null Sun 23 Dec 23:42:03 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 2i51-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i51-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i51-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.4-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/2i51-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.4-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 ============================================================ Sun 23 Dec 23:42:08 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/2i51-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i51-3.4-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 341 and 0 Target number of residues in the AU: 341 Target solvent content: 0.6203 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: 2i51-3.4-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: 2i51-3.4-parrot-mrncs.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 3.400 Wilson plot Bfac: 61.45 6083 reflections ( 85.58 % complete ) and 0 restraints for refining 3437 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3277 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2758 (Rfree = 0.000) for 3437 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 2.90 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: 177 peptides, 34 chains. Longest chain 11 peptides. Score 0.325 Round 2: 247 peptides, 35 chains. Longest chain 15 peptides. Score 0.533 Round 3: 248 peptides, 37 chains. Longest chain 14 peptides. Score 0.511 Round 4: 262 peptides, 36 chains. Longest chain 14 peptides. Score 0.561 Round 5: 263 peptides, 35 chains. Longest chain 23 peptides. Score 0.575 Taking the results from Round 5 Chains 35, Residues 228, Estimated correctness of the model 20.3 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 5928 restraints for refining 2837 atoms. 5033 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2406 (Rfree = 0.000) for 2837 atoms. Found 15 (21 requested) and removed 15 (10 requested) atoms. Cycle 2: After refmac, R = 0.2228 (Rfree = 0.000) for 2815 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 3: After refmac, R = 0.2168 (Rfree = 0.000) for 2798 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. Cycle 4: After refmac, R = 0.2115 (Rfree = 0.000) for 2791 atoms. Found 7 (21 requested) and removed 12 (10 requested) atoms. Cycle 5: After refmac, R = 0.2087 (Rfree = 0.000) for 2782 atoms. Found 4 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 2862 seeds are put forward NCS extension: 45 residues added (1 deleted due to clashes), 2907 seeds are put forward Round 1: 231 peptides, 38 chains. Longest chain 17 peptides. Score 0.448 Round 2: 254 peptides, 36 chains. Longest chain 20 peptides. Score 0.540 Round 3: 266 peptides, 33 chains. Longest chain 27 peptides. Score 0.605 Round 4: 259 peptides, 36 chains. Longest chain 19 peptides. Score 0.553 Round 5: 267 peptides, 33 chains. Longest chain 29 peptides. Score 0.608 Taking the results from Round 5 Chains 33, Residues 234, Estimated correctness of the model 31.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6068 restraints for refining 2837 atoms. 5165 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2248 (Rfree = 0.000) for 2837 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. Cycle 7: After refmac, R = 0.2033 (Rfree = 0.000) for 2844 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 8: After refmac, R = 0.1955 (Rfree = 0.000) for 2835 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 9: After refmac, R = 0.1913 (Rfree = 0.000) for 2822 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 10: After refmac, R = 0.1885 (Rfree = 0.000) for 2812 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 2884 seeds are put forward NCS extension: 46 residues added (7 deleted due to clashes), 2930 seeds are put forward Round 1: 251 peptides, 39 chains. Longest chain 18 peptides. Score 0.495 Round 2: 269 peptides, 39 chains. Longest chain 18 peptides. Score 0.545 Round 3: 264 peptides, 32 chains. Longest chain 18 peptides. Score 0.611 Round 4: 258 peptides, 33 chains. Longest chain 33 peptides. Score 0.585 Round 5: 259 peptides, 32 chains. Longest chain 36 peptides. Score 0.599 Taking the results from Round 3 Chains 32, Residues 232, Estimated correctness of the model 32.2 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6095 restraints for refining 2837 atoms. 5171 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2154 (Rfree = 0.000) for 2837 atoms. Found 15 (21 requested) and removed 11 (10 requested) atoms. Cycle 12: After refmac, R = 0.2005 (Rfree = 0.000) for 2831 atoms. Found 10 (21 requested) and removed 10 (10 requested) atoms. Cycle 13: After refmac, R = 0.1942 (Rfree = 0.000) for 2825 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Cycle 14: After refmac, R = 0.1899 (Rfree = 0.000) for 2820 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 15: After refmac, R = 0.1886 (Rfree = 0.000) for 2811 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 2866 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2881 seeds are put forward Round 1: 225 peptides, 36 chains. Longest chain 17 peptides. Score 0.456 Round 2: 237 peptides, 32 chains. Longest chain 23 peptides. Score 0.542 Round 3: 250 peptides, 31 chains. Longest chain 20 peptides. Score 0.588 Round 4: 246 peptides, 32 chains. Longest chain 20 peptides. Score 0.566 Round 5: 240 peptides, 32 chains. Longest chain 20 peptides. Score 0.550 Taking the results from Round 3 Chains 31, Residues 219, Estimated correctness of the model 24.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6185 restraints for refining 2834 atoms. 5340 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2115 (Rfree = 0.000) for 2834 atoms. Found 17 (21 requested) and removed 10 (10 requested) atoms. Cycle 17: After refmac, R = 0.1978 (Rfree = 0.000) for 2836 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 18: After refmac, R = 0.1956 (Rfree = 0.000) for 2824 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.1919 (Rfree = 0.000) for 2818 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.1910 (Rfree = 0.000) for 2810 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 2857 seeds are put forward NCS extension: 18 residues added (7 deleted due to clashes), 2875 seeds are put forward Round 1: 222 peptides, 39 chains. Longest chain 16 peptides. Score 0.406 Round 2: 237 peptides, 31 chains. Longest chain 20 peptides. Score 0.554 Round 3: 229 peptides, 28 chains. Longest chain 20 peptides. Score 0.569 Round 4: 233 peptides, 33 chains. Longest chain 17 peptides. Score 0.518 Round 5: 234 peptides, 31 chains. Longest chain 20 peptides. Score 0.546 Taking the results from Round 3 Chains 28, Residues 201, Estimated correctness of the model 18.2 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6247 restraints for refining 2837 atoms. 5459 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2083 (Rfree = 0.000) for 2837 atoms. Found 21 (21 requested) and removed 11 (10 requested) atoms. Cycle 22: After refmac, R = 0.1911 (Rfree = 0.000) for 2842 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 23: After refmac, R = 0.1910 (Rfree = 0.000) for 2829 atoms. Found 6 (21 requested) and removed 11 (10 requested) atoms. Cycle 24: After refmac, R = 0.1850 (Rfree = 0.000) for 2822 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.1813 (Rfree = 0.000) for 2820 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.92 Search for helices and strands: 0 residues in 0 chains, 2869 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 2903 seeds are put forward Round 1: 222 peptides, 36 chains. Longest chain 18 peptides. Score 0.447 Round 2: 249 peptides, 32 chains. Longest chain 20 peptides. Score 0.574 Round 3: 234 peptides, 32 chains. Longest chain 19 peptides. Score 0.534 Round 4: 236 peptides, 29 chains. Longest chain 17 peptides. Score 0.575 Round 5: 242 peptides, 32 chains. Longest chain 21 peptides. Score 0.556 Taking the results from Round 4 Chains 29, Residues 207, Estimated correctness of the model 20.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6306 restraints for refining 2837 atoms. 5507 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2111 (Rfree = 0.000) for 2837 atoms. Found 15 (21 requested) and removed 11 (10 requested) atoms. Cycle 27: After refmac, R = 0.1958 (Rfree = 0.000) for 2838 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.1930 (Rfree = 0.000) for 2829 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.1906 (Rfree = 0.000) for 2822 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.1882 (Rfree = 0.000) for 2814 atoms. Found 1 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 2.92 Search for helices and strands: 0 residues in 0 chains, 2858 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2875 seeds are put forward Round 1: 205 peptides, 29 chains. Longest chain 14 peptides. Score 0.489 Round 2: 230 peptides, 26 chains. Longest chain 17 peptides. Score 0.595 Round 3: 238 peptides, 28 chains. Longest chain 17 peptides. Score 0.592 Round 4: 241 peptides, 29 chains. Longest chain 18 peptides. Score 0.588 Round 5: 224 peptides, 29 chains. Longest chain 18 peptides. Score 0.543 Taking the results from Round 2 Chains 26, Residues 204, Estimated correctness of the model 27.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6091 restraints for refining 2837 atoms. 5229 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2087 (Rfree = 0.000) for 2837 atoms. Found 9 (21 requested) and removed 14 (10 requested) atoms. Cycle 32: After refmac, R = 0.1949 (Rfree = 0.000) for 2829 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.1893 (Rfree = 0.000) for 2823 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.1874 (Rfree = 0.000) for 2816 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1846 (Rfree = 0.000) for 2811 atoms. Found 3 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 2847 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2866 seeds are put forward Round 1: 212 peptides, 37 chains. Longest chain 16 peptides. Score 0.401 Round 2: 218 peptides, 34 chains. Longest chain 16 peptides. Score 0.461 Round 3: 205 peptides, 28 chains. Longest chain 18 peptides. Score 0.502 Round 4: 218 peptides, 29 chains. Longest chain 30 peptides. Score 0.527 Round 5: 208 peptides, 28 chains. Longest chain 15 peptides. Score 0.511 Taking the results from Round 4 Chains 29, Residues 189, Estimated correctness of the model 3.1 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6154 restraints for refining 2836 atoms. 5367 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2222 (Rfree = 0.000) for 2836 atoms. Found 14 (21 requested) and removed 11 (10 requested) atoms. Cycle 37: After refmac, R = 0.2088 (Rfree = 0.000) for 2833 atoms. Found 6 (21 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.2040 (Rfree = 0.000) for 2823 atoms. Found 6 (21 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.2011 (Rfree = 0.000) for 2815 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1997 (Rfree = 0.000) for 2805 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 2862 seeds are put forward NCS extension: 62 residues added (3 deleted due to clashes), 2924 seeds are put forward Round 1: 172 peptides, 30 chains. Longest chain 12 peptides. Score 0.368 Round 2: 200 peptides, 28 chains. Longest chain 16 peptides. Score 0.487 Round 3: 203 peptides, 29 chains. Longest chain 15 peptides. Score 0.483 Round 4: 217 peptides, 29 chains. Longest chain 16 peptides. Score 0.524 Round 5: 212 peptides, 29 chains. Longest chain 15 peptides. Score 0.509 Taking the results from Round 4 Chains 30, Residues 188, Estimated correctness of the model 1.9 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6090 restraints for refining 2836 atoms. 5266 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2276 (Rfree = 0.000) for 2836 atoms. Found 14 (21 requested) and removed 12 (10 requested) atoms. Cycle 42: After refmac, R = 0.2116 (Rfree = 0.000) for 2834 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.2070 (Rfree = 0.000) for 2826 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.2052 (Rfree = 0.000) for 2816 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.2027 (Rfree = 0.000) for 2809 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 2844 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2863 seeds are put forward Round 1: 180 peptides, 33 chains. Longest chain 13 peptides. Score 0.351 Round 2: 183 peptides, 28 chains. Longest chain 17 peptides. Score 0.434 Round 3: 205 peptides, 30 chains. Longest chain 17 peptides. Score 0.475 Round 4: 201 peptides, 30 chains. Longest chain 16 peptides. Score 0.463 Round 5: 198 peptides, 30 chains. Longest chain 18 peptides. Score 0.454 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 175, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2i51-3_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (175 residues) following loop building 3 chains (32 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6083 reflections ( 85.58 % complete ) and 6048 restraints for refining 2837 atoms. 5234 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2241 (Rfree = 0.000) for 2837 atoms. Found 0 (21 requested) and removed 8 (10 requested) atoms. Cycle 47: After refmac, R = 0.2125 (Rfree = 0.000) for 2825 atoms. Found 0 (21 requested) and removed 7 (10 requested) atoms. Cycle 48: After refmac, R = 0.2154 (Rfree = 0.000) for 2812 atoms. Found 0 (21 requested) and removed 3 (10 requested) atoms. Cycle 49: After refmac, R = 0.2080 (Rfree = 0.000) for 2806 atoms. Found 0 (21 requested) and removed 2 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:21:18 GMT 2018 Job finished. TimeTaking 39.25 Used memory is bytes: 8594024