null Sun 23 Dec 22:22:41 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 2osd-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2osd-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2osd-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-2.3-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/2osd-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-2.3-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 22:22:50 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/2osd-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2osd-2.3-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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.5937 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 163 Adjusted target solvent content: 0.52 Input MTZ file: 2osd-2.3-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: 96 Cell parameters: 55.786 55.786 118.990 90.000 90.000 90.000 Input sequence file: 2osd-2.3-parrot-hancs.fasta_lf Building free atoms model in initial map for 1304 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: 50.510 2.300 Wilson plot Bfac: 49.91 8896 reflections ( 99.91 % complete ) and 0 restraints for refining 1439 atoms. Observations/parameters ratio is 1.55 ------------------------------------------------------ Starting model: R = 0.3523 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2947 (Rfree = 0.000) for 1439 atoms. Found 17 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 3.01 Round 1: 90 peptides, 15 chains. Longest chain 13 peptides. Score 0.446 Round 2: 107 peptides, 10 chains. Longest chain 21 peptides. Score 0.706 Round 3: 117 peptides, 10 chains. Longest chain 27 peptides. Score 0.752 Round 4: 120 peptides, 10 chains. Longest chain 25 peptides. Score 0.765 Round 5: 122 peptides, 8 chains. Longest chain 25 peptides. Score 0.810 Taking the results from Round 5 Chains 9, Residues 114, Estimated correctness of the model 94.7 % 4 chains (81 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 116 A and 123 A 8 chains (120 residues) following loop building 3 chains (87 residues) in sequence following loop building ------------------------------------------------------ 8896 reflections ( 99.91 % complete ) and 1744 restraints for refining 1274 atoms. 884 conditional restraints added. Observations/parameters ratio is 1.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3332 (Rfree = 0.000) for 1274 atoms. Found 18 (29 requested) and removed 28 (14 requested) atoms. Cycle 2: After refmac, R = 0.3101 (Rfree = 0.000) for 1235 atoms. Found 20 (28 requested) and removed 18 (14 requested) atoms. Cycle 3: After refmac, R = 0.2869 (Rfree = 0.000) for 1226 atoms. Found 15 (27 requested) and removed 17 (14 requested) atoms. Cycle 4: After refmac, R = 0.2841 (Rfree = 0.000) for 1213 atoms. Found 25 (26 requested) and removed 19 (14 requested) atoms. Cycle 5: After refmac, R = 0.2637 (Rfree = 0.000) for 1214 atoms. Found 17 (26 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.65 2.58 Round 1: 119 peptides, 8 chains. Longest chain 25 peptides. Score 0.799 Round 2: 130 peptides, 7 chains. Longest chain 48 peptides. Score 0.850 Round 3: 130 peptides, 9 chains. Longest chain 46 peptides. Score 0.819 Round 4: 127 peptides, 7 chains. Longest chain 30 peptides. Score 0.842 Round 5: 133 peptides, 5 chains. Longest chain 60 peptides. Score 0.885 Taking the results from Round 5 Chains 5, Residues 128, Estimated correctness of the model 97.9 % 2 chains (79 residues) have been docked in sequence Building loops using Loopy2018 5 chains (128 residues) following loop building 2 chains (79 residues) in sequence following loop building ------------------------------------------------------ 8896 reflections ( 99.91 % complete ) and 1719 restraints for refining 1236 atoms. 861 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2890 (Rfree = 0.000) for 1236 atoms. Found 19 (25 requested) and removed 23 (14 requested) atoms. Cycle 7: After refmac, R = 0.2620 (Rfree = 0.000) for 1223 atoms. Found 20 (25 requested) and removed 16 (14 requested) atoms. Cycle 8: After refmac, R = 0.2434 (Rfree = 0.000) for 1226 atoms. Found 12 (24 requested) and removed 17 (14 requested) atoms. Cycle 9: After refmac, R = 0.2373 (Rfree = 0.000) for 1219 atoms. Found 13 (24 requested) and removed 15 (14 requested) atoms. Cycle 10: After refmac, R = 0.2340 (Rfree = 0.000) for 1215 atoms. Found 7 (22 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.65 2.58 Round 1: 129 peptides, 6 chains. Longest chain 60 peptides. Score 0.862 Round 2: 137 peptides, 4 chains. Longest chain 61 peptides. Score 0.905 Round 3: 136 peptides, 5 chains. Longest chain 48 peptides. Score 0.891 Round 4: 130 peptides, 6 chains. Longest chain 39 peptides. Score 0.865 Round 5: 128 peptides, 8 chains. Longest chain 26 peptides. Score 0.829 Taking the results from Round 2 Chains 5, Residues 133, Estimated correctness of the model 98.5 % 3 chains (122 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 98 A 4 chains (142 residues) following loop building 2 chains (131 residues) in sequence following loop building ------------------------------------------------------ 8896 reflections ( 99.91 % complete ) and 1384 restraints for refining 1311 atoms. 238 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2708 (Rfree = 0.000) for 1311 atoms. Found 12 (24 requested) and removed 26 (15 requested) atoms. Cycle 12: After refmac, R = 0.2452 (Rfree = 0.000) for 1291 atoms. Found 9 (23 requested) and removed 15 (14 requested) atoms. Cycle 13: After refmac, R = 0.2294 (Rfree = 0.000) for 1282 atoms. Found 6 (22 requested) and removed 14 (14 requested) atoms. Cycle 14: After refmac, R = 0.2267 (Rfree = 0.000) for 1272 atoms. Found 13 (21 requested) and removed 15 (14 requested) atoms. Cycle 15: After refmac, R = 0.2187 (Rfree = 0.000) for 1268 atoms. Found 7 (21 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.64 2.57 Round 1: 136 peptides, 4 chains. Longest chain 47 peptides. Score 0.903 Round 2: 133 peptides, 8 chains. Longest chain 29 peptides. Score 0.844 Round 3: 132 peptides, 7 chains. Longest chain 50 peptides. Score 0.856 Round 4: 129 peptides, 8 chains. Longest chain 26 peptides. Score 0.832 Round 5: 127 peptides, 9 chains. Longest chain 31 peptides. Score 0.809 Taking the results from Round 1 Chains 4, Residues 132, Estimated correctness of the model 98.5 % 3 chains (120 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 49 A Built loop between residues 88 A and 98 A 2 chains (146 residues) following loop building 1 chains (134 residues) in sequence following loop building ------------------------------------------------------ 8896 reflections ( 99.91 % complete ) and 1409 restraints for refining 1305 atoms. 234 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2690 (Rfree = 0.000) for 1305 atoms. Found 15 (21 requested) and removed 22 (15 requested) atoms. Cycle 17: After refmac, R = 0.2328 (Rfree = 0.000) for 1294 atoms. Found 13 (20 requested) and removed 17 (14 requested) atoms. Cycle 18: After refmac, R = 0.2184 (Rfree = 0.000) for 1289 atoms. Found 15 (19 requested) and removed 15 (14 requested) atoms. Cycle 19: After refmac, R = 0.2092 (Rfree = 0.000) for 1287 atoms. Found 10 (19 requested) and removed 14 (14 requested) atoms. Cycle 20: After refmac, R = 0.2056 (Rfree = 0.000) for 1283 atoms. Found 9 (18 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.66 2.59 Round 1: 136 peptides, 4 chains. Longest chain 47 peptides. Score 0.903 Round 2: 136 peptides, 6 chains. Longest chain 47 peptides. Score 0.879 Round 3: 131 peptides, 8 chains. Longest chain 27 peptides. Score 0.838 Round 4: 131 peptides, 8 chains. Longest chain 26 peptides. Score 0.838 Round 5: 132 peptides, 8 chains. Longest chain 27 peptides. Score 0.841 Taking the results from Round 1 Chains 6, Residues 132, Estimated correctness of the model 98.5 % 3 chains (117 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 49 A Built loop between residues 88 A and 98 A 3 chains (145 residues) following loop building 1 chains (132 residues) in sequence following loop building ------------------------------------------------------ 8896 reflections ( 99.91 % complete ) and 1410 restraints for refining 1306 atoms. 248 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2598 (Rfree = 0.000) for 1306 atoms. Found 17 (18 requested) and removed 24 (15 requested) atoms. Cycle 22: After refmac, R = 0.2258 (Rfree = 0.000) for 1294 atoms. Found 12 (17 requested) and removed 14 (14 requested) atoms. Cycle 23: After refmac, R = 0.2136 (Rfree = 0.000) for 1291 atoms. Found 7 (16 requested) and removed 14 (14 requested) atoms. Cycle 24: After refmac, R = 0.2083 (Rfree = 0.000) for 1281 atoms. Found 6 (16 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.2103 (Rfree = 0.000) for 1271 atoms. Found 6 (15 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.69 2.62 Round 1: 134 peptides, 6 chains. Longest chain 47 peptides. Score 0.874 Round 2: 138 peptides, 5 chains. Longest chain 48 peptides. Score 0.895 Round 3: 136 peptides, 4 chains. Longest chain 61 peptides. Score 0.903 Round 4: 127 peptides, 8 chains. Longest chain 47 peptides. Score 0.826 Round 5: 130 peptides, 6 chains. Longest chain 31 peptides. Score 0.865 Taking the results from Round 3 Chains 5, Residues 132, Estimated correctness of the model 98.5 % 3 chains (118 residues) have been docked in sequence Building loops using Loopy2018 5 chains (132 residues) following loop building 3 chains (118 residues) in sequence following loop building ------------------------------------------------------ 8896 reflections ( 99.91 % complete ) and 1457 restraints for refining 1246 atoms. 408 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2408 (Rfree = 0.000) for 1246 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. Cycle 27: After refmac, R = 0.2197 (Rfree = 0.000) for 1241 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 28: After refmac, R = 0.2094 (Rfree = 0.000) for 1241 atoms. Found 12 (14 requested) and removed 14 (14 requested) atoms. Cycle 29: After refmac, R = 0.2033 (Rfree = 0.000) for 1237 atoms. Found 11 (14 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.2016 (Rfree = 0.000) for 1233 atoms. Found 10 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.65 2.58 Round 1: 130 peptides, 5 chains. Longest chain 47 peptides. Score 0.878 Round 2: 130 peptides, 5 chains. Longest chain 47 peptides. Score 0.878 Round 3: 129 peptides, 8 chains. Longest chain 31 peptides. Score 0.832 Round 4: 130 peptides, 6 chains. Longest chain 51 peptides. Score 0.865 Round 5: 129 peptides, 8 chains. Longest chain 28 peptides. Score 0.832 Taking the results from Round 2 Chains 6, Residues 125, Estimated correctness of the model 97.6 % 3 chains (105 residues) have been docked in sequence Building loops using Loopy2018 6 chains (125 residues) following loop building 3 chains (105 residues) in sequence following loop building ------------------------------------------------------ 8896 reflections ( 99.91 % complete ) and 1521 restraints for refining 1236 atoms. 554 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2306 (Rfree = 0.000) for 1236 atoms. Found 14 (14 requested) and removed 17 (14 requested) atoms. Cycle 32: After refmac, R = 0.2077 (Rfree = 0.000) for 1233 atoms. Found 9 (14 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.2024 (Rfree = 0.000) for 1226 atoms. Found 7 (14 requested) and removed 14 (14 requested) atoms. Cycle 34: After refmac, R = 0.1994 (Rfree = 0.000) for 1218 atoms. Found 1 (14 requested) and removed 9 (14 requested) atoms. Cycle 35: After refmac, R = 0.1989 (Rfree = 0.000) for 1207 atoms. Found 3 (13 requested) and removed 8 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.66 2.59 Round 1: 132 peptides, 4 chains. Longest chain 47 peptides. Score 0.896 Round 2: 131 peptides, 3 chains. Longest chain 61 peptides. Score 0.906 Round 3: 129 peptides, 5 chains. Longest chain 38 peptides. Score 0.876 Round 4: 127 peptides, 7 chains. Longest chain 30 peptides. Score 0.842 Round 5: 126 peptides, 9 chains. Longest chain 23 peptides. Score 0.806 Taking the results from Round 2 Chains 3, Residues 128, Estimated correctness of the model 98.5 % 3 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 51 A Built loop between residues 87 A and 98 A 1 chains (148 residues) following loop building 1 chains (148 residues) in sequence following loop building ------------------------------------------------------ 8896 reflections ( 99.91 % complete ) and 1335 restraints for refining 1339 atoms. 95 conditional restraints added. Observations/parameters ratio is 1.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2668 (Rfree = 0.000) for 1339 atoms. Found 15 (15 requested) and removed 24 (15 requested) atoms. Cycle 37: After refmac, R = 0.2272 (Rfree = 0.000) for 1326 atoms. Found 15 (15 requested) and removed 19 (15 requested) atoms. Cycle 38: After refmac, R = 0.2119 (Rfree = 0.000) for 1322 atoms. Found 6 (15 requested) and removed 15 (15 requested) atoms. Cycle 39: After refmac, R = 0.2102 (Rfree = 0.000) for 1310 atoms. Found 10 (15 requested) and removed 16 (15 requested) atoms. Cycle 40: After refmac, R = 0.2012 (Rfree = 0.000) for 1304 atoms. Found 8 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.65 2.58 Round 1: 133 peptides, 6 chains. Longest chain 47 peptides. Score 0.872 Round 2: 137 peptides, 6 chains. Longest chain 63 peptides. Score 0.881 Round 3: 128 peptides, 8 chains. Longest chain 49 peptides. Score 0.829 Round 4: 132 peptides, 8 chains. Longest chain 50 peptides. Score 0.841 Round 5: 133 peptides, 7 chains. Longest chain 36 peptides. Score 0.858 Taking the results from Round 2 Chains 7, Residues 131, Estimated correctness of the model 97.7 % 3 chains (105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 50 A 5 chains (134 residues) following loop building 2 chains (113 residues) in sequence following loop building ------------------------------------------------------ 8896 reflections ( 99.91 % complete ) and 1564 restraints for refining 1260 atoms. 533 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2574 (Rfree = 0.000) for 1260 atoms. Found 14 (14 requested) and removed 20 (14 requested) atoms. Cycle 42: After refmac, R = 0.2325 (Rfree = 0.000) for 1251 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 43: After refmac, R = 0.2166 (Rfree = 0.000) for 1250 atoms. Found 13 (14 requested) and removed 14 (14 requested) atoms. Cycle 44: After refmac, R = 0.2066 (Rfree = 0.000) for 1249 atoms. Found 4 (14 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.2051 (Rfree = 0.000) for 1238 atoms. Found 7 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.67 2.60 Round 1: 135 peptides, 5 chains. Longest chain 47 peptides. Score 0.889 Round 2: 137 peptides, 4 chains. Longest chain 70 peptides. Score 0.905 Round 3: 127 peptides, 8 chains. Longest chain 36 peptides. Score 0.826 Round 4: 132 peptides, 7 chains. Longest chain 30 peptides. Score 0.856 Round 5: 136 peptides, 6 chains. Longest chain 48 peptides. Score 0.879 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 133, Estimated correctness of the model 98.5 % 3 chains (118 residues) have been docked in sequence Sequence coverage is 88 % All DUM atoms will be removed Building loops using Loopy2018 5 chains (133 residues) following loop building 3 chains (118 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 8896 reflections ( 99.91 % complete ) and 1042 restraints for refining 1024 atoms. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3310 (Rfree = 0.000) for 1024 atoms. Found 9 (11 requested) and removed 0 (11 requested) atoms. Cycle 47: After refmac, R = 0.3085 (Rfree = 0.000) for 1024 atoms. Found 5 (11 requested) and removed 1 (11 requested) atoms. Cycle 48: After refmac, R = 0.2953 (Rfree = 0.000) for 1024 atoms. Found 3 (11 requested) and removed 3 (11 requested) atoms. Cycle 49: After refmac, R = 0.2920 (Rfree = 0.000) for 1024 atoms. Found 5 (11 requested) and removed 3 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:26 GMT 2018 Job finished. TimeTaking 31.76 Used memory is bytes: 11538344