null Mon 24 Dec 07:28:15 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i51-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i51-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i51-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-parrot-noncs ############### 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 07:28:19 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/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-parrot-noncs/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 322 and 0 Target number of residues in the AU: 322 Target solvent content: 0.6415 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: 2i51-3.8-parrot-noncs.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: 2i51-3.8-parrot-noncs.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 3.800 Wilson plot Bfac: 72.52 4372 reflections ( 84.88 % complete ) and 0 restraints for refining 3478 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3538 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3329 (Rfree = 0.000) for 3478 atoms. Found 19 (19 requested) and removed 45 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 3490 seeds are put forward NCS extension: 0 residues added, 3490 seeds are put forward Round 1: 107 peptides, 24 chains. Longest chain 6 peptides. Score 0.216 Round 2: 159 peptides, 31 chains. Longest chain 9 peptides. Score 0.306 Round 3: 183 peptides, 28 chains. Longest chain 15 peptides. Score 0.434 Round 4: 184 peptides, 32 chains. Longest chain 12 peptides. Score 0.379 Round 5: 184 peptides, 30 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 3 Chains 29, Residues 155, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6183 restraints for refining 2821 atoms. 5502 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2904 (Rfree = 0.000) for 2821 atoms. Found 7 (15 requested) and removed 20 (7 requested) atoms. Cycle 2: After refmac, R = 0.2935 (Rfree = 0.000) for 2753 atoms. Found 12 (15 requested) and removed 11 (7 requested) atoms. Cycle 3: After refmac, R = 0.2859 (Rfree = 0.000) for 2736 atoms. Found 9 (15 requested) and removed 14 (7 requested) atoms. Cycle 4: After refmac, R = 0.2719 (Rfree = 0.000) for 2717 atoms. Found 7 (15 requested) and removed 12 (7 requested) atoms. Cycle 5: After refmac, R = 0.2438 (Rfree = 0.000) for 2692 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 2739 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2758 seeds are put forward Round 1: 167 peptides, 36 chains. Longest chain 7 peptides. Score 0.257 Round 2: 193 peptides, 35 chains. Longest chain 11 peptides. Score 0.366 Round 3: 184 peptides, 34 chains. Longest chain 9 peptides. Score 0.350 Round 4: 204 peptides, 34 chains. Longest chain 12 peptides. Score 0.417 Round 5: 206 peptides, 34 chains. Longest chain 13 peptides. Score 0.423 Taking the results from Round 5 Chains 34, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6561 restraints for refining 2822 atoms. 5907 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2594 (Rfree = 0.000) for 2822 atoms. Found 11 (15 requested) and removed 23 (7 requested) atoms. Cycle 7: After refmac, R = 0.2463 (Rfree = 0.000) for 2787 atoms. Found 9 (15 requested) and removed 32 (7 requested) atoms. Cycle 8: After refmac, R = 0.2387 (Rfree = 0.000) for 2750 atoms. Found 14 (15 requested) and removed 23 (7 requested) atoms. Cycle 9: After refmac, R = 0.2222 (Rfree = 0.000) for 2728 atoms. Found 8 (15 requested) and removed 15 (7 requested) atoms. Cycle 10: After refmac, R = 0.1944 (Rfree = 0.000) for 2717 atoms. Found 2 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 2754 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2771 seeds are put forward Round 1: 174 peptides, 36 chains. Longest chain 10 peptides. Score 0.283 Round 2: 201 peptides, 36 chains. Longest chain 10 peptides. Score 0.379 Round 3: 204 peptides, 35 chains. Longest chain 11 peptides. Score 0.403 Round 4: 201 peptides, 33 chains. Longest chain 13 peptides. Score 0.421 Round 5: 206 peptides, 33 chains. Longest chain 13 peptides. Score 0.437 Taking the results from Round 5 Chains 33, Residues 173, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6428 restraints for refining 2822 atoms. 5749 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2330 (Rfree = 0.000) for 2822 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. Cycle 12: After refmac, R = 0.2161 (Rfree = 0.000) for 2804 atoms. Found 2 (15 requested) and removed 11 (7 requested) atoms. Cycle 13: After refmac, R = 0.2080 (Rfree = 0.000) for 2788 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. Cycle 14: After refmac, R = 0.2061 (Rfree = 0.000) for 2774 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Cycle 15: After refmac, R = 0.2040 (Rfree = 0.000) for 2765 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 2817 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2833 seeds are put forward Round 1: 184 peptides, 35 chains. Longest chain 12 peptides. Score 0.335 Round 2: 195 peptides, 35 chains. Longest chain 14 peptides. Score 0.373 Round 3: 201 peptides, 31 chains. Longest chain 15 peptides. Score 0.449 Round 4: 210 peptides, 33 chains. Longest chain 14 peptides. Score 0.450 Round 5: 192 peptides, 28 chains. Longest chain 14 peptides. Score 0.463 Taking the results from Round 5 Chains 28, Residues 164, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6483 restraints for refining 2822 atoms. 5818 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2365 (Rfree = 0.000) for 2822 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Cycle 17: After refmac, R = 0.2258 (Rfree = 0.000) for 2807 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 18: After refmac, R = 0.2339 (Rfree = 0.000) for 2801 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. Cycle 19: After refmac, R = 0.2344 (Rfree = 0.000) for 2789 atoms. Found 2 (15 requested) and removed 10 (7 requested) atoms. Cycle 20: After refmac, R = 0.2298 (Rfree = 0.000) for 2779 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.22 Search for helices and strands: 0 residues in 0 chains, 2812 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2831 seeds are put forward Round 1: 184 peptides, 33 chains. Longest chain 11 peptides. Score 0.364 Round 2: 201 peptides, 29 chains. Longest chain 14 peptides. Score 0.477 Round 3: 197 peptides, 30 chains. Longest chain 14 peptides. Score 0.451 Round 4: 213 peptides, 32 chains. Longest chain 13 peptides. Score 0.473 Round 5: 206 peptides, 31 chains. Longest chain 17 peptides. Score 0.465 Taking the results from Round 2 Chains 29, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6408 restraints for refining 2822 atoms. 5749 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2296 (Rfree = 0.000) for 2822 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.2379 (Rfree = 0.000) for 2805 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. Cycle 23: After refmac, R = 0.2611 (Rfree = 0.000) for 2799 atoms. Found 9 (15 requested) and removed 19 (7 requested) atoms. Cycle 24: After refmac, R = 0.2665 (Rfree = 0.000) for 2787 atoms. Found 5 (15 requested) and removed 54 (7 requested) atoms. Cycle 25: After refmac, R = 0.2597 (Rfree = 0.000) for 2736 atoms. Found 11 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 2786 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2802 seeds are put forward Round 1: 152 peptides, 29 chains. Longest chain 11 peptides. Score 0.311 Round 2: 197 peptides, 34 chains. Longest chain 13 peptides. Score 0.394 Round 3: 188 peptides, 31 chains. Longest chain 13 peptides. Score 0.407 Round 4: 196 peptides, 29 chains. Longest chain 18 peptides. Score 0.461 Round 5: 200 peptides, 32 chains. Longest chain 15 peptides. Score 0.432 Taking the results from Round 4 Chains 29, Residues 167, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6356 restraints for refining 2822 atoms. 5693 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2240 (Rfree = 0.000) for 2822 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. Cycle 27: After refmac, R = 0.2156 (Rfree = 0.000) for 2804 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. Cycle 28: After refmac, R = 0.2242 (Rfree = 0.000) for 2796 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.2176 (Rfree = 0.000) for 2795 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 30: After refmac, R = 0.2026 (Rfree = 0.000) for 2791 atoms. Found 11 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 2836 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 2855 seeds are put forward Round 1: 179 peptides, 36 chains. Longest chain 8 peptides. Score 0.302 Round 2: 174 peptides, 27 chains. Longest chain 16 peptides. Score 0.419 Round 3: 179 peptides, 29 chains. Longest chain 13 peptides. Score 0.407 Round 4: 175 peptides, 27 chains. Longest chain 16 peptides. Score 0.423 Round 5: 182 peptides, 30 chains. Longest chain 14 peptides. Score 0.402 Taking the results from Round 4 Chains 28, Residues 148, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6528 restraints for refining 2822 atoms. 5896 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2178 (Rfree = 0.000) for 2822 atoms. Found 10 (15 requested) and removed 16 (7 requested) atoms. Cycle 32: After refmac, R = 0.2084 (Rfree = 0.000) for 2807 atoms. Found 14 (15 requested) and removed 12 (7 requested) atoms. Cycle 33: After refmac, R = 0.1910 (Rfree = 0.000) for 2807 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.1896 (Rfree = 0.000) for 2798 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.1632 (Rfree = 0.000) for 2795 atoms. Found 6 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 2838 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2856 seeds are put forward Round 1: 140 peptides, 28 chains. Longest chain 12 peptides. Score 0.282 Round 2: 174 peptides, 33 chains. Longest chain 10 peptides. Score 0.329 Round 3: 169 peptides, 29 chains. Longest chain 20 peptides. Score 0.372 Round 4: 166 peptides, 28 chains. Longest chain 12 peptides. Score 0.377 Round 5: 167 peptides, 26 chains. Longest chain 20 peptides. Score 0.411 Taking the results from Round 5 Chains 27, Residues 141, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6578 restraints for refining 2822 atoms. 5965 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2184 (Rfree = 0.000) for 2822 atoms. Found 10 (15 requested) and removed 16 (7 requested) atoms. Cycle 37: After refmac, R = 0.1994 (Rfree = 0.000) for 2803 atoms. Found 2 (15 requested) and removed 17 (7 requested) atoms. Cycle 38: After refmac, R = 0.1978 (Rfree = 0.000) for 2785 atoms. Found 0 (15 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.1962 (Rfree = 0.000) for 2770 atoms. Found 4 (15 requested) and removed 14 (7 requested) atoms. Cycle 40: After refmac, R = 0.1937 (Rfree = 0.000) for 2758 atoms. Found 1 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 2785 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 2803 seeds are put forward Round 1: 142 peptides, 29 chains. Longest chain 9 peptides. Score 0.274 Round 2: 159 peptides, 30 chains. Longest chain 13 peptides. Score 0.321 Round 3: 164 peptides, 26 chains. Longest chain 14 peptides. Score 0.401 Round 4: 167 peptides, 30 chains. Longest chain 11 peptides. Score 0.350 Round 5: 176 peptides, 27 chains. Longest chain 13 peptides. Score 0.426 Taking the results from Round 5 Chains 27, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6654 restraints for refining 2822 atoms. 6085 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2070 (Rfree = 0.000) for 2822 atoms. Found 9 (15 requested) and removed 15 (7 requested) atoms. Cycle 42: After refmac, R = 0.2005 (Rfree = 0.000) for 2803 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. Cycle 43: After refmac, R = 0.2012 (Rfree = 0.000) for 2795 atoms. Found 14 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.2061 (Rfree = 0.000) for 2797 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.1717 (Rfree = 0.000) for 2798 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.24 Search for helices and strands: 0 residues in 0 chains, 2841 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2858 seeds are put forward Round 1: 127 peptides, 29 chains. Longest chain 6 peptides. Score 0.213 Round 2: 130 peptides, 25 chains. Longest chain 9 peptides. Score 0.293 Round 3: 139 peptides, 24 chains. Longest chain 11 peptides. Score 0.344 Round 4: 154 peptides, 28 chains. Longest chain 11 peptides. Score 0.335 Round 5: 163 peptides, 28 chains. Longest chain 11 peptides. Score 0.367 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 135, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2i51-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4372 reflections ( 84.88 % complete ) and 6736 restraints for refining 2822 atoms. 6199 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2092 (Rfree = 0.000) for 2822 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1955 (Rfree = 0.000) for 2810 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1859 (Rfree = 0.000) for 2803 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1884 (Rfree = 0.000) for 2794 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:00:48 GMT 2018 Job finished. TimeTaking 32.56 Used memory is bytes: 7450176