null Sun 23 Dec 22:22:59 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vjn-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:07 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/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-parrot-hancs/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-hancs.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-hancs.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 3898 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.2849 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2846 (Rfree = 0.000) for 3898 atoms. Found 17 (18 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.57 Search for helices and strands: 0 residues in 0 chains, 3939 seeds are put forward NCS extension: 0 residues added, 3939 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 8 peptides. Score 0.245 Round 2: 167 peptides, 33 chains. Longest chain 10 peptides. Score 0.317 Round 3: 192 peptides, 33 chains. Longest chain 14 peptides. Score 0.413 Round 4: 203 peptides, 34 chains. Longest chain 14 peptides. Score 0.437 Round 5: 197 peptides, 32 chains. Longest chain 13 peptides. Score 0.446 Taking the results from Round 5 Chains 32, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 7379 restraints for refining 3071 atoms. 6751 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2583 (Rfree = 0.000) for 3071 atoms. Found 14 (14 requested) and removed 40 (7 requested) atoms. Cycle 2: After refmac, R = 0.2525 (Rfree = 0.000) for 2960 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 3: After refmac, R = 0.2472 (Rfree = 0.000) for 2902 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 4: After refmac, R = 0.2408 (Rfree = 0.000) for 2859 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 5: After refmac, R = 0.2257 (Rfree = 0.000) for 2837 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 2910 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2928 seeds are put forward Round 1: 142 peptides, 30 chains. Longest chain 8 peptides. Score 0.266 Round 2: 183 peptides, 33 chains. Longest chain 14 peptides. Score 0.380 Round 3: 192 peptides, 34 chains. Longest chain 11 peptides. Score 0.397 Round 4: 192 peptides, 35 chains. Longest chain 14 peptides. Score 0.381 Round 5: 208 peptides, 35 chains. Longest chain 13 peptides. Score 0.440 Taking the results from Round 5 Chains 35, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6201 restraints for refining 2767 atoms. 5544 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1976 (Rfree = 0.000) for 2767 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 7: After refmac, R = 0.1906 (Rfree = 0.000) for 2715 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 8: After refmac, R = 0.1868 (Rfree = 0.000) for 2707 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 9: After refmac, R = 0.1829 (Rfree = 0.000) for 2682 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 10: After refmac, R = 0.1376 (Rfree = 0.000) for 2663 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.42 Search for helices and strands: 0 residues in 0 chains, 2742 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 2761 seeds are put forward Round 1: 155 peptides, 33 chains. Longest chain 9 peptides. Score 0.268 Round 2: 183 peptides, 31 chains. Longest chain 13 peptides. Score 0.412 Round 3: 207 peptides, 37 chains. Longest chain 14 peptides. Score 0.405 Round 4: 187 peptides, 33 chains. Longest chain 13 peptides. Score 0.395 Round 5: 185 peptides, 30 chains. Longest chain 17 peptides. Score 0.435 Taking the results from Round 5 Chains 30, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6440 restraints for refining 2818 atoms. 5850 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2259 (Rfree = 0.000) for 2818 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 12: After refmac, R = 0.2008 (Rfree = 0.000) for 2767 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 13: After refmac, R = 0.1837 (Rfree = 0.000) for 2738 atoms. Found 12 (13 requested) and removed 12 (6 requested) atoms. Cycle 14: After refmac, R = 0.1834 (Rfree = 0.000) for 2720 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.1841 (Rfree = 0.000) for 2721 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 2802 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2832 seeds are put forward Round 1: 154 peptides, 32 chains. Longest chain 11 peptides. Score 0.281 Round 2: 202 peptides, 34 chains. Longest chain 13 peptides. Score 0.433 Round 3: 186 peptides, 32 chains. Longest chain 11 peptides. Score 0.407 Round 4: 190 peptides, 31 chains. Longest chain 15 peptides. Score 0.437 Round 5: 200 peptides, 36 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 4 Chains 31, Residues 159, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6655 restraints for refining 2904 atoms. 6035 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2217 (Rfree = 0.000) for 2904 atoms. Found 13 (13 requested) and removed 35 (6 requested) atoms. Cycle 17: After refmac, R = 0.2141 (Rfree = 0.000) for 2845 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 18: After refmac, R = 0.1566 (Rfree = 0.000) for 2823 atoms. Found 7 (13 requested) and removed 15 (6 requested) atoms. Cycle 19: After refmac, R = 0.1459 (Rfree = 0.000) for 2810 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.1461 (Rfree = 0.000) for 2801 atoms. Found 3 (13 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 2862 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2876 seeds are put forward Round 1: 156 peptides, 35 chains. Longest chain 7 peptides. Score 0.237 Round 2: 169 peptides, 31 chains. Longest chain 12 peptides. Score 0.359 Round 3: 166 peptides, 25 chains. Longest chain 12 peptides. Score 0.445 Round 4: 199 peptides, 31 chains. Longest chain 15 peptides. Score 0.468 Round 5: 197 peptides, 34 chains. Longest chain 13 peptides. Score 0.416 Taking the results from Round 4 Chains 31, Residues 168, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6364 restraints for refining 2885 atoms. 5693 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1768 (Rfree = 0.000) for 2885 atoms. Found 11 (13 requested) and removed 24 (6 requested) atoms. Cycle 22: After refmac, R = 0.1816 (Rfree = 0.000) for 2855 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.1556 (Rfree = 0.000) for 2839 atoms. Found 11 (13 requested) and removed 15 (6 requested) atoms. Cycle 24: After refmac, R = 0.1312 (Rfree = 0.000) for 2825 atoms. Found 3 (13 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.1480 (Rfree = 0.000) for 2803 atoms. Found 7 (13 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 2859 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2877 seeds are put forward Round 1: 162 peptides, 32 chains. Longest chain 12 peptides. Score 0.314 Round 2: 190 peptides, 31 chains. Longest chain 12 peptides. Score 0.437 Round 3: 174 peptides, 31 chains. Longest chain 13 peptides. Score 0.378 Round 4: 185 peptides, 30 chains. Longest chain 13 peptides. Score 0.435 Round 5: 190 peptides, 33 chains. Longest chain 12 peptides. Score 0.406 Taking the results from Round 2 Chains 31, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6439 restraints for refining 2846 atoms. 5834 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1910 (Rfree = 0.000) for 2846 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 27: After refmac, R = 0.1763 (Rfree = 0.000) for 2823 atoms. Found 7 (13 requested) and removed 16 (6 requested) atoms. Cycle 28: After refmac, R = 0.1732 (Rfree = 0.000) for 2808 atoms. Found 10 (13 requested) and removed 15 (6 requested) atoms. Cycle 29: After refmac, R = 0.1465 (Rfree = 0.000) for 2801 atoms. Found 2 (13 requested) and removed 11 (6 requested) atoms. Cycle 30: After refmac, R = 0.1515 (Rfree = 0.000) for 2790 atoms. Found 7 (13 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 2875 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2887 seeds are put forward Round 1: 146 peptides, 31 chains. Longest chain 7 peptides. Score 0.265 Round 2: 174 peptides, 32 chains. Longest chain 13 peptides. Score 0.361 Round 3: 183 peptides, 31 chains. Longest chain 12 peptides. Score 0.412 Round 4: 174 peptides, 30 chains. Longest chain 12 peptides. Score 0.394 Round 5: 183 peptides, 33 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 3 Chains 31, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6915 restraints for refining 2949 atoms. 6338 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2095 (Rfree = 0.000) for 2949 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 32: After refmac, R = 0.1846 (Rfree = 0.000) for 2916 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 33: After refmac, R = 0.1711 (Rfree = 0.000) for 2903 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 34: After refmac, R = 0.1319 (Rfree = 0.000) for 2897 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.1319 (Rfree = 0.000) for 2879 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2954 seeds are put forward Round 1: 154 peptides, 34 chains. Longest chain 8 peptides. Score 0.246 Round 2: 167 peptides, 29 chains. Longest chain 12 peptides. Score 0.384 Round 3: 167 peptides, 30 chains. Longest chain 12 peptides. Score 0.367 Round 4: 151 peptides, 28 chains. Longest chain 12 peptides. Score 0.338 Round 5: 162 peptides, 31 chains. Longest chain 12 peptides. Score 0.331 Taking the results from Round 2 Chains 29, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6705 restraints for refining 2898 atoms. 6182 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2126 (Rfree = 0.000) for 2898 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 37: After refmac, R = 0.1941 (Rfree = 0.000) for 2880 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 38: After refmac, R = 0.1403 (Rfree = 0.000) for 2864 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1253 (Rfree = 0.000) for 2856 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1324 (Rfree = 0.000) for 2849 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 2913 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2926 seeds are put forward Round 1: 122 peptides, 28 chains. Longest chain 6 peptides. Score 0.214 Round 2: 135 peptides, 27 chains. Longest chain 8 peptides. Score 0.289 Round 3: 140 peptides, 26 chains. Longest chain 9 peptides. Score 0.328 Round 4: 148 peptides, 24 chains. Longest chain 11 peptides. Score 0.395 Round 5: 146 peptides, 26 chains. Longest chain 9 peptides. Score 0.353 Taking the results from Round 4 Chains 24, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6583 restraints for refining 2790 atoms. 6111 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1979 (Rfree = 0.000) for 2790 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 42: After refmac, R = 0.1753 (Rfree = 0.000) for 2767 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 43: After refmac, R = 0.1661 (Rfree = 0.000) for 2761 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1313 (Rfree = 0.000) for 2762 atoms. Found 10 (13 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.1296 (Rfree = 0.000) for 2755 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.54 Search for helices and strands: 0 residues in 0 chains, 2811 seeds are put forward NCS extension: 0 residues added, 2811 seeds are put forward Round 1: 118 peptides, 26 chains. Longest chain 8 peptides. Score 0.233 Round 2: 137 peptides, 26 chains. Longest chain 11 peptides. Score 0.316 Round 3: 146 peptides, 27 chains. Longest chain 10 peptides. Score 0.335 Round 4: 144 peptides, 26 chains. Longest chain 10 peptides. Score 0.345 Round 5: 145 peptides, 29 chains. Longest chain 10 peptides. Score 0.296 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 118, 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 6421 restraints for refining 2744 atoms. 5975 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1923 (Rfree = 0.000) for 2744 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1872 (Rfree = 0.000) for 2721 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1463 (Rfree = 0.000) for 2710 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1367 (Rfree = 0.000) for 2696 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:14:16 GMT 2018 Job finished. TimeTaking 51.29 Used memory is bytes: 16999480