Sun 23 Dec 22:22:42 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 2oc6-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oc6-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oc6-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-1.8-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/2oc6-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-1.8-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 22:23:44 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/2oc6-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc6-1.8-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 250 and 0 Target number of residues in the AU: 250 Target solvent content: 0.5124 Checking the provided sequence file Detected sequence length: 124 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 248 Adjusted target solvent content: 0.52 Input MTZ file: 2oc6-1.8-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: 3 Cell parameters: 48.794 46.883 64.576 90.000 110.073 90.000 Input sequence file: 2oc6-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.60 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: 60.653 1.751 Wilson plot Bfac: 25.86 21417 reflections ( 85.37 % complete ) and 0 restraints for refining 2217 atoms. Observations/parameters ratio is 2.42 ------------------------------------------------------ Starting model: R = 0.3480 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3017 (Rfree = 0.000) for 2217 atoms. Found 63 (110 requested) and removed 56 (55 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.10 2.04 NCS extension: 0 residues added, 2224 seeds are put forward Round 1: 193 peptides, 18 chains. Longest chain 41 peptides. Score 0.761 Round 2: 224 peptides, 11 chains. Longest chain 49 peptides. Score 0.890 Round 3: 229 peptides, 7 chains. Longest chain 103 peptides. Score 0.923 Round 4: 236 peptides, 5 chains. Longest chain 82 peptides. Score 0.941 Round 5: 237 peptides, 5 chains. Longest chain 82 peptides. Score 0.941 Taking the results from Round 5 Chains 6, Residues 232, Estimated correctness of the model 99.7 % 5 chains (231 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 76 A Built loop between residues 12 B and 15 B Built loop between residues 38 B and 43 B 2 chains (240 residues) following loop building 2 chains (240 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2203 restraints for refining 2237 atoms. 155 conditional restraints added. Observations/parameters ratio is 2.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2818 (Rfree = 0.000) for 2237 atoms. Found 80 (111 requested) and removed 61 (55 requested) atoms. Cycle 2: After refmac, R = 0.2504 (Rfree = 0.000) for 2245 atoms. Found 70 (110 requested) and removed 37 (56 requested) atoms. Cycle 3: After refmac, R = 0.2340 (Rfree = 0.000) for 2264 atoms. Found 52 (108 requested) and removed 25 (56 requested) atoms. Cycle 4: After refmac, R = 0.2224 (Rfree = 0.000) for 2281 atoms. Found 44 (109 requested) and removed 11 (57 requested) atoms. Cycle 5: After refmac, R = 0.2122 (Rfree = 0.000) for 2309 atoms. Found 51 (110 requested) and removed 15 (57 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.02 1.97 NCS extension: 0 residues added, 2348 seeds are put forward Round 1: 244 peptides, 2 chains. Longest chain 122 peptides. Score 0.961 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 245 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 5: 243 peptides, 4 chains. Longest chain 123 peptides. Score 0.951 Taking the results from Round 3 Chains 2, Residues 243, Estimated correctness of the model 99.9 % 2 chains (243 residues) have been docked in sequence Building loops using Loopy2018 2 chains (243 residues) following loop building 2 chains (243 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2187 restraints for refining 2258 atoms. 115 conditional restraints added. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2135 (Rfree = 0.000) for 2258 atoms. Found 92 (108 requested) and removed 39 (56 requested) atoms. Cycle 7: After refmac, R = 0.2041 (Rfree = 0.000) for 2311 atoms. Found 65 (110 requested) and removed 31 (57 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1927 (Rfree = 0.000) for 2343 atoms. Found 53 (112 requested) and removed 22 (58 requested) atoms. Cycle 9: After refmac, R = 0.1869 (Rfree = 0.000) for 2369 atoms. Found 41 (113 requested) and removed 34 (59 requested) atoms. Cycle 10: After refmac, R = 0.1823 (Rfree = 0.000) for 2374 atoms. Found 53 (111 requested) and removed 27 (59 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.02 1.97 NCS extension: 0 residues added, 2400 seeds are put forward Round 1: 245 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 5: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Taking the results from Round 5 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2210 restraints for refining 2298 atoms. 130 conditional restraints added. Observations/parameters ratio is 2.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1992 (Rfree = 0.000) for 2298 atoms. Found 77 (105 requested) and removed 30 (57 requested) atoms. Cycle 12: After refmac, R = 0.1902 (Rfree = 0.000) for 2343 atoms. Found 55 (108 requested) and removed 28 (58 requested) atoms. Cycle 13: After refmac, R = 0.1851 (Rfree = 0.000) for 2368 atoms. Found 56 (106 requested) and removed 24 (59 requested) atoms. Cycle 14: After refmac, R = 0.1802 (Rfree = 0.000) for 2400 atoms. Found 37 (107 requested) and removed 25 (59 requested) atoms. Cycle 15: After refmac, R = 0.1765 (Rfree = 0.000) for 2410 atoms. Found 44 (106 requested) and removed 26 (60 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2429 seeds are put forward Round 1: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 5: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Taking the results from Round 4 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2226 restraints for refining 2324 atoms. 146 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1939 (Rfree = 0.000) for 2324 atoms. Found 82 (100 requested) and removed 30 (58 requested) atoms. Cycle 17: After refmac, R = 0.1873 (Rfree = 0.000) for 2376 atoms. Found 47 (101 requested) and removed 29 (59 requested) atoms. Cycle 18: After refmac, R = 0.1790 (Rfree = 0.000) for 2392 atoms. Found 44 (100 requested) and removed 20 (59 requested) atoms. Cycle 19: After refmac, R = 0.1771 (Rfree = 0.000) for 2414 atoms. Found 43 (101 requested) and removed 34 (60 requested) atoms. Cycle 20: After refmac, R = 0.1736 (Rfree = 0.000) for 2422 atoms. Found 44 (99 requested) and removed 39 (60 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2428 seeds are put forward Round 1: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 4: 246 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 5: 244 peptides, 3 chains. Longest chain 123 peptides. Score 0.956 Taking the results from Round 2 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2220 restraints for refining 2329 atoms. 140 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1948 (Rfree = 0.000) for 2329 atoms. Found 93 (93 requested) and removed 28 (58 requested) atoms. Cycle 22: After refmac, R = 0.1849 (Rfree = 0.000) for 2392 atoms. Found 48 (95 requested) and removed 35 (59 requested) atoms. Cycle 23: After refmac, R = 0.1783 (Rfree = 0.000) for 2402 atoms. Found 57 (94 requested) and removed 24 (60 requested) atoms. Cycle 24: After refmac, R = 0.1768 (Rfree = 0.000) for 2432 atoms. Found 53 (94 requested) and removed 42 (60 requested) atoms. Cycle 25: After refmac, R = 0.1742 (Rfree = 0.000) for 2441 atoms. Found 50 (93 requested) and removed 43 (61 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2449 seeds are put forward Round 1: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 5: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Taking the results from Round 3 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2232 restraints for refining 2336 atoms. 152 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1930 (Rfree = 0.000) for 2336 atoms. Found 79 (86 requested) and removed 29 (58 requested) atoms. Cycle 27: After refmac, R = 0.1827 (Rfree = 0.000) for 2386 atoms. Found 50 (88 requested) and removed 30 (59 requested) atoms. Cycle 28: After refmac, R = 0.1789 (Rfree = 0.000) for 2404 atoms. Found 55 (86 requested) and removed 35 (60 requested) atoms. Cycle 29: After refmac, R = 0.1766 (Rfree = 0.000) for 2422 atoms. Found 48 (85 requested) and removed 44 (60 requested) atoms. Cycle 30: After refmac, R = 0.1764 (Rfree = 0.000) for 2425 atoms. Found 54 (82 requested) and removed 43 (60 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2437 seeds are put forward Round 1: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 4: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 5: 243 peptides, 4 chains. Longest chain 110 peptides. Score 0.951 Taking the results from Round 4 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2212 restraints for refining 2330 atoms. 132 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1931 (Rfree = 0.000) for 2330 atoms. Found 77 (77 requested) and removed 32 (58 requested) atoms. Cycle 32: After refmac, R = 0.1836 (Rfree = 0.000) for 2374 atoms. Found 51 (78 requested) and removed 32 (59 requested) atoms. Cycle 33: After refmac, R = 0.1793 (Rfree = 0.000) for 2390 atoms. Found 57 (76 requested) and removed 28 (59 requested) atoms. Cycle 34: After refmac, R = 0.1759 (Rfree = 0.000) for 2419 atoms. Found 39 (77 requested) and removed 46 (60 requested) atoms. Cycle 35: After refmac, R = 0.1753 (Rfree = 0.000) for 2411 atoms. Found 50 (74 requested) and removed 32 (60 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2430 seeds are put forward Round 1: 244 peptides, 3 chains. Longest chain 123 peptides. Score 0.956 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 4: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 5: 245 peptides, 4 chains. Longest chain 123 peptides. Score 0.952 Taking the results from Round 3 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2219 restraints for refining 2329 atoms. 139 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1942 (Rfree = 0.000) for 2329 atoms. Found 70 (70 requested) and removed 26 (58 requested) atoms. Cycle 37: After refmac, R = 0.1849 (Rfree = 0.000) for 2373 atoms. Found 47 (71 requested) and removed 21 (59 requested) atoms. Cycle 38: After refmac, R = 0.1782 (Rfree = 0.000) for 2399 atoms. Found 43 (71 requested) and removed 28 (59 requested) atoms. Cycle 39: After refmac, R = 0.1774 (Rfree = 0.000) for 2412 atoms. Found 51 (70 requested) and removed 33 (60 requested) atoms. Cycle 40: After refmac, R = 0.1753 (Rfree = 0.000) for 2430 atoms. Found 44 (68 requested) and removed 47 (60 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.02 1.97 NCS extension: 0 residues added, 2428 seeds are put forward Round 1: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 4: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 5: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Taking the results from Round 4 Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2230 restraints for refining 2338 atoms. 150 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1939 (Rfree = 0.000) for 2338 atoms. Found 63 (63 requested) and removed 28 (58 requested) atoms. Cycle 42: After refmac, R = 0.1836 (Rfree = 0.000) for 2371 atoms. Found 49 (64 requested) and removed 18 (59 requested) atoms. Cycle 43: After refmac, R = 0.1785 (Rfree = 0.000) for 2400 atoms. Found 46 (65 requested) and removed 31 (60 requested) atoms. Cycle 44: After refmac, R = 0.1749 (Rfree = 0.000) for 2412 atoms. Found 36 (62 requested) and removed 32 (60 requested) atoms. Cycle 45: After refmac, R = 0.1743 (Rfree = 0.000) for 2412 atoms. Found 50 (60 requested) and removed 27 (60 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.02 1.97 NCS extension: 0 residues added, 2436 seeds are put forward Round 1: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 3: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 4: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 5: 244 peptides, 4 chains. Longest chain 75 peptides. Score 0.951 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 244, Estimated correctness of the model 99.9 % 2 chains (244 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (244 residues) following loop building 2 chains (244 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 21417 reflections ( 85.37 % complete ) and 2080 restraints for refining 2020 atoms. Observations/parameters ratio is 2.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2445 (Rfree = 0.000) for 2020 atoms. Found 36 (50 requested) and removed 0 (50 requested) atoms. Cycle 47: After refmac, R = 0.2283 (Rfree = 0.000) for 2020 atoms. Found 12 (51 requested) and removed 1 (51 requested) atoms. Cycle 48: After refmac, R = 0.2170 (Rfree = 0.000) for 2020 atoms. Found 9 (51 requested) and removed 0 (51 requested) atoms. Cycle 49: After refmac, R = 0.2108 (Rfree = 0.000) for 2020 atoms. Found 4 (51 requested) and removed 2 (51 requested) atoms. Writing output files ... TimeTaking 91.02