null Sun 23 Dec 22:23:08 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 1o6a-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1o6a-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-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/1o6a-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-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 ============================================================ Sun 23 Dec 22:23:18 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/1o6a-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1o6a-3.6-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 136 and 0 Target number of residues in the AU: 136 Target solvent content: 0.6582 Checking the provided sequence file Detected sequence length: 96 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 192 Adjusted target solvent content: 0.52 Input MTZ file: 1o6a-3.6-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: 92 Cell parameters: 61.652 61.652 113.295 90.000 90.000 90.000 Input sequence file: 1o6a-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1536 target number of atoms Had to go as low as 0.65 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. Conditional restraints will be used 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: 41.713 3.601 Wilson plot Bfac: 83.20 2821 reflections ( 99.86 % complete ) and 0 restraints for refining 1713 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.4251 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3842 (Rfree = 0.000) for 1713 atoms. Found 4 (10 requested) and removed 19 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.21 4.10 Search for helices and strands: 0 residues in 0 chains, 1719 seeds are put forward NCS extension: 0 residues added, 1719 seeds are put forward Round 1: 66 peptides, 13 chains. Longest chain 10 peptides. Score 0.295 Round 2: 96 peptides, 15 chains. Longest chain 15 peptides. Score 0.459 Round 3: 94 peptides, 14 chains. Longest chain 18 peptides. Score 0.476 Round 4: 98 peptides, 14 chains. Longest chain 12 peptides. Score 0.503 Round 5: 96 peptides, 13 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 5 Chains 13, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3195 restraints for refining 1364 atoms. 2876 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3618 (Rfree = 0.000) for 1364 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 2: After refmac, R = 0.3462 (Rfree = 0.000) for 1338 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 3: After refmac, R = 0.3337 (Rfree = 0.000) for 1330 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.3716 (Rfree = 0.000) for 1320 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.3514 (Rfree = 0.000) for 1293 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 1339 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1358 seeds are put forward Round 1: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.402 Round 2: 102 peptides, 17 chains. Longest chain 17 peptides. Score 0.441 Round 3: 110 peptides, 15 chains. Longest chain 15 peptides. Score 0.550 Round 4: 111 peptides, 14 chains. Longest chain 18 peptides. Score 0.583 Round 5: 111 peptides, 14 chains. Longest chain 20 peptides. Score 0.583 Taking the results from Round 5 Chains 14, Residues 97, Estimated correctness of the model 7.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 2927 restraints for refining 1298 atoms. 2553 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3726 (Rfree = 0.000) for 1298 atoms. Found 3 (8 requested) and removed 23 (4 requested) atoms. Cycle 7: After refmac, R = 0.3954 (Rfree = 0.000) for 1266 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 8: After refmac, R = 0.3722 (Rfree = 0.000) for 1247 atoms. Found 4 (8 requested) and removed 17 (4 requested) atoms. Cycle 9: After refmac, R = 0.3220 (Rfree = 0.000) for 1226 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 10: After refmac, R = 0.3160 (Rfree = 0.000) for 1220 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 1290 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 1320 seeds are put forward Round 1: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.379 Round 2: 97 peptides, 13 chains. Longest chain 20 peptides. Score 0.525 Round 3: 104 peptides, 14 chains. Longest chain 16 peptides. Score 0.541 Round 4: 92 peptides, 11 chains. Longest chain 19 peptides. Score 0.551 Round 5: 100 peptides, 13 chains. Longest chain 17 peptides. Score 0.544 Taking the results from Round 4 Chains 11, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 2915 restraints for refining 1306 atoms. 2602 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3205 (Rfree = 0.000) for 1306 atoms. Found 5 (8 requested) and removed 13 (4 requested) atoms. Cycle 12: After refmac, R = 0.3264 (Rfree = 0.000) for 1288 atoms. Found 7 (8 requested) and removed 12 (4 requested) atoms. Cycle 13: After refmac, R = 0.3458 (Rfree = 0.000) for 1274 atoms. Found 6 (8 requested) and removed 12 (4 requested) atoms. Cycle 14: After refmac, R = 0.3396 (Rfree = 0.000) for 1260 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.3248 (Rfree = 0.000) for 1241 atoms. Found 3 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 1282 seeds are put forward NCS extension: 0 residues added, 1282 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 11 peptides. Score 0.264 Round 2: 75 peptides, 12 chains. Longest chain 12 peptides. Score 0.402 Round 3: 82 peptides, 11 chains. Longest chain 13 peptides. Score 0.486 Round 4: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.404 Round 5: 89 peptides, 13 chains. Longest chain 13 peptides. Score 0.472 Taking the results from Round 3 Chains 11, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 2889 restraints for refining 1263 atoms. 2616 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3472 (Rfree = 0.000) for 1263 atoms. Found 4 (8 requested) and removed 13 (4 requested) atoms. Cycle 17: After refmac, R = 0.3356 (Rfree = 0.000) for 1243 atoms. Found 7 (8 requested) and removed 12 (4 requested) atoms. Cycle 18: After refmac, R = 0.3061 (Rfree = 0.000) for 1234 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 19: After refmac, R = 0.2877 (Rfree = 0.000) for 1227 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2863 (Rfree = 0.000) for 1222 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 1252 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1266 seeds are put forward Round 1: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.324 Round 2: 86 peptides, 13 chains. Longest chain 15 peptides. Score 0.451 Round 3: 84 peptides, 13 chains. Longest chain 14 peptides. Score 0.436 Round 4: 89 peptides, 12 chains. Longest chain 14 peptides. Score 0.502 Round 5: 92 peptides, 11 chains. Longest chain 22 peptides. Score 0.551 Taking the results from Round 5 Chains 11, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 2815 restraints for refining 1293 atoms. 2502 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3454 (Rfree = 0.000) for 1293 atoms. Found 1 (8 requested) and removed 15 (4 requested) atoms. Cycle 22: After refmac, R = 0.3160 (Rfree = 0.000) for 1269 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.3076 (Rfree = 0.000) for 1259 atoms. Found 1 (8 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.3066 (Rfree = 0.000) for 1251 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2987 (Rfree = 0.000) for 1246 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 1288 seeds are put forward NCS extension: 0 residues added, 1288 seeds are put forward Round 1: 74 peptides, 14 chains. Longest chain 13 peptides. Score 0.326 Round 2: 89 peptides, 13 chains. Longest chain 12 peptides. Score 0.472 Round 3: 91 peptides, 13 chains. Longest chain 12 peptides. Score 0.486 Round 4: 95 peptides, 12 chains. Longest chain 15 peptides. Score 0.541 Round 5: 96 peptides, 13 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 4 Chains 12, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 2934 restraints for refining 1315 atoms. 2614 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3141 (Rfree = 0.000) for 1315 atoms. Found 3 (8 requested) and removed 13 (4 requested) atoms. Cycle 27: After refmac, R = 0.2901 (Rfree = 0.000) for 1293 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.3064 (Rfree = 0.000) for 1288 atoms. Found 2 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.2736 (Rfree = 0.000) for 1274 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.2684 (Rfree = 0.000) for 1272 atoms. Found 0 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 1303 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1322 seeds are put forward Round 1: 91 peptides, 17 chains. Longest chain 15 peptides. Score 0.359 Round 2: 89 peptides, 15 chains. Longest chain 16 peptides. Score 0.409 Round 3: 83 peptides, 14 chains. Longest chain 11 peptides. Score 0.397 Round 4: 84 peptides, 13 chains. Longest chain 16 peptides. Score 0.436 Round 5: 92 peptides, 14 chains. Longest chain 15 peptides. Score 0.462 Taking the results from Round 5 Chains 14, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3093 restraints for refining 1352 atoms. 2795 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3128 (Rfree = 0.000) for 1352 atoms. Found 7 (8 requested) and removed 17 (4 requested) atoms. Cycle 32: After refmac, R = 0.2896 (Rfree = 0.000) for 1335 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.2838 (Rfree = 0.000) for 1326 atoms. Found 4 (8 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.2717 (Rfree = 0.000) for 1318 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2732 (Rfree = 0.000) for 1311 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 1334 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1354 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 11 peptides. Score 0.316 Round 2: 79 peptides, 14 chains. Longest chain 9 peptides. Score 0.366 Round 3: 87 peptides, 14 chains. Longest chain 17 peptides. Score 0.426 Round 4: 89 peptides, 14 chains. Longest chain 11 peptides. Score 0.441 Round 5: 96 peptides, 13 chains. Longest chain 18 peptides. Score 0.519 Taking the results from Round 5 Chains 13, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3004 restraints for refining 1362 atoms. 2685 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3112 (Rfree = 0.000) for 1362 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 37: After refmac, R = 0.2958 (Rfree = 0.000) for 1347 atoms. Found 5 (8 requested) and removed 12 (4 requested) atoms. Cycle 38: After refmac, R = 0.3052 (Rfree = 0.000) for 1328 atoms. Found 3 (8 requested) and removed 10 (4 requested) atoms. Cycle 39: After refmac, R = 0.2825 (Rfree = 0.000) for 1314 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.2781 (Rfree = 0.000) for 1308 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 1340 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1358 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 9 peptides. Score 0.231 Round 2: 66 peptides, 10 chains. Longest chain 16 peptides. Score 0.402 Round 3: 67 peptides, 11 chains. Longest chain 10 peptides. Score 0.375 Round 4: 79 peptides, 13 chains. Longest chain 11 peptides. Score 0.399 Round 5: 80 peptides, 11 chains. Longest chain 13 peptides. Score 0.472 Taking the results from Round 5 Chains 11, Residues 69, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2821 reflections ( 99.86 % complete ) and 3062 restraints for refining 1368 atoms. 2797 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3101 (Rfree = 0.000) for 1368 atoms. Found 2 (8 requested) and removed 16 (4 requested) atoms. Cycle 42: After refmac, R = 0.3077 (Rfree = 0.000) for 1345 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 43: After refmac, R = 0.3064 (Rfree = 0.000) for 1337 atoms. Found 5 (8 requested) and removed 11 (4 requested) atoms. Cycle 44: After refmac, R = 0.2731 (Rfree = 0.000) for 1330 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.2708 (Rfree = 0.000) for 1320 atoms. Found 3 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 1337 seeds are put forward NCS extension: 0 residues added, 1337 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 8 peptides. Score 0.273 Round 2: 79 peptides, 13 chains. Longest chain 15 peptides. Score 0.399 Round 3: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.387 Round 4: 85 peptides, 13 chains. Longest chain 12 peptides. Score 0.444 Round 5: 84 peptides, 14 chains. Longest chain 9 peptides. Score 0.404 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1o6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2821 reflections ( 99.86 % complete ) and 3104 restraints for refining 1365 atoms. 2829 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3607 (Rfree = 0.000) for 1365 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2948 (Rfree = 0.000) for 1349 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2741 (Rfree = 0.000) for 1343 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2675 (Rfree = 0.000) for 1339 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:16 GMT 2018 Job finished. TimeTaking 27.14 Used memory is bytes: 21255112