162 chains. Longest chain 26 peptides. Score 0.391 Round 5: 1223 peptides, 157 chains. Longest chain 29 peptides. Score 0.398 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 158, Residues 1066, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2aam-3_warpNtrace.pdb as input Building loops using Loopy2018 158 chains (1066 residues) following loop building 5 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 54333 reflections ( 98.81 % complete ) and 4186 restraints for refining 15683 atoms. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2515 (Rfree = 0.000) for 15683 atoms. Found 0 (86 requested) and removed 43 (43 requested) atoms. Cycle 47: After refmac, R = 0.2512 (Rfree = 0.000) for 15640 atoms. Found 0 (86 requested) and removed 43 (43 requested) atoms. Cycle 48: After refmac, R = 0.2480 (Rfree = 0.000) for 15597 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Cycle 49: After refmac, R = 0.2496 (Rfree = 0.000) for 15555 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:52:05 GMT 2018 Job finished. TimeTaking 201.68 Used memory is bytes: 27130824