Mon 24 Dec 01:06:01 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 1vjn-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vjn-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vjn-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-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/1vjn-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-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 01:06:05 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/1vjn-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-4.0-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 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-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: 1 Cell parameters: 43.059 45.719 63.384 73.681 89.271 64.860 Input sequence file: 1vjn-4.0-parrot-mrncs.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 3904 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.2866 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2770 (Rfree = 0.000) for 3904 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 3945 seeds are put forward NCS extension: 0 residues added, 3945 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 11 peptides. Score 0.270 Round 2: 155 peptides, 30 chains. Longest chain 11 peptides. Score 0.320 Round 3: 196 peptides, 39 chains. Longest chain 11 peptides. Score 0.332 Round 4: 211 peptides, 37 chains. Longest chain 12 peptides. Score 0.420 Round 5: 220 peptides, 40 chains. Longest chain 15 peptides. Score 0.406 Taking the results from Round 4 Chains 37, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 7411 restraints for refining 3097 atoms. 6752 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2515 (Rfree = 0.000) for 3097 atoms. Found 14 (14 requested) and removed 27 (7 requested) atoms. Cycle 2: After refmac, R = 0.2546 (Rfree = 0.000) for 3008 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 3: After refmac, R = 0.2716 (Rfree = 0.000) for 2948 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 4: After refmac, R = 0.2572 (Rfree = 0.000) for 2906 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 5: After refmac, R = 0.2384 (Rfree = 0.000) for 2879 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 2973 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2990 seeds are put forward Round 1: 148 peptides, 31 chains. Longest chain 10 peptides. Score 0.273 Round 2: 202 peptides, 38 chains. Longest chain 14 peptides. Score 0.371 Round 3: 205 peptides, 37 chains. Longest chain 17 peptides. Score 0.398 Round 4: 204 peptides, 34 chains. Longest chain 15 peptides. Score 0.441 Round 5: 207 peptides, 32 chains. Longest chain 14 peptides. Score 0.481 Taking the results from Round 5 Chains 32, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6464 restraints for refining 2856 atoms. 5796 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2014 (Rfree = 0.000) for 2856 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 7: After refmac, R = 0.1983 (Rfree = 0.000) for 2803 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 8: After refmac, R = 0.1808 (Rfree = 0.000) for 2779 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.1775 (Rfree = 0.000) for 2767 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 10: After refmac, R = 0.1387 (Rfree = 0.000) for 2751 atoms. Found 5 (13 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 2814 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2831 seeds are put forward Round 1: 168 peptides, 34 chains. Longest chain 11 peptides. Score 0.304 Round 2: 204 peptides, 41 chains. Longest chain 12 peptides. Score 0.331 Round 3: 225 peptides, 39 chains. Longest chain 13 peptides. Score 0.439 Round 4: 198 peptides, 33 chains. Longest chain 15 peptides. Score 0.435 Round 5: 202 peptides, 34 chains. Longest chain 10 peptides. Score 0.433 Taking the results from Round 3 Chains 39, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6423 restraints for refining 2838 atoms. 5718 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1725 (Rfree = 0.000) for 2838 atoms. Found 9 (13 requested) and removed 21 (6 requested) atoms. Cycle 12: After refmac, R = 0.1564 (Rfree = 0.000) for 2812 atoms. Found 3 (13 requested) and removed 13 (6 requested) atoms. Cycle 13: After refmac, R = 0.1532 (Rfree = 0.000) for 2794 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.1517 (Rfree = 0.000) for 2785 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.1496 (Rfree = 0.000) for 2778 atoms. Found 0 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 2834 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2856 seeds are put forward Round 1: 161 peptides, 34 chains. Longest chain 8 peptides. Score 0.275 Round 2: 183 peptides, 31 chains. Longest chain 12 peptides. Score 0.412 Round 3: 193 peptides, 30 chains. Longest chain 14 peptides. Score 0.463 Round 4: 209 peptides, 30 chains. Longest chain 14 peptides. Score 0.516 Round 5: 194 peptides, 29 chains. Longest chain 18 peptides. Score 0.481 Taking the results from Round 4 Chains 30, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6563 restraints for refining 2895 atoms. 5877 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1698 (Rfree = 0.000) for 2895 atoms. Found 11 (13 requested) and removed 28 (6 requested) atoms. Cycle 17: After refmac, R = 0.1693 (Rfree = 0.000) for 2849 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 18: After refmac, R = 0.1964 (Rfree = 0.000) for 2829 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.1513 (Rfree = 0.000) for 2810 atoms. Found 4 (13 requested) and removed 12 (6 requested) atoms. Cycle 20: After refmac, R = 0.1749 (Rfree = 0.000) for 2794 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.57 Search for helices and strands: 0 residues in 0 chains, 2896 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2912 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 9 peptides. Score 0.283 Round 2: 182 peptides, 32 chains. Longest chain 13 peptides. Score 0.392 Round 3: 184 peptides, 32 chains. Longest chain 13 peptides. Score 0.399 Round 4: 192 peptides, 32 chains. Longest chain 11 peptides. Score 0.429 Round 5: 195 peptides, 28 chains. Longest chain 17 peptides. Score 0.499 Taking the results from Round 5 Chains 28, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6649 restraints for refining 2908 atoms. 6009 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1971 (Rfree = 0.000) for 2908 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 22: After refmac, R = 0.1893 (Rfree = 0.000) for 2873 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 23: After refmac, R = 0.2118 (Rfree = 0.000) for 2846 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 24: After refmac, R = 0.1815 (Rfree = 0.000) for 2823 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 25: After refmac, R = 0.1453 (Rfree = 0.000) for 2811 atoms. Found 4 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.56 Search for helices and strands: 0 residues in 0 chains, 2893 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2909 seeds are put forward Round 1: 156 peptides, 32 chains. Longest chain 10 peptides. Score 0.289 Round 2: 182 peptides, 31 chains. Longest chain 12 peptides. Score 0.408 Round 3: 189 peptides, 32 chains. Longest chain 16 peptides. Score 0.418 Round 4: 191 peptides, 30 chains. Longest chain 16 peptides. Score 0.456 Round 5: 195 peptides, 30 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 5 Chains 30, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6659 restraints for refining 2908 atoms. 6029 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2015 (Rfree = 0.000) for 2908 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 27: After refmac, R = 0.1907 (Rfree = 0.000) for 2868 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 28: After refmac, R = 0.1408 (Rfree = 0.000) for 2848 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.1323 (Rfree = 0.000) for 2840 atoms. Found 3 (13 requested) and removed 12 (6 requested) atoms. Cycle 30: After refmac, R = 0.1361 (Rfree = 0.000) for 2829 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 2894 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2913 seeds are put forward Round 1: 173 peptides, 36 chains. Longest chain 10 peptides. Score 0.291 Round 2: 174 peptides, 33 chains. Longest chain 11 peptides. Score 0.345 Round 3: 174 peptides, 29 chains. Longest chain 10 peptides. Score 0.410 Round 4: 178 peptides, 34 chains. Longest chain 11 peptides. Score 0.344 Round 5: 187 peptides, 31 chains. Longest chain 15 peptides. Score 0.426 Taking the results from Round 5 Chains 31, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6897 restraints for refining 2982 atoms. 6304 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1929 (Rfree = 0.000) for 2982 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 32: After refmac, R = 0.1850 (Rfree = 0.000) for 2942 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 33: After refmac, R = 0.2034 (Rfree = 0.000) for 2927 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 34: After refmac, R = 0.1740 (Rfree = 0.000) for 2907 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 35: After refmac, R = 0.2155 (Rfree = 0.000) for 2897 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.52 Search for helices and strands: 0 residues in 0 chains, 2956 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2975 seeds are put forward Round 1: 124 peptides, 28 chains. Longest chain 8 peptides. Score 0.223 Round 2: 138 peptides, 28 chains. Longest chain 8 peptides. Score 0.284 Round 3: 161 peptides, 30 chains. Longest chain 10 peptides. Score 0.344 Round 4: 162 peptides, 30 chains. Longest chain 8 peptides. Score 0.348 Round 5: 162 peptides, 27 chains. Longest chain 11 peptides. Score 0.398 Taking the results from Round 5 Chains 27, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 6976 restraints for refining 2987 atoms. 6463 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2175 (Rfree = 0.000) for 2987 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 37: After refmac, R = 0.1780 (Rfree = 0.000) for 2954 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 38: After refmac, R = 0.1335 (Rfree = 0.000) for 2944 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.1329 (Rfree = 0.000) for 2941 atoms. Found 2 (13 requested) and removed 15 (6 requested) atoms. Cycle 40: After refmac, R = 0.1498 (Rfree = 0.000) for 2927 atoms. Found 5 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.55 Search for helices and strands: 0 residues in 0 chains, 2979 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2990 seeds are put forward Round 1: 125 peptides, 29 chains. Longest chain 7 peptides. Score 0.209 Round 2: 137 peptides, 25 chains. Longest chain 13 peptides. Score 0.334 Round 3: 150 peptides, 28 chains. Longest chain 11 peptides. Score 0.334 Round 4: 156 peptides, 29 chains. Longest chain 13 peptides. Score 0.341 Round 5: 159 peptides, 29 chains. Longest chain 10 peptides. Score 0.353 Taking the results from Round 5 Chains 29, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3444 reflections ( 98.04 % complete ) and 7184 restraints for refining 3053 atoms. 6693 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2164 (Rfree = 0.000) for 3053 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 42: After refmac, R = 0.1943 (Rfree = 0.000) for 3017 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 43: After refmac, R = 0.1929 (Rfree = 0.000) for 3003 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 44: After refmac, R = 0.1253 (Rfree = 0.000) for 2995 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.0998 (Rfree = 0.000) for 2990 atoms. Found 2 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 3058 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 3066 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 6 peptides. Score 0.240 Round 2: 122 peptides, 23 chains. Longest chain 10 peptides. Score 0.307 Round 3: 125 peptides, 22 chains. Longest chain 10 peptides. Score 0.338 Round 4: 124 peptides, 22 chains. Longest chain 11 peptides. Score 0.334 Round 5: 135 peptides, 22 chains. Longest chain 15 peptides. Score 0.379 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 113, 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 6924 restraints for refining 2975 atoms. 6494 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1765 (Rfree = 0.000) for 2975 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1841 (Rfree = 0.000) for 2961 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1241 (Rfree = 0.000) for 2946 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1663 (Rfree = 0.000) for 2933 atoms. TimeTaking 32.23