Sun 23 Dec 22:22:44 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 2ou6-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-4.0-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/2ou6-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-4.0-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 22:22:53 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/2ou6-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-4.0-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 149 and 0 Target number of residues in the AU: 149 Target solvent content: 0.6681 Checking the provided sequence file Detected sequence length: 190 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 190 Adjusted target solvent content: 0.58 Input MTZ file: 2ou6-4.0-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: 179 Cell parameters: 57.933 57.933 250.773 90.000 90.000 120.000 Input sequence file: 2ou6-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.85 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 Loops will be built when appropriate and at the last cycle Resolution range: 50.171 4.001 Wilson plot Bfac: 90.17 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2474 reflections ( 99.68 % complete ) and 0 restraints for refining 1684 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3843 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3888 (Rfree = 0.000) for 1684 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.45 Search for helices and strands: 0 residues in 0 chains, 1732 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.243 Round 2: 95 peptides, 13 chains. Longest chain 13 peptides. Score 0.484 Round 3: 98 peptides, 15 chains. Longest chain 11 peptides. Score 0.447 Round 4: 101 peptides, 10 chains. Longest chain 27 peptides. Score 0.596 Round 5: 91 peptides, 13 chains. Longest chain 13 peptides. Score 0.460 Taking the results from Round 4 Chains 10, Residues 91, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.68 % complete ) and 2884 restraints for refining 1343 atoms. 2498 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3209 (Rfree = 0.000) for 1343 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.2966 (Rfree = 0.000) for 1307 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.2838 (Rfree = 0.000) for 1277 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2839 (Rfree = 0.000) for 1260 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.2798 (Rfree = 0.000) for 1245 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.39 Search for helices and strands: 0 residues in 0 chains, 1288 seeds are put forward Round 1: 71 peptides, 13 chains. Longest chain 8 peptides. Score 0.322 Round 2: 96 peptides, 13 chains. Longest chain 22 peptides. Score 0.490 Round 3: 94 peptides, 14 chains. Longest chain 12 peptides. Score 0.450 Round 4: 97 peptides, 13 chains. Longest chain 17 peptides. Score 0.496 Round 5: 102 peptides, 14 chains. Longest chain 13 peptides. Score 0.499 Taking the results from Round 5 Chains 14, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.68 % complete ) and 2942 restraints for refining 1311 atoms. 2604 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2997 (Rfree = 0.000) for 1311 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2841 (Rfree = 0.000) for 1275 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 8: After refmac, R = 0.2735 (Rfree = 0.000) for 1260 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 9: After refmac, R = 0.2694 (Rfree = 0.000) for 1248 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.2328 (Rfree = 0.000) for 1237 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.39 Search for helices and strands: 0 residues in 0 chains, 1297 seeds are put forward Round 1: 93 peptides, 16 chains. Longest chain 10 peptides. Score 0.386 Round 2: 105 peptides, 14 chains. Longest chain 15 peptides. Score 0.517 Round 3: 97 peptides, 15 chains. Longest chain 10 peptides. Score 0.441 Round 4: 106 peptides, 15 chains. Longest chain 13 peptides. Score 0.496 Round 5: 110 peptides, 14 chains. Longest chain 13 peptides. Score 0.545 Taking the results from Round 5 Chains 14, Residues 96, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.68 % complete ) and 2754 restraints for refining 1300 atoms. 2347 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2995 (Rfree = 0.000) for 1300 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 12: After refmac, R = 0.2728 (Rfree = 0.000) for 1264 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 13: After refmac, R = 0.2741 (Rfree = 0.000) for 1255 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 14: After refmac, R = 0.2604 (Rfree = 0.000) for 1246 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 15: After refmac, R = 0.2177 (Rfree = 0.000) for 1237 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 3.41 Search for helices and strands: 0 residues in 0 chains, 1297 seeds are put forward Round 1: 80 peptides, 15 chains. Longest chain 11 peptides. Score 0.325 Round 2: 102 peptides, 15 chains. Longest chain 13 peptides. Score 0.472 Round 3: 105 peptides, 14 chains. Longest chain 15 peptides. Score 0.517 Round 4: 101 peptides, 13 chains. Longest chain 15 peptides. Score 0.520 Round 5: 102 peptides, 14 chains. Longest chain 14 peptides. Score 0.499 Taking the results from Round 4 Chains 14, Residues 88, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.68 % complete ) and 2722 restraints for refining 1373 atoms. 2299 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3174 (Rfree = 0.000) for 1373 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 17: After refmac, R = 0.3050 (Rfree = 0.000) for 1341 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 18: After refmac, R = 0.2970 (Rfree = 0.000) for 1315 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 19: After refmac, R = 0.2667 (Rfree = 0.000) for 1298 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.2858 (Rfree = 0.000) for 1285 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.79 3.40 Search for helices and strands: 0 residues in 0 chains, 1328 seeds are put forward Round 1: 79 peptides, 12 chains. Longest chain 21 peptides. Score 0.411 Round 2: 94 peptides, 13 chains. Longest chain 25 peptides. Score 0.478 Round 3: 94 peptides, 14 chains. Longest chain 17 peptides. Score 0.450 Round 4: 106 peptides, 13 chains. Longest chain 18 peptides. Score 0.548 Round 5: 102 peptides, 13 chains. Longest chain 18 peptides. Score 0.525 Taking the results from Round 4 Chains 13, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.68 % complete ) and 2851 restraints for refining 1310 atoms. 2492 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3026 (Rfree = 0.000) for 1310 atoms. Found 6 (6 requested) and removed 24 (3 requested) atoms. Cycle 22: After refmac, R = 0.2701 (Rfree = 0.000) for 1269 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 23: After refmac, R = 0.2669 (Rfree = 0.000) for 1253 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.2659 (Rfree = 0.000) for 1250 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 25: After refmac, R = 0.2617 (Rfree = 0.000) for 1246 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.37 Search for helices and strands: 0 residues in 0 chains, 1324 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.316 Round 2: 96 peptides, 13 chains. Longest chain 12 peptides. Score 0.490 Round 3: 105 peptides, 14 chains. Longest chain 14 peptides. Score 0.517 Round 4: 108 peptides, 15 chains. Longest chain 15 peptides. Score 0.508 Round 5: 103 peptides, 13 chains. Longest chain 14 peptides. Score 0.531 Taking the results from Round 5 Chains 13, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.68 % complete ) and 2859 restraints for refining 1346 atoms. 2512 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2903 (Rfree = 0.000) for 1346 atoms. Found 6 (6 requested) and removed 19 (3 requested) atoms. Cycle 27: After refmac, R = 0.2844 (Rfree = 0.000) for 1314 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 28: After refmac, R = 0.2723 (Rfree = 0.000) for 1298 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 29: After refmac, R = 0.2464 (Rfree = 0.000) for 1286 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 30: After refmac, R = 0.2622 (Rfree = 0.000) for 1280 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.39 Search for helices and strands: 0 residues in 0 chains, 1347 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 7 peptides. Score 0.285 Round 2: 92 peptides, 15 chains. Longest chain 10 peptides. Score 0.409 Round 3: 89 peptides, 12 chains. Longest chain 14 peptides. Score 0.475 Round 4: 98 peptides, 13 chains. Longest chain 12 peptides. Score 0.502 Round 5: 92 peptides, 12 chains. Longest chain 19 peptides. Score 0.494 Taking the results from Round 4 Chains 13, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.68 % complete ) and 2931 restraints for refining 1349 atoms. 2604 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2830 (Rfree = 0.000) for 1349 atoms. Found 6 (6 requested) and removed 16 (3 requested) atoms. Cycle 32: After refmac, R = 0.2691 (Rfree = 0.000) for 1325 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 33: After refmac, R = 0.2690 (Rfree = 0.000) for 1313 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 34: After refmac, R = 0.2699 (Rfree = 0.000) for 1298 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 35: After refmac, R = 0.2641 (Rfree = 0.000) for 1294 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.35 Search for helices and strands: 0 residues in 0 chains, 1360 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.225 Round 2: 80 peptides, 15 chains. Longest chain 8 peptides. Score 0.325 Round 3: 87 peptides, 14 chains. Longest chain 11 peptides. Score 0.405 Round 4: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.370 Round 5: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.387 Taking the results from Round 3 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.68 % complete ) and 2750 restraints for refining 1308 atoms. 2440 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2892 (Rfree = 0.000) for 1308 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 37: After refmac, R = 0.2808 (Rfree = 0.000) for 1296 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.2684 (Rfree = 0.000) for 1286 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 39: After refmac, R = 0.2887 (Rfree = 0.000) for 1279 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 40: After refmac, R = 0.2512 (Rfree = 0.000) for 1267 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.34 Search for helices and strands: 0 residues in 0 chains, 1310 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 9 peptides. Score 0.300 Round 2: 92 peptides, 17 chains. Longest chain 7 peptides. Score 0.350 Round 3: 95 peptides, 18 chains. Longest chain 8 peptides. Score 0.341 Round 4: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.379 Round 5: 91 peptides, 17 chains. Longest chain 9 peptides. Score 0.343 Taking the results from Round 4 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2474 reflections ( 99.68 % complete ) and 2997 restraints for refining 1340 atoms. 2709 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2949 (Rfree = 0.000) for 1340 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 42: After refmac, R = 0.2850 (Rfree = 0.000) for 1325 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 43: After refmac, R = 0.2868 (Rfree = 0.000) for 1308 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2722 (Rfree = 0.000) for 1298 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.3120 (Rfree = 0.000) for 1288 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 3.40 Search for helices and strands: 0 residues in 0 chains, 1333 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 10 peptides. Score 0.276 Round 2: 81 peptides, 15 chains. Longest chain 12 peptides. Score 0.332 Round 3: 78 peptides, 14 chains. Longest chain 8 peptides. Score 0.342 Round 4: 77 peptides, 14 chains. Longest chain 9 peptides. Score 0.335 Round 5: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 64, 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 2ou6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2474 reflections ( 99.68 % complete ) and 2820 restraints for refining 1271 atoms. 2578 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3157 (Rfree = 0.000) for 1271 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3013 (Rfree = 0.000) for 1260 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2975 (Rfree = 0.000) for 1249 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2946 (Rfree = 0.000) for 1238 atoms. TimeTaking 27.95