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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aam-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aam-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aam-3.8-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 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-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-3.8-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 3.800 Wilson plot Bfac: 70.79 54333 reflections ( 98.81 % complete ) and 0 restraints for refining 18502 atoms. Observations/parameters ratio is 0.73 ------------------------------------------------------ Starting model: R = 0.3400 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2988 (Rfree = 0.000) for 18502 atoms. Found 101 (101 requested) and removed 107 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 2.12 Search for helices and strands: 0 residues in 0 chains, 18844 seeds are put forward NCS extension: 0 residues added, 18844 seeds are put forward Round 1: 1154 peptides, 136 chains. Longest chain 39 peptides. Score 0.409 Round 2: 1197 peptides, 132 chains. Longest chain 29 peptides. Score 0.428 Round 3: 1221 peptides, 138 chains. Longest chain 25 peptides. Score 0.426 Round 4: 1216 peptides, 129 chains. Longest chain 30 peptides. Score 0.438 Round 5: 1232 peptides, 126 chains. Longest chain 27 peptides. Score 0.448 Taking the results from Round 5 Chains 129, Residues 1106, Estimated correctness of the model 0.0 % 4 chains (52 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4566 restraints for refining 15855 atoms. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2409 (Rfree = 0.000) for 15855 atoms. Found 87 (87 requested) and removed 66 (43 requested) atoms. Cycle 2: After refmac, R = 0.2280 (Rfree = 0.000) for 15876 atoms. Found 87 (87 requested) and removed 59 (43 requested) atoms. Cycle 3: After refmac, R = 0.2210 (Rfree = 0.000) for 15904 atoms. Found 87 (87 requested) and removed 75 (43 requested) atoms. Cycle 4: After refmac, R = 0.2185 (Rfree = 0.000) for 15916 atoms. Found 87 (87 requested) and removed 81 (43 requested) atoms. Cycle 5: After refmac, R = 0.2186 (Rfree = 0.000) for 15922 atoms. Found 87 (87 requested) and removed 76 (43 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 2.08 Search for helices and strands: 0 residues in 0 chains, 16455 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 16493 seeds are put forward Round 1: 1258 peptides, 127 chains. Longest chain 34 peptides. Score 0.454 Round 2: 1279 peptides, 121 chains. Longest chain 33 peptides. Score 0.468 Round 3: 1288 peptides, 122 chains. Longest chain 52 peptides. Score 0.470 Round 4: 1272 peptides, 114 chains. Longest chain 49 peptides. Score 0.477 Round 5: 1249 peptides, 118 chains. Longest chain 36 peptides. Score 0.464 Taking the results from Round 4 Chains 122, Residues 1158, Estimated correctness of the model 0.0 % 9 chains (143 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 5162 restraints for refining 15635 atoms. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2371 (Rfree = 0.000) for 15635 atoms. Found 85 (85 requested) and removed 54 (42 requested) atoms. Cycle 7: After refmac, R = 0.2306 (Rfree = 0.000) for 15666 atoms. Found 86 (86 requested) and removed 65 (43 requested) atoms. Cycle 8: After refmac, R = 0.2268 (Rfree = 0.000) for 15687 atoms. Found 86 (86 requested) and removed 79 (43 requested) atoms. Cycle 9: After refmac, R = 0.2259 (Rfree = 0.000) for 15694 atoms. Found 86 (86 requested) and removed 74 (43 requested) atoms. Cycle 10: After refmac, R = 0.2064 (Rfree = 0.000) for 15706 atoms. Found 44 (86 requested) and removed 67 (43 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 2.03 Search for helices and strands: 0 residues in 0 chains, 16226 seeds are put forward NCS extension: 46 residues added (2 deleted due to clashes), 16272 seeds are put forward Round 1: 1241 peptides, 148 chains. Longest chain 28 peptides. Score 0.417 Round 2: 1300 peptides, 142 chains. Longest chain 35 peptides. Score 0.444 Round 3: 1309 peptides, 147 chains. Longest chain 35 peptides. Score 0.439 Round 4: 1285 peptides, 135 chains. Longest chain 42 peptides. Score 0.450 Round 5: 1304 peptides, 148 chains. Longest chain 28 peptides. Score 0.436 Taking the results from Round 4 Chains 141, Residues 1150, Estimated correctness of the model 0.0 % 7 chains (132 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 5126 restraints for refining 15752 atoms. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2418 (Rfree = 0.000) for 15752 atoms. Found 86 (86 requested) and removed 56 (43 requested) atoms. Cycle 12: After refmac, R = 0.2388 (Rfree = 0.000) for 15782 atoms. Found 86 (86 requested) and removed 56 (43 requested) atoms. Cycle 13: After refmac, R = 0.2390 (Rfree = 0.000) for 15812 atoms. Found 86 (86 requested) and removed 59 (43 requested) atoms. Cycle 14: After refmac, R = 0.2406 (Rfree = 0.000) for 15839 atoms. Found 87 (87 requested) and removed 72 (43 requested) atoms. Cycle 15: After refmac, R = 0.2424 (Rfree = 0.000) for 15854 atoms. Found 87 (87 requested) and removed 67 (43 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 2.00 Search for helices and strands: 0 residues in 0 chains, 16460 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 16494 seeds are put forward Round 1: 1243 peptides, 163 chains. Longest chain 34 peptides. Score 0.395 Round 2: 1289 peptides, 150 chains. Longest chain 29 peptides. Score 0.429 Round 3: 1290 peptides, 138 chains. Longest chain 37 peptides. Score 0.447 Round 4: 1314 peptides, 151 chains. Longest chain 31 peptides. Score 0.435 Round 5: 1334 peptides, 158 chains. Longest chain 29 peptides. Score 0.431 Taking the results from Round 3 Chains 144, Residues 1152, Estimated correctness of the model 0.0 % 8 chains (148 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 5140 restraints for refining 15919 atoms. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2504 (Rfree = 0.000) for 15919 atoms. Found 87 (87 requested) and removed 57 (43 requested) atoms. Cycle 17: After refmac, R = 0.2504 (Rfree = 0.000) for 15949 atoms. Found 87 (87 requested) and removed 64 (43 requested) atoms. Cycle 18: After refmac, R = 0.2460 (Rfree = 0.000) for 15972 atoms. Found 87 (87 requested) and removed 62 (43 requested) atoms. Cycle 19: After refmac, R = 0.2451 (Rfree = 0.000) for 15997 atoms. Found 87 (87 requested) and removed 77 (43 requested) atoms. Cycle 20: After refmac, R = 0.2484 (Rfree = 0.000) for 16007 atoms. Found 88 (88 requested) and removed 63 (44 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 2.00 Search for helices and strands: 0 residues in 0 chains, 16593 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 16624 seeds are put forward Round 1: 1193 peptides, 166 chains. Longest chain 27 peptides. Score 0.375 Round 2: 1311 peptides, 160 chains. Longest chain 45 peptides. Score 0.421 Round 3: 1338 peptides, 156 chains. Longest chain 28 peptides. Score 0.435 Round 4: 1325 peptides, 145 chains. Longest chain 31 peptides. Score 0.447 Round 5: 1313 peptides, 152 chains. Longest chain 29 peptides. Score 0.433 Taking the results from Round 4 Chains 151, Residues 1180, Estimated correctness of the model 0.0 % 6 chains (58 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4844 restraints for refining 15883 atoms. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2587 (Rfree = 0.000) for 15883 atoms. Found 87 (87 requested) and removed 49 (43 requested) atoms. Cycle 22: After refmac, R = 0.2622 (Rfree = 0.000) for 15921 atoms. Found 87 (87 requested) and removed 54 (43 requested) atoms. Cycle 23: After refmac, R = 0.2602 (Rfree = 0.000) for 15954 atoms. Found 87 (87 requested) and removed 61 (43 requested) atoms. Cycle 24: After refmac, R = 0.2606 (Rfree = 0.000) for 15980 atoms. Found 87 (87 requested) and removed 65 (43 requested) atoms. Cycle 25: After refmac, R = 0.2602 (Rfree = 0.000) for 16002 atoms. Found 88 (88 requested) and removed 63 (44 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.01 Search for helices and strands: 0 residues in 0 chains, 16771 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 16801 seeds are put forward Round 1: 1137 peptides, 166 chains. Longest chain 19 peptides. Score 0.356 Round 2: 1308 peptides, 163 chains. Longest chain 26 peptides. Score 0.415 Round 3: 1278 peptides, 152 chains. Longest chain 33 peptides. Score 0.423 Round 4: 1274 peptides, 148 chains. Longest chain 28 peptides. Score 0.427 Round 5: 1324 peptides, 159 chains. Longest chain 39 peptides. Score 0.426 Taking the results from Round 4 Chains 149, Residues 1126, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4468 restraints for refining 15781 atoms. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2458 (Rfree = 0.000) for 15781 atoms. Found 86 (86 requested) and removed 51 (43 requested) atoms. Cycle 27: After refmac, R = 0.2608 (Rfree = 0.000) for 15816 atoms. Found 86 (86 requested) and removed 63 (43 requested) atoms. Cycle 28: After refmac, R = 0.2592 (Rfree = 0.000) for 15839 atoms. Found 87 (87 requested) and removed 62 (43 requested) atoms. Cycle 29: After refmac, R = 0.2520 (Rfree = 0.000) for 15864 atoms. Found 87 (87 requested) and removed 75 (43 requested) atoms. Cycle 30: After refmac, R = 0.2565 (Rfree = 0.000) for 15876 atoms. Found 87 (87 requested) and removed 64 (43 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 2.02 Search for helices and strands: 0 residues in 0 chains, 16481 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 16498 seeds are put forward Round 1: 1216 peptides, 179 chains. Longest chain 21 peptides. Score 0.362 Round 2: 1299 peptides, 163 chains. Longest chain 34 peptides. Score 0.413 Round 3: 1262 peptides, 154 chains. Longest chain 40 peptides. Score 0.415 Round 4: 1282 peptides, 159 chains. Longest chain 22 peptides. Score 0.413 Round 5: 1301 peptides, 155 chains. Longest chain 42 peptides. Score 0.425 Taking the results from Round 5 Chains 161, Residues 1146, Estimated correctness of the model 0.0 % 6 chains (53 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4642 restraints for refining 16158 atoms. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2548 (Rfree = 0.000) for 16158 atoms. Found 88 (88 requested) and removed 51 (44 requested) atoms. Cycle 32: After refmac, R = 0.2536 (Rfree = 0.000) for 16195 atoms. Found 89 (89 requested) and removed 57 (44 requested) atoms. Cycle 33: After refmac, R = 0.2530 (Rfree = 0.000) for 16227 atoms. Found 89 (89 requested) and removed 71 (44 requested) atoms. Cycle 34: After refmac, R = 0.2515 (Rfree = 0.000) for 16245 atoms. Found 89 (89 requested) and removed 63 (44 requested) atoms. Cycle 35: After refmac, R = 0.2517 (Rfree = 0.000) for 16271 atoms. Found 89 (89 requested) and removed 77 (44 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 2.01 Search for helices and strands: 0 residues in 0 chains, 16808 seeds are put forward NCS extension: 51 residues added (0 deleted due to clashes), 16859 seeds are put forward Round 1: 1143 peptides, 179 chains. Longest chain 26 peptides. Score 0.338 Round 2: 1258 peptides, 160 chains. Longest chain 28 peptides. Score 0.404 Round 3: 1237 peptides, 159 chains. Longest chain 30 peptides. Score 0.399 Round 4: 1264 peptides, 156 chains. Longest chain 27 peptides. Score 0.412 Round 5: 1238 peptides, 151 chains. Longest chain 32 peptides. Score 0.412 Taking the results from Round 5 Chains 155, Residues 1087, Estimated correctness of the model 0.0 % 4 chains (68 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4505 restraints for refining 16003 atoms. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2515 (Rfree = 0.000) for 16003 atoms. Found 88 (88 requested) and removed 46 (44 requested) atoms. Cycle 37: After refmac, R = 0.2513 (Rfree = 0.000) for 16045 atoms. Found 88 (88 requested) and removed 56 (44 requested) atoms. Cycle 38: After refmac, R = 0.2501 (Rfree = 0.000) for 16077 atoms. Found 88 (88 requested) and removed 64 (44 requested) atoms. Cycle 39: After refmac, R = 0.2457 (Rfree = 0.000) for 16101 atoms. Found 88 (88 requested) and removed 68 (44 requested) atoms. Cycle 40: After refmac, R = 0.2115 (Rfree = 0.000) for 16121 atoms. Found 48 (88 requested) and removed 59 (44 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 1.99 Search for helices and strands: 0 residues in 0 chains, 16563 seeds are put forward NCS extension: 48 residues added (6 deleted due to clashes), 16611 seeds are put forward Round 1: 1142 peptides, 189 chains. Longest chain 15 peptides. Score 0.322 Round 2: 1321 peptides, 179 chains. Longest chain 25 peptides. Score 0.396 Round 3: 1256 peptides, 173 chains. Longest chain 23 peptides. Score 0.384 Round 4: 1225 peptides, 162 chains. Longest chain 22 peptides. Score 0.391 Round 5: 1237 peptides, 160 chains. Longest chain 24 peptides. Score 0.398 Taking the results from Round 5 Chains 163, Residues 1077, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 54333 reflections ( 98.81 % complete ) and 4333 restraints for refining 15926 atoms. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2462 (Rfree = 0.000) for 15926 atoms. Found 87 (87 requested) and removed 50 (43 requested) atoms. Cycle 42: After refmac, R = 0.2520 (Rfree = 0.000) for 15963 atoms. Found 87 (87 requested) and removed 56 (43 requested) atoms. Cycle 43: After refmac, R = 0.2516 (Rfree = 0.000) for 15994 atoms. Found 87 (87 requested) and removed 62 (43 requested) atoms. Cycle 44: After refmac, R = 0.2477 (Rfree = 0.000) for 16019 atoms. Found 88 (88 requested) and removed 73 (44 requested) atoms. Cycle 45: After refmac, R = 0.2096 (Rfree = 0.000) for 16034 atoms. Found 36 (88 requested) and removed 63 (44 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 1.96 Search for helices and strands: 0 residues in 0 chains, 16546 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 16578 seeds are put forward Round 1: 1112 peptides, 190 chains. Longest chain 19 peptides. Score 0.309 Round 2: 1207 peptides, 179 chains. Longest chain 24 peptides. Score 0.359 Round 3: 1240 peptides, 181 chains. Longest chain 22 peptides. Score 0.367 Round 4: 1234 peptides, 176 chains. Longest chain 19 peptides. Score 0.373 Round 5: 1246 peptides, 181 chains. Longest chain 22 peptides. Score 0.369 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 177, Residues 1058, Estimated correctness of the model 0.0 % 5 chains (33 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 177 chains (1058 residues) following loop building 5 chains (33 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 54333 reflections ( 98.81 % complete ) and 4181 restraints for refining 15591 atoms. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2607 (Rfree = 0.000) for 15591 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Cycle 47: After refmac, R = 0.2641 (Rfree = 0.000) for 15549 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Cycle 48: After refmac, R = 0.2570 (Rfree = 0.000) for 15507 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Cycle 49: After refmac, R = 0.2595 (Rfree = 0.000) for 15465 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 23:39:40 GMT 2018 Job finished. TimeTaking 251.72 Used memory is bytes: 10522536