null Tue 25 Dec 19:27:55 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 2i8d-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-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/2i8d-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-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 ============================================================ Tue 25 Dec 19:28:04 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/2i8d-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-1.7-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 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-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: 19 Cell parameters: 47.981 69.366 90.889 90.000 90.000 90.000 Input sequence file: 2i8d-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 1968 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 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 2175 atoms. Observations/parameters ratio is 3.04 ------------------------------------------------------ Starting model: R = 0.3340 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2777 (Rfree = 0.000) for 2175 atoms. Found 120 (120 requested) and removed 51 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.90 1.75 NCS extension: 0 residues added, 2244 seeds are put forward Round 1: 202 peptides, 12 chains. Longest chain 37 peptides. Score 0.826 Round 2: 220 peptides, 5 chains. Longest chain 58 peptides. Score 0.912 Round 3: 223 peptides, 5 chains. Longest chain 75 peptides. Score 0.915 Round 4: 224 peptides, 5 chains. Longest chain 71 peptides. Score 0.916 Round 5: 226 peptides, 4 chains. Longest chain 108 peptides. Score 0.924 Taking the results from Round 5 Chains 4, Residues 222, Estimated correctness of the model 99.6 % 3 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 B and 65 B 3 chains (224 residues) following loop building 2 chains (218 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2321 restraints for refining 2206 atoms. 420 conditional restraints added. Observations/parameters ratio is 3.00 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2691 (Rfree = 0.000) for 2206 atoms. Found 96 (122 requested) and removed 47 (61 requested) atoms. Cycle 2: After refmac, R = 0.2304 (Rfree = 0.000) for 2251 atoms. Found 83 (124 requested) and removed 20 (62 requested) atoms. Cycle 3: After refmac, R = 0.2154 (Rfree = 0.000) for 2306 atoms. Found 61 (127 requested) and removed 15 (63 requested) atoms. Cycle 4: After refmac, R = 0.2038 (Rfree = 0.000) for 2344 atoms. Found 63 (129 requested) and removed 24 (64 requested) atoms. Cycle 5: After refmac, R = 0.1961 (Rfree = 0.000) for 2370 atoms. Found 66 (131 requested) and removed 22 (65 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.89 1.74 NCS extension: 1 residues added (2 deleted due to clashes), 2415 seeds are put forward Round 1: 234 peptides, 2 chains. Longest chain 119 peptides. Score 0.943 Round 2: 233 peptides, 3 chains. Longest chain 119 peptides. Score 0.936 Round 3: 234 peptides, 2 chains. Longest chain 119 peptides. Score 0.943 Round 4: 233 peptides, 2 chains. Longest chain 119 peptides. Score 0.942 Round 5: 230 peptides, 2 chains. Longest chain 119 peptides. Score 0.940 Taking the results from Round 3 Chains 2, Residues 232, Estimated correctness of the model 99.8 % 2 chains (232 residues) have been docked in sequence Building loops using Loopy2018 2 chains (232 residues) following loop building 2 chains (232 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2286 restraints for refining 2330 atoms. 276 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2010 (Rfree = 0.000) for 2330 atoms. Found 96 (128 requested) and removed 43 (64 requested) atoms. Cycle 7: After refmac, R = 0.1940 (Rfree = 0.000) for 2377 atoms. Found 73 (131 requested) and removed 25 (65 requested) atoms. Cycle 8: After refmac, R = 0.1868 (Rfree = 0.000) for 2425 atoms. Found 68 (134 requested) and removed 24 (67 requested) atoms. Cycle 9: After refmac, R = 0.1836 (Rfree = 0.000) for 2463 atoms. Found 58 (136 requested) and removed 27 (68 requested) atoms. Cycle 10: After refmac, R = 0.1798 (Rfree = 0.000) for 2489 atoms. Found 67 (137 requested) and removed 27 (68 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.89 1.74 NCS extension: 3 residues added (1 deleted due to clashes), 2532 seeds are put forward Round 1: 234 peptides, 2 chains. Longest chain 119 peptides. Score 0.943 Round 2: 233 peptides, 3 chains. Longest chain 119 peptides. Score 0.936 Round 3: 232 peptides, 3 chains. Longest chain 119 peptides. Score 0.936 Round 4: 235 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 5: 234 peptides, 2 chains. Longest chain 119 peptides. Score 0.943 Taking the results from Round 4 Chains 4, Residues 233, Estimated correctness of the model 99.8 % 2 chains (228 residues) have been docked in sequence Building loops using Loopy2018 4 chains (233 residues) following loop building 2 chains (228 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2340 restraints for refining 2388 atoms. 353 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1935 (Rfree = 0.000) for 2388 atoms. Found 99 (131 requested) and removed 47 (65 requested) atoms. Cycle 12: After refmac, R = 0.1852 (Rfree = 0.000) for 2435 atoms. Found 65 (134 requested) and removed 24 (67 requested) atoms. Cycle 13: After refmac, R = 0.1794 (Rfree = 0.000) for 2469 atoms. Found 57 (136 requested) and removed 30 (68 requested) atoms. Cycle 14: After refmac, R = 0.1773 (Rfree = 0.000) for 2494 atoms. Found 52 (134 requested) and removed 32 (68 requested) atoms. Cycle 15: After refmac, R = 0.1758 (Rfree = 0.000) for 2510 atoms. Found 56 (132 requested) and removed 36 (69 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.89 1.74 NCS extension: 4 residues added (4 deleted due to clashes), 2535 seeds are put forward Round 1: 235 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 2: 232 peptides, 3 chains. Longest chain 119 peptides. Score 0.936 Round 3: 235 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 4: 235 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 5: 237 peptides, 2 chains. Longest chain 119 peptides. Score 0.945 Taking the results from Round 5 Chains 3, Residues 235, Estimated correctness of the model 99.8 % 2 chains (232 residues) have been docked in sequence Building loops using Loopy2018 3 chains (235 residues) following loop building 2 chains (232 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2325 restraints for refining 2400 atoms. 304 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1911 (Rfree = 0.000) for 2400 atoms. Found 96 (124 requested) and removed 43 (66 requested) atoms. Cycle 17: After refmac, R = 0.1855 (Rfree = 0.000) for 2448 atoms. Found 59 (127 requested) and removed 40 (67 requested) atoms. Cycle 18: After refmac, R = 0.1801 (Rfree = 0.000) for 2461 atoms. Found 69 (125 requested) and removed 23 (68 requested) atoms. Cycle 19: After refmac, R = 0.1797 (Rfree = 0.000) for 2502 atoms. Found 60 (127 requested) and removed 27 (69 requested) atoms. Cycle 20: After refmac, R = 0.1792 (Rfree = 0.000) for 2529 atoms. Found 52 (129 requested) and removed 30 (70 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.90 1.75 NCS extension: 0 residues added, 2552 seeds are put forward Round 1: 234 peptides, 3 chains. Longest chain 119 peptides. Score 0.937 Round 2: 236 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 3: 235 peptides, 2 chains. Longest chain 120 peptides. Score 0.944 Round 4: 235 peptides, 3 chains. Longest chain 120 peptides. Score 0.938 Round 5: 232 peptides, 3 chains. Longest chain 119 peptides. Score 0.936 Taking the results from Round 3 Chains 3, Residues 233, Estimated correctness of the model 99.8 % 3 chains (233 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 B and 43 B 2 chains (234 residues) following loop building 2 chains (234 residues) in sequence following loop building ------------------------------------------------------ 26455 reflections ( 99.69 % complete ) and 2299 restraints for refining 2423 atoms. 262 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1946 (Rfree = 0.000) for 2423 atoms. Found 98 (120 requested) and removed 45 (66 requested) atoms. Cycle 22: After refmac, R = 0.1871 (Rfree = 0.000) for 2471 atoms. Found 69 (122 requested) and removed 34 (68 requested) atoms. Cycle 23: After refmac, R = 0.1822 (Rfree = 0.000) for 2497 atoms. Found 61 (124 requested) and removed 20 (69 requested) atoms. Cycle 24: After refmac, R = 0.1797 (Rfree = 0.000) for 2535 atoms. Found 52 (126 requested) and removed 38 (70 requested) atoms. Cycle 25: After refmac, R = 0.1770 (Rfree = 0.000) for 2542 atoms. Found 64 (123 requested) and removed 25 (70 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.89 1.74 NCS extension: 2 residues added (1 deleted due to clashes), 2584 seeds are put forward Round 1: 233 peptides, 4 chains. Longest chain 120 peptides. Score 0.930 Round 2: 235 peptides, 3 chains. Longest chain 120 peptides. Score 0.938 Round 3: 235 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 Round 4: 238 peptides, 2 chains. Longest chain 120 peptides. Score 0.946 Round 5: 236 peptides, 2 chains. Longest chain 119 peptides. Score 0.944 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 2356 restraints for refining 2433 atoms. 324 conditional restraints added. Observations/parameters ratio is 2.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1902 (Rfree = 0.000) for 2433 atoms. Found 85 (118 requested) and removed 45 (67 requested) atoms. Cycle 27: After refmac, R = 0.1833 (Rfree = 0.000) for 2467 atoms. Found 56 (117 requested) and removed 27 (68 requested) atoms. Cycle 28: After refmac, R = 0.1771 (Rfree = 0.000) for 2493 atoms. Found 52 (118 requested) and removed 12 (68 requested) atoms. Cycle 29: After refmac, R = 0.1742 (Rfree = 0.000) for 2530 atoms. Found 54 (120 requested) and removed 33 (69 requested) atoms. Cycle 30: After refmac, R = 0.1741 (Rfree = 0.000) for 2548 atoms. Found 61 (118 requested) and removed 33 (70 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.89 1.74 NCS extension: 0 residues added (3 deleted due to clashes), 2576 seeds are put forward Round 1: 237 peptides, 3 chains. Longest chain 120 peptides. Score 0.940 Round 2: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 3: 236 peptides, 4 chains. Longest chain 120 peptides. Score 0.933 Round 4: 237 peptides, 3 chains. Longest chain 120 peptides. Score 0.940 Round 5: 237 peptides, 3 chains. Longest chain 120 peptides. Score 0.940 Taking the results from Round 2 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 2321 restraints for refining 2419 atoms. 275 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1888 (Rfree = 0.000) for 2419 atoms. Found 109 (109 requested) and removed 45 (66 requested) atoms. Cycle 32: After refmac, R = 0.1835 (Rfree = 0.000) for 2480 atoms. Found 74 (112 requested) and removed 37 (68 requested) atoms. Cycle 33: After refmac, R = 0.1788 (Rfree = 0.000) for 2514 atoms. Found 66 (114 requested) and removed 47 (69 requested) atoms. Cycle 34: After refmac, R = 0.1776 (Rfree = 0.000) for 2527 atoms. Found 63 (111 requested) and removed 42 (69 requested) atoms. Cycle 35: After refmac, R = 0.1768 (Rfree = 0.000) for 2545 atoms. Found 63 (109 requested) and removed 45 (70 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.90 1.75 NCS extension: 0 residues added, 2563 seeds are put forward Round 1: 235 peptides, 4 chains. Longest chain 120 peptides. Score 0.932 Round 2: 236 peptides, 3 chains. Longest chain 120 peptides. Score 0.939 Round 3: 237 peptides, 2 chains. Longest chain 120 peptides. Score 0.945 Round 4: 236 peptides, 3 chains. Longest chain 120 peptides. Score 0.939 Round 5: 236 peptides, 3 chains. Longest chain 120 peptides. Score 0.939 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 2335 restraints for refining 2436 atoms. 289 conditional restraints added. Observations/parameters ratio is 2.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1892 (Rfree = 0.000) for 2436 atoms. Found 102 (102 requested) and removed 45 (67 requested) atoms. Cycle 37: After refmac, R = 0.1859 (Rfree = 0.000) for 2488 atoms. Found 69 (104 requested) and removed 35 (68 requested) atoms. Cycle 38: After refmac, R = 0.1793 (Rfree = 0.000) for 2519 atoms. Found 61 (103 requested) and removed 29 (69 requested) atoms. Cycle 39: After refmac, R = 0.1774 (Rfree = 0.000) for 2546 atoms. Found 51 (104 requested) and removed 36 (70 requested) atoms. Cycle 40: After refmac, R = 0.1752 (Rfree = 0.000) for 2554 atoms. Found 64 (102 requested) and removed 35 (70 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.88 1.73 NCS extension: 0 residues added, 2583 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: 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: 236 peptides, 3 chains. Longest chain 120 peptides. Score 0.939 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 2334 restraints for refining 2425 atoms. 302 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1910 (Rfree = 0.000) for 2425 atoms. Found 93 (94 requested) and removed 50 (67 requested) atoms. Cycle 42: After refmac, R = 0.1864 (Rfree = 0.000) for 2464 atoms. Found 54 (92 requested) and removed 40 (68 requested) atoms. Cycle 43: After refmac, R = 0.1792 (Rfree = 0.000) for 2472 atoms. Found 59 (90 requested) and removed 22 (68 requested) atoms. Cycle 44: After refmac, R = 0.1798 (Rfree = 0.000) for 2504 atoms. Found 49 (91 requested) and removed 33 (69 requested) atoms. Cycle 45: After refmac, R = 0.1790 (Rfree = 0.000) for 2516 atoms. Found 49 (89 requested) and removed 33 (69 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.90 1.75 NCS extension: 0 residues added (3 deleted due to clashes), 2533 seeds are put forward Round 1: 233 peptides, 3 chains. Longest chain 120 peptides. Score 0.936 Round 2: 234 peptides, 2 chains. Longest chain 120 peptides. Score 0.943 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: 233 peptides, 3 chains. Longest chain 120 peptides. Score 0.936 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 232, Estimated correctness of the model 99.8 % 2 chains (232 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (232 residues) following loop building 2 chains (232 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 26455 reflections ( 99.69 % complete ) and 2012 restraints for refining 1948 atoms. Observations/parameters ratio is 3.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2638 (Rfree = 0.000) for 1948 atoms. Found 66 (66 requested) and removed 0 (66 requested) atoms. Cycle 47: After refmac, R = 0.2369 (Rfree = 0.000) for 1948 atoms. Found 44 (69 requested) and removed 1 (55 requested) atoms. Cycle 48: After refmac, R = 0.2216 (Rfree = 0.000) for 1948 atoms. Found 25 (70 requested) and removed 0 (56 requested) atoms. Cycle 49: After refmac, R = 0.2122 (Rfree = 0.000) for 1948 atoms. Found 14 (71 requested) and removed 4 (57 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:15:58 GMT 2018 Job finished. TimeTaking 48.06 Used memory is bytes: 3101512