Sun 23 Dec 22:22:43 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 2etd-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etd-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etd-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-3.2-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/2etd-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-3.2-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 22:22:52 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/2etd-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-3.2-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 128 and 0 Target number of residues in the AU: 128 Target solvent content: 0.6213 Checking the provided sequence file Detected sequence length: 171 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 171 Adjusted target solvent content: 0.49 Input MTZ file: 2etd-3.2-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: 21 Cell parameters: 80.417 85.225 53.388 90.000 90.000 90.000 Input sequence file: 2etd-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1368 target number of atoms Had to go as low as 0.55 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. 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: 58.489 3.200 Wilson plot Bfac: 61.39 2784 reflections ( 86.03 % complete ) and 0 restraints for refining 1518 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3744 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3576 (Rfree = 0.000) for 1518 atoms. Found 12 (13 requested) and removed 31 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 1527 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 6 peptides. Score 0.251 Round 2: 57 peptides, 12 chains. Longest chain 6 peptides. Score 0.263 Round 3: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.301 Round 4: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.376 Round 5: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.382 Taking the results from Round 5 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2784 reflections ( 86.03 % complete ) and 2665 restraints for refining 1162 atoms. 2423 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3310 (Rfree = 0.000) for 1162 atoms. Found 2 (10 requested) and removed 16 (5 requested) atoms. Cycle 2: After refmac, R = 0.3194 (Rfree = 0.000) for 1127 atoms. Found 7 (10 requested) and removed 12 (5 requested) atoms. Cycle 3: After refmac, R = 0.3014 (Rfree = 0.000) for 1106 atoms. Found 1 (10 requested) and removed 15 (5 requested) atoms. Cycle 4: After refmac, R = 0.3207 (Rfree = 0.000) for 1082 atoms. Found 2 (9 requested) and removed 10 (4 requested) atoms. Cycle 5: After refmac, R = 0.2494 (Rfree = 0.000) for 1067 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.45 Search for helices and strands: 0 residues in 0 chains, 1133 seeds are put forward Round 1: 62 peptides, 13 chains. Longest chain 6 peptides. Score 0.272 Round 2: 84 peptides, 13 chains. Longest chain 14 peptides. Score 0.470 Round 3: 78 peptides, 10 chains. Longest chain 23 peptides. Score 0.528 Round 4: 79 peptides, 11 chains. Longest chain 23 peptides. Score 0.501 Round 5: 80 peptides, 11 chains. Longest chain 15 peptides. Score 0.508 Taking the results from Round 3 Chains 10, Residues 68, Estimated correctness of the model 20.2 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 2784 reflections ( 86.03 % complete ) and 1945 restraints for refining 1082 atoms. 1582 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3017 (Rfree = 0.000) for 1082 atoms. Found 7 (9 requested) and removed 27 (4 requested) atoms. Cycle 7: After refmac, R = 0.2711 (Rfree = 0.000) for 1056 atoms. Found 8 (9 requested) and removed 45 (4 requested) atoms. Cycle 8: After refmac, R = 0.2852 (Rfree = 0.000) for 1017 atoms. Found 7 (9 requested) and removed 12 (4 requested) atoms. Cycle 9: After refmac, R = 0.2682 (Rfree = 0.000) for 1004 atoms. Found 3 (9 requested) and removed 9 (4 requested) atoms. Cycle 10: After refmac, R = 0.2991 (Rfree = 0.000) for 995 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 1072 seeds are put forward Round 1: 72 peptides, 14 chains. Longest chain 7 peptides. Score 0.328 Round 2: 72 peptides, 11 chains. Longest chain 10 peptides. Score 0.443 Round 3: 71 peptides, 11 chains. Longest chain 10 peptides. Score 0.435 Round 4: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.382 Round 5: 64 peptides, 10 chains. Longest chain 12 peptides. Score 0.413 Taking the results from Round 2 Chains 11, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2784 reflections ( 86.03 % complete ) and 2248 restraints for refining 1079 atoms. 2015 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2603 (Rfree = 0.000) for 1079 atoms. Found 7 (9 requested) and removed 28 (4 requested) atoms. Cycle 12: After refmac, R = 0.2948 (Rfree = 0.000) for 1056 atoms. Found 4 (9 requested) and removed 11 (4 requested) atoms. Cycle 13: After refmac, R = 0.2944 (Rfree = 0.000) for 1042 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.2778 (Rfree = 0.000) for 1034 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2472 (Rfree = 0.000) for 1030 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 1094 seeds are put forward Round 1: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.342 Round 2: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.398 Round 3: 80 peptides, 11 chains. Longest chain 14 peptides. Score 0.508 Round 4: 88 peptides, 12 chains. Longest chain 12 peptides. Score 0.535 Round 5: 91 peptides, 12 chains. Longest chain 12 peptides. Score 0.557 Taking the results from Round 5 Chains 13, Residues 79, Estimated correctness of the model 28.9 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2784 reflections ( 86.03 % complete ) and 2331 restraints for refining 1222 atoms. 1960 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2446 (Rfree = 0.000) for 1222 atoms. Found 10 (10 requested) and removed 71 (5 requested) atoms. Cycle 17: After refmac, R = 0.2481 (Rfree = 0.000) for 1152 atoms. Found 5 (10 requested) and removed 15 (5 requested) atoms. Cycle 18: After refmac, R = 0.2425 (Rfree = 0.000) for 1138 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.2013 (Rfree = 0.000) for 1126 atoms. Found 0 (10 requested) and removed 8 (5 requested) atoms. Cycle 20: After refmac, R = 0.1883 (Rfree = 0.000) for 1116 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.25 Search for helices and strands: 0 residues in 0 chains, 1180 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 7 peptides. Score 0.332 Round 2: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.369 Round 3: 87 peptides, 14 chains. Longest chain 14 peptides. Score 0.459 Round 4: 87 peptides, 14 chains. Longest chain 10 peptides. Score 0.459 Round 5: 87 peptides, 17 chains. Longest chain 8 peptides. Score 0.350 Taking the results from Round 4 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2784 reflections ( 86.03 % complete ) and 2579 restraints for refining 1239 atoms. 2269 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2392 (Rfree = 0.000) for 1239 atoms. Found 10 (11 requested) and removed 19 (5 requested) atoms. Cycle 22: After refmac, R = 0.2053 (Rfree = 0.000) for 1228 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.1896 (Rfree = 0.000) for 1225 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.1835 (Rfree = 0.000) for 1222 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.1839 (Rfree = 0.000) for 1220 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 1279 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.339 Round 2: 76 peptides, 12 chains. Longest chain 16 peptides. Score 0.440 Round 3: 73 peptides, 11 chains. Longest chain 11 peptides. Score 0.452 Round 4: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.418 Round 5: 63 peptides, 11 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 3 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2784 reflections ( 86.03 % complete ) and 2776 restraints for refining 1249 atoms. 2539 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2504 (Rfree = 0.000) for 1249 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 27: After refmac, R = 0.2294 (Rfree = 0.000) for 1245 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2275 (Rfree = 0.000) for 1239 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2059 (Rfree = 0.000) for 1234 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2079 (Rfree = 0.000) for 1230 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.20 Search for helices and strands: 0 residues in 0 chains, 1281 seeds are put forward Round 1: 66 peptides, 12 chains. Longest chain 8 peptides. Score 0.351 Round 2: 72 peptides, 11 chains. Longest chain 12 peptides. Score 0.443 Round 3: 68 peptides, 10 chains. Longest chain 10 peptides. Score 0.447 Round 4: 78 peptides, 11 chains. Longest chain 15 peptides. Score 0.493 Round 5: 79 peptides, 11 chains. Longest chain 15 peptides. Score 0.501 Taking the results from Round 5 Chains 12, Residues 68, Estimated correctness of the model 11.7 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2784 reflections ( 86.03 % complete ) and 2647 restraints for refining 1249 atoms. 2332 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2376 (Rfree = 0.000) for 1249 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 32: After refmac, R = 0.2007 (Rfree = 0.000) for 1251 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.1900 (Rfree = 0.000) for 1243 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1954 (Rfree = 0.000) for 1241 atoms. Found 4 (11 requested) and removed 12 (5 requested) atoms. Cycle 35: After refmac, R = 0.1872 (Rfree = 0.000) for 1232 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.20 Search for helices and strands: 0 residues in 0 chains, 1270 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 13 peptides. Score 0.339 Round 2: 78 peptides, 13 chains. Longest chain 16 peptides. Score 0.420 Round 3: 84 peptides, 12 chains. Longest chain 12 peptides. Score 0.505 Round 4: 86 peptides, 13 chains. Longest chain 16 peptides. Score 0.486 Round 5: 78 peptides, 13 chains. Longest chain 12 peptides. Score 0.420 Taking the results from Round 3 Chains 13, Residues 72, Estimated correctness of the model 12.9 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2784 reflections ( 86.03 % complete ) and 2589 restraints for refining 1249 atoms. 2280 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2280 (Rfree = 0.000) for 1249 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 37: After refmac, R = 0.1980 (Rfree = 0.000) for 1246 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.1870 (Rfree = 0.000) for 1244 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1876 (Rfree = 0.000) for 1238 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.1682 (Rfree = 0.000) for 1233 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 1284 seeds are put forward Round 1: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.329 Round 2: 60 peptides, 10 chains. Longest chain 8 peptides. Score 0.376 Round 3: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.391 Round 4: 71 peptides, 11 chains. Longest chain 10 peptides. Score 0.435 Round 5: 68 peptides, 11 chains. Longest chain 12 peptides. Score 0.409 Taking the results from Round 4 Chains 11, Residues 60, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2784 reflections ( 86.03 % complete ) and 2695 restraints for refining 1245 atoms. 2440 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2137 (Rfree = 0.000) for 1245 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 42: After refmac, R = 0.1841 (Rfree = 0.000) for 1232 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.1881 (Rfree = 0.000) for 1227 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1902 (Rfree = 0.000) for 1225 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.1850 (Rfree = 0.000) for 1223 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 1273 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 8 peptides. Score 0.232 Round 2: 73 peptides, 15 chains. Longest chain 8 peptides. Score 0.298 Round 3: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.342 Round 4: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.313 Round 5: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.349 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 57, 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 2etd-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2784 reflections ( 86.03 % complete ) and 2791 restraints for refining 1249 atoms. 2576 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2438 (Rfree = 0.000) for 1249 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2155 (Rfree = 0.000) for 1244 atoms. Found 0 (11 requested) and removed 2 (5 requested) atoms. Cycle 48: After refmac, R = 0.2093 (Rfree = 0.000) for 1242 atoms. Found 0 (11 requested) and removed 0 (5 requested) atoms. Cycle 49: After refmac, R = 0.2063 (Rfree = 0.000) for 1242 atoms. TimeTaking 26.88