null Mon 24 Dec 00:24:30 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 2i51-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i51-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i51-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-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/2i51-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-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 00:24:35 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/2i51-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-4.0-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 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-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: 19 Cell parameters: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3120 target number of atoms Had to go as low as 0.90 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 3443 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3499 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3410 (Rfree = 0.000) for 3443 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 3482 seeds are put forward NCS extension: 0 residues added, 3482 seeds are put forward Round 1: 116 peptides, 25 chains. Longest chain 9 peptides. Score 0.237 Round 2: 168 peptides, 34 chains. Longest chain 11 peptides. Score 0.292 Round 3: 180 peptides, 33 chains. Longest chain 12 peptides. Score 0.351 Round 4: 185 peptides, 32 chains. Longest chain 12 peptides. Score 0.383 Round 5: 198 peptides, 34 chains. Longest chain 12 peptides. Score 0.397 Taking the results from Round 5 Chains 34, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6513 restraints for refining 2816 atoms. 5891 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2710 (Rfree = 0.000) for 2816 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. Cycle 2: After refmac, R = 0.2735 (Rfree = 0.000) for 2734 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 3: After refmac, R = 0.2668 (Rfree = 0.000) for 2695 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2613 (Rfree = 0.000) for 2664 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2160 (Rfree = 0.000) for 2649 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.34 Search for helices and strands: 0 residues in 0 chains, 2715 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2731 seeds are put forward Round 1: 142 peptides, 30 chains. Longest chain 7 peptides. Score 0.257 Round 2: 167 peptides, 31 chains. Longest chain 9 peptides. Score 0.335 Round 3: 174 peptides, 28 chains. Longest chain 18 peptides. Score 0.405 Round 4: 179 peptides, 31 chains. Longest chain 13 peptides. Score 0.377 Round 5: 177 peptides, 30 chains. Longest chain 13 peptides. Score 0.385 Taking the results from Round 3 Chains 29, Residues 146, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 5619 restraints for refining 2525 atoms. 5017 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2129 (Rfree = 0.000) for 2525 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 7: After refmac, R = 0.1917 (Rfree = 0.000) for 2490 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 8: After refmac, R = 0.1800 (Rfree = 0.000) for 2477 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.1774 (Rfree = 0.000) for 2463 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.1760 (Rfree = 0.000) for 2456 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 3.30 Search for helices and strands: 0 residues in 0 chains, 2521 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2547 seeds are put forward Round 1: 170 peptides, 31 chains. Longest chain 9 peptides. Score 0.346 Round 2: 206 peptides, 36 chains. Longest chain 8 peptides. Score 0.395 Round 3: 206 peptides, 36 chains. Longest chain 9 peptides. Score 0.395 Round 4: 197 peptides, 31 chains. Longest chain 10 peptides. Score 0.437 Round 5: 205 peptides, 34 chains. Longest chain 12 peptides. Score 0.420 Taking the results from Round 4 Chains 31, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6042 restraints for refining 2651 atoms. 5409 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2167 (Rfree = 0.000) for 2651 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 12: After refmac, R = 0.2017 (Rfree = 0.000) for 2618 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.1971 (Rfree = 0.000) for 2606 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.1953 (Rfree = 0.000) for 2595 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.1943 (Rfree = 0.000) for 2588 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 3.32 Search for helices and strands: 0 residues in 0 chains, 2638 seeds are put forward NCS extension: 0 residues added, 2638 seeds are put forward Round 1: 163 peptides, 33 chains. Longest chain 8 peptides. Score 0.289 Round 2: 176 peptides, 30 chains. Longest chain 11 peptides. Score 0.382 Round 3: 180 peptides, 31 chains. Longest chain 10 peptides. Score 0.380 Round 4: 189 peptides, 30 chains. Longest chain 11 peptides. Score 0.425 Round 5: 188 peptides, 30 chains. Longest chain 11 peptides. Score 0.422 Taking the results from Round 4 Chains 30, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6208 restraints for refining 2710 atoms. 5602 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2411 (Rfree = 0.000) for 2710 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 17: After refmac, R = 0.2285 (Rfree = 0.000) for 2697 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. Cycle 18: After refmac, R = 0.2219 (Rfree = 0.000) for 2688 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 19: After refmac, R = 0.2168 (Rfree = 0.000) for 2683 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2151 (Rfree = 0.000) for 2679 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 2720 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2734 seeds are put forward Round 1: 155 peptides, 32 chains. Longest chain 10 peptides. Score 0.275 Round 2: 185 peptides, 29 chains. Longest chain 12 peptides. Score 0.426 Round 3: 178 peptides, 30 chains. Longest chain 12 peptides. Score 0.388 Round 4: 178 peptides, 30 chains. Longest chain 11 peptides. Score 0.388 Round 5: 165 peptides, 28 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 2 Chains 30, Residues 156, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6219 restraints for refining 2762 atoms. 5587 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2479 (Rfree = 0.000) for 2762 atoms. Found 8 (13 requested) and removed 13 (6 requested) atoms. Cycle 22: After refmac, R = 0.2365 (Rfree = 0.000) for 2749 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.2332 (Rfree = 0.000) for 2739 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.2303 (Rfree = 0.000) for 2725 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.2286 (Rfree = 0.000) for 2717 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.33 Search for helices and strands: 0 residues in 0 chains, 2741 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2756 seeds are put forward Round 1: 155 peptides, 32 chains. Longest chain 9 peptides. Score 0.275 Round 2: 181 peptides, 33 chains. Longest chain 10 peptides. Score 0.354 Round 3: 185 peptides, 32 chains. Longest chain 12 peptides. Score 0.383 Round 4: 171 peptides, 27 chains. Longest chain 11 peptides. Score 0.409 Round 5: 174 peptides, 27 chains. Longest chain 16 peptides. Score 0.419 Taking the results from Round 5 Chains 27, Residues 147, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6733 restraints for refining 2816 atoms. 6172 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2301 (Rfree = 0.000) for 2816 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 27: After refmac, R = 0.2129 (Rfree = 0.000) for 2796 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.2361 (Rfree = 0.000) for 2788 atoms. Found 7 (13 requested) and removed 11 (6 requested) atoms. Cycle 29: After refmac, R = 0.2126 (Rfree = 0.000) for 2767 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2058 (Rfree = 0.000) for 2763 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.31 Search for helices and strands: 0 residues in 0 chains, 2799 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2816 seeds are put forward Round 1: 152 peptides, 32 chains. Longest chain 7 peptides. Score 0.264 Round 2: 172 peptides, 33 chains. Longest chain 9 peptides. Score 0.322 Round 3: 183 peptides, 30 chains. Longest chain 14 peptides. Score 0.405 Round 4: 173 peptides, 30 chains. Longest chain 11 peptides. Score 0.371 Round 5: 178 peptides, 31 chains. Longest chain 12 peptides. Score 0.374 Taking the results from Round 3 Chains 30, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6608 restraints for refining 2815 atoms. 6026 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2217 (Rfree = 0.000) for 2815 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 32: After refmac, R = 0.2056 (Rfree = 0.000) for 2807 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2000 (Rfree = 0.000) for 2798 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.1965 (Rfree = 0.000) for 2791 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1947 (Rfree = 0.000) for 2786 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 2819 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2835 seeds are put forward Round 1: 156 peptides, 33 chains. Longest chain 7 peptides. Score 0.263 Round 2: 170 peptides, 31 chains. Longest chain 10 peptides. Score 0.346 Round 3: 170 peptides, 28 chains. Longest chain 15 peptides. Score 0.391 Round 4: 168 peptides, 30 chains. Longest chain 13 peptides. Score 0.354 Round 5: 179 peptides, 29 chains. Longest chain 14 peptides. Score 0.407 Taking the results from Round 5 Chains 29, Residues 150, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6694 restraints for refining 2817 atoms. 6098 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2182 (Rfree = 0.000) for 2817 atoms. Found 8 (13 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.1988 (Rfree = 0.000) for 2798 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.1964 (Rfree = 0.000) for 2789 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.1950 (Rfree = 0.000) for 2784 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1986 (Rfree = 0.000) for 2776 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.36 Search for helices and strands: 0 residues in 0 chains, 2809 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2835 seeds are put forward Round 1: 142 peptides, 32 chains. Longest chain 6 peptides. Score 0.224 Round 2: 147 peptides, 28 chains. Longest chain 10 peptides. Score 0.309 Round 3: 153 peptides, 27 chains. Longest chain 12 peptides. Score 0.347 Round 4: 157 peptides, 27 chains. Longest chain 9 peptides. Score 0.361 Round 5: 172 peptides, 28 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 5 Chains 28, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3751 reflections ( 84.54 % complete ) and 6725 restraints for refining 2817 atoms. 6177 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2181 (Rfree = 0.000) for 2817 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.2051 (Rfree = 0.000) for 2810 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.1980 (Rfree = 0.000) for 2804 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1969 (Rfree = 0.000) for 2795 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1958 (Rfree = 0.000) for 2788 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 2833 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2847 seeds are put forward Round 1: 122 peptides, 26 chains. Longest chain 8 peptides. Score 0.244 Round 2: 133 peptides, 26 chains. Longest chain 11 peptides. Score 0.288 Round 3: 143 peptides, 27 chains. Longest chain 9 peptides. Score 0.310 Round 4: 144 peptides, 26 chains. Longest chain 10 peptides. Score 0.330 Round 5: 142 peptides, 26 chains. Longest chain 9 peptides. Score 0.322 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 118, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2i51-4_warpNtrace.pdb as input Building loops using Loopy2018 26 chains (118 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3751 reflections ( 84.54 % complete ) and 6898 restraints for refining 2817 atoms. 6429 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2094 (Rfree = 0.000) for 2817 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1969 (Rfree = 0.000) for 2803 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1928 (Rfree = 0.000) for 2790 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1875 (Rfree = 0.000) for 2781 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:00:53 GMT 2018 Job finished. TimeTaking 36.38 Used memory is bytes: 21167056