Sun 23 Dec 23:52:32 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vjn-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vjn-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.8-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-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.8-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 ============================================================ Sun 23 Dec 23:52:36 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-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.8-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 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-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-3.8-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 3.800 Wilson plot Bfac: 46.27 4023 reflections ( 98.05 % complete ) and 0 restraints for refining 3885 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.2846 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2873 (Rfree = 0.000) for 3885 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, 3915 seeds are put forward NCS extension: 0 residues added, 3915 seeds are put forward Round 1: 142 peptides, 31 chains. Longest chain 7 peptides. Score 0.248 Round 2: 185 peptides, 36 chains. Longest chain 10 peptides. Score 0.338 Round 3: 209 peptides, 35 chains. Longest chain 11 peptides. Score 0.443 Round 4: 209 peptides, 32 chains. Longest chain 19 peptides. Score 0.487 Round 5: 200 peptides, 30 chains. Longest chain 14 peptides. Score 0.487 Taking the results from Round 5 Chains 30, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7531 restraints for refining 3156 atoms. 6881 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2069 (Rfree = 0.000) for 3156 atoms. Found 16 (17 requested) and removed 36 (8 requested) atoms. Cycle 2: After refmac, R = 0.1877 (Rfree = 0.000) for 3093 atoms. Found 15 (17 requested) and removed 19 (8 requested) atoms. Cycle 3: After refmac, R = 0.1896 (Rfree = 0.000) for 3066 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 4: After refmac, R = 0.1691 (Rfree = 0.000) for 3049 atoms. Found 15 (16 requested) and removed 12 (8 requested) atoms. Cycle 5: After refmac, R = 0.1373 (Rfree = 0.000) for 3035 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 3117 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3132 seeds are put forward Round 1: 181 peptides, 38 chains. Longest chain 12 peptides. Score 0.289 Round 2: 211 peptides, 38 chains. Longest chain 13 peptides. Score 0.404 Round 3: 215 peptides, 37 chains. Longest chain 17 peptides. Score 0.434 Round 4: 240 peptides, 41 chains. Longest chain 11 peptides. Score 0.461 Round 5: 250 peptides, 43 chains. Longest chain 12 peptides. Score 0.466 Taking the results from Round 5 Chains 43, Residues 207, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7023 restraints for refining 3030 atoms. 6238 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2149 (Rfree = 0.000) for 3030 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 7: After refmac, R = 0.1988 (Rfree = 0.000) for 2989 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 8: After refmac, R = 0.1988 (Rfree = 0.000) for 2960 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 9: After refmac, R = 0.1511 (Rfree = 0.000) for 2946 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.1475 (Rfree = 0.000) for 2930 atoms. Found 9 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.41 Search for helices and strands: 0 residues in 0 chains, 3012 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3025 seeds are put forward Round 1: 175 peptides, 34 chains. Longest chain 12 peptides. Score 0.332 Round 2: 201 peptides, 37 chains. Longest chain 12 peptides. Score 0.383 Round 3: 201 peptides, 33 chains. Longest chain 12 peptides. Score 0.445 Round 4: 198 peptides, 36 chains. Longest chain 13 peptides. Score 0.388 Round 5: 196 peptides, 34 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 3 Chains 34, Residues 168, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 6938 restraints for refining 3055 atoms. 6243 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2051 (Rfree = 0.000) for 3055 atoms. Found 16 (16 requested) and removed 35 (8 requested) atoms. Cycle 12: After refmac, R = 0.1650 (Rfree = 0.000) for 3014 atoms. Found 14 (16 requested) and removed 16 (8 requested) atoms. Cycle 13: After refmac, R = 0.1619 (Rfree = 0.000) for 2994 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 14: After refmac, R = 0.1450 (Rfree = 0.000) for 2990 atoms. Found 13 (16 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.1510 (Rfree = 0.000) for 2984 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 3083 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3094 seeds are put forward Round 1: 160 peptides, 32 chains. Longest chain 9 peptides. Score 0.306 Round 2: 183 peptides, 33 chains. Longest chain 10 peptides. Score 0.380 Round 3: 193 peptides, 36 chains. Longest chain 13 peptides. Score 0.369 Round 4: 195 peptides, 34 chains. Longest chain 12 peptides. Score 0.408 Round 5: 183 peptides, 30 chains. Longest chain 16 peptides. Score 0.427 Taking the results from Round 5 Chains 30, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7629 restraints for refining 3143 atoms. 7047 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1764 (Rfree = 0.000) for 3143 atoms. Found 12 (17 requested) and removed 24 (8 requested) atoms. Cycle 17: After refmac, R = 0.1559 (Rfree = 0.000) for 3109 atoms. Found 8 (17 requested) and removed 17 (8 requested) atoms. Cycle 18: After refmac, R = 0.1446 (Rfree = 0.000) for 3094 atoms. Found 5 (17 requested) and removed 14 (8 requested) atoms. Cycle 19: After refmac, R = 0.1432 (Rfree = 0.000) for 3082 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.1375 (Rfree = 0.000) for 3078 atoms. Found 8 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 3154 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3176 seeds are put forward Round 1: 179 peptides, 41 chains. Longest chain 8 peptides. Score 0.231 Round 2: 189 peptides, 38 chains. Longest chain 10 peptides. Score 0.321 Round 3: 190 peptides, 34 chains. Longest chain 13 peptides. Score 0.390 Round 4: 191 peptides, 38 chains. Longest chain 13 peptides. Score 0.329 Round 5: 183 peptides, 30 chains. Longest chain 14 peptides. Score 0.427 Taking the results from Round 5 Chains 30, Residues 153, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7513 restraints for refining 3184 atoms. 6890 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1896 (Rfree = 0.000) for 3184 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 22: After refmac, R = 0.1740 (Rfree = 0.000) for 3157 atoms. Found 15 (17 requested) and removed 20 (8 requested) atoms. Cycle 23: After refmac, R = 0.1295 (Rfree = 0.000) for 3140 atoms. Found 6 (17 requested) and removed 19 (8 requested) atoms. Cycle 24: After refmac, R = 0.1377 (Rfree = 0.000) for 3122 atoms. Found 5 (17 requested) and removed 13 (8 requested) atoms. Cycle 25: After refmac, R = 0.1447 (Rfree = 0.000) for 3106 atoms. Found 7 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 3186 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3201 seeds are put forward Round 1: 155 peptides, 33 chains. Longest chain 9 peptides. Score 0.268 Round 2: 176 peptides, 33 chains. Longest chain 11 peptides. Score 0.353 Round 3: 159 peptides, 28 chains. Longest chain 12 peptides. Score 0.370 Round 4: 183 peptides, 32 chains. Longest chain 10 peptides. Score 0.396 Round 5: 191 peptides, 34 chains. Longest chain 9 peptides. Score 0.394 Taking the results from Round 4 Chains 32, Residues 151, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7570 restraints for refining 3184 atoms. 6986 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1892 (Rfree = 0.000) for 3184 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 27: After refmac, R = 0.2008 (Rfree = 0.000) for 3168 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 28: After refmac, R = 0.1428 (Rfree = 0.000) for 3160 atoms. Found 5 (17 requested) and removed 18 (8 requested) atoms. Cycle 29: After refmac, R = 0.1341 (Rfree = 0.000) for 3138 atoms. Found 4 (17 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.1333 (Rfree = 0.000) for 3129 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.40 Search for helices and strands: 0 residues in 0 chains, 3193 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3204 seeds are put forward Round 1: 163 peptides, 36 chains. Longest chain 10 peptides. Score 0.249 Round 2: 174 peptides, 29 chains. Longest chain 10 peptides. Score 0.410 Round 3: 194 peptides, 31 chains. Longest chain 13 peptides. Score 0.451 Round 4: 190 peptides, 29 chains. Longest chain 16 peptides. Score 0.468 Round 5: 183 peptides, 29 chains. Longest chain 11 peptides. Score 0.443 Taking the results from Round 4 Chains 29, Residues 161, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7590 restraints for refining 3184 atoms. 6953 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2147 (Rfree = 0.000) for 3184 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 32: After refmac, R = 0.2031 (Rfree = 0.000) for 3159 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 33: After refmac, R = 0.1856 (Rfree = 0.000) for 3152 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 34: After refmac, R = 0.1477 (Rfree = 0.000) for 3148 atoms. Found 6 (17 requested) and removed 13 (8 requested) atoms. Cycle 35: After refmac, R = 0.1400 (Rfree = 0.000) for 3137 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.39 Search for helices and strands: 0 residues in 0 chains, 3191 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3212 seeds are put forward Round 1: 152 peptides, 30 chains. Longest chain 9 peptides. Score 0.307 Round 2: 166 peptides, 29 chains. Longest chain 10 peptides. Score 0.380 Round 3: 160 peptides, 29 chains. Longest chain 11 peptides. Score 0.357 Round 4: 177 peptides, 30 chains. Longest chain 10 peptides. Score 0.405 Round 5: 192 peptides, 33 chains. Longest chain 15 peptides. Score 0.413 Taking the results from Round 5 Chains 33, Residues 159, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7495 restraints for refining 3184 atoms. 6865 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2173 (Rfree = 0.000) for 3184 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 37: After refmac, R = 0.2231 (Rfree = 0.000) for 3162 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 38: After refmac, R = 0.2134 (Rfree = 0.000) for 3147 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 39: After refmac, R = 0.1627 (Rfree = 0.000) for 3141 atoms. Found 7 (17 requested) and removed 13 (8 requested) atoms. Cycle 40: After refmac, R = 0.1505 (Rfree = 0.000) for 3134 atoms. Found 3 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 3185 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3206 seeds are put forward Round 1: 145 peptides, 30 chains. Longest chain 9 peptides. Score 0.278 Round 2: 173 peptides, 31 chains. Longest chain 11 peptides. Score 0.374 Round 3: 173 peptides, 30 chains. Longest chain 20 peptides. Score 0.390 Round 4: 189 peptides, 33 chains. Longest chain 15 peptides. Score 0.402 Round 5: 169 peptides, 30 chains. Longest chain 16 peptides. Score 0.375 Taking the results from Round 4 Chains 33, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 98.05 % complete ) and 7620 restraints for refining 3184 atoms. 7029 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1946 (Rfree = 0.000) for 3184 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 42: After refmac, R = 0.1999 (Rfree = 0.000) for 3174 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 43: After refmac, R = 0.1903 (Rfree = 0.000) for 3174 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 44: After refmac, R = 0.1765 (Rfree = 0.000) for 3162 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 45: After refmac, R = 0.1571 (Rfree = 0.000) for 3163 atoms. Found 13 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 3238 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 3256 seeds are put forward Round 1: 129 peptides, 26 chains. Longest chain 7 peptides. Score 0.282 Round 2: 157 peptides, 27 chains. Longest chain 13 peptides. Score 0.379 Round 3: 145 peptides, 25 chains. Longest chain 13 peptides. Score 0.366 Round 4: 147 peptides, 25 chains. Longest chain 11 peptides. Score 0.374 Round 5: 156 peptides, 25 chains. Longest chain 13 peptides. Score 0.408 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 131, 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 7568 restraints for refining 3183 atoms. 7069 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1840 (Rfree = 0.000) for 3183 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2023 (Rfree = 0.000) for 3169 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1579 (Rfree = 0.000) for 3156 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1553 (Rfree = 0.000) for 3143 atoms. TimeTaking 36.13