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 2o8q-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o8q-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o8q-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-3.6-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/2o8q-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-3.6-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 19:28:05 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/2o8q-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-3.6-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 264 and 0 Target number of residues in the AU: 264 Target solvent content: 0.6405 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 268 Adjusted target solvent content: 0.64 Input MTZ file: 2o8q-3.6-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: 94 Cell parameters: 103.170 103.170 74.680 90.000 90.000 90.000 Input sequence file: 2o8q-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2144 target number of atoms Had to go as low as 0.85 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 3 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: 29.026 3.601 Wilson plot Bfac: 71.81 4947 reflections ( 98.53 % complete ) and 0 restraints for refining 2394 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3059 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3164 (Rfree = 0.000) for 2394 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 2.85 Search for helices and strands: 0 residues in 0 chains, 2420 seeds are put forward NCS extension: 0 residues added, 2420 seeds are put forward Round 1: 154 peptides, 24 chains. Longest chain 14 peptides. Score 0.432 Round 2: 186 peptides, 22 chains. Longest chain 21 peptides. Score 0.578 Round 3: 186 peptides, 22 chains. Longest chain 21 peptides. Score 0.578 Round 4: 188 peptides, 22 chains. Longest chain 17 peptides. Score 0.584 Round 5: 194 peptides, 20 chains. Longest chain 27 peptides. Score 0.630 Taking the results from Round 5 Chains 24, Residues 174, Estimated correctness of the model 25.9 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3720 restraints for refining 1940 atoms. 2911 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2676 (Rfree = 0.000) for 1940 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 2: After refmac, R = 0.2489 (Rfree = 0.000) for 1899 atoms. Found 9 (12 requested) and removed 17 (6 requested) atoms. Cycle 3: After refmac, R = 0.2404 (Rfree = 0.000) for 1874 atoms. Found 8 (12 requested) and removed 14 (6 requested) atoms. Cycle 4: After refmac, R = 0.2335 (Rfree = 0.000) for 1861 atoms. Found 3 (11 requested) and removed 10 (5 requested) atoms. Cycle 5: After refmac, R = 0.2316 (Rfree = 0.000) for 1853 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 2.81 Search for helices and strands: 0 residues in 0 chains, 1891 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 1914 seeds are put forward Round 1: 165 peptides, 23 chains. Longest chain 18 peptides. Score 0.491 Round 2: 179 peptides, 22 chains. Longest chain 23 peptides. Score 0.555 Round 3: 184 peptides, 19 chains. Longest chain 32 peptides. Score 0.615 Round 4: 189 peptides, 23 chains. Longest chain 20 peptides. Score 0.573 Round 5: 196 peptides, 21 chains. Longest chain 20 peptides. Score 0.623 Taking the results from Round 5 Chains 23, Residues 175, Estimated correctness of the model 23.4 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3953 restraints for refining 1944 atoms. 3189 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2708 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.2534 (Rfree = 0.000) for 1908 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.2485 (Rfree = 0.000) for 1906 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.2381 (Rfree = 0.000) for 1902 atoms. Found 4 (12 requested) and removed 12 (6 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2345 (Rfree = 0.000) for 1890 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 2.83 Search for helices and strands: 0 residues in 0 chains, 1927 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 1951 seeds are put forward Round 1: 169 peptides, 25 chains. Longest chain 15 peptides. Score 0.472 Round 2: 177 peptides, 19 chains. Longest chain 21 peptides. Score 0.593 Round 3: 175 peptides, 19 chains. Longest chain 23 peptides. Score 0.587 Round 4: 181 peptides, 18 chains. Longest chain 41 peptides. Score 0.620 Round 5: 181 peptides, 21 chains. Longest chain 20 peptides. Score 0.577 Taking the results from Round 4 Chains 18, Residues 163, Estimated correctness of the model 22.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 4261 restraints for refining 1944 atoms. 3627 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2640 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 12: After refmac, R = 0.2436 (Rfree = 0.000) for 1932 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2427 (Rfree = 0.000) for 1920 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.2265 (Rfree = 0.000) for 1922 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 15: After refmac, R = 0.2268 (Rfree = 0.000) for 1921 atoms. Found 4 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 2.83 Search for helices and strands: 0 residues in 0 chains, 1972 seeds are put forward NCS extension: 61 residues added (1 deleted due to clashes), 2033 seeds are put forward Round 1: 163 peptides, 24 chains. Longest chain 19 peptides. Score 0.467 Round 2: 170 peptides, 23 chains. Longest chain 19 peptides. Score 0.509 Round 3: 173 peptides, 22 chains. Longest chain 26 peptides. Score 0.535 Round 4: 170 peptides, 21 chains. Longest chain 16 peptides. Score 0.540 Round 5: 175 peptides, 21 chains. Longest chain 25 peptides. Score 0.557 Taking the results from Round 5 Chains 21, Residues 154, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4947 reflections ( 98.53 % complete ) and 4149 restraints for refining 1944 atoms. 3522 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2646 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2544 (Rfree = 0.000) for 1914 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 18: After refmac, R = 0.2457 (Rfree = 0.000) for 1897 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.2369 (Rfree = 0.000) for 1888 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2263 (Rfree = 0.000) for 1890 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 2.82 Search for helices and strands: 0 residues in 0 chains, 1951 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 1985 seeds are put forward Round 1: 159 peptides, 21 chains. Longest chain 21 peptides. Score 0.502 Round 2: 172 peptides, 20 chains. Longest chain 23 peptides. Score 0.562 Round 3: 173 peptides, 19 chains. Longest chain 32 peptides. Score 0.581 Round 4: 171 peptides, 19 chains. Longest chain 27 peptides. Score 0.574 Round 5: 177 peptides, 20 chains. Longest chain 26 peptides. Score 0.579 Taking the results from Round 3 Chains 19, Residues 154, Estimated correctness of the model 7.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4947 reflections ( 98.53 % complete ) and 4217 restraints for refining 1944 atoms. 3603 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2396 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 22: After refmac, R = 0.2423 (Rfree = 0.000) for 1940 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.2282 (Rfree = 0.000) for 1931 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 24: After refmac, R = 0.2450 (Rfree = 0.000) for 1928 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 25: After refmac, R = 0.2325 (Rfree = 0.000) for 1926 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 2.81 Search for helices and strands: 0 residues in 0 chains, 1988 seeds are put forward NCS extension: 62 residues added (1 deleted due to clashes), 2050 seeds are put forward Round 1: 166 peptides, 26 chains. Longest chain 26 peptides. Score 0.444 Round 2: 190 peptides, 24 chains. Longest chain 28 peptides. Score 0.561 Round 3: 183 peptides, 19 chains. Longest chain 33 peptides. Score 0.612 Round 4: 187 peptides, 22 chains. Longest chain 22 peptides. Score 0.581 Round 5: 179 peptides, 20 chains. Longest chain 26 peptides. Score 0.585 Taking the results from Round 3 Chains 20, Residues 164, Estimated correctness of the model 19.2 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 4029 restraints for refining 1944 atoms. 3342 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2653 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 27: After refmac, R = 0.2465 (Rfree = 0.000) for 1931 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2540 (Rfree = 0.000) for 1923 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 29: After refmac, R = 0.2461 (Rfree = 0.000) for 1917 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2293 (Rfree = 0.000) for 1914 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 2.81 Search for helices and strands: 0 residues in 0 chains, 1987 seeds are put forward NCS extension: 57 residues added (3 deleted due to clashes), 2044 seeds are put forward Round 1: 159 peptides, 26 chains. Longest chain 14 peptides. Score 0.417 Round 2: 170 peptides, 19 chains. Longest chain 40 peptides. Score 0.571 Round 3: 164 peptides, 17 chains. Longest chain 19 peptides. Score 0.582 Round 4: 168 peptides, 17 chains. Longest chain 20 peptides. Score 0.595 Round 5: 186 peptides, 15 chains. Longest chain 33 peptides. Score 0.674 Taking the results from Round 5 Chains 15, Residues 171, Estimated correctness of the model 41.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 4145 restraints for refining 1943 atoms. 3476 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2718 (Rfree = 0.000) for 1943 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 32: After refmac, R = 0.2659 (Rfree = 0.000) for 1930 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 33: After refmac, R = 0.2587 (Rfree = 0.000) for 1920 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2494 (Rfree = 0.000) for 1918 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.2475 (Rfree = 0.000) for 1922 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 2.79 Search for helices and strands: 0 residues in 0 chains, 1978 seeds are put forward NCS extension: 34 residues added (16 deleted due to clashes), 2012 seeds are put forward Round 1: 155 peptides, 22 chains. Longest chain 20 peptides. Score 0.470 Round 2: 167 peptides, 20 chains. Longest chain 29 peptides. Score 0.546 Round 3: 165 peptides, 19 chains. Longest chain 30 peptides. Score 0.555 Round 4: 169 peptides, 18 chains. Longest chain 25 peptides. Score 0.583 Round 5: 179 peptides, 20 chains. Longest chain 26 peptides. Score 0.585 Taking the results from Round 5 Chains 20, Residues 159, Estimated correctness of the model 8.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 4268 restraints for refining 1944 atoms. 3652 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2673 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 37: After refmac, R = 0.2598 (Rfree = 0.000) for 1936 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2544 (Rfree = 0.000) for 1929 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2623 (Rfree = 0.000) for 1924 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 40: After refmac, R = 0.2678 (Rfree = 0.000) for 1924 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 2.78 Search for helices and strands: 0 residues in 0 chains, 1983 seeds are put forward NCS extension: 24 residues added (13 deleted due to clashes), 2007 seeds are put forward Round 1: 163 peptides, 26 chains. Longest chain 15 peptides. Score 0.433 Round 2: 176 peptides, 24 chains. Longest chain 18 peptides. Score 0.514 Round 3: 179 peptides, 25 chains. Longest chain 25 peptides. Score 0.509 Round 4: 186 peptides, 22 chains. Longest chain 25 peptides. Score 0.578 Round 5: 176 peptides, 20 chains. Longest chain 31 peptides. Score 0.576 Taking the results from Round 4 Chains 23, Residues 164, Estimated correctness of the model 5.8 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3962 restraints for refining 1944 atoms. 3256 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2831 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 42: After refmac, R = 0.2599 (Rfree = 0.000) for 1928 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 43: After refmac, R = 0.2643 (Rfree = 0.000) for 1918 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 44: After refmac, R = 0.2480 (Rfree = 0.000) for 1912 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.2425 (Rfree = 0.000) for 1911 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 2.72 Search for helices and strands: 0 residues in 0 chains, 1968 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1986 seeds are put forward Round 1: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.416 Round 2: 175 peptides, 23 chains. Longest chain 27 peptides. Score 0.526 Round 3: 175 peptides, 20 chains. Longest chain 22 peptides. Score 0.572 Round 4: 174 peptides, 21 chains. Longest chain 19 peptides. Score 0.554 Round 5: 173 peptides, 19 chains. Longest chain 22 peptides. Score 0.581 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 154, Estimated correctness of the model 7.0 % 4 chains (40 residues) have been docked in sequence Sequence coverage is 25 % Consider running further cycles of model building using 2o8q-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 27 A and 38 A 20 chains (160 residues) following loop building 3 chains (50 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4947 reflections ( 98.53 % complete ) and 3622 restraints for refining 1944 atoms. 2895 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2789 (Rfree = 0.000) for 1944 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2701 (Rfree = 0.000) for 1922 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2655 (Rfree = 0.000) for 1908 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2586 (Rfree = 0.000) for 1896 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:13:49 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 45.9