Tue 25 Dec 19:30:29 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 2okf-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2okf-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2okf-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okf-3.2-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/2okf-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okf-3.2-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 ============================================================ Tue 25 Dec 19:30:39 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/2okf-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okf-3.2-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 209 and 0 Target number of residues in the AU: 209 Target solvent content: 0.6269 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 280 Adjusted target solvent content: 0.50 Input MTZ file: 2okf-3.2-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: 144 Cell parameters: 59.870 59.870 73.240 90.000 90.000 120.000 Input sequence file: 2okf-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2240 target number of atoms Had to go as low as 0.70 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: 27.710 3.201 Wilson plot Bfac: 64.57 4845 reflections ( 99.65 % complete ) and 0 restraints for refining 2473 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3174 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3093 (Rfree = 0.000) for 2473 atoms. Found 22 (22 requested) and removed 44 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 3.10 Search for helices and strands: 0 residues in 0 chains, 2499 seeds are put forward NCS extension: 0 residues added, 2499 seeds are put forward Round 1: 143 peptides, 29 chains. Longest chain 10 peptides. Score 0.324 Round 2: 166 peptides, 27 chains. Longest chain 17 peptides. Score 0.485 Round 3: 181 peptides, 26 chains. Longest chain 17 peptides. Score 0.569 Round 4: 189 peptides, 24 chains. Longest chain 30 peptides. Score 0.634 Round 5: 200 peptides, 23 chains. Longest chain 30 peptides. Score 0.686 Taking the results from Round 5 Chains 26, Residues 177, Estimated correctness of the model 62.1 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3718 restraints for refining 2045 atoms. 2805 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2743 (Rfree = 0.000) for 2045 atoms. Found 15 (18 requested) and removed 28 (9 requested) atoms. Cycle 2: After refmac, R = 0.2791 (Rfree = 0.000) for 2005 atoms. Found 11 (18 requested) and removed 29 (9 requested) atoms. Cycle 3: After refmac, R = 0.2538 (Rfree = 0.000) for 1977 atoms. Found 11 (17 requested) and removed 21 (8 requested) atoms. Cycle 4: After refmac, R = 0.2643 (Rfree = 0.000) for 1961 atoms. Found 9 (17 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.2598 (Rfree = 0.000) for 1947 atoms. Found 12 (17 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.10 Search for helices and strands: 0 residues in 0 chains, 2024 seeds are put forward NCS extension: 32 residues added (14 deleted due to clashes), 2056 seeds are put forward Round 1: 166 peptides, 20 chains. Longest chain 31 peptides. Score 0.616 Round 2: 195 peptides, 21 chains. Longest chain 27 peptides. Score 0.699 Round 3: 205 peptides, 22 chains. Longest chain 25 peptides. Score 0.715 Round 4: 200 peptides, 20 chains. Longest chain 27 peptides. Score 0.728 Round 5: 192 peptides, 22 chains. Longest chain 23 peptides. Score 0.675 Taking the results from Round 4 Chains 22, Residues 180, Estimated correctness of the model 70.9 % 2 chains (44 residues) have been docked in sequence Building loops using Loopy2018 22 chains (180 residues) following loop building 2 chains (44 residues) in sequence following loop building ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3772 restraints for refining 2045 atoms. 2872 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2461 (Rfree = 0.000) for 2045 atoms. Found 6 (18 requested) and removed 20 (9 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2287 (Rfree = 0.000) for 2018 atoms. Found 8 (18 requested) and removed 12 (9 requested) atoms. Cycle 8: After refmac, R = 0.2227 (Rfree = 0.000) for 2008 atoms. Found 5 (17 requested) and removed 12 (9 requested) atoms. Cycle 9: After refmac, R = 0.2435 (Rfree = 0.000) for 1996 atoms. Found 9 (16 requested) and removed 18 (8 requested) atoms. Cycle 10: After refmac, R = 0.1953 (Rfree = 0.000) for 1981 atoms. Found 11 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.14 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 2078 seeds are put forward Round 1: 193 peptides, 20 chains. Longest chain 31 peptides. Score 0.707 Round 2: 198 peptides, 24 chains. Longest chain 27 peptides. Score 0.665 Round 3: 194 peptides, 21 chains. Longest chain 23 peptides. Score 0.696 Round 4: 207 peptides, 24 chains. Longest chain 24 peptides. Score 0.694 Round 5: 198 peptides, 22 chains. Longest chain 23 peptides. Score 0.694 Taking the results from Round 1 Chains 22, Residues 173, Estimated correctness of the model 66.6 % 3 chains (69 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 102 A and 111 A 20 chains (178 residues) following loop building 2 chains (77 residues) in sequence following loop building ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3317 restraints for refining 2045 atoms. 2252 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2473 (Rfree = 0.000) for 2045 atoms. Found 10 (16 requested) and removed 24 (9 requested) atoms. Cycle 12: After refmac, R = 0.2217 (Rfree = 0.000) for 2020 atoms. Found 14 (16 requested) and removed 13 (9 requested) atoms. Cycle 13: After refmac, R = 0.2133 (Rfree = 0.000) for 2011 atoms. Found 4 (15 requested) and removed 16 (9 requested) atoms. Cycle 14: After refmac, R = 0.2002 (Rfree = 0.000) for 1996 atoms. Found 9 (14 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.1923 (Rfree = 0.000) for 1988 atoms. Found 7 (14 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 3.12 Search for helices and strands: 0 residues in 0 chains, 2058 seeds are put forward NCS extension: 50 residues added (66 deleted due to clashes), 2108 seeds are put forward Round 1: 171 peptides, 18 chains. Longest chain 23 peptides. Score 0.667 Round 2: 185 peptides, 19 chains. Longest chain 31 peptides. Score 0.697 Round 3: 192 peptides, 20 chains. Longest chain 27 peptides. Score 0.705 Round 4: 185 peptides, 19 chains. Longest chain 33 peptides. Score 0.697 Round 5: 189 peptides, 20 chains. Longest chain 35 peptides. Score 0.695 Taking the results from Round 3 Chains 23, Residues 172, Estimated correctness of the model 66.2 % 3 chains (62 residues) have been docked in sequence Building loops using Loopy2018 23 chains (172 residues) following loop building 3 chains (62 residues) in sequence following loop building ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3553 restraints for refining 2045 atoms. 2595 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2236 (Rfree = 0.000) for 2045 atoms. Found 10 (14 requested) and removed 16 (9 requested) atoms. Cycle 17: After refmac, R = 0.2008 (Rfree = 0.000) for 2033 atoms. Found 1 (14 requested) and removed 14 (9 requested) atoms. Cycle 18: After refmac, R = 0.2134 (Rfree = 0.000) for 2020 atoms. Found 4 (14 requested) and removed 11 (9 requested) atoms. Cycle 19: After refmac, R = 0.2056 (Rfree = 0.000) for 2013 atoms. Found 4 (13 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2145 (Rfree = 0.000) for 2004 atoms. Found 6 (12 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 3.10 Search for helices and strands: 0 residues in 0 chains, 2052 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 2087 seeds are put forward Round 1: 173 peptides, 20 chains. Longest chain 24 peptides. Score 0.642 Round 2: 186 peptides, 22 chains. Longest chain 37 peptides. Score 0.655 Round 3: 177 peptides, 21 chains. Longest chain 25 peptides. Score 0.640 Round 4: 174 peptides, 20 chains. Longest chain 28 peptides. Score 0.645 Round 5: 180 peptides, 22 chains. Longest chain 27 peptides. Score 0.634 Taking the results from Round 2 Chains 24, Residues 164, Estimated correctness of the model 55.0 % 2 chains (47 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4845 reflections ( 99.65 % complete ) and 3749 restraints for refining 2045 atoms. 2887 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2104 (Rfree = 0.000) for 2045 atoms. Found 6 (13 requested) and removed 22 (9 requested) atoms. Cycle 22: After refmac, R = 0.1946 (Rfree = 0.000) for 2027 atoms. Found 5 (13 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1932 (Rfree = 0.000) for 2013 atoms. Found 2 (13 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1935 (Rfree = 0.000) for 2001 atoms. Found 1 (12 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1890 (Rfree = 0.000) for 1994 atoms. Found 2 (12 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.14 Search for helices and strands: 0 residues in 0 chains, 2032 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 2047 seeds are put forward Round 1: 162 peptides, 17 chains. Longest chain 38 peptides. Score 0.652 Round 2: 175 peptides, 19 chains. Longest chain 32 peptides. Score 0.665 Round 3: 171 peptides, 20 chains. Longest chain 31 peptides. Score 0.634 Round 4: 167 peptides, 17 chains. Longest chain 54 peptides. Score 0.669 Round 5: 176 peptides, 21 chains. Longest chain 29 peptides. Score 0.636 Taking the results from Round 4 Chains 17, Residues 150, Estimated correctness of the model 58.3 % 1 chains (53 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3668 restraints for refining 2045 atoms. 2828 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2151 (Rfree = 0.000) for 2045 atoms. Found 8 (13 requested) and removed 19 (9 requested) atoms. Cycle 27: After refmac, R = 0.2023 (Rfree = 0.000) for 2029 atoms. Found 12 (13 requested) and removed 13 (9 requested) atoms. Cycle 28: After refmac, R = 0.1937 (Rfree = 0.000) for 2026 atoms. Found 7 (13 requested) and removed 10 (9 requested) atoms. Cycle 29: After refmac, R = 0.1848 (Rfree = 0.000) for 2020 atoms. Found 5 (13 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1784 (Rfree = 0.000) for 2007 atoms. Found 1 (13 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 3.12 Search for helices and strands: 0 residues in 0 chains, 2051 seeds are put forward NCS extension: 70 residues added (17 deleted due to clashes), 2121 seeds are put forward Round 1: 151 peptides, 21 chains. Longest chain 21 peptides. Score 0.536 Round 2: 158 peptides, 19 chains. Longest chain 24 peptides. Score 0.602 Round 3: 168 peptides, 17 chains. Longest chain 36 peptides. Score 0.673 Round 4: 172 peptides, 18 chains. Longest chain 24 peptides. Score 0.670 Round 5: 164 peptides, 21 chains. Longest chain 19 peptides. Score 0.590 Taking the results from Round 3 Chains 19, Residues 151, Estimated correctness of the model 59.2 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3838 restraints for refining 2045 atoms. 3101 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2105 (Rfree = 0.000) for 2045 atoms. Found 5 (13 requested) and removed 14 (9 requested) atoms. Cycle 32: After refmac, R = 0.1963 (Rfree = 0.000) for 2031 atoms. Found 7 (13 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.2115 (Rfree = 0.000) for 2026 atoms. Found 13 (13 requested) and removed 11 (9 requested) atoms. Cycle 34: After refmac, R = 0.1869 (Rfree = 0.000) for 2024 atoms. Found 5 (13 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.1775 (Rfree = 0.000) for 2015 atoms. Found 5 (13 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.15 Search for helices and strands: 0 residues in 0 chains, 2061 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 2072 seeds are put forward Round 1: 131 peptides, 21 chains. Longest chain 18 peptides. Score 0.441 Round 2: 139 peptides, 16 chains. Longest chain 24 peptides. Score 0.581 Round 3: 148 peptides, 18 chains. Longest chain 25 peptides. Score 0.580 Round 4: 145 peptides, 20 chains. Longest chain 15 peptides. Score 0.529 Round 5: 133 peptides, 19 chains. Longest chain 13 peptides. Score 0.494 Taking the results from Round 2 Chains 16, Residues 123, Estimated correctness of the model 35.8 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 4220 restraints for refining 2045 atoms. 3645 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2003 (Rfree = 0.000) for 2045 atoms. Found 3 (13 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1987 (Rfree = 0.000) for 2036 atoms. Found 5 (13 requested) and removed 11 (9 requested) atoms. Cycle 38: After refmac, R = 0.2156 (Rfree = 0.000) for 2027 atoms. Found 5 (13 requested) and removed 10 (9 requested) atoms. Cycle 39: After refmac, R = 0.1863 (Rfree = 0.000) for 2020 atoms. Found 2 (13 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1837 (Rfree = 0.000) for 2010 atoms. Found 3 (13 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.15 Search for helices and strands: 0 residues in 0 chains, 2068 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 2090 seeds are put forward Round 1: 127 peptides, 19 chains. Longest chain 13 peptides. Score 0.465 Round 2: 139 peptides, 19 chains. Longest chain 18 peptides. Score 0.522 Round 3: 144 peptides, 19 chains. Longest chain 18 peptides. Score 0.544 Round 4: 139 peptides, 20 chains. Longest chain 18 peptides. Score 0.501 Round 5: 146 peptides, 17 chains. Longest chain 21 peptides. Score 0.591 Taking the results from Round 5 Chains 17, Residues 129, Estimated correctness of the model 38.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 4483 restraints for refining 2045 atoms. 3984 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2050 (Rfree = 0.000) for 2045 atoms. Found 6 (13 requested) and removed 11 (9 requested) atoms. Cycle 42: After refmac, R = 0.2292 (Rfree = 0.000) for 2037 atoms. Found 13 (13 requested) and removed 10 (9 requested) atoms. Cycle 43: After refmac, R = 0.2124 (Rfree = 0.000) for 2037 atoms. Found 7 (13 requested) and removed 13 (9 requested) atoms. Cycle 44: After refmac, R = 0.2008 (Rfree = 0.000) for 2028 atoms. Found 1 (13 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2048 (Rfree = 0.000) for 2018 atoms. Found 7 (13 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.13 Search for helices and strands: 0 residues in 0 chains, 2073 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 2099 seeds are put forward Round 1: 111 peptides, 20 chains. Longest chain 13 peptides. Score 0.357 Round 2: 136 peptides, 20 chains. Longest chain 16 peptides. Score 0.487 Round 3: 141 peptides, 21 chains. Longest chain 13 peptides. Score 0.490 Round 4: 150 peptides, 20 chains. Longest chain 16 peptides. Score 0.551 Round 5: 150 peptides, 19 chains. Longest chain 16 peptides. Score 0.570 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 131, Estimated correctness of the model 32.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2okf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4845 reflections ( 99.65 % complete ) and 4356 restraints for refining 2034 atoms. 3851 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2019 (Rfree = 0.000) for 2034 atoms. Found 0 (13 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1914 (Rfree = 0.000) for 2024 atoms. Found 0 (13 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1967 (Rfree = 0.000) for 2013 atoms. Found 0 (13 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1913 (Rfree = 0.000) for 2003 atoms. Found 0 (12 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:35:57 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 65.48