Mon 24 Dec 07:51:26 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 1vjn-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-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/1vjn-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-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 07:51:30 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/1vjn-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-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 320 and 0 Target number of residues in the AU: 320 Target solvent content: 0.5976 Checking the provided sequence file Detected sequence length: 220 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 440 Adjusted target solvent content: 0.45 Input MTZ file: 1vjn-4.0-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: 43.059 45.719 63.384 73.681 89.271 64.860 Input sequence file: 1vjn-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.60 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: 60.370 4.001 Wilson plot Bfac: 51.53 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3444 reflections ( 98.04 % complete ) and 0 restraints for refining 3890 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.2984 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2824 (Rfree = 0.000) for 3890 atoms. Found 18 (18 requested) and removed 32 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 3906 seeds are put forward NCS extension: 0 residues added, 3906 seeds are put forward Round 1: 98 peptides, 22 chains. Longest chain 9 peptides. Score 0.217 Round 2: 140 peptides, 29 chains. Longest chain 11 peptides. Score 0.275 Round 3: 174 peptides, 32 chains. Longest chain 13 peptides. Score 0.361 Round 4: 193 peptides, 33 chains. Longest chain 13 peptides. Score 0.417 Round 5: 181 peptides, 32 chains. Longest chain 14 peptides. Score 0.388 Taking the results from Round 4 Chains 33, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 7375 restraints for refining 3065 atoms. 6768 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2506 (Rfree = 0.000) for 3065 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 2: After refmac, R = 0.2465 (Rfree = 0.000) for 2968 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 3: After refmac, R = 0.2349 (Rfree = 0.000) for 2929 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 4: After refmac, R = 0.1718 (Rfree = 0.000) for 2892 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 5: After refmac, R = 0.2099 (Rfree = 0.000) for 2875 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 2964 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2976 seeds are put forward Round 1: 175 peptides, 36 chains. Longest chain 11 peptides. Score 0.299 Round 2: 189 peptides, 32 chains. Longest chain 14 peptides. Score 0.418 Round 3: 199 peptides, 36 chains. Longest chain 11 peptides. Score 0.392 Round 4: 208 peptides, 36 chains. Longest chain 14 peptides. Score 0.424 Round 5: 193 peptides, 33 chains. Longest chain 11 peptides. Score 0.417 Taking the results from Round 4 Chains 36, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6514 restraints for refining 2836 atoms. 5862 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1841 (Rfree = 0.000) for 2836 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 7: After refmac, R = 0.1821 (Rfree = 0.000) for 2816 atoms. Found 9 (13 requested) and removed 22 (6 requested) atoms. Cycle 8: After refmac, R = 0.1761 (Rfree = 0.000) for 2801 atoms. Found 4 (13 requested) and removed 18 (6 requested) atoms. Cycle 9: After refmac, R = 0.1734 (Rfree = 0.000) for 2784 atoms. Found 2 (13 requested) and removed 13 (6 requested) atoms. Cycle 10: After refmac, R = 0.1742 (Rfree = 0.000) for 2771 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 2834 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2852 seeds are put forward Round 1: 172 peptides, 35 chains. Longest chain 10 peptides. Score 0.303 Round 2: 194 peptides, 32 chains. Longest chain 18 peptides. Score 0.436 Round 3: 185 peptides, 28 chains. Longest chain 19 peptides. Score 0.466 Round 4: 196 peptides, 29 chains. Longest chain 13 peptides. Score 0.488 Round 5: 197 peptides, 31 chains. Longest chain 13 peptides. Score 0.462 Taking the results from Round 4 Chains 29, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6645 restraints for refining 2896 atoms. 6006 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2304 (Rfree = 0.000) for 2896 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 12: After refmac, R = 0.1943 (Rfree = 0.000) for 2854 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 13: After refmac, R = 0.2158 (Rfree = 0.000) for 2825 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 14: After refmac, R = 0.1623 (Rfree = 0.000) for 2801 atoms. Found 12 (13 requested) and removed 17 (6 requested) atoms. Cycle 15: After refmac, R = 0.1479 (Rfree = 0.000) for 2782 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 2835 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2852 seeds are put forward Round 1: 159 peptides, 32 chains. Longest chain 10 peptides. Score 0.302 Round 2: 186 peptides, 32 chains. Longest chain 11 peptides. Score 0.407 Round 3: 191 peptides, 31 chains. Longest chain 15 peptides. Score 0.440 Round 4: 183 peptides, 30 chains. Longest chain 12 peptides. Score 0.427 Round 5: 183 peptides, 29 chains. Longest chain 12 peptides. Score 0.443 Taking the results from Round 5 Chains 29, Residues 154, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6717 restraints for refining 2925 atoms. 6101 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2321 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 38 (6 requested) atoms. Cycle 17: After refmac, R = 0.2057 (Rfree = 0.000) for 2882 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 18: After refmac, R = 0.2241 (Rfree = 0.000) for 2869 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 19: After refmac, R = 0.2195 (Rfree = 0.000) for 2852 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 20: After refmac, R = 0.1497 (Rfree = 0.000) for 2839 atoms. Found 7 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.52 Search for helices and strands: 0 residues in 0 chains, 2915 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2932 seeds are put forward Round 1: 159 peptides, 35 chains. Longest chain 10 peptides. Score 0.250 Round 2: 171 peptides, 34 chains. Longest chain 10 peptides. Score 0.316 Round 3: 189 peptides, 35 chains. Longest chain 10 peptides. Score 0.370 Round 4: 194 peptides, 34 chains. Longest chain 11 peptides. Score 0.405 Round 5: 182 peptides, 31 chains. Longest chain 11 peptides. Score 0.408 Taking the results from Round 5 Chains 31, Residues 151, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 7175 restraints for refining 3001 atoms. 6585 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2156 (Rfree = 0.000) for 3001 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 22: After refmac, R = 0.2210 (Rfree = 0.000) for 2965 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 23: After refmac, R = 0.2107 (Rfree = 0.000) for 2931 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 24: After refmac, R = 0.1605 (Rfree = 0.000) for 2897 atoms. Found 10 (13 requested) and removed 15 (6 requested) atoms. Cycle 25: After refmac, R = 0.1475 (Rfree = 0.000) for 2876 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 2937 seeds are put forward Round 1: 133 peptides, 28 chains. Longest chain 9 peptides. Score 0.263 Round 2: 169 peptides, 30 chains. Longest chain 12 peptides. Score 0.375 Round 3: 174 peptides, 29 chains. Longest chain 10 peptides. Score 0.410 Round 4: 173 peptides, 30 chains. Longest chain 14 peptides. Score 0.390 Round 5: 171 peptides, 30 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 3 Chains 29, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6672 restraints for refining 2833 atoms. 6121 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2100 (Rfree = 0.000) for 2833 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 27: After refmac, R = 0.1537 (Rfree = 0.000) for 2816 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.1329 (Rfree = 0.000) for 2801 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.1324 (Rfree = 0.000) for 2790 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.1391 (Rfree = 0.000) for 2785 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 2858 seeds are put forward NCS extension: 0 residues added, 2858 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 8 peptides. Score 0.271 Round 2: 162 peptides, 27 chains. Longest chain 11 peptides. Score 0.398 Round 3: 158 peptides, 26 chains. Longest chain 10 peptides. Score 0.399 Round 4: 158 peptides, 28 chains. Longest chain 10 peptides. Score 0.366 Round 5: 168 peptides, 27 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 5 Chains 27, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6769 restraints for refining 2910 atoms. 6232 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2356 (Rfree = 0.000) for 2910 atoms. Found 13 (13 requested) and removed 36 (6 requested) atoms. Cycle 32: After refmac, R = 0.2044 (Rfree = 0.000) for 2869 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 33: After refmac, R = 0.2080 (Rfree = 0.000) for 2855 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 34: After refmac, R = 0.1991 (Rfree = 0.000) for 2845 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 35: After refmac, R = 0.1711 (Rfree = 0.000) for 2836 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 2886 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 2898 seeds are put forward Round 1: 115 peptides, 24 chains. Longest chain 8 peptides. Score 0.257 Round 2: 137 peptides, 27 chains. Longest chain 8 peptides. Score 0.298 Round 3: 156 peptides, 29 chains. Longest chain 10 peptides. Score 0.341 Round 4: 159 peptides, 27 chains. Longest chain 10 peptides. Score 0.387 Round 5: 160 peptides, 26 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 5 Chains 26, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6880 restraints for refining 2912 atoms. 6370 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2154 (Rfree = 0.000) for 2912 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 37: After refmac, R = 0.2389 (Rfree = 0.000) for 2889 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 38: After refmac, R = 0.2206 (Rfree = 0.000) for 2863 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 39: After refmac, R = 0.2070 (Rfree = 0.000) for 2848 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 40: After refmac, R = 0.1942 (Rfree = 0.000) for 2844 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 2889 seeds are put forward NCS extension: 0 residues added, 2889 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 9 peptides. Score 0.242 Round 2: 128 peptides, 24 chains. Longest chain 10 peptides. Score 0.314 Round 3: 127 peptides, 21 chains. Longest chain 15 peptides. Score 0.364 Round 4: 134 peptides, 24 chains. Longest chain 11 peptides. Score 0.339 Round 5: 139 peptides, 23 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 5 Chains 23, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6934 restraints for refining 2909 atoms. 6493 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2389 (Rfree = 0.000) for 2909 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 42: After refmac, R = 0.2043 (Rfree = 0.000) for 2885 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 43: After refmac, R = 0.2015 (Rfree = 0.000) for 2865 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 44: After refmac, R = 0.2123 (Rfree = 0.000) for 2855 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 45: After refmac, R = 0.1957 (Rfree = 0.000) for 2851 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.63 Search for helices and strands: 0 residues in 0 chains, 2919 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2931 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 7 peptides. Score 0.258 Round 2: 125 peptides, 22 chains. Longest chain 12 peptides. Score 0.338 Round 3: 122 peptides, 23 chains. Longest chain 10 peptides. Score 0.307 Round 4: 135 peptides, 24 chains. Longest chain 9 peptides. Score 0.343 Round 5: 120 peptides, 21 chains. Longest chain 12 peptides. Score 0.335 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 111, 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 1vjn-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3444 reflections ( 98.04 % complete ) and 6601 restraints for refining 2788 atoms. 6181 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2076 (Rfree = 0.000) for 2788 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2002 (Rfree = 0.000) for 2773 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1809 (Rfree = 0.000) for 2760 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1329 (Rfree = 0.000) for 2748 atoms. TimeTaking 34.87