Mon 24 Dec 00:30:28 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 2oc6-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oc6-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oc6-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oc6-1.8-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/2oc6-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oc6-1.8-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 00:30:32 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/2oc6-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oc6-1.8-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 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-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: 3 Cell parameters: 48.794 46.883 64.576 90.000 110.073 90.000 Input sequence file: 2oc6-1.8-parrot-mrncs.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 2218 atoms. Observations/parameters ratio is 2.41 ------------------------------------------------------ Starting model: R = 0.3501 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3004 (Rfree = 0.000) for 2218 atoms. Found 68 (110 requested) and removed 57 (55 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.08 2.03 NCS extension: 0 residues added, 2229 seeds are put forward Round 1: 169 peptides, 22 chains. Longest chain 24 peptides. Score 0.618 Round 2: 213 peptides, 16 chains. Longest chain 29 peptides. Score 0.830 Round 3: 228 peptides, 10 chains. Longest chain 51 peptides. Score 0.902 Round 4: 231 peptides, 8 chains. Longest chain 48 peptides. Score 0.919 Round 5: 239 peptides, 4 chains. Longest chain 109 peptides. Score 0.948 Taking the results from Round 5 Chains 4, Residues 235, Estimated correctness of the model 99.8 % 3 chains (226 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 B and 43 B 3 chains (238 residues) following loop building 2 chains (229 residues) in sequence following loop building ------------------------------------------------------ 21417 reflections ( 85.37 % complete ) and 2295 restraints for refining 2250 atoms. 297 conditional restraints added. Observations/parameters ratio is 2.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2881 (Rfree = 0.000) for 2250 atoms. Found 62 (112 requested) and removed 60 (56 requested) atoms. Cycle 2: After refmac, R = 0.2571 (Rfree = 0.000) for 2232 atoms. Found 76 (110 requested) and removed 56 (56 requested) atoms. Cycle 3: After refmac, R = 0.2382 (Rfree = 0.000) for 2245 atoms. Found 66 (108 requested) and removed 18 (56 requested) atoms. Cycle 4: After refmac, R = 0.2219 (Rfree = 0.000) for 2283 atoms. Found 63 (109 requested) and removed 17 (57 requested) atoms. Cycle 5: After refmac, R = 0.2108 (Rfree = 0.000) for 2324 atoms. Found 47 (111 requested) and removed 25 (58 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.02 1.97 NCS extension: 1 residues added (12 deleted due to clashes), 2347 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: 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 2201 restraints for refining 2288 atoms. 121 conditional restraints added. Observations/parameters ratio is 2.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2153 (Rfree = 0.000) for 2288 atoms. Found 89 (107 requested) and removed 43 (57 requested) atoms. Cycle 7: After refmac, R = 0.2011 (Rfree = 0.000) for 2330 atoms. Found 58 (109 requested) and removed 25 (58 requested) atoms. Cycle 8: After refmac, R = 0.1917 (Rfree = 0.000) for 2362 atoms. Found 57 (111 requested) and removed 26 (59 requested) atoms. Cycle 9: After refmac, R = 0.1868 (Rfree = 0.000) for 2389 atoms. Found 45 (112 requested) and removed 30 (59 requested) atoms. Cycle 10: After refmac, R = 0.1819 (Rfree = 0.000) for 2402 atoms. Found 49 (110 requested) and removed 24 (60 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2427 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: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 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 2216 restraints for refining 2321 atoms. 136 conditional restraints added. Observations/parameters ratio is 2.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1996 (Rfree = 0.000) for 2321 atoms. Found 89 (107 requested) and removed 30 (58 requested) atoms. Cycle 12: After refmac, R = 0.1906 (Rfree = 0.000) for 2377 atoms. Found 44 (109 requested) and removed 32 (59 requested) atoms. Cycle 13: After refmac, R = 0.1824 (Rfree = 0.000) for 2388 atoms. Found 60 (107 requested) and removed 25 (59 requested) atoms. Cycle 14: After refmac, R = 0.1803 (Rfree = 0.000) for 2421 atoms. Found 41 (109 requested) and removed 40 (60 requested) atoms. Cycle 15: After refmac, R = 0.1764 (Rfree = 0.000) for 2420 atoms. Found 58 (106 requested) and removed 28 (60 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2450 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: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 5: 244 peptides, 4 chains. Longest chain 73 peptides. Score 0.951 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 2237 restraints for refining 2333 atoms. 157 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1926 (Rfree = 0.000) for 2333 atoms. Found 79 (102 requested) and removed 29 (58 requested) atoms. Cycle 17: After refmac, R = 0.1857 (Rfree = 0.000) for 2381 atoms. Found 45 (105 requested) and removed 37 (59 requested) atoms. Cycle 18: After refmac, R = 0.1792 (Rfree = 0.000) for 2387 atoms. Found 52 (102 requested) and removed 29 (59 requested) atoms. Cycle 19: After refmac, R = 0.1764 (Rfree = 0.000) for 2410 atoms. Found 45 (101 requested) and removed 36 (60 requested) atoms. Cycle 20: After refmac, R = 0.1731 (Rfree = 0.000) for 2418 atoms. Found 52 (98 requested) and removed 31 (60 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2440 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: 244 peptides, 4 chains. Longest chain 123 peptides. Score 0.951 Round 5: 243 peptides, 3 chains. Longest chain 123 peptides. Score 0.956 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 2243 restraints for refining 2336 atoms. 163 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1938 (Rfree = 0.000) for 2336 atoms. Found 80 (93 requested) and removed 30 (58 requested) atoms. Cycle 22: After refmac, R = 0.1874 (Rfree = 0.000) for 2385 atoms. Found 35 (95 requested) and removed 37 (59 requested) atoms. Cycle 23: After refmac, R = 0.1802 (Rfree = 0.000) for 2382 atoms. Found 57 (92 requested) and removed 20 (59 requested) atoms. Cycle 24: After refmac, R = 0.1765 (Rfree = 0.000) for 2419 atoms. Found 39 (94 requested) and removed 29 (60 requested) atoms. Cycle 25: After refmac, R = 0.1722 (Rfree = 0.000) for 2428 atoms. Found 44 (92 requested) and removed 23 (60 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.02 1.97 NCS extension: 0 residues added, 2450 seeds are put forward Round 1: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 2: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 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: 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 2227 restraints for refining 2326 atoms. 147 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1938 (Rfree = 0.000) for 2326 atoms. Found 86 (86 requested) and removed 29 (58 requested) atoms. Cycle 27: After refmac, R = 0.1867 (Rfree = 0.000) for 2383 atoms. Found 42 (88 requested) and removed 30 (59 requested) atoms. Cycle 28: After refmac, R = 0.1796 (Rfree = 0.000) for 2392 atoms. Found 44 (86 requested) and removed 25 (59 requested) atoms. Cycle 29: After refmac, R = 0.1758 (Rfree = 0.000) for 2408 atoms. Found 42 (84 requested) and removed 34 (60 requested) atoms. Cycle 30: After refmac, R = 0.1740 (Rfree = 0.000) for 2414 atoms. Found 51 (82 requested) and removed 28 (60 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2438 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: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 5: 244 peptides, 3 chains. Longest chain 123 peptides. Score 0.956 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 2232 restraints for refining 2335 atoms. 152 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1925 (Rfree = 0.000) for 2335 atoms. Found 70 (77 requested) and removed 30 (58 requested) atoms. Cycle 32: After refmac, R = 0.1844 (Rfree = 0.000) for 2373 atoms. Found 44 (78 requested) and removed 37 (59 requested) atoms. Cycle 33: After refmac, R = 0.1790 (Rfree = 0.000) for 2380 atoms. Found 48 (76 requested) and removed 27 (59 requested) atoms. Cycle 34: After refmac, R = 0.1751 (Rfree = 0.000) for 2398 atoms. Found 43 (74 requested) and removed 34 (60 requested) atoms. Cycle 35: After refmac, R = 0.1758 (Rfree = 0.000) for 2406 atoms. Found 49 (72 requested) and removed 32 (60 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.03 1.98 NCS extension: 0 residues added, 2424 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 2239 restraints for refining 2331 atoms. 159 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1935 (Rfree = 0.000) for 2331 atoms. Found 67 (67 requested) and removed 34 (58 requested) atoms. Cycle 37: After refmac, R = 0.1846 (Rfree = 0.000) for 2362 atoms. Found 51 (66 requested) and removed 27 (59 requested) atoms. Cycle 38: After refmac, R = 0.1781 (Rfree = 0.000) for 2383 atoms. Found 43 (64 requested) and removed 26 (59 requested) atoms. Cycle 39: After refmac, R = 0.1749 (Rfree = 0.000) for 2398 atoms. Found 38 (62 requested) and removed 29 (59 requested) atoms. Cycle 40: After refmac, R = 0.1726 (Rfree = 0.000) for 2406 atoms. Found 40 (60 requested) and removed 25 (60 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.04 1.99 NCS extension: 0 residues added, 2422 seeds are put forward Round 1: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 2: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 3: 243 peptides, 3 chains. Longest chain 123 peptides. Score 0.956 Round 4: 243 peptides, 4 chains. Longest chain 101 peptides. Score 0.951 Round 5: 244 peptides, 4 chains. Longest chain 123 peptides. Score 0.951 Taking the results from Round 2 Chains 3, Residues 242, Estimated correctness of the model 99.9 % 3 chains (242 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 B and 63 B 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 2330 atoms. 152 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1949 (Rfree = 0.000) for 2330 atoms. Found 58 (58 requested) and removed 29 (58 requested) atoms. Cycle 42: After refmac, R = 0.1857 (Rfree = 0.000) for 2359 atoms. Found 44 (58 requested) and removed 19 (58 requested) atoms. Cycle 43: After refmac, R = 0.1793 (Rfree = 0.000) for 2381 atoms. Found 41 (59 requested) and removed 23 (59 requested) atoms. Cycle 44: After refmac, R = 0.1769 (Rfree = 0.000) for 2399 atoms. Found 44 (59 requested) and removed 29 (59 requested) atoms. Cycle 45: After refmac, R = 0.1722 (Rfree = 0.000) for 2412 atoms. Found 49 (60 requested) and removed 37 (60 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.02 1.97 NCS extension: 0 residues added, 2424 seeds are put forward Round 1: 246 peptides, 2 chains. Longest chain 123 peptides. Score 0.962 Round 2: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Round 3: 243 peptides, 3 chains. Longest chain 123 peptides. Score 0.956 Round 4: 243 peptides, 4 chains. Longest chain 101 peptides. Score 0.951 Round 5: 245 peptides, 3 chains. Longest chain 123 peptides. Score 0.957 Taking the results from Round 1 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 = 0.2426 (Rfree = 0.000) for 2020 atoms. Found 35 (50 requested) and removed 0 (50 requested) atoms. Cycle 47: After refmac, R = 0.2270 (Rfree = 0.000) for 2020 atoms. Found 16 (51 requested) and removed 0 (51 requested) atoms. Cycle 48: After refmac, R = 0.2164 (Rfree = 0.000) for 2020 atoms. Found 5 (51 requested) and removed 1 (51 requested) atoms. Cycle 49: After refmac, R = 0.2108 (Rfree = 0.000) for 2020 atoms. TimeTaking 33.6