null Sun 23 Dec 22:23:02 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 2i51-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i51-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i51-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-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/2i51-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-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 22:23:11 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/2i51-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-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 314 and 0 Target number of residues in the AU: 314 Target solvent content: 0.6504 Checking the provided sequence file Detected sequence length: 195 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 390 Adjusted target solvent content: 0.57 Input MTZ file: 2i51-4.0-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: 19 Cell parameters: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3120 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: 56.880 4.000 Wilson plot Bfac: 77.89 3751 reflections ( 84.54 % complete ) and 0 restraints for refining 3479 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3550 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3550 (Rfree = 0.000) for 3479 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 3501 seeds are put forward NCS extension: 0 residues added, 3501 seeds are put forward Round 1: 98 peptides, 22 chains. Longest chain 8 peptides. Score 0.213 Round 2: 142 peptides, 27 chains. Longest chain 10 peptides. Score 0.306 Round 3: 164 peptides, 28 chains. Longest chain 12 peptides. Score 0.370 Round 4: 171 peptides, 29 chains. Longest chain 12 peptides. Score 0.379 Round 5: 175 peptides, 31 chains. Longest chain 11 peptides. Score 0.363 Taking the results from Round 4 Chains 29, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6677 restraints for refining 2815 atoms. 6138 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2811 (Rfree = 0.000) for 2815 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 2: After refmac, R = 0.2949 (Rfree = 0.000) for 2767 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 3: After refmac, R = 0.2484 (Rfree = 0.000) for 2754 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2384 (Rfree = 0.000) for 2730 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2570 (Rfree = 0.000) for 2713 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 2769 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2786 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 12 peptides. Score 0.239 Round 2: 140 peptides, 28 chains. Longest chain 8 peptides. Score 0.282 Round 3: 152 peptides, 27 chains. Longest chain 12 peptides. Score 0.343 Round 4: 161 peptides, 30 chains. Longest chain 11 peptides. Score 0.329 Round 5: 155 peptides, 26 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 5 Chains 26, Residues 129, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 5859 restraints for refining 2570 atoms. 5340 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2639 (Rfree = 0.000) for 2570 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 7: After refmac, R = 0.2314 (Rfree = 0.000) for 2548 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 8: After refmac, R = 0.2169 (Rfree = 0.000) for 2530 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2082 (Rfree = 0.000) for 2522 atoms. Found 9 (12 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.2135 (Rfree = 0.000) for 2510 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 2573 seeds are put forward NCS extension: 0 residues added, 2573 seeds are put forward Round 1: 150 peptides, 31 chains. Longest chain 10 peptides. Score 0.272 Round 2: 171 peptides, 29 chains. Longest chain 13 peptides. Score 0.379 Round 3: 182 peptides, 29 chains. Longest chain 15 peptides. Score 0.416 Round 4: 176 peptides, 28 chains. Longest chain 17 peptides. Score 0.411 Round 5: 183 peptides, 29 chains. Longest chain 16 peptides. Score 0.420 Taking the results from Round 5 Chains 29, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 5985 restraints for refining 2652 atoms. 5398 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2324 (Rfree = 0.000) for 2652 atoms. Found 10 (12 requested) and removed 26 (6 requested) atoms. Cycle 12: After refmac, R = 0.1936 (Rfree = 0.000) for 2612 atoms. Found 9 (12 requested) and removed 14 (6 requested) atoms. Cycle 13: After refmac, R = 0.1857 (Rfree = 0.000) for 2599 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.1638 (Rfree = 0.000) for 2585 atoms. Found 2 (12 requested) and removed 12 (6 requested) atoms. Cycle 15: After refmac, R = 0.1571 (Rfree = 0.000) for 2568 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 2632 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2650 seeds are put forward Round 1: 185 peptides, 35 chains. Longest chain 11 peptides. Score 0.338 Round 2: 187 peptides, 32 chains. Longest chain 13 peptides. Score 0.389 Round 3: 203 peptides, 35 chains. Longest chain 15 peptides. Score 0.400 Round 4: 207 peptides, 36 chains. Longest chain 16 peptides. Score 0.399 Round 5: 194 peptides, 33 chains. Longest chain 11 peptides. Score 0.398 Taking the results from Round 3 Chains 35, Residues 168, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6207 restraints for refining 2811 atoms. 5533 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1943 (Rfree = 0.000) for 2811 atoms. Found 7 (13 requested) and removed 71 (6 requested) atoms. Cycle 17: After refmac, R = 0.1998 (Rfree = 0.000) for 2714 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 18: After refmac, R = 0.1963 (Rfree = 0.000) for 2699 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.1875 (Rfree = 0.000) for 2689 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 20: After refmac, R = 0.1759 (Rfree = 0.000) for 2683 atoms. Found 11 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.30 Search for helices and strands: 0 residues in 0 chains, 2723 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2744 seeds are put forward Round 1: 177 peptides, 36 chains. Longest chain 9 peptides. Score 0.294 Round 2: 201 peptides, 36 chains. Longest chain 11 peptides. Score 0.379 Round 3: 186 peptides, 31 chains. Longest chain 14 peptides. Score 0.401 Round 4: 191 peptides, 33 chains. Longest chain 15 peptides. Score 0.388 Round 5: 185 peptides, 31 chains. Longest chain 16 peptides. Score 0.397 Taking the results from Round 3 Chains 31, Residues 155, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6379 restraints for refining 2817 atoms. 5748 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2021 (Rfree = 0.000) for 2817 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 22: After refmac, R = 0.1892 (Rfree = 0.000) for 2799 atoms. Found 12 (13 requested) and removed 18 (6 requested) atoms. Cycle 23: After refmac, R = 0.1568 (Rfree = 0.000) for 2780 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 24: After refmac, R = 0.1437 (Rfree = 0.000) for 2771 atoms. Found 2 (13 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.1409 (Rfree = 0.000) for 2758 atoms. Found 3 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.30 Search for helices and strands: 0 residues in 0 chains, 2808 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2824 seeds are put forward Round 1: 155 peptides, 32 chains. Longest chain 8 peptides. Score 0.275 Round 2: 187 peptides, 34 chains. Longest chain 12 peptides. Score 0.360 Round 3: 185 peptides, 32 chains. Longest chain 16 peptides. Score 0.383 Round 4: 191 peptides, 31 chains. Longest chain 13 peptides. Score 0.417 Round 5: 187 peptides, 33 chains. Longest chain 10 peptides. Score 0.375 Taking the results from Round 4 Chains 31, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6422 restraints for refining 2817 atoms. 5813 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2022 (Rfree = 0.000) for 2817 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 27: After refmac, R = 0.2160 (Rfree = 0.000) for 2795 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 28: After refmac, R = 0.1979 (Rfree = 0.000) for 2791 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 29: After refmac, R = 0.1470 (Rfree = 0.000) for 2781 atoms. Found 4 (13 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.1718 (Rfree = 0.000) for 2771 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 2824 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2844 seeds are put forward Round 1: 155 peptides, 32 chains. Longest chain 8 peptides. Score 0.275 Round 2: 159 peptides, 27 chains. Longest chain 11 peptides. Score 0.368 Round 3: 180 peptides, 31 chains. Longest chain 15 peptides. Score 0.380 Round 4: 176 peptides, 28 chains. Longest chain 11 peptides. Score 0.411 Round 5: 190 peptides, 31 chains. Longest chain 11 peptides. Score 0.414 Taking the results from Round 5 Chains 31, Residues 159, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6446 restraints for refining 2817 atoms. 5798 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2142 (Rfree = 0.000) for 2817 atoms. Found 6 (13 requested) and removed 11 (6 requested) atoms. Cycle 32: After refmac, R = 0.2133 (Rfree = 0.000) for 2791 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 33: After refmac, R = 0.1893 (Rfree = 0.000) for 2771 atoms. Found 11 (13 requested) and removed 16 (6 requested) atoms. Cycle 34: After refmac, R = 0.1482 (Rfree = 0.000) for 2760 atoms. Found 2 (13 requested) and removed 16 (6 requested) atoms. Cycle 35: After refmac, R = 0.1740 (Rfree = 0.000) for 2745 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 2819 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2833 seeds are put forward Round 1: 139 peptides, 30 chains. Longest chain 8 peptides. Score 0.245 Round 2: 155 peptides, 28 chains. Longest chain 10 peptides. Score 0.338 Round 3: 146 peptides, 26 chains. Longest chain 11 peptides. Score 0.337 Round 4: 164 peptides, 28 chains. Longest chain 11 peptides. Score 0.370 Round 5: 139 peptides, 25 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 4 Chains 28, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6656 restraints for refining 2817 atoms. 6140 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2161 (Rfree = 0.000) for 2817 atoms. Found 13 (13 requested) and removed 34 (6 requested) atoms. Cycle 37: After refmac, R = 0.2112 (Rfree = 0.000) for 2782 atoms. Found 13 (13 requested) and removed 33 (6 requested) atoms. Cycle 38: After refmac, R = 0.2181 (Rfree = 0.000) for 2752 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 39: After refmac, R = 0.2193 (Rfree = 0.000) for 2726 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 40: After refmac, R = 0.2011 (Rfree = 0.000) for 2709 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 2758 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2770 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 6 peptides. Score 0.222 Round 2: 121 peptides, 26 chains. Longest chain 9 peptides. Score 0.240 Round 3: 125 peptides, 21 chains. Longest chain 12 peptides. Score 0.341 Round 4: 129 peptides, 24 chains. Longest chain 10 peptides. Score 0.306 Round 5: 127 peptides, 22 chains. Longest chain 11 peptides. Score 0.332 Taking the results from Round 3 Chains 21, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6209 restraints for refining 2665 atoms. 5814 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2143 (Rfree = 0.000) for 2665 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 42: After refmac, R = 0.2173 (Rfree = 0.000) for 2654 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 43: After refmac, R = 0.1999 (Rfree = 0.000) for 2634 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 44: After refmac, R = 0.2183 (Rfree = 0.000) for 2626 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 45: After refmac, R = 0.2171 (Rfree = 0.000) for 2617 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.27 Search for helices and strands: 0 residues in 0 chains, 2679 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2694 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 10 peptides. Score 0.243 Round 2: 140 peptides, 28 chains. Longest chain 9 peptides. Score 0.282 Round 3: 142 peptides, 25 chains. Longest chain 11 peptides. Score 0.338 Round 4: 143 peptides, 24 chains. Longest chain 11 peptides. Score 0.358 Round 5: 148 peptides, 24 chains. Longest chain 13 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 124, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2i51-4_warpNtrace.pdb as input Building loops using Loopy2018 24 chains (124 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3751 reflections ( 84.54 % complete ) and 5845 restraints for refining 2686 atoms. 5303 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2332 (Rfree = 0.000) for 2686 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1990 (Rfree = 0.000) for 2666 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1534 (Rfree = 0.000) for 2650 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2043 (Rfree = 0.000) for 2639 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:43 GMT 2018 Job finished. TimeTaking 47.69 Used memory is bytes: 21602000