Mon 24 Dec 08:00:04 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 1vk8-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.4-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/1vk8-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.4-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 08:00:08 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/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-3.4-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 278 and 0 Target number of residues in the AU: 278 Target solvent content: 0.6028 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: 1vk8-3.4-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: 1vk8-3.4-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 3.400 Wilson plot Bfac: 53.37 4829 reflections ( 96.04 % complete ) and 0 restraints for refining 3748 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3240 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2819 (Rfree = 0.000) for 3748 atoms. Found 14 (28 requested) and removed 59 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 3.61 Search for helices and strands: 0 residues in 0 chains, 3752 seeds are put forward NCS extension: 0 residues added, 3752 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 7 peptides. Score 0.243 Round 2: 136 peptides, 27 chains. Longest chain 12 peptides. Score 0.306 Round 3: 142 peptides, 27 chains. Longest chain 12 peptides. Score 0.334 Round 4: 147 peptides, 27 chains. Longest chain 9 peptides. Score 0.356 Round 5: 151 peptides, 24 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 5 Chains 24, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 7295 restraints for refining 3083 atoms. 6811 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2325 (Rfree = 0.000) for 3083 atoms. Found 7 (23 requested) and removed 23 (11 requested) atoms. Cycle 2: After refmac, R = 0.2232 (Rfree = 0.000) for 3023 atoms. Found 13 (23 requested) and removed 18 (11 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2148 (Rfree = 0.000) for 3000 atoms. Found 10 (22 requested) and removed 20 (11 requested) atoms. Cycle 4: After refmac, R = 0.1879 (Rfree = 0.000) for 2973 atoms. Found 8 (22 requested) and removed 16 (11 requested) atoms. Cycle 5: After refmac, R = 0.1712 (Rfree = 0.000) for 2959 atoms. Found 8 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 3.55 Search for helices and strands: 0 residues in 0 chains, 3060 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 3072 seeds are put forward Round 1: 110 peptides, 25 chains. Longest chain 6 peptides. Score 0.220 Round 2: 138 peptides, 27 chains. Longest chain 10 peptides. Score 0.315 Round 3: 138 peptides, 28 chains. Longest chain 7 peptides. Score 0.296 Round 4: 145 peptides, 27 chains. Longest chain 10 peptides. Score 0.347 Round 5: 149 peptides, 26 chains. Longest chain 10 peptides. Score 0.384 Taking the results from Round 5 Chains 26, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4829 reflections ( 96.04 % complete ) and 6472 restraints for refining 2815 atoms. 6006 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1684 (Rfree = 0.000) for 2815 atoms. Found 11 (21 requested) and removed 23 (10 requested) atoms. Cycle 7: After refmac, R = 0.1743 (Rfree = 0.000) for 2797 atoms. Found 15 (21 requested) and removed 26 (10 requested) atoms. Cycle 8: After refmac, R = 0.1399 (Rfree = 0.000) for 2781 atoms. Found 2 (21 requested) and removed 14 (10 requested) atoms. Cycle 9: After refmac, R = 0.1932 (Rfree = 0.000) for 2765 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 10: After refmac, R = 0.1383 (Rfree = 0.000) for 2768 atoms. Found 4 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.56 Search for helices and strands: 0 residues in 0 chains, 2838 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 2846 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 9 peptides. Score 0.313 Round 2: 184 peptides, 33 chains. Longest chain 12 peptides. Score 0.405 Round 3: 178 peptides, 33 chains. Longest chain 11 peptides. Score 0.380 Round 4: 171 peptides, 32 chains. Longest chain 9 peptides. Score 0.368 Round 5: 174 peptides, 29 chains. Longest chain 15 peptides. Score 0.434 Taking the results from Round 5 Chains 29, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6408 restraints for refining 2846 atoms. 5857 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1937 (Rfree = 0.000) for 2846 atoms. Found 10 (21 requested) and removed 31 (10 requested) atoms. Cycle 12: After refmac, R = 0.1832 (Rfree = 0.000) for 2819 atoms. Found 17 (21 requested) and removed 21 (10 requested) atoms. Cycle 13: After refmac, R = 0.1803 (Rfree = 0.000) for 2806 atoms. Found 13 (21 requested) and removed 19 (10 requested) atoms. Cycle 14: After refmac, R = 0.1678 (Rfree = 0.000) for 2793 atoms. Found 8 (21 requested) and removed 17 (10 requested) atoms. Cycle 15: After refmac, R = 0.1715 (Rfree = 0.000) for 2778 atoms. Found 14 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 3.62 Search for helices and strands: 0 residues in 0 chains, 2856 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 2881 seeds are put forward Round 1: 134 peptides, 29 chains. Longest chain 9 peptides. Score 0.257 Round 2: 168 peptides, 30 chains. Longest chain 11 peptides. Score 0.392 Round 3: 173 peptides, 27 chains. Longest chain 21 peptides. Score 0.465 Round 4: 170 peptides, 28 chains. Longest chain 14 peptides. Score 0.436 Round 5: 174 peptides, 30 chains. Longest chain 15 peptides. Score 0.417 Taking the results from Round 3 Chains 27, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 5903 restraints for refining 2740 atoms. 5346 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1680 (Rfree = 0.000) for 2740 atoms. Found 12 (20 requested) and removed 15 (10 requested) atoms. Cycle 17: After refmac, R = 0.1617 (Rfree = 0.000) for 2731 atoms. Found 7 (20 requested) and removed 18 (10 requested) atoms. Cycle 18: After refmac, R = 0.1599 (Rfree = 0.000) for 2718 atoms. Found 9 (20 requested) and removed 14 (10 requested) atoms. Cycle 19: After refmac, R = 0.1595 (Rfree = 0.000) for 2709 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. Cycle 20: After refmac, R = 0.1573 (Rfree = 0.000) for 2709 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.64 Search for helices and strands: 0 residues in 0 chains, 2794 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 2816 seeds are put forward Round 1: 137 peptides, 28 chains. Longest chain 9 peptides. Score 0.291 Round 2: 162 peptides, 27 chains. Longest chain 19 peptides. Score 0.421 Round 3: 147 peptides, 26 chains. Longest chain 12 peptides. Score 0.375 Round 4: 145 peptides, 23 chains. Longest chain 15 peptides. Score 0.423 Round 5: 159 peptides, 29 chains. Longest chain 14 peptides. Score 0.371 Taking the results from Round 4 Chains 23, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6308 restraints for refining 2785 atoms. 5843 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1721 (Rfree = 0.000) for 2785 atoms. Found 12 (21 requested) and removed 16 (10 requested) atoms. Cycle 22: After refmac, R = 0.2405 (Rfree = 0.000) for 2775 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 23: After refmac, R = 0.1913 (Rfree = 0.000) for 2772 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 24: After refmac, R = 0.2090 (Rfree = 0.000) for 2771 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 25: After refmac, R = 0.1394 (Rfree = 0.000) for 2774 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.67 Search for helices and strands: 0 residues in 0 chains, 2856 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2875 seeds are put forward Round 1: 131 peptides, 28 chains. Longest chain 9 peptides. Score 0.263 Round 2: 134 peptides, 24 chains. Longest chain 12 peptides. Score 0.356 Round 3: 146 peptides, 25 chains. Longest chain 12 peptides. Score 0.390 Round 4: 147 peptides, 23 chains. Longest chain 17 peptides. Score 0.431 Round 5: 129 peptides, 22 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 4 Chains 23, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6174 restraints for refining 2793 atoms. 5701 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1617 (Rfree = 0.000) for 2793 atoms. Found 12 (21 requested) and removed 17 (10 requested) atoms. Cycle 27: After refmac, R = 0.1652 (Rfree = 0.000) for 2779 atoms. Found 12 (21 requested) and removed 13 (10 requested) atoms. Cycle 28: After refmac, R = 0.1412 (Rfree = 0.000) for 2773 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.1712 (Rfree = 0.000) for 2762 atoms. Found 14 (20 requested) and removed 13 (10 requested) atoms. Cycle 30: After refmac, R = 0.1437 (Rfree = 0.000) for 2759 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.71 Search for helices and strands: 0 residues in 0 chains, 2837 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2857 seeds are put forward Round 1: 120 peptides, 24 chains. Longest chain 11 peptides. Score 0.290 Round 2: 141 peptides, 24 chains. Longest chain 14 peptides. Score 0.387 Round 3: 134 peptides, 22 chains. Longest chain 13 peptides. Score 0.394 Round 4: 129 peptides, 22 chains. Longest chain 13 peptides. Score 0.372 Round 5: 137 peptides, 22 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 5 Chains 22, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6078 restraints for refining 2749 atoms. 5640 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1747 (Rfree = 0.000) for 2749 atoms. Found 18 (20 requested) and removed 36 (10 requested) atoms. Cycle 32: After refmac, R = 0.1634 (Rfree = 0.000) for 2723 atoms. Found 12 (20 requested) and removed 13 (10 requested) atoms. Cycle 33: After refmac, R = 0.1525 (Rfree = 0.000) for 2722 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.1981 (Rfree = 0.000) for 2714 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 35: After refmac, R = 0.1405 (Rfree = 0.000) for 2709 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 3.66 Search for helices and strands: 0 residues in 0 chains, 2759 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2774 seeds are put forward Round 1: 143 peptides, 28 chains. Longest chain 11 peptides. Score 0.319 Round 2: 163 peptides, 29 chains. Longest chain 14 peptides. Score 0.389 Round 3: 165 peptides, 29 chains. Longest chain 12 peptides. Score 0.397 Round 4: 168 peptides, 29 chains. Longest chain 11 peptides. Score 0.410 Round 5: 161 peptides, 28 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 4 Chains 29, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6045 restraints for refining 2747 atoms. 5518 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1521 (Rfree = 0.000) for 2747 atoms. Found 9 (20 requested) and removed 13 (10 requested) atoms. Cycle 37: After refmac, R = 0.1827 (Rfree = 0.000) for 2742 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 38: After refmac, R = 0.1872 (Rfree = 0.000) for 2745 atoms. Found 17 (20 requested) and removed 18 (10 requested) atoms. Cycle 39: After refmac, R = 0.1441 (Rfree = 0.000) for 2740 atoms. Found 6 (20 requested) and removed 14 (10 requested) atoms. Cycle 40: After refmac, R = 0.1403 (Rfree = 0.000) for 2730 atoms. Found 5 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.10 3.60 Search for helices and strands: 0 residues in 0 chains, 2797 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2812 seeds are put forward Round 1: 109 peptides, 25 chains. Longest chain 7 peptides. Score 0.214 Round 2: 145 peptides, 30 chains. Longest chain 14 peptides. Score 0.289 Round 3: 146 peptides, 28 chains. Longest chain 10 peptides. Score 0.333 Round 4: 146 peptides, 28 chains. Longest chain 14 peptides. Score 0.333 Round 5: 142 peptides, 27 chains. Longest chain 10 peptides. Score 0.334 Taking the results from Round 5 Chains 27, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4829 reflections ( 96.04 % complete ) and 6367 restraints for refining 2800 atoms. 5934 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1690 (Rfree = 0.000) for 2800 atoms. Found 15 (21 requested) and removed 19 (10 requested) atoms. Cycle 42: After refmac, R = 0.1492 (Rfree = 0.000) for 2783 atoms. Found 14 (21 requested) and removed 16 (10 requested) atoms. Cycle 43: After refmac, R = 0.1324 (Rfree = 0.000) for 2773 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.1264 (Rfree = 0.000) for 2764 atoms. Found 15 (20 requested) and removed 13 (10 requested) atoms. Cycle 45: After refmac, R = 0.1133 (Rfree = 0.000) for 2763 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.63 Search for helices and strands: 0 residues in 0 chains, 2843 seeds are put forward NCS extension: 0 residues added, 2843 seeds are put forward Round 1: 102 peptides, 24 chains. Longest chain 5 peptides. Score 0.199 Round 2: 126 peptides, 25 chains. Longest chain 9 peptides. Score 0.299 Round 3: 125 peptides, 24 chains. Longest chain 10 peptides. Score 0.314 Round 4: 130 peptides, 26 chains. Longest chain 10 peptides. Score 0.298 Round 5: 129 peptides, 23 chains. Longest chain 9 peptides. Score 0.353 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 106, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vk8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4829 reflections ( 96.04 % complete ) and 6282 restraints for refining 2829 atoms. 5854 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1577 (Rfree = 0.000) for 2829 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1482 (Rfree = 0.000) for 2811 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1412 (Rfree = 0.000) for 2797 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1247 (Rfree = 0.000) for 2780 atoms. TimeTaking 33.42