null Mon 24 Dec 08:03:06 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i8d-1.7-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-1.7-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-1.7-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-parrot-noncs ############### 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 08:03:11 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/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 1968 target number of atoms Had to go as low as 0.40 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 2192 atoms. Observations/parameters ratio is 3.02 ------------------------------------------------------ Starting model: R = 0.3245 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2743 (Rfree = 0.000) for 2192 atoms. Found 121 (121 requested) and removed 53 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.92 1.77 NCS extension: 0 residues added, 2260 seeds are put forward Round 1: 213 peptides, 13 chains. Longest chain 46 peptides. Score 0.837 Round 2: 233 peptides, 4 chains. Longest chain 120 peptides. Score 0.930 Round 3: 236 peptides, 4 chains. Longest chain 90 peptides. Score 0.933 Round 4: 236 peptides, 4 chains. Longest chain 114 peptides. Score 0.933 Round 5: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Taking the results from Round 5 Chains 2, Residues 236, Estimated correctness of the model 99.8 % 2 chains (236 residues) have been docked in sequence Building loops using Loopy2018 2 chains (236 residues) following loop building 2 chains (236 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2249 restraints for refining 2247 atoms. 198 conditional restraints added. Observations/parameters ratio is 2.94 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2682 (Rfree = 0.000) for 2247 atoms. Found 94 (124 requested) and removed 64 (62 requested) atoms. Cycle 2: After refmac, R = 0.2311 (Rfree = 0.000) for 2270 atoms. Found 77 (122 requested) and removed 22 (62 requested) atoms. Cycle 3: After refmac, R = 0.2152 (Rfree = 0.000) for 2314 atoms. Found 74 (125 requested) and removed 12 (64 requested) atoms. Cycle 4: After refmac, R = 0.2041 (Rfree = 0.000) for 2371 atoms. Found 50 (128 requested) and removed 32 (65 requested) atoms. Cycle 5: After refmac, R = 0.1969 (Rfree = 0.000) for 2384 atoms. Found 72 (127 requested) and removed 19 (66 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added, 2437 seeds are put forward Round 1: 235 peptides, 3 chains. Longest chain 119 peptides. Score 0.938 Round 2: 232 peptides, 2 chains. Longest chain 119 peptides. Score 0.941 Round 3: 234 peptides, 3 chains. Longest chain 119 peptides. Score 0.937 Round 4: 236 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 5: 235 peptides, 3 chains. Longest chain 119 peptides. Score 0.938 Taking the results from Round 4 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 2288 restraints for refining 2341 atoms. 253 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2040 (Rfree = 0.000) for 2341 atoms. Found 85 (124 requested) and removed 48 (64 requested) atoms. Cycle 7: After refmac, R = 0.1948 (Rfree = 0.000) for 2372 atoms. Found 79 (123 requested) and removed 23 (65 requested) atoms. Cycle 8: After refmac, R = 0.1893 (Rfree = 0.000) for 2423 atoms. Found 56 (126 requested) and removed 31 (67 requested) atoms. Cycle 9: After refmac, R = 0.1841 (Rfree = 0.000) for 2444 atoms. Found 59 (124 requested) and removed 16 (67 requested) atoms. Cycle 10: After refmac, R = 0.1847 (Rfree = 0.000) for 2481 atoms. Found 52 (126 requested) and removed 34 (68 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added, 2499 seeds are put forward Round 1: 234 peptides, 3 chains. Longest chain 120 peptides. Score 0.937 Round 2: 235 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 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: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Taking the results from Round 5 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 2294 restraints for refining 2381 atoms. 248 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1968 (Rfree = 0.000) for 2381 atoms. Found 91 (118 requested) and removed 33 (65 requested) atoms. Cycle 12: After refmac, R = 0.1933 (Rfree = 0.000) for 2429 atoms. Found 65 (121 requested) and removed 38 (67 requested) atoms. Cycle 13: After refmac, R = 0.1872 (Rfree = 0.000) for 2453 atoms. Found 72 (119 requested) and removed 26 (67 requested) atoms. Cycle 14: After refmac, R = 0.1860 (Rfree = 0.000) for 2494 atoms. Found 42 (121 requested) and removed 36 (69 requested) atoms. Cycle 15: After refmac, R = 0.1819 (Rfree = 0.000) for 2493 atoms. Found 69 (119 requested) and removed 31 (69 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added, 2532 seeds are put forward Round 1: 232 peptides, 4 chains. Longest chain 120 peptides. Score 0.930 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, 4 chains. Longest chain 120 peptides. Score 0.932 Taking the results from Round 4 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 2374 restraints for refining 2399 atoms. 353 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1938 (Rfree = 0.000) for 2399 atoms. Found 99 (114 requested) and removed 38 (66 requested) atoms. Cycle 17: After refmac, R = 0.1888 (Rfree = 0.000) for 2452 atoms. Found 63 (116 requested) and removed 30 (67 requested) atoms. Cycle 18: After refmac, R = 0.1822 (Rfree = 0.000) for 2482 atoms. Found 55 (118 requested) and removed 16 (68 requested) atoms. Cycle 19: After refmac, R = 0.1793 (Rfree = 0.000) for 2517 atoms. Found 42 (120 requested) and removed 33 (69 requested) atoms. Cycle 20: After refmac, R = 0.1781 (Rfree = 0.000) for 2517 atoms. Found 56 (117 requested) and removed 30 (69 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added (3 deleted due to clashes), 2544 seeds are put forward Round 1: 233 peptides, 4 chains. Longest chain 120 peptides. Score 0.930 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: 234 peptides, 3 chains. Longest chain 120 peptides. Score 0.937 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 2348 restraints for refining 2397 atoms. 327 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1936 (Rfree = 0.000) for 2397 atoms. Found 87 (108 requested) and removed 46 (66 requested) atoms. Cycle 22: After refmac, R = 0.1860 (Rfree = 0.000) for 2434 atoms. Found 71 (107 requested) and removed 27 (67 requested) atoms. Cycle 23: After refmac, R = 0.1820 (Rfree = 0.000) for 2475 atoms. Found 63 (109 requested) and removed 32 (68 requested) atoms. Cycle 24: After refmac, R = 0.1809 (Rfree = 0.000) for 2503 atoms. Found 53 (108 requested) and removed 38 (69 requested) atoms. Cycle 25: After refmac, R = 0.1790 (Rfree = 0.000) for 2514 atoms. Found 63 (106 requested) and removed 39 (69 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.88 1.73 NCS extension: 0 residues added (3 deleted due to clashes), 2539 seeds are put forward Round 1: 233 peptides, 2 chains. Longest chain 120 peptides. Score 0.942 Round 2: 236 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Round 3: 234 peptides, 2 chains. Longest chain 120 peptides. Score 0.943 Round 4: 234 peptides, 2 chains. Longest chain 120 peptides. Score 0.943 Round 5: 234 peptides, 3 chains. Longest chain 120 peptides. Score 0.937 Taking the results from Round 2 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 2300 restraints for refining 2409 atoms. 263 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1946 (Rfree = 0.000) for 2409 atoms. Found 98 (98 requested) and removed 47 (66 requested) atoms. Cycle 27: After refmac, R = 0.1873 (Rfree = 0.000) for 2453 atoms. Found 66 (100 requested) and removed 42 (67 requested) atoms. Cycle 28: After refmac, R = 0.1832 (Rfree = 0.000) for 2471 atoms. Found 55 (98 requested) and removed 26 (68 requested) atoms. Cycle 29: After refmac, R = 0.1808 (Rfree = 0.000) for 2493 atoms. Found 58 (99 requested) and removed 34 (69 requested) atoms. Cycle 30: After refmac, R = 0.1801 (Rfree = 0.000) for 2509 atoms. Found 51 (97 requested) and removed 38 (69 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.89 1.74 NCS extension: 2 residues added (1 deleted due to clashes), 2525 seeds are put forward Round 1: 236 peptides, 3 chains. Longest chain 120 peptides. Score 0.939 Round 2: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 3: 237 peptides, 3 chains. Longest chain 120 peptides. Score 0.940 Round 4: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 5: 232 peptides, 3 chains. Longest chain 120 peptides. Score 0.936 Taking the results from Round 4 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 2337 restraints for refining 2402 atoms. 305 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1934 (Rfree = 0.000) for 2402 atoms. Found 90 (90 requested) and removed 42 (66 requested) atoms. Cycle 32: After refmac, R = 0.1859 (Rfree = 0.000) for 2444 atoms. Found 47 (92 requested) and removed 22 (67 requested) atoms. Cycle 33: After refmac, R = 0.1814 (Rfree = 0.000) for 2467 atoms. Found 43 (92 requested) and removed 20 (68 requested) atoms. Cycle 34: After refmac, R = 0.1773 (Rfree = 0.000) for 2489 atoms. Found 33 (93 requested) and removed 27 (68 requested) atoms. Cycle 35: After refmac, R = 0.1763 (Rfree = 0.000) for 2488 atoms. Found 46 (90 requested) and removed 27 (68 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added (3 deleted due to clashes), 2508 seeds are put forward Round 1: 234 peptides, 3 chains. Longest chain 120 peptides. Score 0.937 Round 2: 235 peptides, 3 chains. Longest chain 120 peptides. Score 0.938 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 2317 restraints for refining 2401 atoms. 271 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1922 (Rfree = 0.000) for 2401 atoms. Found 84 (84 requested) and removed 46 (66 requested) atoms. Cycle 37: After refmac, R = 0.1860 (Rfree = 0.000) for 2436 atoms. Found 50 (83 requested) and removed 37 (67 requested) atoms. Cycle 38: After refmac, R = 0.1808 (Rfree = 0.000) for 2447 atoms. Found 62 (81 requested) and removed 18 (67 requested) atoms. Cycle 39: After refmac, R = 0.1786 (Rfree = 0.000) for 2489 atoms. Found 36 (82 requested) and removed 37 (68 requested) atoms. Cycle 40: After refmac, R = 0.1760 (Rfree = 0.000) for 2481 atoms. Found 70 (79 requested) and removed 20 (68 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.88 1.73 NCS extension: 0 residues added, 2531 seeds are put forward Round 1: 234 peptides, 4 chains. Longest chain 120 peptides. Score 0.931 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, 2 chains. Longest chain 120 peptides. Score 0.944 Round 5: 236 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Taking the results from Round 5 Chains 3, Residues 234, Estimated correctness of the model 99.8 % 2 chains (233 residues) have been docked in sequence Building loops using Loopy2018 3 chains (234 residues) following loop building 3 chains (234 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2342 restraints for refining 2387 atoms. 318 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1914 (Rfree = 0.000) for 2387 atoms. Found 76 (76 requested) and removed 50 (65 requested) atoms. Cycle 42: After refmac, R = 0.1852 (Rfree = 0.000) for 2405 atoms. Found 65 (74 requested) and removed 31 (66 requested) atoms. Cycle 43: After refmac, R = 0.1799 (Rfree = 0.000) for 2438 atoms. Found 65 (75 requested) and removed 23 (67 requested) atoms. Cycle 44: After refmac, R = 0.1772 (Rfree = 0.000) for 2480 atoms. Found 47 (77 requested) and removed 31 (68 requested) atoms. Cycle 45: After refmac, R = 0.1753 (Rfree = 0.000) for 2489 atoms. Found 56 (74 requested) and removed 32 (68 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added (4 deleted due to clashes), 2514 seeds are put forward Round 1: 236 peptides, 3 chains. Longest chain 120 peptides. Score 0.939 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: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 5: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 235, Estimated correctness of the model 99.8 % 2 chains (235 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (235 residues) following loop building 2 chains (235 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 26455 reflections ( 99.69 % complete ) and 2046 restraints for refining 1980 atoms. Observations/parameters ratio is 3.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2589 (Rfree = 0.000) for 1980 atoms. Found 57 (57 requested) and removed 0 (57 requested) atoms. Cycle 47: After refmac, R = 0.2352 (Rfree = 0.000) for 1980 atoms. Found 58 (58 requested) and removed 1 (56 requested) atoms. Cycle 48: After refmac, R = 0.2168 (Rfree = 0.000) for 1980 atoms. Found 24 (60 requested) and removed 2 (57 requested) atoms. Cycle 49: After refmac, R = 0.2080 (Rfree = 0.000) for 1980 atoms. Found 8 (60 requested) and removed 2 (58 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:39:54 GMT 2018 Job finished. TimeTaking 36.81 Used memory is bytes: 521536