null Mon 24 Dec 01:01:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fzt-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fzt-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fzt-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 01:01:12 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-parrot-mrncs/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 165 and 0 Target number of residues in the AU: 165 Target solvent content: 0.4860 Checking the provided sequence file Detected sequence length: 79 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 158 Adjusted target solvent content: 0.51 Input MTZ file: 2fzt-2.0-parrot-mrncs.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: 4 Cell parameters: 49.630 27.430 65.380 90.000 102.600 90.000 Input sequence file: 2fzt-2.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1264 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 63.805 2.000 Wilson plot Bfac: 20.33 11159 reflections ( 99.79 % complete ) and 0 restraints for refining 1391 atoms. Observations/parameters ratio is 2.01 ------------------------------------------------------ Starting model: R = 0.3478 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2945 (Rfree = 0.000) for 1391 atoms. Found 47 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.99 1.96 NCS extension: 0 residues added, 1415 seeds are put forward Round 1: 108 peptides, 16 chains. Longest chain 13 peptides. Score 0.565 Round 2: 141 peptides, 8 chains. Longest chain 45 peptides. Score 0.877 Round 3: 146 peptides, 6 chains. Longest chain 48 peptides. Score 0.910 Round 4: 147 peptides, 4 chains. Longest chain 51 peptides. Score 0.931 Round 5: 149 peptides, 6 chains. Longest chain 59 peptides. Score 0.915 Taking the results from Round 4 Chains 7, Residues 143, Estimated correctness of the model 99.5 % 4 chains (139 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 52 A Built loop between residues 53 B and 58 B 3 chains (149 residues) following loop building 2 chains (147 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1440 restraints for refining 1424 atoms. 196 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2982 (Rfree = 0.000) for 1424 atoms. Found 33 (48 requested) and removed 24 (24 requested) atoms. Cycle 2: After refmac, R = 0.2737 (Rfree = 0.000) for 1427 atoms. Found 30 (48 requested) and removed 25 (24 requested) atoms. Cycle 3: After refmac, R = 0.2585 (Rfree = 0.000) for 1430 atoms. Found 31 (47 requested) and removed 24 (24 requested) atoms. Cycle 4: After refmac, R = 0.2456 (Rfree = 0.000) for 1435 atoms. Found 39 (46 requested) and removed 19 (24 requested) atoms. Cycle 5: After refmac, R = 0.2354 (Rfree = 0.000) for 1451 atoms. Found 36 (46 requested) and removed 20 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.92 1.89 NCS extension: 0 residues added, 1468 seeds are put forward Round 1: 153 peptides, 2 chains. Longest chain 79 peptides. Score 0.955 Round 2: 153 peptides, 4 chains. Longest chain 76 peptides. Score 0.939 Round 3: 154 peptides, 4 chains. Longest chain 77 peptides. Score 0.940 Round 4: 150 peptides, 6 chains. Longest chain 50 peptides. Score 0.916 Round 5: 151 peptides, 4 chains. Longest chain 78 peptides. Score 0.936 Taking the results from Round 1 Chains 3, Residues 151, Estimated correctness of the model 99.8 % 2 chains (147 residues) have been docked in sequence Building loops using Loopy2018 3 chains (151 residues) following loop building 2 chains (147 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1457 restraints for refining 1462 atoms. 203 conditional restraints added. Observations/parameters ratio is 1.91 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2401 (Rfree = 0.000) for 1462 atoms. Found 46 (46 requested) and removed 25 (25 requested) atoms. Cycle 7: After refmac, R = 0.2287 (Rfree = 0.000) for 1481 atoms. Found 29 (45 requested) and removed 15 (25 requested) atoms. Cycle 8: After refmac, R = 0.2194 (Rfree = 0.000) for 1495 atoms. Found 26 (45 requested) and removed 13 (25 requested) atoms. Cycle 9: After refmac, R = 0.2141 (Rfree = 0.000) for 1507 atoms. Found 31 (45 requested) and removed 17 (25 requested) atoms. Cycle 10: After refmac, R = 0.2079 (Rfree = 0.000) for 1520 atoms. Found 32 (45 requested) and removed 14 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.93 1.90 NCS extension: 4 residues added (3 deleted due to clashes), 1542 seeds are put forward Round 1: 157 peptides, 2 chains. Longest chain 79 peptides. Score 0.959 Round 2: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 3: 151 peptides, 4 chains. Longest chain 78 peptides. Score 0.936 Round 4: 157 peptides, 2 chains. Longest chain 79 peptides. Score 0.959 Round 5: 148 peptides, 8 chains. Longest chain 36 peptides. Score 0.892 Taking the results from Round 4 Chains 3, Residues 155, Estimated correctness of the model 99.8 % 2 chains (151 residues) have been docked in sequence Building loops using Loopy2018 3 chains (155 residues) following loop building 2 chains (151 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1395 restraints for refining 1493 atoms. 109 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2233 (Rfree = 0.000) for 1493 atoms. Found 44 (44 requested) and removed 25 (25 requested) atoms. Cycle 12: After refmac, R = 0.2149 (Rfree = 0.000) for 1509 atoms. Found 35 (43 requested) and removed 21 (25 requested) atoms. Cycle 13: After refmac, R = 0.2083 (Rfree = 0.000) for 1522 atoms. Found 24 (43 requested) and removed 14 (26 requested) atoms. Cycle 14: After refmac, R = 0.2026 (Rfree = 0.000) for 1531 atoms. Found 29 (42 requested) and removed 14 (26 requested) atoms. Cycle 15: After refmac, R = 0.2003 (Rfree = 0.000) for 1544 atoms. Found 24 (42 requested) and removed 19 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.94 1.91 NCS extension: 2 residues added (1 deleted due to clashes), 1551 seeds are put forward Round 1: 157 peptides, 2 chains. Longest chain 79 peptides. Score 0.959 Round 2: 156 peptides, 3 chains. Longest chain 78 peptides. Score 0.950 Round 3: 148 peptides, 6 chains. Longest chain 55 peptides. Score 0.913 Round 4: 155 peptides, 4 chains. Longest chain 56 peptides. Score 0.941 Round 5: 154 peptides, 5 chains. Longest chain 71 peptides. Score 0.931 Taking the results from Round 1 Chains 3, Residues 155, Estimated correctness of the model 99.8 % 2 chains (151 residues) have been docked in sequence Building loops using Loopy2018 3 chains (155 residues) following loop building 2 chains (151 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1403 restraints for refining 1521 atoms. 117 conditional restraints added. Observations/parameters ratio is 1.83 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2135 (Rfree = 0.000) for 1521 atoms. Found 35 (41 requested) and removed 26 (26 requested) atoms. Cycle 17: After refmac, R = 0.2029 (Rfree = 0.000) for 1529 atoms. Found 34 (40 requested) and removed 10 (26 requested) atoms. Cycle 18: After refmac, R = 0.1983 (Rfree = 0.000) for 1552 atoms. Found 26 (40 requested) and removed 18 (26 requested) atoms. Cycle 19: After refmac, R = 0.1961 (Rfree = 0.000) for 1557 atoms. Found 36 (39 requested) and removed 21 (26 requested) atoms. Cycle 20: After refmac, R = 0.1941 (Rfree = 0.000) for 1572 atoms. Found 27 (38 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.94 1.91 NCS extension: 2 residues added (1 deleted due to clashes), 1575 seeds are put forward Round 1: 157 peptides, 2 chains. Longest chain 79 peptides. Score 0.959 Round 2: 155 peptides, 3 chains. Longest chain 78 peptides. Score 0.949 Round 3: 151 peptides, 7 chains. Longest chain 56 peptides. Score 0.908 Round 4: 156 peptides, 4 chains. Longest chain 60 peptides. Score 0.942 Round 5: 153 peptides, 5 chains. Longest chain 78 peptides. Score 0.930 Taking the results from Round 1 Chains 3, Residues 155, Estimated correctness of the model 99.8 % 2 chains (151 residues) have been docked in sequence Building loops using Loopy2018 3 chains (155 residues) following loop building 2 chains (151 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1412 restraints for refining 1527 atoms. 126 conditional restraints added. Observations/parameters ratio is 1.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2083 (Rfree = 0.000) for 1527 atoms. Found 36 (36 requested) and removed 28 (26 requested) atoms. Cycle 22: After refmac, R = 0.2008 (Rfree = 0.000) for 1531 atoms. Found 31 (35 requested) and removed 10 (26 requested) atoms. Cycle 23: After refmac, R = 0.1951 (Rfree = 0.000) for 1550 atoms. Found 22 (36 requested) and removed 12 (26 requested) atoms. Cycle 24: After refmac, R = 0.1926 (Rfree = 0.000) for 1558 atoms. Found 27 (35 requested) and removed 11 (26 requested) atoms. Cycle 25: After refmac, R = 0.1906 (Rfree = 0.000) for 1574 atoms. Found 22 (35 requested) and removed 14 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.93 1.90 NCS extension: 2 residues added (1 deleted due to clashes), 1584 seeds are put forward Round 1: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Round 2: 153 peptides, 5 chains. Longest chain 61 peptides. Score 0.930 Round 3: 151 peptides, 7 chains. Longest chain 39 peptides. Score 0.908 Round 4: 153 peptides, 5 chains. Longest chain 61 peptides. Score 0.930 Round 5: 154 peptides, 3 chains. Longest chain 78 peptides. Score 0.948 Taking the results from Round 1 Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1434 restraints for refining 1534 atoms. 157 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2082 (Rfree = 0.000) for 1534 atoms. Found 33 (33 requested) and removed 27 (26 requested) atoms. Cycle 27: After refmac, R = 0.1965 (Rfree = 0.000) for 1538 atoms. Found 32 (32 requested) and removed 8 (26 requested) atoms. Cycle 28: After refmac, R = 0.1929 (Rfree = 0.000) for 1562 atoms. Found 20 (33 requested) and removed 13 (26 requested) atoms. Cycle 29: After refmac, R = 0.1901 (Rfree = 0.000) for 1568 atoms. Found 28 (32 requested) and removed 19 (26 requested) atoms. Cycle 30: After refmac, R = 0.1893 (Rfree = 0.000) for 1576 atoms. Found 31 (31 requested) and removed 20 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.93 1.90 NCS extension: 0 residues added, 1587 seeds are put forward Round 1: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Round 2: 154 peptides, 6 chains. Longest chain 61 peptides. Score 0.922 Round 3: 155 peptides, 3 chains. Longest chain 78 peptides. Score 0.949 Round 4: 146 peptides, 8 chains. Longest chain 39 peptides. Score 0.888 Round 5: 153 peptides, 5 chains. Longest chain 78 peptides. Score 0.930 Taking the results from Round 1 Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1419 restraints for refining 1520 atoms. 142 conditional restraints added. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2072 (Rfree = 0.000) for 1520 atoms. Found 29 (29 requested) and removed 27 (26 requested) atoms. Cycle 32: After refmac, R = 0.1987 (Rfree = 0.000) for 1521 atoms. Found 28 (28 requested) and removed 9 (26 requested) atoms. Cycle 33: After refmac, R = 0.1948 (Rfree = 0.000) for 1540 atoms. Found 28 (28 requested) and removed 16 (26 requested) atoms. Cycle 34: After refmac, R = 0.1919 (Rfree = 0.000) for 1551 atoms. Found 28 (28 requested) and removed 12 (26 requested) atoms. Cycle 35: After refmac, R = 0.1894 (Rfree = 0.000) for 1567 atoms. Found 28 (28 requested) and removed 15 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.93 1.90 NCS extension: 0 residues added, 1580 seeds are put forward Round 1: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 2: 153 peptides, 3 chains. Longest chain 76 peptides. Score 0.947 Round 3: 148 peptides, 6 chains. Longest chain 78 peptides. Score 0.913 Round 4: 151 peptides, 5 chains. Longest chain 56 peptides. Score 0.927 Round 5: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Taking the results from Round 5 Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1431 restraints for refining 1526 atoms. 154 conditional restraints added. Observations/parameters ratio is 1.83 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2075 (Rfree = 0.000) for 1526 atoms. Found 26 (26 requested) and removed 26 (26 requested) atoms. Cycle 37: After refmac, R = 0.1973 (Rfree = 0.000) for 1524 atoms. Found 26 (26 requested) and removed 5 (26 requested) atoms. Cycle 38: After refmac, R = 0.1921 (Rfree = 0.000) for 1544 atoms. Found 26 (26 requested) and removed 13 (26 requested) atoms. Cycle 39: After refmac, R = 0.1872 (Rfree = 0.000) for 1556 atoms. Found 23 (26 requested) and removed 12 (26 requested) atoms. Cycle 40: After refmac, R = 0.1863 (Rfree = 0.000) for 1566 atoms. Found 22 (26 requested) and removed 14 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.92 1.89 NCS extension: 0 residues added, 1574 seeds are put forward Round 1: 156 peptides, 3 chains. Longest chain 79 peptides. Score 0.950 Round 2: 155 peptides, 3 chains. Longest chain 78 peptides. Score 0.949 Round 3: 149 peptides, 6 chains. Longest chain 56 peptides. Score 0.915 Round 4: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 5: 153 peptides, 5 chains. Longest chain 78 peptides. Score 0.930 Taking the results from Round 1 Chains 4, Residues 153, Estimated correctness of the model 99.7 % 2 chains (137 residues) have been docked in sequence Building loops using Loopy2018 4 chains (153 residues) following loop building 2 chains (137 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1567 restraints for refining 1536 atoms. 350 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2077 (Rfree = 0.000) for 1536 atoms. Found 26 (26 requested) and removed 26 (26 requested) atoms. Cycle 42: After refmac, R = 0.1969 (Rfree = 0.000) for 1535 atoms. Found 26 (26 requested) and removed 3 (26 requested) atoms. Cycle 43: After refmac, R = 0.1899 (Rfree = 0.000) for 1558 atoms. Found 21 (26 requested) and removed 10 (26 requested) atoms. Cycle 44: After refmac, R = 0.1866 (Rfree = 0.000) for 1569 atoms. Found 21 (26 requested) and removed 13 (26 requested) atoms. Cycle 45: After refmac, R = 0.1848 (Rfree = 0.000) for 1576 atoms. Found 27 (27 requested) and removed 14 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.92 1.89 NCS extension: 2 residues added (15 deleted due to clashes), 1591 seeds are put forward Round 1: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Round 2: 152 peptides, 4 chains. Longest chain 76 peptides. Score 0.938 Round 3: 151 peptides, 7 chains. Longest chain 61 peptides. Score 0.908 Round 4: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 5: 152 peptides, 6 chains. Longest chain 68 peptides. Score 0.919 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 11159 reflections ( 99.79 % complete ) and 1277 restraints for refining 1273 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2723 (Rfree = 0.000) for 1273 atoms. Found 13 (21 requested) and removed 0 (21 requested) atoms. Cycle 47: After refmac, R = 0.2608 (Rfree = 0.000) for 1273 atoms. Found 5 (22 requested) and removed 0 (22 requested) atoms. Cycle 48: After refmac, R = 0.2540 (Rfree = 0.000) for 1273 atoms. Found 1 (22 requested) and removed 0 (22 requested) atoms. Cycle 49: After refmac, R = 0.2510 (Rfree = 0.000) for 1273 atoms. Found 2 (22 requested) and removed 0 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:25:20 GMT 2018 Job finished. TimeTaking 24.2 Used memory is bytes: 4379568