Mon 24 Dec 07:39:25 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 1vk8-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.2-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/1vk8-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.2-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 07:39:30 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/1vk8-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.2-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 284 and 0 Target number of residues in the AU: 284 Target solvent content: 0.5942 Checking the provided sequence file Detected sequence length: 106 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 424 Adjusted target solvent content: 0.39 Input MTZ file: 1vk8-3.2-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: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.55 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: 41.711 3.200 Wilson plot Bfac: 50.12 5809 reflections ( 96.00 % complete ) and 0 restraints for refining 3758 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3327 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2541 (Rfree = 0.000) for 3758 atoms. Found 25 (33 requested) and removed 65 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.99 3.47 Search for helices and strands: 0 residues in 0 chains, 3769 seeds are put forward NCS extension: 0 residues added, 3769 seeds are put forward Round 1: 133 peptides, 30 chains. Longest chain 8 peptides. Score 0.232 Round 2: 166 peptides, 32 chains. Longest chain 11 peptides. Score 0.347 Round 3: 193 peptides, 37 chains. Longest chain 9 peptides. Score 0.372 Round 4: 198 peptides, 36 chains. Longest chain 13 peptides. Score 0.410 Round 5: 202 peptides, 36 chains. Longest chain 12 peptides. Score 0.427 Taking the results from Round 5 Chains 36, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 7073 restraints for refining 3096 atoms. 6445 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2171 (Rfree = 0.000) for 3096 atoms. Found 17 (27 requested) and removed 31 (13 requested) atoms. Cycle 2: After refmac, R = 0.2250 (Rfree = 0.000) for 3051 atoms. Found 13 (27 requested) and removed 17 (13 requested) atoms. Cycle 3: After refmac, R = 0.1820 (Rfree = 0.000) for 3021 atoms. Found 5 (27 requested) and removed 16 (13 requested) atoms. Cycle 4: After refmac, R = 0.2023 (Rfree = 0.000) for 2995 atoms. Found 15 (27 requested) and removed 17 (13 requested) atoms. Cycle 5: After refmac, R = 0.1713 (Rfree = 0.000) for 2983 atoms. Found 10 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 3.52 Search for helices and strands: 0 residues in 0 chains, 3099 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3112 seeds are put forward Round 1: 142 peptides, 31 chains. Longest chain 7 peptides. Score 0.256 Round 2: 175 peptides, 32 chains. Longest chain 14 peptides. Score 0.385 Round 3: 161 peptides, 29 chains. Longest chain 10 peptides. Score 0.380 Round 4: 191 peptides, 34 chains. Longest chain 14 peptides. Score 0.416 Round 5: 183 peptides, 31 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 5 Chains 31, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6770 restraints for refining 2973 atoms. 6193 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2019 (Rfree = 0.000) for 2973 atoms. Found 19 (26 requested) and removed 22 (13 requested) atoms. Cycle 7: After refmac, R = 0.1906 (Rfree = 0.000) for 2955 atoms. Found 20 (26 requested) and removed 15 (13 requested) atoms. Cycle 8: After refmac, R = 0.1743 (Rfree = 0.000) for 2954 atoms. Found 6 (26 requested) and removed 13 (13 requested) atoms. Cycle 9: After refmac, R = 0.1670 (Rfree = 0.000) for 2941 atoms. Found 12 (26 requested) and removed 13 (13 requested) atoms. Cycle 10: After refmac, R = 0.1613 (Rfree = 0.000) for 2933 atoms. Found 10 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.06 3.55 Search for helices and strands: 0 residues in 0 chains, 3023 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3039 seeds are put forward Round 1: 151 peptides, 32 chains. Longest chain 7 peptides. Score 0.279 Round 2: 170 peptides, 32 chains. Longest chain 11 peptides. Score 0.364 Round 3: 178 peptides, 34 chains. Longest chain 8 peptides. Score 0.362 Round 4: 182 peptides, 32 chains. Longest chain 12 peptides. Score 0.414 Round 5: 207 peptides, 39 chains. Longest chain 10 peptides. Score 0.396 Taking the results from Round 4 Chains 32, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6786 restraints for refining 2975 atoms. 6218 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1906 (Rfree = 0.000) for 2975 atoms. Found 22 (26 requested) and removed 22 (13 requested) atoms. Cycle 12: After refmac, R = 0.1790 (Rfree = 0.000) for 2966 atoms. Found 14 (26 requested) and removed 15 (13 requested) atoms. Cycle 13: After refmac, R = 0.1632 (Rfree = 0.000) for 2957 atoms. Found 12 (26 requested) and removed 18 (13 requested) atoms. Cycle 14: After refmac, R = 0.1585 (Rfree = 0.000) for 2946 atoms. Found 8 (26 requested) and removed 14 (13 requested) atoms. Cycle 15: After refmac, R = 0.1563 (Rfree = 0.000) for 2934 atoms. Found 6 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.00 3.48 Search for helices and strands: 0 residues in 0 chains, 3018 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3033 seeds are put forward Round 1: 145 peptides, 31 chains. Longest chain 7 peptides. Score 0.270 Round 2: 166 peptides, 33 chains. Longest chain 8 peptides. Score 0.328 Round 3: 181 peptides, 31 chains. Longest chain 10 peptides. Score 0.428 Round 4: 191 peptides, 37 chains. Longest chain 11 peptides. Score 0.364 Round 5: 175 peptides, 30 chains. Longest chain 10 peptides. Score 0.421 Taking the results from Round 3 Chains 31, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6748 restraints for refining 2941 atoms. 6179 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1791 (Rfree = 0.000) for 2941 atoms. Found 11 (26 requested) and removed 18 (13 requested) atoms. Cycle 17: After refmac, R = 0.1685 (Rfree = 0.000) for 2927 atoms. Found 12 (26 requested) and removed 15 (13 requested) atoms. Cycle 18: After refmac, R = 0.1458 (Rfree = 0.000) for 2921 atoms. Found 7 (26 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.1672 (Rfree = 0.000) for 2910 atoms. Found 21 (26 requested) and removed 17 (13 requested) atoms. Cycle 20: After refmac, R = 0.1464 (Rfree = 0.000) for 2911 atoms. Found 7 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.04 3.53 Search for helices and strands: 0 residues in 0 chains, 2975 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2987 seeds are put forward Round 1: 153 peptides, 33 chains. Longest chain 7 peptides. Score 0.269 Round 2: 190 peptides, 35 chains. Longest chain 13 peptides. Score 0.395 Round 3: 183 peptides, 33 chains. Longest chain 10 peptides. Score 0.401 Round 4: 185 peptides, 32 chains. Longest chain 12 peptides. Score 0.427 Round 5: 179 peptides, 31 chains. Longest chain 12 peptides. Score 0.420 Taking the results from Round 4 Chains 32, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6510 restraints for refining 2934 atoms. 5930 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1728 (Rfree = 0.000) for 2934 atoms. Found 21 (26 requested) and removed 18 (13 requested) atoms. Cycle 22: After refmac, R = 0.1681 (Rfree = 0.000) for 2930 atoms. Found 12 (26 requested) and removed 15 (13 requested) atoms. Cycle 23: After refmac, R = 0.1596 (Rfree = 0.000) for 2924 atoms. Found 10 (26 requested) and removed 13 (13 requested) atoms. Cycle 24: After refmac, R = 0.1498 (Rfree = 0.000) for 2919 atoms. Found 6 (26 requested) and removed 15 (13 requested) atoms. Cycle 25: After refmac, R = 0.1351 (Rfree = 0.000) for 2909 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 3.56 Search for helices and strands: 0 residues in 0 chains, 2967 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2981 seeds are put forward Round 1: 144 peptides, 30 chains. Longest chain 8 peptides. Score 0.285 Round 2: 145 peptides, 26 chains. Longest chain 9 peptides. Score 0.366 Round 3: 149 peptides, 27 chains. Longest chain 9 peptides. Score 0.365 Round 4: 151 peptides, 25 chains. Longest chain 11 peptides. Score 0.411 Round 5: 151 peptides, 25 chains. Longest chain 10 peptides. Score 0.411 Taking the results from Round 5 Chains 25, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6928 restraints for refining 2981 atoms. 6449 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1634 (Rfree = 0.000) for 2981 atoms. Found 12 (26 requested) and removed 18 (13 requested) atoms. Cycle 27: After refmac, R = 0.1612 (Rfree = 0.000) for 2970 atoms. Found 8 (26 requested) and removed 13 (13 requested) atoms. Cycle 28: After refmac, R = 0.1610 (Rfree = 0.000) for 2963 atoms. Found 15 (26 requested) and removed 13 (13 requested) atoms. Cycle 29: After refmac, R = 0.1383 (Rfree = 0.000) for 2964 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.1426 (Rfree = 0.000) for 2955 atoms. Found 6 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 3039 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3042 seeds are put forward Round 1: 150 peptides, 31 chains. Longest chain 8 peptides. Score 0.293 Round 2: 164 peptides, 28 chains. Longest chain 10 peptides. Score 0.411 Round 3: 163 peptides, 26 chains. Longest chain 10 peptides. Score 0.442 Round 4: 166 peptides, 27 chains. Longest chain 10 peptides. Score 0.437 Round 5: 160 peptides, 28 chains. Longest chain 11 peptides. Score 0.394 Taking the results from Round 3 Chains 26, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6953 restraints for refining 3000 atoms. 6431 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1677 (Rfree = 0.000) for 3000 atoms. Found 14 (26 requested) and removed 16 (13 requested) atoms. Cycle 32: After refmac, R = 0.1578 (Rfree = 0.000) for 2992 atoms. Found 10 (26 requested) and removed 15 (13 requested) atoms. Cycle 33: After refmac, R = 0.1497 (Rfree = 0.000) for 2983 atoms. Found 6 (26 requested) and removed 14 (13 requested) atoms. Cycle 34: After refmac, R = 0.1418 (Rfree = 0.000) for 2972 atoms. Found 9 (26 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.1406 (Rfree = 0.000) for 2961 atoms. Found 7 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 3.55 Search for helices and strands: 0 residues in 0 chains, 3027 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3039 seeds are put forward Round 1: 151 peptides, 30 chains. Longest chain 10 peptides. Score 0.317 Round 2: 142 peptides, 26 chains. Longest chain 10 peptides. Score 0.353 Round 3: 149 peptides, 28 chains. Longest chain 10 peptides. Score 0.346 Round 4: 151 peptides, 26 chains. Longest chain 14 peptides. Score 0.392 Round 5: 163 peptides, 26 chains. Longest chain 19 peptides. Score 0.442 Taking the results from Round 5 Chains 26, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 6966 restraints for refining 3017 atoms. 6444 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1631 (Rfree = 0.000) for 3017 atoms. Found 8 (27 requested) and removed 15 (13 requested) atoms. Cycle 37: After refmac, R = 0.1580 (Rfree = 0.000) for 3005 atoms. Found 7 (27 requested) and removed 14 (13 requested) atoms. Cycle 38: After refmac, R = 0.1592 (Rfree = 0.000) for 2994 atoms. Found 13 (26 requested) and removed 14 (13 requested) atoms. Cycle 39: After refmac, R = 0.1473 (Rfree = 0.000) for 2989 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1546 (Rfree = 0.000) for 2980 atoms. Found 9 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 3.55 Search for helices and strands: 0 residues in 0 chains, 3065 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3091 seeds are put forward Round 1: 112 peptides, 24 chains. Longest chain 7 peptides. Score 0.251 Round 2: 134 peptides, 23 chains. Longest chain 10 peptides. Score 0.375 Round 3: 137 peptides, 26 chains. Longest chain 9 peptides. Score 0.330 Round 4: 137 peptides, 26 chains. Longest chain 11 peptides. Score 0.330 Round 5: 143 peptides, 26 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 2 Chains 23, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5809 reflections ( 96.00 % complete ) and 7029 restraints for refining 2980 atoms. 6608 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1528 (Rfree = 0.000) for 2980 atoms. Found 8 (26 requested) and removed 16 (13 requested) atoms. Cycle 42: After refmac, R = 0.1432 (Rfree = 0.000) for 2970 atoms. Found 12 (26 requested) and removed 14 (13 requested) atoms. Cycle 43: After refmac, R = 0.1348 (Rfree = 0.000) for 2966 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.1328 (Rfree = 0.000) for 2956 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.1325 (Rfree = 0.000) for 2947 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 3.56 Search for helices and strands: 0 residues in 0 chains, 3012 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3018 seeds are put forward Round 1: 109 peptides, 22 chains. Longest chain 7 peptides. Score 0.278 Round 2: 138 peptides, 24 chains. Longest chain 10 peptides. Score 0.374 Round 3: 144 peptides, 27 chains. Longest chain 9 peptides. Score 0.343 Round 4: 150 peptides, 25 chains. Longest chain 10 peptides. Score 0.407 Round 5: 148 peptides, 24 chains. Longest chain 11 peptides. Score 0.417 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 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vk8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5809 reflections ( 96.00 % complete ) and 6999 restraints for refining 2998 atoms. 6527 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1475 (Rfree = 0.000) for 2998 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1496 (Rfree = 0.000) for 2979 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1386 (Rfree = 0.000) for 2964 atoms. Found 0 (26 requested) and removed 6 (13 requested) atoms. Cycle 49: After refmac, R = 0.1371 (Rfree = 0.000) for 2957 atoms. TimeTaking 35.15