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 2etd-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etd-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etd-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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/2etd-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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 22:23:18 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/2etd-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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 160 and 0 Target number of residues in the AU: 160 Target solvent content: 0.5267 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-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: 21 Cell parameters: 80.417 85.225 53.388 90.000 90.000 90.000 Input sequence file: 2etd-2.3-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 1 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 2.280 Wilson plot Bfac: 29.32 8217 reflections ( 94.54 % complete ) and 0 restraints for refining 1517 atoms. Observations/parameters ratio is 1.35 ------------------------------------------------------ Starting model: R = 0.3791 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3271 (Rfree = 0.000) for 1517 atoms. Found 16 (35 requested) and removed 33 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.25 2.28 Round 1: 87 peptides, 15 chains. Longest chain 12 peptides. Score 0.423 Round 2: 93 peptides, 12 chains. Longest chain 21 peptides. Score 0.571 Round 3: 103 peptides, 10 chains. Longest chain 22 peptides. Score 0.689 Round 4: 110 peptides, 12 chains. Longest chain 31 peptides. Score 0.676 Round 5: 118 peptides, 11 chains. Longest chain 31 peptides. Score 0.739 Taking the results from Round 5 Chains 13, Residues 107, Estimated correctness of the model 90.8 % 3 chains (55 residues) have been docked in sequence Building loops using Loopy2018 13 chains (107 residues) following loop building 3 chains (55 residues) in sequence following loop building ------------------------------------------------------ 8217 reflections ( 94.54 % complete ) and 2134 restraints for refining 1299 atoms. 1486 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3758 (Rfree = 0.000) for 1299 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 2: After refmac, R = 0.3494 (Rfree = 0.000) for 1297 atoms. Found 13 (29 requested) and removed 19 (15 requested) atoms. Cycle 3: After refmac, R = 0.3341 (Rfree = 0.000) for 1269 atoms. Found 9 (29 requested) and removed 16 (15 requested) atoms. Cycle 4: After refmac, R = 0.3196 (Rfree = 0.000) for 1258 atoms. Found 11 (27 requested) and removed 16 (14 requested) atoms. Cycle 5: After refmac, R = 0.3103 (Rfree = 0.000) for 1245 atoms. Found 10 (27 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.26 2.29 Round 1: 107 peptides, 9 chains. Longest chain 27 peptides. Score 0.733 Round 2: 114 peptides, 7 chains. Longest chain 32 peptides. Score 0.803 Round 3: 114 peptides, 7 chains. Longest chain 51 peptides. Score 0.803 Round 4: 114 peptides, 7 chains. Longest chain 47 peptides. Score 0.803 Round 5: 117 peptides, 5 chains. Longest chain 51 peptides. Score 0.848 Taking the results from Round 5 Chains 6, Residues 112, Estimated correctness of the model 96.6 % 2 chains (83 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 94 A and 99 A 4 chains (115 residues) following loop building 1 chains (87 residues) in sequence following loop building ------------------------------------------------------ 8217 reflections ( 94.54 % complete ) and 1696 restraints for refining 1271 atoms. 910 conditional restraints added. Observations/parameters ratio is 1.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3315 (Rfree = 0.000) for 1271 atoms. Found 15 (27 requested) and removed 20 (15 requested) atoms. Cycle 7: After refmac, R = 0.3078 (Rfree = 0.000) for 1252 atoms. Found 7 (26 requested) and removed 14 (14 requested) atoms. Cycle 8: After refmac, R = 0.2935 (Rfree = 0.000) for 1241 atoms. Found 14 (25 requested) and removed 14 (14 requested) atoms. Cycle 9: After refmac, R = 0.2862 (Rfree = 0.000) for 1240 atoms. Found 8 (24 requested) and removed 14 (14 requested) atoms. Cycle 10: After refmac, R = 0.2788 (Rfree = 0.000) for 1234 atoms. Found 16 (24 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.28 2.31 Round 1: 117 peptides, 6 chains. Longest chain 63 peptides. Score 0.831 Round 2: 118 peptides, 6 chains. Longest chain 83 peptides. Score 0.834 Round 3: 120 peptides, 6 chains. Longest chain 85 peptides. Score 0.841 Round 4: 119 peptides, 6 chains. Longest chain 74 peptides. Score 0.838 Round 5: 120 peptides, 4 chains. Longest chain 105 peptides. Score 0.872 Taking the results from Round 5 Chains 4, Residues 116, Estimated correctness of the model 97.5 % 1 chains (104 residues) have been docked in sequence ------------------------------------------------------ 8217 reflections ( 94.54 % complete ) and 1549 restraints for refining 1280 atoms. 684 conditional restraints added. Observations/parameters ratio is 1.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2999 (Rfree = 0.000) for 1280 atoms. Found 24 (24 requested) and removed 17 (15 requested) atoms. Cycle 12: After refmac, R = 0.2772 (Rfree = 0.000) for 1284 atoms. Found 19 (23 requested) and removed 15 (15 requested) atoms. Cycle 13: After refmac, R = 0.2646 (Rfree = 0.000) for 1279 atoms. Found 21 (23 requested) and removed 15 (15 requested) atoms. Cycle 14: After refmac, R = 0.2524 (Rfree = 0.000) for 1283 atoms. Found 21 (22 requested) and removed 15 (15 requested) atoms. Cycle 15: After refmac, R = 0.2414 (Rfree = 0.000) for 1287 atoms. Found 15 (22 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.23 2.26 Round 1: 121 peptides, 4 chains. Longest chain 88 peptides. Score 0.874 Round 2: 122 peptides, 3 chains. Longest chain 113 peptides. Score 0.890 Round 3: 123 peptides, 3 chains. Longest chain 113 peptides. Score 0.893 Round 4: 121 peptides, 6 chains. Longest chain 51 peptides. Score 0.843 Round 5: 125 peptides, 4 chains. Longest chain 90 peptides. Score 0.883 Taking the results from Round 3 Chains 4, Residues 120, Estimated correctness of the model 98.2 % 1 chains (109 residues) have been docked in sequence ------------------------------------------------------ 8217 reflections ( 94.54 % complete ) and 1479 restraints for refining 1299 atoms. 575 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2618 (Rfree = 0.000) for 1299 atoms. Found 21 (21 requested) and removed 16 (15 requested) atoms. Cycle 17: After refmac, R = 0.2415 (Rfree = 0.000) for 1302 atoms. Found 20 (20 requested) and removed 15 (15 requested) atoms. Cycle 18: After refmac, R = 0.2350 (Rfree = 0.000) for 1305 atoms. Found 20 (20 requested) and removed 15 (15 requested) atoms. Cycle 19: After refmac, R = 0.2260 (Rfree = 0.000) for 1310 atoms. Found 16 (19 requested) and removed 15 (15 requested) atoms. Cycle 20: After refmac, R = 0.2244 (Rfree = 0.000) for 1310 atoms. Found 13 (19 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.23 2.26 Round 1: 122 peptides, 3 chains. Longest chain 113 peptides. Score 0.890 Round 2: 122 peptides, 4 chains. Longest chain 100 peptides. Score 0.876 Round 3: 123 peptides, 4 chains. Longest chain 95 peptides. Score 0.879 Round 4: 125 peptides, 3 chains. Longest chain 96 peptides. Score 0.897 Round 5: 123 peptides, 5 chains. Longest chain 84 peptides. Score 0.864 Taking the results from Round 4 Chains 5, Residues 122, Estimated correctness of the model 98.3 % 2 chains (115 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 111 A 3 chains (124 residues) following loop building 1 chains (118 residues) in sequence following loop building ------------------------------------------------------ 8217 reflections ( 94.54 % complete ) and 1391 restraints for refining 1299 atoms. 436 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2573 (Rfree = 0.000) for 1299 atoms. Found 18 (18 requested) and removed 17 (15 requested) atoms. Cycle 22: After refmac, R = 0.2326 (Rfree = 0.000) for 1300 atoms. Found 17 (17 requested) and removed 15 (15 requested) atoms. Cycle 23: After refmac, R = 0.2221 (Rfree = 0.000) for 1302 atoms. Found 9 (17 requested) and removed 15 (15 requested) atoms. Cycle 24: After refmac, R = 0.2180 (Rfree = 0.000) for 1296 atoms. Found 14 (16 requested) and removed 14 (15 requested) atoms. Cycle 25: After refmac, R = 0.2155 (Rfree = 0.000) for 1296 atoms. Found 13 (16 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.24 2.27 Round 1: 126 peptides, 2 chains. Longest chain 121 peptides. Score 0.911 Round 2: 126 peptides, 2 chains. Longest chain 121 peptides. Score 0.911 Round 3: 126 peptides, 3 chains. Longest chain 108 peptides. Score 0.899 Round 4: 124 peptides, 4 chains. Longest chain 60 peptides. Score 0.881 Round 5: 123 peptides, 5 chains. Longest chain 61 peptides. Score 0.864 Taking the results from Round 2 Chains 2, Residues 124, Estimated correctness of the model 98.7 % 1 chains (120 residues) have been docked in sequence ------------------------------------------------------ 8217 reflections ( 94.54 % complete ) and 1360 restraints for refining 1299 atoms. 394 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2429 (Rfree = 0.000) for 1299 atoms. Found 15 (15 requested) and removed 16 (15 requested) atoms. Cycle 27: After refmac, R = 0.2238 (Rfree = 0.000) for 1298 atoms. Found 12 (15 requested) and removed 15 (15 requested) atoms. Cycle 28: After refmac, R = 0.2145 (Rfree = 0.000) for 1294 atoms. Found 7 (15 requested) and removed 14 (15 requested) atoms. Cycle 29: After refmac, R = 0.2116 (Rfree = 0.000) for 1286 atoms. Found 15 (15 requested) and removed 6 (15 requested) atoms. Cycle 30: After refmac, R = 0.2087 (Rfree = 0.000) for 1294 atoms. Found 9 (15 requested) and removed 14 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.23 2.26 Round 1: 129 peptides, 3 chains. Longest chain 107 peptides. Score 0.905 Round 2: 131 peptides, 2 chains. Longest chain 126 peptides. Score 0.920 Round 3: 128 peptides, 3 chains. Longest chain 117 peptides. Score 0.903 Round 4: 131 peptides, 3 chains. Longest chain 88 peptides. Score 0.908 Round 5: 128 peptides, 4 chains. Longest chain 56 peptides. Score 0.890 Taking the results from Round 2 Chains 3, Residues 129, Estimated correctness of the model 98.9 % 1 chains (124 residues) have been docked in sequence ------------------------------------------------------ 8217 reflections ( 94.54 % complete ) and 1303 restraints for refining 1299 atoms. 301 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2381 (Rfree = 0.000) for 1299 atoms. Found 15 (15 requested) and removed 16 (15 requested) atoms. Cycle 32: After refmac, R = 0.2187 (Rfree = 0.000) for 1295 atoms. Found 15 (15 requested) and removed 15 (15 requested) atoms. Cycle 33: After refmac, R = 0.2118 (Rfree = 0.000) for 1295 atoms. Found 14 (15 requested) and removed 15 (15 requested) atoms. Cycle 34: After refmac, R = 0.2070 (Rfree = 0.000) for 1293 atoms. Found 14 (15 requested) and removed 10 (15 requested) atoms. Cycle 35: After refmac, R = 0.2043 (Rfree = 0.000) for 1296 atoms. Found 14 (15 requested) and removed 12 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.22 2.25 Round 1: 130 peptides, 3 chains. Longest chain 121 peptides. Score 0.906 Round 2: 132 peptides, 2 chains. Longest chain 126 peptides. Score 0.921 Round 3: 128 peptides, 3 chains. Longest chain 110 peptides. Score 0.903 Round 4: 128 peptides, 4 chains. Longest chain 64 peptides. Score 0.890 Round 5: 131 peptides, 4 chains. Longest chain 81 peptides. Score 0.896 Taking the results from Round 2 Chains 3, Residues 130, Estimated correctness of the model 99.0 % 1 chains (124 residues) have been docked in sequence ------------------------------------------------------ 8217 reflections ( 94.54 % complete ) and 1290 restraints for refining 1299 atoms. 284 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2320 (Rfree = 0.000) for 1299 atoms. Found 15 (15 requested) and removed 16 (15 requested) atoms. Cycle 37: After refmac, R = 0.2155 (Rfree = 0.000) for 1298 atoms. Found 15 (15 requested) and removed 15 (15 requested) atoms. Cycle 38: After refmac, R = 0.2060 (Rfree = 0.000) for 1298 atoms. Found 10 (15 requested) and removed 13 (15 requested) atoms. Cycle 39: After refmac, R = 0.2047 (Rfree = 0.000) for 1294 atoms. Found 15 (15 requested) and removed 9 (15 requested) atoms. Cycle 40: After refmac, R = 0.2037 (Rfree = 0.000) for 1300 atoms. Found 13 (15 requested) and removed 10 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.24 2.27 Round 1: 132 peptides, 3 chains. Longest chain 121 peptides. Score 0.910 Round 2: 133 peptides, 3 chains. Longest chain 70 peptides. Score 0.912 Round 3: 132 peptides, 4 chains. Longest chain 110 peptides. Score 0.898 Round 4: 134 peptides, 2 chains. Longest chain 126 peptides. Score 0.925 Round 5: 135 peptides, 2 chains. Longest chain 126 peptides. Score 0.926 Taking the results from Round 5 Chains 3, Residues 133, Estimated correctness of the model 99.1 % 1 chains (124 residues) have been docked in sequence ------------------------------------------------------ 8217 reflections ( 94.54 % complete ) and 1308 restraints for refining 1299 atoms. 290 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2354 (Rfree = 0.000) for 1299 atoms. Found 15 (15 requested) and removed 16 (15 requested) atoms. Cycle 42: After refmac, R = 0.2170 (Rfree = 0.000) for 1298 atoms. Found 13 (15 requested) and removed 15 (15 requested) atoms. Cycle 43: After refmac, R = 0.2100 (Rfree = 0.000) for 1295 atoms. Found 15 (15 requested) and removed 14 (15 requested) atoms. Cycle 44: After refmac, R = 0.2040 (Rfree = 0.000) for 1296 atoms. Found 15 (15 requested) and removed 14 (15 requested) atoms. Cycle 45: After refmac, R = 0.2019 (Rfree = 0.000) for 1297 atoms. Found 15 (15 requested) and removed 12 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.25 2.28 Round 1: 135 peptides, 2 chains. Longest chain 126 peptides. Score 0.926 Round 2: 133 peptides, 4 chains. Longest chain 56 peptides. Score 0.900 Round 3: 134 peptides, 3 chains. Longest chain 71 peptides. Score 0.914 Round 4: 132 peptides, 5 chains. Longest chain 97 peptides. Score 0.886 Round 5: 135 peptides, 3 chains. Longest chain 98 peptides. Score 0.915 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 133, Estimated correctness of the model 99.1 % 1 chains (125 residues) have been docked in sequence Sequence coverage is 93 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 8217 reflections ( 94.54 % complete ) and 1023 restraints for refining 1015 atoms. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3006 (Rfree = 0.000) for 1015 atoms. Found 6 (11 requested) and removed 0 (11 requested) atoms. Cycle 47: After refmac, R = 0.2855 (Rfree = 0.000) for 1015 atoms. Found 4 (12 requested) and removed 0 (12 requested) atoms. Cycle 48: After refmac, R = 0.2766 (Rfree = 0.000) for 1015 atoms. Found 5 (12 requested) and removed 2 (12 requested) atoms. Cycle 49: After refmac, R = 0.2731 (Rfree = 0.000) for 1015 atoms. Found 2 (12 requested) and removed 2 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:57 GMT 2018 Job finished. TimeTaking 28.83 Used memory is bytes: 10479136