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 2okf-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okf-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okf-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-3.2-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/2okf-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-3.2-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/2okf-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okf-3.2-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 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-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: 144 Cell parameters: 59.870 59.870 73.240 90.000 90.000 120.000 Input sequence file: 2okf-3.2-parrot-hancs.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 2504 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3223 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2928 (Rfree = 0.000) for 2504 atoms. Found 21 (22 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 2546 seeds are put forward NCS extension: 0 residues added, 2546 seeds are put forward Round 1: 132 peptides, 24 chains. Longest chain 11 peptides. Score 0.379 Round 2: 162 peptides, 25 chains. Longest chain 14 peptides. Score 0.506 Round 3: 170 peptides, 26 chains. Longest chain 13 peptides. Score 0.522 Round 4: 181 peptides, 25 chains. Longest chain 21 peptides. Score 0.587 Round 5: 197 peptides, 25 chains. Longest chain 22 peptides. Score 0.647 Taking the results from Round 5 Chains 27, Residues 172, Estimated correctness of the model 53.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 4284 restraints for refining 2044 atoms. 3593 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2521 (Rfree = 0.000) for 2044 atoms. Found 13 (18 requested) and removed 16 (9 requested) atoms. Cycle 2: After refmac, R = 0.2362 (Rfree = 0.000) for 2023 atoms. Found 8 (18 requested) and removed 18 (9 requested) atoms. Cycle 3: After refmac, R = 0.2323 (Rfree = 0.000) for 2003 atoms. Found 7 (18 requested) and removed 33 (9 requested) atoms. Cycle 4: After refmac, R = 0.2186 (Rfree = 0.000) for 1970 atoms. Found 4 (17 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.2123 (Rfree = 0.000) for 1954 atoms. Found 3 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.13 Search for helices and strands: 0 residues in 0 chains, 2030 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 2045 seeds are put forward Round 1: 154 peptides, 21 chains. Longest chain 22 peptides. Score 0.549 Round 2: 184 peptides, 24 chains. Longest chain 27 peptides. Score 0.616 Round 3: 184 peptides, 20 chains. Longest chain 28 peptides. Score 0.679 Round 4: 181 peptides, 19 chains. Longest chain 23 peptides. Score 0.685 Round 5: 181 peptides, 23 chains. Longest chain 22 peptides. Score 0.621 Taking the results from Round 4 Chains 19, Residues 162, Estimated correctness of the model 61.9 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 4397 restraints for refining 2045 atoms. 3719 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2475 (Rfree = 0.000) for 2045 atoms. Found 7 (18 requested) and removed 17 (9 requested) atoms. Cycle 7: After refmac, R = 0.2312 (Rfree = 0.000) for 2030 atoms. Found 6 (18 requested) and removed 16 (9 requested) atoms. Cycle 8: After refmac, R = 0.2475 (Rfree = 0.000) for 2013 atoms. Found 11 (18 requested) and removed 18 (9 requested) atoms. Cycle 9: After refmac, R = 0.2277 (Rfree = 0.000) for 1999 atoms. Found 4 (17 requested) and removed 16 (8 requested) atoms. Cycle 10: After refmac, R = 0.2542 (Rfree = 0.000) for 1984 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 3.11 Search for helices and strands: 0 residues in 0 chains, 2030 seeds are put forward NCS extension: 24 residues added (10 deleted due to clashes), 2054 seeds are put forward Round 1: 168 peptides, 21 chains. Longest chain 35 peptides. Score 0.606 Round 2: 174 peptides, 20 chains. Longest chain 22 peptides. Score 0.645 Round 3: 192 peptides, 20 chains. Longest chain 39 peptides. Score 0.705 Round 4: 189 peptides, 21 chains. Longest chain 37 peptides. Score 0.681 Round 5: 202 peptides, 22 chains. Longest chain 39 peptides. Score 0.707 Taking the results from Round 5 Chains 28, Residues 180, Estimated correctness of the model 66.6 % 4 chains (63 residues) have been docked in sequence Building loops using Loopy2018 28 chains (180 residues) following loop building 4 chains (63 residues) in sequence following loop building ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3487 restraints for refining 2045 atoms. 2490 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2716 (Rfree = 0.000) for 2045 atoms. Found 12 (18 requested) and removed 21 (9 requested) atoms. Cycle 12: After refmac, R = 0.2528 (Rfree = 0.000) for 2011 atoms. Found 9 (18 requested) and removed 23 (9 requested) atoms. Cycle 13: After refmac, R = 0.2505 (Rfree = 0.000) for 1990 atoms. Found 9 (16 requested) and removed 17 (8 requested) atoms. Cycle 14: After refmac, R = 0.2420 (Rfree = 0.000) for 1980 atoms. Found 7 (16 requested) and removed 15 (8 requested) atoms. Cycle 15: After refmac, R = 0.1936 (Rfree = 0.000) for 1965 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.15 Search for helices and strands: 0 residues in 0 chains, 2065 seeds are put forward NCS extension: 38 residues added (8 deleted due to clashes), 2103 seeds are put forward Round 1: 171 peptides, 23 chains. Longest chain 23 peptides. Score 0.582 Round 2: 188 peptides, 21 chains. Longest chain 32 peptides. Score 0.677 Round 3: 191 peptides, 21 chains. Longest chain 20 peptides. Score 0.687 Round 4: 195 peptides, 25 chains. Longest chain 22 peptides. Score 0.639 Round 5: 190 peptides, 23 chains. Longest chain 22 peptides. Score 0.653 Taking the results from Round 3 Chains 25, Residues 170, Estimated correctness of the model 62.3 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3826 restraints for refining 2045 atoms. 2942 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2287 (Rfree = 0.000) for 2045 atoms. Found 5 (16 requested) and removed 16 (9 requested) atoms. Cycle 17: After refmac, R = 0.2048 (Rfree = 0.000) for 2026 atoms. Found 2 (16 requested) and removed 13 (9 requested) atoms. Cycle 18: After refmac, R = 0.1917 (Rfree = 0.000) for 2012 atoms. Found 1 (16 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.1873 (Rfree = 0.000) for 2004 atoms. Found 1 (15 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.1889 (Rfree = 0.000) for 1997 atoms. Found 0 (15 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 2061 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 2077 seeds are put forward Round 1: 177 peptides, 21 chains. Longest chain 20 peptides. Score 0.640 Round 2: 192 peptides, 21 chains. Longest chain 37 peptides. Score 0.690 Round 3: 197 peptides, 21 chains. Longest chain 37 peptides. Score 0.705 Round 4: 202 peptides, 24 chains. Longest chain 20 peptides. Score 0.678 Round 5: 198 peptides, 22 chains. Longest chain 24 peptides. Score 0.694 Taking the results from Round 3 Chains 25, Residues 176, Estimated correctness of the model 66.2 % 3 chains (53 residues) have been docked in sequence Building loops using Loopy2018 25 chains (176 residues) following loop building 3 chains (53 residues) in sequence following loop building ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3712 restraints for refining 2043 atoms. 2780 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2384 (Rfree = 0.000) for 2043 atoms. Found 8 (16 requested) and removed 21 (9 requested) atoms. Cycle 22: After refmac, R = 0.2181 (Rfree = 0.000) for 2025 atoms. Found 6 (16 requested) and removed 9 (9 requested) atoms. Cycle 23: After refmac, R = 0.2111 (Rfree = 0.000) for 2016 atoms. Found 7 (15 requested) and removed 12 (9 requested) atoms. Cycle 24: After refmac, R = 0.2317 (Rfree = 0.000) for 2006 atoms. Found 6 (15 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1953 (Rfree = 0.000) for 1997 atoms. Found 3 (14 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 2063 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 2082 seeds are put forward Round 1: 156 peptides, 24 chains. Longest chain 16 peptides. Score 0.498 Round 2: 176 peptides, 21 chains. Longest chain 22 peptides. Score 0.636 Round 3: 162 peptides, 18 chains. Longest chain 26 peptides. Score 0.635 Round 4: 164 peptides, 20 chains. Longest chain 23 peptides. Score 0.608 Round 5: 165 peptides, 21 chains. Longest chain 16 peptides. Score 0.594 Taking the results from Round 2 Chains 23, Residues 155, Estimated correctness of the model 50.4 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 4312 restraints for refining 2044 atoms. 3668 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2064 (Rfree = 0.000) for 2044 atoms. Found 5 (14 requested) and removed 11 (9 requested) atoms. Cycle 27: After refmac, R = 0.1889 (Rfree = 0.000) for 2035 atoms. Found 5 (14 requested) and removed 10 (9 requested) atoms. Cycle 28: After refmac, R = 0.1901 (Rfree = 0.000) for 2028 atoms. Found 5 (14 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.2278 (Rfree = 0.000) for 2020 atoms. Found 14 (14 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1825 (Rfree = 0.000) for 2019 atoms. Found 2 (14 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 2077 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2093 seeds are put forward Round 1: 159 peptides, 19 chains. Longest chain 37 peptides. Score 0.606 Round 2: 168 peptides, 17 chains. Longest chain 37 peptides. Score 0.673 Round 3: 168 peptides, 20 chains. Longest chain 37 peptides. Score 0.623 Round 4: 155 peptides, 18 chains. Longest chain 20 peptides. Score 0.609 Round 5: 154 peptides, 20 chains. Longest chain 15 peptides. Score 0.568 Taking the results from Round 2 Chains 17, Residues 151, Estimated correctness of the model 59.2 % 1 chains (36 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3870 restraints for refining 2043 atoms. 3099 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1841 (Rfree = 0.000) for 2043 atoms. Found 2 (14 requested) and removed 11 (9 requested) atoms. Cycle 32: After refmac, R = 0.1721 (Rfree = 0.000) for 2030 atoms. Found 2 (14 requested) and removed 9 (9 requested) atoms. Cycle 33: After refmac, R = 0.1686 (Rfree = 0.000) for 2022 atoms. Found 3 (14 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.1706 (Rfree = 0.000) for 2015 atoms. Found 1 (14 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.1775 (Rfree = 0.000) for 2005 atoms. Found 2 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.19 Search for helices and strands: 0 residues in 0 chains, 2071 seeds are put forward NCS extension: 37 residues added (25 deleted due to clashes), 2108 seeds are put forward Round 1: 139 peptides, 22 chains. Longest chain 20 peptides. Score 0.459 Round 2: 158 peptides, 20 chains. Longest chain 37 peptides. Score 0.584 Round 3: 166 peptides, 19 chains. Longest chain 37 peptides. Score 0.633 Round 4: 167 peptides, 20 chains. Longest chain 21 peptides. Score 0.620 Round 5: 159 peptides, 20 chains. Longest chain 22 peptides. Score 0.588 Taking the results from Round 3 Chains 19, Residues 147, Estimated correctness of the model 49.6 % 1 chains (36 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 3890 restraints for refining 2045 atoms. 3137 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2658 (Rfree = 0.000) for 2045 atoms. Found 8 (14 requested) and removed 27 (9 requested) atoms. Cycle 37: After refmac, R = 0.2364 (Rfree = 0.000) for 2020 atoms. Found 3 (14 requested) and removed 11 (9 requested) atoms. Cycle 38: After refmac, R = 0.2085 (Rfree = 0.000) for 2012 atoms. Found 1 (14 requested) and removed 11 (9 requested) atoms. Cycle 39: After refmac, R = 0.2086 (Rfree = 0.000) for 2001 atoms. Found 3 (14 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.1969 (Rfree = 0.000) for 1993 atoms. Found 2 (14 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 49 residues added (18 deleted due to clashes), 2084 seeds are put forward Round 1: 131 peptides, 20 chains. Longest chain 17 peptides. Score 0.463 Round 2: 154 peptides, 22 chains. Longest chain 18 peptides. Score 0.529 Round 3: 149 peptides, 19 chains. Longest chain 22 peptides. Score 0.566 Round 4: 155 peptides, 18 chains. Longest chain 22 peptides. Score 0.609 Round 5: 147 peptides, 18 chains. Longest chain 17 peptides. Score 0.576 Taking the results from Round 4 Chains 18, Residues 137, Estimated correctness of the model 43.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4845 reflections ( 99.65 % complete ) and 4311 restraints for refining 2045 atoms. 3781 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2085 (Rfree = 0.000) for 2045 atoms. Found 4 (14 requested) and removed 11 (9 requested) atoms. Cycle 42: After refmac, R = 0.2014 (Rfree = 0.000) for 2037 atoms. Found 4 (14 requested) and removed 13 (9 requested) atoms. Cycle 43: After refmac, R = 0.1961 (Rfree = 0.000) for 2022 atoms. Found 8 (14 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.1847 (Rfree = 0.000) for 2021 atoms. Found 4 (14 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2275 (Rfree = 0.000) for 2014 atoms. Found 14 (14 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 2083 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 2113 seeds are put forward Round 1: 139 peptides, 25 chains. Longest chain 13 peptides. Score 0.393 Round 2: 153 peptides, 19 chains. Longest chain 20 peptides. Score 0.582 Round 3: 150 peptides, 18 chains. Longest chain 27 peptides. Score 0.589 Round 4: 147 peptides, 16 chains. Longest chain 20 peptides. Score 0.613 Round 5: 146 peptides, 19 chains. Longest chain 20 peptides. Score 0.553 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 131, Estimated correctness of the model 44.5 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 9 % 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 4237 restraints for refining 2045 atoms. 3674 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2026 (Rfree = 0.000) for 2045 atoms. Found 0 (14 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1903 (Rfree = 0.000) for 2032 atoms. Found 0 (14 requested) and removed 8 (9 requested) atoms. Cycle 48: After refmac, R = 0.2224 (Rfree = 0.000) for 2020 atoms. Found 0 (14 requested) and removed 8 (9 requested) atoms. Cycle 49: After refmac, R = 0.1940 (Rfree = 0.000) for 2010 atoms. Found 0 (14 requested) and removed 7 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:12:32 GMT 2018 Job finished. TimeTaking 44.61 Used memory is bytes: 9043416