null Mon 24 Dec 00:12:52 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 2i8d-1.7-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-1.7-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-1.7-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-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/2i8d-1.7-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-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 00:12:57 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/2i8d-1.7-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-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 287 and 0 Target number of residues in the AU: 287 Target solvent content: 0.4865 Checking the provided sequence file Detected sequence length: 123 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 246 Adjusted target solvent content: 0.56 Input MTZ file: 2i8d-1.7-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: 19 Cell parameters: 47.981 69.366 90.889 90.000 90.000 90.000 Input sequence file: 2i8d-1.7-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1968 target number of atoms Had to go as low as 0.45 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: 55.142 1.691 Wilson plot Bfac: 20.57 26455 reflections ( 99.69 % complete ) and 0 restraints for refining 2173 atoms. Observations/parameters ratio is 3.04 ------------------------------------------------------ Starting model: R = 0.3336 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2748 (Rfree = 0.000) for 2173 atoms. Found 120 (120 requested) and removed 59 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.92 1.77 NCS extension: 0 residues added, 2234 seeds are put forward Round 1: 219 peptides, 15 chains. Longest chain 38 peptides. Score 0.829 Round 2: 225 peptides, 7 chains. Longest chain 67 peptides. Score 0.903 Round 3: 234 peptides, 6 chains. Longest chain 120 peptides. Score 0.919 Round 4: 237 peptides, 3 chains. Longest chain 120 peptides. Score 0.940 Round 5: 238 peptides, 3 chains. Longest chain 120 peptides. Score 0.940 Taking the results from Round 5 Chains 4, Residues 235, Estimated correctness of the model 99.8 % 3 chains (232 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 58 B and 62 B 3 chains (238 residues) following loop building 2 chains (235 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2222 restraints for refining 2238 atoms. 177 conditional restraints added. Observations/parameters ratio is 2.96 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2669 (Rfree = 0.000) for 2238 atoms. Found 87 (123 requested) and removed 55 (61 requested) atoms. Cycle 2: After refmac, R = 0.2273 (Rfree = 0.000) for 2266 atoms. Found 93 (122 requested) and removed 25 (62 requested) atoms. Cycle 3: After refmac, R = 0.2127 (Rfree = 0.000) for 2327 atoms. Found 81 (125 requested) and removed 32 (64 requested) atoms. Cycle 4: After refmac, R = 0.2007 (Rfree = 0.000) for 2374 atoms. Found 79 (128 requested) and removed 22 (65 requested) atoms. Cycle 5: After refmac, R = 0.1947 (Rfree = 0.000) for 2426 atoms. Found 71 (131 requested) and removed 37 (67 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.88 1.73 NCS extension: 0 residues added (3 deleted due to clashes), 2464 seeds are put forward Round 1: 236 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 2: 236 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 3: 236 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 4: 236 peptides, 4 chains. Longest chain 119 peptides. Score 0.933 Round 5: 238 peptides, 2 chains. Longest chain 119 peptides. Score 0.946 Taking the results from Round 5 Chains 4, Residues 236, Estimated correctness of the model 99.8 % 3 chains (232 residues) have been docked in sequence Building loops using Loopy2018 4 chains (236 residues) following loop building 3 chains (232 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2295 restraints for refining 2341 atoms. 282 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2062 (Rfree = 0.000) for 2341 atoms. Found 96 (124 requested) and removed 55 (64 requested) atoms. Cycle 7: After refmac, R = 0.1963 (Rfree = 0.000) for 2379 atoms. Found 73 (123 requested) and removed 31 (65 requested) atoms. Cycle 8: After refmac, R = 0.1912 (Rfree = 0.000) for 2415 atoms. Found 71 (125 requested) and removed 31 (66 requested) atoms. Cycle 9: After refmac, R = 0.1882 (Rfree = 0.000) for 2453 atoms. Found 75 (127 requested) and removed 37 (67 requested) atoms. Cycle 10: After refmac, R = 0.1850 (Rfree = 0.000) for 2483 atoms. Found 67 (129 requested) and removed 51 (68 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.89 1.74 NCS extension: 15 residues added (107 deleted due to clashes), 2516 seeds are put forward Round 1: 239 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 2: 239 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 3: 239 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 4: 239 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 5: 239 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Taking the results from Round 5 Chains 2, Residues 237, Estimated correctness of the model 99.8 % 2 chains (237 residues) have been docked in sequence Building loops using Loopy2018 2 chains (237 residues) following loop building 2 chains (237 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2264 restraints for refining 2382 atoms. 205 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1940 (Rfree = 0.000) for 2382 atoms. Found 106 (121 requested) and removed 48 (65 requested) atoms. Cycle 12: After refmac, R = 0.1906 (Rfree = 0.000) for 2435 atoms. Found 59 (123 requested) and removed 50 (67 requested) atoms. Cycle 13: After refmac, R = 0.1847 (Rfree = 0.000) for 2438 atoms. Found 73 (121 requested) and removed 34 (67 requested) atoms. Cycle 14: After refmac, R = 0.1816 (Rfree = 0.000) for 2475 atoms. Found 61 (122 requested) and removed 33 (68 requested) atoms. Cycle 15: After refmac, R = 0.1794 (Rfree = 0.000) for 2499 atoms. Found 58 (121 requested) and removed 34 (69 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added, 2525 seeds are put forward Round 1: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 2: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 3: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 4: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 5: 236 peptides, 3 chains. Longest chain 120 peptides. Score 0.939 Taking the results from Round 2 Chains 3, Residues 236, Estimated correctness of the model 99.8 % 2 chains (233 residues) have been docked in sequence Building loops using Loopy2018 3 chains (236 residues) following loop building 2 chains (233 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2315 restraints for refining 2395 atoms. 283 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1938 (Rfree = 0.000) for 2395 atoms. Found 104 (114 requested) and removed 46 (66 requested) atoms. Cycle 17: After refmac, R = 0.1901 (Rfree = 0.000) for 2450 atoms. Found 67 (116 requested) and removed 50 (67 requested) atoms. Cycle 18: After refmac, R = 0.1863 (Rfree = 0.000) for 2464 atoms. Found 61 (114 requested) and removed 39 (68 requested) atoms. Cycle 19: After refmac, R = 0.1815 (Rfree = 0.000) for 2483 atoms. Found 56 (112 requested) and removed 41 (68 requested) atoms. Cycle 20: After refmac, R = 0.1825 (Rfree = 0.000) for 2496 atoms. Found 67 (110 requested) and removed 39 (69 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added (3 deleted due to clashes), 2525 seeds are put forward Round 1: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 2: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 3: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 4: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 5: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Taking the results from Round 5 Chains 3, Residues 236, Estimated correctness of the model 99.8 % 2 chains (233 residues) have been docked in sequence Building loops using Loopy2018 3 chains (236 residues) following loop building 2 chains (233 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2307 restraints for refining 2385 atoms. 275 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1947 (Rfree = 0.000) for 2385 atoms. Found 94 (102 requested) and removed 46 (65 requested) atoms. Cycle 22: After refmac, R = 0.1888 (Rfree = 0.000) for 2430 atoms. Found 57 (105 requested) and removed 42 (67 requested) atoms. Cycle 23: After refmac, R = 0.1845 (Rfree = 0.000) for 2442 atoms. Found 57 (103 requested) and removed 26 (67 requested) atoms. Cycle 24: After refmac, R = 0.1820 (Rfree = 0.000) for 2469 atoms. Found 58 (103 requested) and removed 31 (68 requested) atoms. Cycle 25: After refmac, R = 0.1794 (Rfree = 0.000) for 2491 atoms. Found 51 (101 requested) and removed 27 (68 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added (3 deleted due to clashes), 2516 seeds are put forward Round 1: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 2: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 3: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 4: 235 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Round 5: 235 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Taking the results from Round 3 Chains 2, Residues 235, Estimated correctness of the model 99.8 % 2 chains (235 residues) have been docked in sequence Building loops using Loopy2018 2 chains (235 residues) following loop building 2 chains (235 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2298 restraints for refining 2394 atoms. 252 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1962 (Rfree = 0.000) for 2394 atoms. Found 95 (95 requested) and removed 52 (66 requested) atoms. Cycle 27: After refmac, R = 0.1889 (Rfree = 0.000) for 2432 atoms. Found 63 (94 requested) and removed 36 (67 requested) atoms. Cycle 28: After refmac, R = 0.1857 (Rfree = 0.000) for 2455 atoms. Found 57 (92 requested) and removed 33 (67 requested) atoms. Cycle 29: After refmac, R = 0.1812 (Rfree = 0.000) for 2473 atoms. Found 52 (90 requested) and removed 26 (68 requested) atoms. Cycle 30: After refmac, R = 0.1784 (Rfree = 0.000) for 2494 atoms. Found 54 (91 requested) and removed 31 (69 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added, 2517 seeds are put forward Round 1: 234 peptides, 3 chains. Longest chain 120 peptides. Score 0.937 Round 2: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 3: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 4: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 5: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Taking the results from Round 5 Chains 3, Residues 236, Estimated correctness of the model 99.8 % 2 chains (233 residues) have been docked in sequence Building loops using Loopy2018 3 chains (236 residues) following loop building 2 chains (233 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2317 restraints for refining 2400 atoms. 285 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1947 (Rfree = 0.000) for 2400 atoms. Found 84 (84 requested) and removed 44 (66 requested) atoms. Cycle 32: After refmac, R = 0.1868 (Rfree = 0.000) for 2434 atoms. Found 68 (83 requested) and removed 19 (67 requested) atoms. Cycle 33: After refmac, R = 0.1835 (Rfree = 0.000) for 2480 atoms. Found 53 (85 requested) and removed 25 (68 requested) atoms. Cycle 34: After refmac, R = 0.1810 (Rfree = 0.000) for 2504 atoms. Found 44 (86 requested) and removed 28 (69 requested) atoms. Cycle 35: After refmac, R = 0.1771 (Rfree = 0.000) for 2517 atoms. Found 40 (83 requested) and removed 28 (69 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added (3 deleted due to clashes), 2530 seeds are put forward Round 1: 235 peptides, 3 chains. Longest chain 120 peptides. Score 0.938 Round 2: 236 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Round 3: 236 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Round 4: 236 peptides, 3 chains. Longest chain 120 peptides. Score 0.939 Round 5: 236 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Taking the results from Round 5 Chains 2, Residues 234, Estimated correctness of the model 99.8 % 2 chains (234 residues) have been docked in sequence Building loops using Loopy2018 2 chains (234 residues) following loop building 2 chains (234 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2313 restraints for refining 2398 atoms. 276 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1940 (Rfree = 0.000) for 2398 atoms. Found 77 (77 requested) and removed 47 (66 requested) atoms. Cycle 37: After refmac, R = 0.1848 (Rfree = 0.000) for 2424 atoms. Found 54 (75 requested) and removed 18 (67 requested) atoms. Cycle 38: After refmac, R = 0.1808 (Rfree = 0.000) for 2456 atoms. Found 55 (76 requested) and removed 18 (67 requested) atoms. Cycle 39: After refmac, R = 0.1781 (Rfree = 0.000) for 2491 atoms. Found 45 (77 requested) and removed 34 (68 requested) atoms. Cycle 40: After refmac, R = 0.1768 (Rfree = 0.000) for 2500 atoms. Found 43 (75 requested) and removed 31 (69 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added (3 deleted due to clashes), 2512 seeds are put forward Round 1: 234 peptides, 2 chains. Longest chain 120 peptides. Score 0.943 Round 2: 235 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Round 3: 235 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Round 4: 235 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Round 5: 235 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Taking the results from Round 5 Chains 2, Residues 233, Estimated correctness of the model 99.8 % 2 chains (233 residues) have been docked in sequence Building loops using Loopy2018 2 chains (233 residues) following loop building 2 chains (233 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2344 restraints for refining 2395 atoms. 323 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1941 (Rfree = 0.000) for 2395 atoms. Found 69 (69 requested) and removed 39 (66 requested) atoms. Cycle 42: After refmac, R = 0.1863 (Rfree = 0.000) for 2424 atoms. Found 67 (67 requested) and removed 22 (67 requested) atoms. Cycle 43: After refmac, R = 0.1842 (Rfree = 0.000) for 2465 atoms. Found 52 (68 requested) and removed 30 (68 requested) atoms. Cycle 44: After refmac, R = 0.1817 (Rfree = 0.000) for 2483 atoms. Found 62 (68 requested) and removed 27 (68 requested) atoms. Cycle 45: After refmac, R = 0.1805 (Rfree = 0.000) for 2515 atoms. Found 60 (69 requested) and removed 43 (69 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added (3 deleted due to clashes), 2532 seeds are put forward Round 1: 235 peptides, 3 chains. Longest chain 120 peptides. Score 0.938 Round 2: 235 peptides, 3 chains. Longest chain 120 peptides. Score 0.938 Round 3: 233 peptides, 2 chains. Longest chain 120 peptides. Score 0.942 Round 4: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 5: 234 peptides, 2 chains. Longest chain 120 peptides. Score 0.943 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 235, Estimated correctness of the model 99.8 % 2 chains (233 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 3 chains (235 residues) following loop building 2 chains (233 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 26455 reflections ( 99.69 % complete ) and 2035 restraints for refining 1970 atoms. Observations/parameters ratio is 3.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2587 (Rfree = 0.000) for 1970 atoms. Found 54 (54 requested) and removed 0 (54 requested) atoms. Cycle 47: After refmac, R = 0.2340 (Rfree = 0.000) for 1970 atoms. Found 55 (55 requested) and removed 1 (55 requested) atoms. Cycle 48: After refmac, R = 0.2164 (Rfree = 0.000) for 1970 atoms. Found 25 (57 requested) and removed 1 (57 requested) atoms. Cycle 49: After refmac, R = 0.2070 (Rfree = 0.000) for 1970 atoms. Found 14 (58 requested) and removed 2 (58 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:52:59 GMT 2018 Job finished. TimeTaking 40.12 Used memory is bytes: 16901928