null Mon 24 Dec 07:26:13 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.8-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 07:26:17 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.8-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 331 and 0 Target number of residues in the AU: 331 Target solvent content: 0.5837 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 46.27 4023 reflections ( 98.05 % complete ) and 0 restraints for refining 3897 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.2953 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2970 (Rfree = 0.000) for 3897 atoms. Found 21 (21 requested) and removed 38 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 3922 seeds are put forward NCS extension: 0 residues added, 3922 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 7 peptides. Score 0.245 Round 2: 152 peptides, 30 chains. Longest chain 9 peptides. Score 0.307 Round 3: 176 peptides, 31 chains. Longest chain 10 peptides. Score 0.385 Round 4: 164 peptides, 28 chains. Longest chain 10 peptides. Score 0.389 Round 5: 174 peptides, 32 chains. Longest chain 11 peptides. Score 0.361 Taking the results from Round 4 Chains 28, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7712 restraints for refining 3158 atoms. 7196 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2605 (Rfree = 0.000) for 3158 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 2: After refmac, R = 0.2499 (Rfree = 0.000) for 3094 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. Cycle 3: After refmac, R = 0.2132 (Rfree = 0.000) for 3063 atoms. Found 12 (16 requested) and removed 19 (8 requested) atoms. Cycle 4: After refmac, R = 0.1679 (Rfree = 0.000) for 3040 atoms. Found 7 (16 requested) and removed 15 (8 requested) atoms. Cycle 5: After refmac, R = 0.1458 (Rfree = 0.000) for 3022 atoms. Found 5 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.40 Search for helices and strands: 0 residues in 0 chains, 3100 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 3105 seeds are put forward Round 1: 146 peptides, 31 chains. Longest chain 8 peptides. Score 0.265 Round 2: 182 peptides, 34 chains. Longest chain 10 peptides. Score 0.359 Round 3: 208 peptides, 37 chains. Longest chain 13 peptides. Score 0.409 Round 4: 199 peptides, 33 chains. Longest chain 12 peptides. Score 0.438 Round 5: 201 peptides, 34 chains. Longest chain 12 peptides. Score 0.430 Taking the results from Round 4 Chains 33, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7078 restraints for refining 3020 atoms. 6447 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1967 (Rfree = 0.000) for 3020 atoms. Found 16 (16 requested) and removed 37 (8 requested) atoms. Cycle 7: After refmac, R = 0.1851 (Rfree = 0.000) for 2963 atoms. Found 16 (16 requested) and removed 37 (8 requested) atoms. Cycle 8: After refmac, R = 0.1448 (Rfree = 0.000) for 2936 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.1375 (Rfree = 0.000) for 2923 atoms. Found 5 (16 requested) and removed 14 (8 requested) atoms. Cycle 10: After refmac, R = 0.1339 (Rfree = 0.000) for 2911 atoms. Found 3 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.40 Search for helices and strands: 0 residues in 0 chains, 2982 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2999 seeds are put forward Round 1: 184 peptides, 37 chains. Longest chain 11 peptides. Score 0.318 Round 2: 194 peptides, 34 chains. Longest chain 13 peptides. Score 0.405 Round 3: 199 peptides, 35 chains. Longest chain 14 peptides. Score 0.407 Round 4: 197 peptides, 33 chains. Longest chain 12 peptides. Score 0.431 Round 5: 186 peptides, 32 chains. Longest chain 10 peptides. Score 0.407 Taking the results from Round 4 Chains 33, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7323 restraints for refining 3103 atoms. 6700 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2316 (Rfree = 0.000) for 3103 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. Cycle 12: After refmac, R = 0.2102 (Rfree = 0.000) for 3064 atoms. Found 16 (16 requested) and removed 34 (8 requested) atoms. Cycle 13: After refmac, R = 0.2194 (Rfree = 0.000) for 3032 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 14: After refmac, R = 0.2001 (Rfree = 0.000) for 3016 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 15: After refmac, R = 0.1635 (Rfree = 0.000) for 3003 atoms. Found 10 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.35 Search for helices and strands: 0 residues in 0 chains, 3065 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3082 seeds are put forward Round 1: 151 peptides, 31 chains. Longest chain 9 peptides. Score 0.286 Round 2: 187 peptides, 35 chains. Longest chain 10 peptides. Score 0.362 Round 3: 198 peptides, 36 chains. Longest chain 10 peptides. Score 0.388 Round 4: 205 peptides, 34 chains. Longest chain 14 peptides. Score 0.444 Round 5: 203 peptides, 31 chains. Longest chain 17 peptides. Score 0.482 Taking the results from Round 5 Chains 31, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7264 restraints for refining 3108 atoms. 6607 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2371 (Rfree = 0.000) for 3108 atoms. Found 17 (17 requested) and removed 37 (8 requested) atoms. Cycle 17: After refmac, R = 0.2386 (Rfree = 0.000) for 3067 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 18: After refmac, R = 0.2249 (Rfree = 0.000) for 3043 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 19: After refmac, R = 0.1862 (Rfree = 0.000) for 3021 atoms. Found 11 (16 requested) and removed 16 (8 requested) atoms. Cycle 20: After refmac, R = 0.1757 (Rfree = 0.000) for 3007 atoms. Found 14 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 3090 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3106 seeds are put forward Round 1: 161 peptides, 33 chains. Longest chain 8 peptides. Score 0.293 Round 2: 200 peptides, 36 chains. Longest chain 10 peptides. Score 0.395 Round 3: 189 peptides, 30 chains. Longest chain 16 peptides. Score 0.449 Round 4: 197 peptides, 35 chains. Longest chain 11 peptides. Score 0.400 Round 5: 201 peptides, 33 chains. Longest chain 12 peptides. Score 0.445 Taking the results from Round 3 Chains 30, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7054 restraints for refining 3044 atoms. 6448 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2069 (Rfree = 0.000) for 3044 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 22: After refmac, R = 0.2066 (Rfree = 0.000) for 3030 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 23: After refmac, R = 0.1944 (Rfree = 0.000) for 3011 atoms. Found 14 (16 requested) and removed 14 (8 requested) atoms. Cycle 24: After refmac, R = 0.1666 (Rfree = 0.000) for 3002 atoms. Found 9 (16 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.1630 (Rfree = 0.000) for 2988 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 3052 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3065 seeds are put forward Round 1: 151 peptides, 28 chains. Longest chain 11 peptides. Score 0.338 Round 2: 202 peptides, 37 chains. Longest chain 12 peptides. Score 0.387 Round 3: 192 peptides, 33 chains. Longest chain 14 peptides. Score 0.413 Round 4: 194 peptides, 32 chains. Longest chain 14 peptides. Score 0.436 Round 5: 197 peptides, 32 chains. Longest chain 14 peptides. Score 0.446 Taking the results from Round 5 Chains 32, Residues 165, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7245 restraints for refining 3093 atoms. 6585 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2235 (Rfree = 0.000) for 3093 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. Cycle 27: After refmac, R = 0.2122 (Rfree = 0.000) for 3060 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 28: After refmac, R = 0.1993 (Rfree = 0.000) for 3051 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.1964 (Rfree = 0.000) for 3044 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 30: After refmac, R = 0.2033 (Rfree = 0.000) for 3039 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 3098 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3118 seeds are put forward Round 1: 130 peptides, 29 chains. Longest chain 10 peptides. Score 0.231 Round 2: 159 peptides, 31 chains. Longest chain 10 peptides. Score 0.319 Round 3: 160 peptides, 30 chains. Longest chain 11 peptides. Score 0.340 Round 4: 163 peptides, 31 chains. Longest chain 12 peptides. Score 0.335 Round 5: 182 peptides, 33 chains. Longest chain 13 peptides. Score 0.376 Taking the results from Round 5 Chains 33, Residues 149, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7153 restraints for refining 3072 atoms. 6554 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1895 (Rfree = 0.000) for 3072 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 32: After refmac, R = 0.1822 (Rfree = 0.000) for 3045 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 33: After refmac, R = 0.1818 (Rfree = 0.000) for 3033 atoms. Found 10 (16 requested) and removed 17 (8 requested) atoms. Cycle 34: After refmac, R = 0.1725 (Rfree = 0.000) for 3014 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.1552 (Rfree = 0.000) for 2997 atoms. Found 14 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.41 Search for helices and strands: 0 residues in 0 chains, 3060 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3079 seeds are put forward Round 1: 149 peptides, 31 chains. Longest chain 10 peptides. Score 0.278 Round 2: 176 peptides, 36 chains. Longest chain 10 peptides. Score 0.303 Round 3: 182 peptides, 36 chains. Longest chain 14 peptides. Score 0.327 Round 4: 168 peptides, 33 chains. Longest chain 11 peptides. Score 0.321 Round 5: 179 peptides, 35 chains. Longest chain 11 peptides. Score 0.331 Taking the results from Round 5 Chains 35, Residues 144, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7073 restraints for refining 3059 atoms. 6485 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1891 (Rfree = 0.000) for 3059 atoms. Found 10 (16 requested) and removed 21 (8 requested) atoms. Cycle 37: After refmac, R = 0.1550 (Rfree = 0.000) for 3040 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. Cycle 38: After refmac, R = 0.1459 (Rfree = 0.000) for 3028 atoms. Found 0 (16 requested) and removed 13 (8 requested) atoms. Cycle 39: After refmac, R = 0.1418 (Rfree = 0.000) for 3011 atoms. Found 3 (16 requested) and removed 11 (8 requested) atoms. Cycle 40: After refmac, R = 0.1383 (Rfree = 0.000) for 3001 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.07 3.28 Search for helices and strands: 0 residues in 0 chains, 3081 seeds are put forward NCS extension: 0 residues added, 3081 seeds are put forward Round 1: 116 peptides, 26 chains. Longest chain 6 peptides. Score 0.224 Round 2: 148 peptides, 29 chains. Longest chain 12 peptides. Score 0.308 Round 3: 164 peptides, 29 chains. Longest chain 13 peptides. Score 0.372 Round 4: 164 peptides, 31 chains. Longest chain 9 peptides. Score 0.339 Round 5: 168 peptides, 31 chains. Longest chain 10 peptides. Score 0.355 Taking the results from Round 3 Chains 29, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7351 restraints for refining 3070 atoms. 6840 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1585 (Rfree = 0.000) for 3070 atoms. Found 12 (16 requested) and removed 18 (8 requested) atoms. Cycle 42: After refmac, R = 0.1475 (Rfree = 0.000) for 3062 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. Cycle 43: After refmac, R = 0.1414 (Rfree = 0.000) for 3054 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.1382 (Rfree = 0.000) for 3048 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1381 (Rfree = 0.000) for 3044 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 3111 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3129 seeds are put forward Round 1: 140 peptides, 31 chains. Longest chain 9 peptides. Score 0.239 Round 2: 174 peptides, 31 chains. Longest chain 11 peptides. Score 0.378 Round 3: 160 peptides, 31 chains. Longest chain 11 peptides. Score 0.323 Round 4: 154 peptides, 28 chains. Longest chain 13 peptides. Score 0.350 Round 5: 156 peptides, 28 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 143, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4023 reflections ( 98.05 % complete ) and 7379 restraints for refining 3087 atoms. 6838 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1698 (Rfree = 0.000) for 3087 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1654 (Rfree = 0.000) for 3076 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1536 (Rfree = 0.000) for 3061 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1559 (Rfree = 0.000) for 3050 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:01:48 GMT 2018 Job finished. TimeTaking 35.59 Used memory is bytes: 13255864