Sun 23 Dec 22:22:46 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 1vjf-2.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-2.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjf-2.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-2.6-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/1vjf-2.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-2.6-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 22:22:56 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/1vjf-2.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjf-2.6-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 167 and 0 Target number of residues in the AU: 167 Target solvent content: 0.4254 Checking the provided sequence file Detected sequence length: 180 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 180 Adjusted target solvent content: 0.38 Input MTZ file: 1vjf-2.6-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: 96 Cell parameters: 50.903 50.903 121.411 90.000 90.000 90.000 Input sequence file: 1vjf-2.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1440 target number of atoms Had to go as low as 0.50 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: 46.944 2.600 Wilson plot Bfac: 11.12 5350 reflections ( 99.85 % complete ) and 0 restraints for refining 1608 atoms. Observations/parameters ratio is 0.83 ------------------------------------------------------ Starting model: R = 0.3125 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2376 (Rfree = 0.000) for 1608 atoms. Found 18 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.89 2.22 Round 1: 102 peptides, 17 chains. Longest chain 12 peptides. Score 0.512 Round 2: 125 peptides, 12 chains. Longest chain 21 peptides. Score 0.792 Round 3: 137 peptides, 8 chains. Longest chain 32 peptides. Score 0.890 Round 4: 140 peptides, 9 chains. Longest chain 40 peptides. Score 0.884 Round 5: 144 peptides, 7 chains. Longest chain 55 peptides. Score 0.914 Taking the results from Round 5 Chains 7, Residues 137, Estimated correctness of the model 98.2 % 3 chains (104 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 114 A and 119 A 6 chains (141 residues) following loop building 2 chains (108 residues) in sequence following loop building ------------------------------------------------------ 5350 reflections ( 99.85 % complete ) and 1787 restraints for refining 1367 atoms. 816 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2712 (Rfree = 0.000) for 1367 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 2: After refmac, R = 0.2355 (Rfree = 0.000) for 1358 atoms. Found 18 (22 requested) and removed 12 (11 requested) atoms. Cycle 3: After refmac, R = 0.2221 (Rfree = 0.000) for 1359 atoms. Found 12 (21 requested) and removed 12 (11 requested) atoms. Cycle 4: After refmac, R = 0.2130 (Rfree = 0.000) for 1356 atoms. Found 13 (21 requested) and removed 12 (11 requested) atoms. Cycle 5: After refmac, R = 0.2058 (Rfree = 0.000) for 1353 atoms. Found 7 (19 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.93 2.27 Round 1: 149 peptides, 6 chains. Longest chain 41 peptides. Score 0.931 Round 2: 152 peptides, 7 chains. Longest chain 50 peptides. Score 0.926 Round 3: 146 peptides, 7 chains. Longest chain 41 peptides. Score 0.917 Round 4: 155 peptides, 5 chains. Longest chain 50 peptides. Score 0.946 Round 5: 156 peptides, 7 chains. Longest chain 48 peptides. Score 0.931 Taking the results from Round 4 Chains 5, Residues 150, Estimated correctness of the model 99.2 % 5 chains (150 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 69 A Built loop between residues 75 A and 81 A Built loop between residues 104 A and 107 A Built loop between residues 134 A and 137 A 1 chains (165 residues) following loop building 1 chains (165 residues) in sequence following loop building ------------------------------------------------------ 5350 reflections ( 99.85 % complete ) and 1401 restraints for refining 1428 atoms. 108 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2293 (Rfree = 0.000) for 1428 atoms. Found 18 (21 requested) and removed 17 (11 requested) atoms. Cycle 7: After refmac, R = 0.2039 (Rfree = 0.000) for 1426 atoms. Found 16 (20 requested) and removed 11 (11 requested) atoms. Cycle 8: After refmac, R = 0.1941 (Rfree = 0.000) for 1429 atoms. Found 14 (20 requested) and removed 11 (11 requested) atoms. Cycle 9: After refmac, R = 0.1869 (Rfree = 0.000) for 1428 atoms. Found 11 (19 requested) and removed 11 (11 requested) atoms. Cycle 10: After refmac, R = 0.1804 (Rfree = 0.000) for 1426 atoms. Found 9 (19 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.90 2.24 Round 1: 163 peptides, 4 chains. Longest chain 64 peptides. Score 0.960 Round 2: 165 peptides, 1 chains. Longest chain 165 peptides. Score 0.980 Round 3: 160 peptides, 4 chains. Longest chain 100 peptides. Score 0.958 Round 4: 160 peptides, 5 chains. Longest chain 57 peptides. Score 0.951 Round 5: 162 peptides, 5 chains. Longest chain 63 peptides. Score 0.953 Taking the results from Round 2 Chains 1, Residues 164, Estimated correctness of the model 99.9 % 1 chains (164 residues) have been docked in sequence ------------------------------------------------------ 5350 reflections ( 99.85 % complete ) and 1392 restraints for refining 1393 atoms. 108 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2043 (Rfree = 0.000) for 1393 atoms. Found 18 (18 requested) and removed 14 (11 requested) atoms. Cycle 12: After refmac, R = 0.1904 (Rfree = 0.000) for 1396 atoms. Found 17 (17 requested) and removed 12 (11 requested) atoms. Cycle 13: After refmac, R = 0.1810 (Rfree = 0.000) for 1399 atoms. Found 17 (17 requested) and removed 11 (11 requested) atoms. Cycle 14: After refmac, R = 0.1696 (Rfree = 0.000) for 1402 atoms. Found 12 (16 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.1647 (Rfree = 0.000) for 1401 atoms. Found 14 (16 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.88 2.21 Round 1: 164 peptides, 3 chains. Longest chain 106 peptides. Score 0.967 Round 2: 166 peptides, 2 chains. Longest chain 111 peptides. Score 0.975 Round 3: 162 peptides, 4 chains. Longest chain 63 peptides. Score 0.960 Round 4: 163 peptides, 5 chains. Longest chain 56 peptides. Score 0.954 Round 5: 165 peptides, 4 chains. Longest chain 65 peptides. Score 0.962 Taking the results from Round 2 Chains 3, Residues 164, Estimated correctness of the model 99.8 % 2 chains (163 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 122 A and 125 A 1 chains (165 residues) following loop building 1 chains (165 residues) in sequence following loop building ------------------------------------------------------ 5350 reflections ( 99.85 % complete ) and 1371 restraints for refining 1395 atoms. 78 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1907 (Rfree = 0.000) for 1395 atoms. Found 15 (15 requested) and removed 15 (11 requested) atoms. Cycle 17: After refmac, R = 0.1730 (Rfree = 0.000) for 1394 atoms. Found 15 (15 requested) and removed 11 (11 requested) atoms. Cycle 18: After refmac, R = 0.1659 (Rfree = 0.000) for 1397 atoms. Found 15 (15 requested) and removed 11 (11 requested) atoms. Cycle 19: After refmac, R = 0.1612 (Rfree = 0.000) for 1397 atoms. Found 14 (14 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.1590 (Rfree = 0.000) for 1399 atoms. Found 14 (14 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.85 2.18 Round 1: 164 peptides, 3 chains. Longest chain 125 peptides. Score 0.967 Round 2: 164 peptides, 3 chains. Longest chain 101 peptides. Score 0.967 Round 3: 165 peptides, 3 chains. Longest chain 105 peptides. Score 0.968 Round 4: 163 peptides, 5 chains. Longest chain 63 peptides. Score 0.954 Round 5: 164 peptides, 4 chains. Longest chain 65 peptides. Score 0.961 Taking the results from Round 3 Chains 3, Residues 162, Estimated correctness of the model 99.7 % 3 chains (162 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 116 A and 119 A Built loop between residues 153 A and 156 A 1 chains (166 residues) following loop building 1 chains (166 residues) in sequence following loop building ------------------------------------------------------ 5350 reflections ( 99.85 % complete ) and 1363 restraints for refining 1395 atoms. 62 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1953 (Rfree = 0.000) for 1395 atoms. Found 13 (13 requested) and removed 15 (11 requested) atoms. Cycle 22: After refmac, R = 0.1790 (Rfree = 0.000) for 1393 atoms. Found 13 (13 requested) and removed 11 (11 requested) atoms. Cycle 23: After refmac, R = 0.1737 (Rfree = 0.000) for 1391 atoms. Found 12 (12 requested) and removed 11 (11 requested) atoms. Cycle 24: After refmac, R = 0.1670 (Rfree = 0.000) for 1391 atoms. Found 12 (12 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.1617 (Rfree = 0.000) for 1391 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.91 2.25 Round 1: 165 peptides, 2 chains. Longest chain 124 peptides. Score 0.974 Round 2: 166 peptides, 4 chains. Longest chain 62 peptides. Score 0.962 Round 3: 164 peptides, 2 chains. Longest chain 125 peptides. Score 0.974 Round 4: 152 peptides, 7 chains. Longest chain 49 peptides. Score 0.926 Round 5: 156 peptides, 6 chains. Longest chain 55 peptides. Score 0.940 Taking the results from Round 3 Chains 2, Residues 162, Estimated correctness of the model 99.8 % 2 chains (162 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A 1 chains (164 residues) following loop building 1 chains (164 residues) in sequence following loop building ------------------------------------------------------ 5350 reflections ( 99.85 % complete ) and 1372 restraints for refining 1380 atoms. 86 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1959 (Rfree = 0.000) for 1380 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 27: After refmac, R = 0.1838 (Rfree = 0.000) for 1378 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 28: After refmac, R = 0.1682 (Rfree = 0.000) for 1377 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.1609 (Rfree = 0.000) for 1376 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.1602 (Rfree = 0.000) for 1375 atoms. Found 11 (11 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.88 2.21 Round 1: 165 peptides, 2 chains. Longest chain 125 peptides. Score 0.974 Round 2: 164 peptides, 3 chains. Longest chain 125 peptides. Score 0.967 Round 3: 164 peptides, 3 chains. Longest chain 104 peptides. Score 0.967 Round 4: 162 peptides, 4 chains. Longest chain 61 peptides. Score 0.960 Round 5: 156 peptides, 7 chains. Longest chain 42 peptides. Score 0.931 Taking the results from Round 1 Chains 2, Residues 163, Estimated correctness of the model 99.8 % 2 chains (163 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A 1 chains (165 residues) following loop building 1 chains (165 residues) in sequence following loop building ------------------------------------------------------ 5350 reflections ( 99.85 % complete ) and 1373 restraints for refining 1380 atoms. 80 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1864 (Rfree = 0.000) for 1380 atoms. Found 11 (11 requested) and removed 15 (11 requested) atoms. Cycle 32: After refmac, R = 0.1687 (Rfree = 0.000) for 1376 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.1625 (Rfree = 0.000) for 1374 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 34: After refmac, R = 0.1578 (Rfree = 0.000) for 1373 atoms. Found 11 (11 requested) and removed 9 (11 requested) atoms. Cycle 35: After refmac, R = 0.1563 (Rfree = 0.000) for 1374 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.91 2.25 Round 1: 164 peptides, 2 chains. Longest chain 124 peptides. Score 0.974 Round 2: 164 peptides, 3 chains. Longest chain 104 peptides. Score 0.967 Round 3: 163 peptides, 4 chains. Longest chain 90 peptides. Score 0.960 Round 4: 166 peptides, 1 chains. Longest chain 166 peptides. Score 0.980 Round 5: 165 peptides, 2 chains. Longest chain 159 peptides. Score 0.974 Taking the results from Round 4 Chains 1, Residues 165, Estimated correctness of the model 99.9 % 1 chains (165 residues) have been docked in sequence ------------------------------------------------------ 5350 reflections ( 99.85 % complete ) and 1363 restraints for refining 1383 atoms. 70 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1889 (Rfree = 0.000) for 1383 atoms. Found 11 (11 requested) and removed 13 (11 requested) atoms. Cycle 37: After refmac, R = 0.1704 (Rfree = 0.000) for 1379 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.1663 (Rfree = 0.000) for 1377 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 39: After refmac, R = 0.1585 (Rfree = 0.000) for 1376 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1551 (Rfree = 0.000) for 1376 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.91 2.25 Round 1: 165 peptides, 2 chains. Longest chain 125 peptides. Score 0.974 Round 2: 164 peptides, 3 chains. Longest chain 104 peptides. Score 0.967 Round 3: 161 peptides, 4 chains. Longest chain 62 peptides. Score 0.959 Round 4: 162 peptides, 4 chains. Longest chain 62 peptides. Score 0.960 Round 5: 156 peptides, 5 chains. Longest chain 87 peptides. Score 0.947 Taking the results from Round 1 Chains 2, Residues 163, Estimated correctness of the model 99.8 % 2 chains (163 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A 1 chains (165 residues) following loop building 1 chains (165 residues) in sequence following loop building ------------------------------------------------------ 5350 reflections ( 99.85 % complete ) and 1350 restraints for refining 1377 atoms. 57 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1826 (Rfree = 0.000) for 1377 atoms. Found 11 (11 requested) and removed 13 (11 requested) atoms. Cycle 42: After refmac, R = 0.1652 (Rfree = 0.000) for 1374 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 43: After refmac, R = 0.1643 (Rfree = 0.000) for 1371 atoms. Found 11 (11 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.1593 (Rfree = 0.000) for 1369 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1561 (Rfree = 0.000) for 1369 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.87 2.20 Round 1: 164 peptides, 2 chains. Longest chain 124 peptides. Score 0.974 Round 2: 166 peptides, 1 chains. Longest chain 166 peptides. Score 0.980 Round 3: 161 peptides, 4 chains. Longest chain 101 peptides. Score 0.959 Round 4: 162 peptides, 5 chains. Longest chain 65 peptides. Score 0.953 Round 5: 163 peptides, 3 chains. Longest chain 98 peptides. Score 0.967 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 165, Estimated correctness of the model 99.9 % 1 chains (165 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 5350 reflections ( 99.85 % complete ) and 1293 restraints for refining 1266 atoms. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2248 (Rfree = 0.000) for 1266 atoms. Found 6 (10 requested) and removed 0 (10 requested) atoms. Cycle 47: After refmac, R = 0.2146 (Rfree = 0.000) for 1266 atoms. Found 4 (10 requested) and removed 0 (10 requested) atoms. Cycle 48: After refmac, R = 0.2067 (Rfree = 0.000) for 1266 atoms. Found 2 (10 requested) and removed 0 (10 requested) atoms. Cycle 49: After refmac, R = 0.2073 (Rfree = 0.000) for 1266 atoms. TimeTaking 31.12