null Mon 24 Dec 00:59:39 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 2oyo-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oyo-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oyo-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-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/2oyo-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-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 00:59:43 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/2oyo-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-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 288 and 0 Target number of residues in the AU: 288 Target solvent content: 0.6274 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.49 Input MTZ file: 2oyo-3.2-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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.80 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: 83.295 3.200 Wilson plot Bfac: 64.87 7050 reflections ( 99.87 % complete ) and 0 restraints for refining 3504 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3107 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2398 (Rfree = 0.000) for 3504 atoms. Found 30 (31 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 3596 seeds are put forward NCS extension: 0 residues added, 3596 seeds are put forward Round 1: 205 peptides, 36 chains. Longest chain 15 peptides. Score 0.419 Round 2: 232 peptides, 37 chains. Longest chain 15 peptides. Score 0.498 Round 3: 252 peptides, 36 chains. Longest chain 16 peptides. Score 0.574 Round 4: 254 peptides, 30 chains. Longest chain 18 peptides. Score 0.653 Round 5: 268 peptides, 32 chains. Longest chain 18 peptides. Score 0.665 Taking the results from Round 5 Chains 34, Residues 236, Estimated correctness of the model 57.4 % 6 chains (55 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5593 restraints for refining 2859 atoms. 4489 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2415 (Rfree = 0.000) for 2859 atoms. Found 23 (25 requested) and removed 19 (12 requested) atoms. Cycle 2: After refmac, R = 0.2144 (Rfree = 0.000) for 2842 atoms. Found 11 (25 requested) and removed 15 (12 requested) atoms. Cycle 3: After refmac, R = 0.2062 (Rfree = 0.000) for 2825 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. Cycle 4: After refmac, R = 0.1992 (Rfree = 0.000) for 2808 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 5: After refmac, R = 0.1960 (Rfree = 0.000) for 2795 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.21 Search for helices and strands: 0 residues in 0 chains, 2916 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 2933 seeds are put forward Round 1: 234 peptides, 36 chains. Longest chain 16 peptides. Score 0.519 Round 2: 256 peptides, 31 chains. Longest chain 36 peptides. Score 0.646 Round 3: 262 peptides, 29 chains. Longest chain 26 peptides. Score 0.683 Round 4: 263 peptides, 28 chains. Longest chain 22 peptides. Score 0.696 Round 5: 260 peptides, 31 chains. Longest chain 21 peptides. Score 0.656 Taking the results from Round 4 Chains 34, Residues 235, Estimated correctness of the model 64.3 % 6 chains (62 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5656 restraints for refining 2862 atoms. 4523 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2324 (Rfree = 0.000) for 2862 atoms. Found 21 (25 requested) and removed 21 (12 requested) atoms. Cycle 7: After refmac, R = 0.2176 (Rfree = 0.000) for 2854 atoms. Found 13 (25 requested) and removed 16 (12 requested) atoms. Cycle 8: After refmac, R = 0.2327 (Rfree = 0.000) for 2845 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 9: After refmac, R = 0.2285 (Rfree = 0.000) for 2850 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 10: After refmac, R = 0.2255 (Rfree = 0.000) for 2852 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 2979 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2992 seeds are put forward Round 1: 248 peptides, 34 chains. Longest chain 19 peptides. Score 0.588 Round 2: 245 peptides, 25 chains. Longest chain 57 peptides. Score 0.687 Round 3: 258 peptides, 28 chains. Longest chain 31 peptides. Score 0.685 Round 4: 245 peptides, 29 chains. Longest chain 30 peptides. Score 0.641 Round 5: 269 peptides, 26 chains. Longest chain 31 peptides. Score 0.729 Taking the results from Round 5 Chains 28, Residues 243, Estimated correctness of the model 71.1 % 3 chains (42 residues) have been docked in sequence Building loops using Loopy2018 28 chains (243 residues) following loop building 3 chains (42 residues) in sequence following loop building ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5723 restraints for refining 2862 atoms. 4582 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2265 (Rfree = 0.000) for 2862 atoms. Found 18 (25 requested) and removed 24 (12 requested) atoms. Cycle 12: After refmac, R = 0.1993 (Rfree = 0.000) for 2848 atoms. Found 11 (24 requested) and removed 16 (12 requested) atoms. Cycle 13: After refmac, R = 0.2000 (Rfree = 0.000) for 2839 atoms. Found 10 (24 requested) and removed 14 (12 requested) atoms. Cycle 14: After refmac, R = 0.1762 (Rfree = 0.000) for 2832 atoms. Found 7 (23 requested) and removed 14 (12 requested) atoms. Cycle 15: After refmac, R = 0.1674 (Rfree = 0.000) for 2824 atoms. Found 3 (23 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.17 Search for helices and strands: 0 residues in 0 chains, 2957 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 2981 seeds are put forward Round 1: 214 peptides, 35 chains. Longest chain 18 peptides. Score 0.466 Round 2: 240 peptides, 29 chains. Longest chain 18 peptides. Score 0.628 Round 3: 247 peptides, 30 chains. Longest chain 16 peptides. Score 0.635 Round 4: 248 peptides, 31 chains. Longest chain 20 peptides. Score 0.625 Round 5: 248 peptides, 31 chains. Longest chain 22 peptides. Score 0.625 Taking the results from Round 3 Chains 32, Residues 217, Estimated correctness of the model 50.2 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6273 restraints for refining 2861 atoms. 5332 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2137 (Rfree = 0.000) for 2861 atoms. Found 21 (22 requested) and removed 15 (12 requested) atoms. Cycle 17: After refmac, R = 0.1946 (Rfree = 0.000) for 2862 atoms. Found 11 (22 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.1834 (Rfree = 0.000) for 2855 atoms. Found 4 (22 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.1872 (Rfree = 0.000) for 2845 atoms. Found 4 (22 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.1764 (Rfree = 0.000) for 2834 atoms. Found 8 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 3.17 Search for helices and strands: 0 residues in 0 chains, 2958 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2971 seeds are put forward Round 1: 211 peptides, 34 chains. Longest chain 14 peptides. Score 0.471 Round 2: 243 peptides, 30 chains. Longest chain 28 peptides. Score 0.624 Round 3: 244 peptides, 33 chains. Longest chain 19 peptides. Score 0.590 Round 4: 252 peptides, 28 chains. Longest chain 21 peptides. Score 0.670 Round 5: 245 peptides, 32 chains. Longest chain 21 peptides. Score 0.605 Taking the results from Round 4 Chains 28, Residues 224, Estimated correctness of the model 58.5 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5958 restraints for refining 2863 atoms. 4938 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2220 (Rfree = 0.000) for 2863 atoms. Found 22 (22 requested) and removed 21 (12 requested) atoms. Cycle 22: After refmac, R = 0.2065 (Rfree = 0.000) for 2858 atoms. Found 10 (22 requested) and removed 16 (12 requested) atoms. Cycle 23: After refmac, R = 0.1870 (Rfree = 0.000) for 2850 atoms. Found 6 (22 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.1821 (Rfree = 0.000) for 2843 atoms. Found 2 (22 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.1824 (Rfree = 0.000) for 2832 atoms. Found 6 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 3.15 Search for helices and strands: 0 residues in 0 chains, 2959 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 2986 seeds are put forward Round 1: 218 peptides, 36 chains. Longest chain 16 peptides. Score 0.465 Round 2: 243 peptides, 35 chains. Longest chain 16 peptides. Score 0.561 Round 3: 249 peptides, 33 chains. Longest chain 24 peptides. Score 0.604 Round 4: 248 peptides, 32 chains. Longest chain 29 peptides. Score 0.613 Round 5: 249 peptides, 35 chains. Longest chain 20 peptides. Score 0.579 Taking the results from Round 4 Chains 32, Residues 216, Estimated correctness of the model 44.5 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5733 restraints for refining 2863 atoms. 4688 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2219 (Rfree = 0.000) for 2863 atoms. Found 22 (22 requested) and removed 18 (12 requested) atoms. Cycle 27: After refmac, R = 0.2000 (Rfree = 0.000) for 2864 atoms. Found 9 (22 requested) and removed 15 (12 requested) atoms. Cycle 28: After refmac, R = 0.1835 (Rfree = 0.000) for 2856 atoms. Found 4 (22 requested) and removed 13 (12 requested) atoms. Cycle 29: After refmac, R = 0.1830 (Rfree = 0.000) for 2843 atoms. Found 7 (22 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.1948 (Rfree = 0.000) for 2835 atoms. Found 14 (22 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.17 Search for helices and strands: 0 residues in 0 chains, 2965 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 2992 seeds are put forward Round 1: 194 peptides, 31 chains. Longest chain 13 peptides. Score 0.457 Round 2: 207 peptides, 29 chains. Longest chain 19 peptides. Score 0.531 Round 3: 228 peptides, 31 chains. Longest chain 19 peptides. Score 0.569 Round 4: 217 peptides, 33 chains. Longest chain 12 peptides. Score 0.506 Round 5: 217 peptides, 33 chains. Longest chain 16 peptides. Score 0.506 Taking the results from Round 3 Chains 32, Residues 197, Estimated correctness of the model 32.4 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6095 restraints for refining 2863 atoms. 5223 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2012 (Rfree = 0.000) for 2863 atoms. Found 14 (22 requested) and removed 21 (12 requested) atoms. Cycle 32: After refmac, R = 0.1811 (Rfree = 0.000) for 2851 atoms. Found 6 (22 requested) and removed 14 (12 requested) atoms. Cycle 33: After refmac, R = 0.1645 (Rfree = 0.000) for 2836 atoms. Found 3 (22 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.1647 (Rfree = 0.000) for 2822 atoms. Found 4 (22 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1564 (Rfree = 0.000) for 2812 atoms. Found 6 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.16 Search for helices and strands: 0 residues in 0 chains, 2934 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 2948 seeds are put forward Round 1: 187 peptides, 34 chains. Longest chain 17 peptides. Score 0.383 Round 2: 217 peptides, 34 chains. Longest chain 18 peptides. Score 0.491 Round 3: 225 peptides, 37 chains. Longest chain 15 peptides. Score 0.475 Round 4: 215 peptides, 32 chains. Longest chain 15 peptides. Score 0.514 Round 5: 203 peptides, 33 chains. Longest chain 14 peptides. Score 0.458 Taking the results from Round 4 Chains 33, Residues 183, Estimated correctness of the model 15.8 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6185 restraints for refining 2863 atoms. 5380 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1991 (Rfree = 0.000) for 2863 atoms. Found 22 (22 requested) and removed 14 (12 requested) atoms. Cycle 37: After refmac, R = 0.1798 (Rfree = 0.000) for 2869 atoms. Found 13 (22 requested) and removed 13 (12 requested) atoms. Cycle 38: After refmac, R = 0.1744 (Rfree = 0.000) for 2866 atoms. Found 6 (22 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.1683 (Rfree = 0.000) for 2858 atoms. Found 5 (22 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.1657 (Rfree = 0.000) for 2850 atoms. Found 4 (22 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 2970 seeds are put forward NCS extension: 4 residues added (3 deleted due to clashes), 2974 seeds are put forward Round 1: 186 peptides, 34 chains. Longest chain 13 peptides. Score 0.379 Round 2: 203 peptides, 29 chains. Longest chain 25 peptides. Score 0.518 Round 3: 214 peptides, 34 chains. Longest chain 14 peptides. Score 0.481 Round 4: 216 peptides, 32 chains. Longest chain 16 peptides. Score 0.517 Round 5: 208 peptides, 32 chains. Longest chain 25 peptides. Score 0.490 Taking the results from Round 2 Chains 32, Residues 174, Estimated correctness of the model 17.1 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6163 restraints for refining 2863 atoms. 5399 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1927 (Rfree = 0.000) for 2863 atoms. Found 15 (22 requested) and removed 16 (12 requested) atoms. Cycle 42: After refmac, R = 0.1790 (Rfree = 0.000) for 2858 atoms. Found 1 (22 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.1776 (Rfree = 0.000) for 2844 atoms. Found 5 (22 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.1787 (Rfree = 0.000) for 2836 atoms. Found 9 (22 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.1759 (Rfree = 0.000) for 2831 atoms. Found 2 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 2959 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 2972 seeds are put forward Round 1: 149 peptides, 29 chains. Longest chain 9 peptides. Score 0.316 Round 2: 166 peptides, 28 chains. Longest chain 12 peptides. Score 0.401 Round 3: 182 peptides, 28 chains. Longest chain 16 peptides. Score 0.461 Round 4: 166 peptides, 25 chains. Longest chain 17 peptides. Score 0.451 Round 5: 177 peptides, 29 chains. Longest chain 15 peptides. Score 0.427 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 154, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2oyo-3_warpNtrace.pdb as input Building loops using Loopy2018 29 chains (154 residues) following loop building 3 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7050 reflections ( 99.87 % complete ) and 6363 restraints for refining 2863 atoms. 5701 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1897 (Rfree = 0.000) for 2863 atoms. Found 0 (22 requested) and removed 5 (12 requested) atoms. Cycle 47: After refmac, R = 0.1801 (Rfree = 0.000) for 2856 atoms. Found 0 (22 requested) and removed 3 (12 requested) atoms. Cycle 48: After refmac, R = 0.1976 (Rfree = 0.000) for 2853 atoms. Found 0 (22 requested) and removed 9 (12 requested) atoms. Cycle 49: After refmac, R = 0.1757 (Rfree = 0.000) for 2839 atoms. Found 0 (22 requested) and removed 10 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:42:18 GMT 2018 Job finished. TimeTaking 42.66 Used memory is bytes: 14928056