null Mon 24 Dec 07:39:22 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 2fea-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fea-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fea-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-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/2fea-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-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 07:39:27 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/2fea-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-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 353 and 0 Target number of residues in the AU: 353 Target solvent content: 0.6531 Checking the provided sequence file Detected sequence length: 236 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 472 Adjusted target solvent content: 0.54 Input MTZ file: 2fea-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: 4 Cell parameters: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3776 target number of atoms Had to go as low as 0.65 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: 22.949 3.800 Wilson plot Bfac: 80.04 5507 reflections ( 98.22 % complete ) and 0 restraints for refining 4160 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3371 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3303 (Rfree = 0.000) for 4160 atoms. Found 22 (22 requested) and removed 69 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 4212 seeds are put forward NCS extension: 0 residues added, 4212 seeds are put forward Round 1: 169 peptides, 33 chains. Longest chain 8 peptides. Score 0.299 Round 2: 203 peptides, 36 chains. Longest chain 11 peptides. Score 0.366 Round 3: 226 peptides, 35 chains. Longest chain 13 peptides. Score 0.446 Round 4: 246 peptides, 35 chains. Longest chain 19 peptides. Score 0.500 Round 5: 252 peptides, 36 chains. Longest chain 16 peptides. Score 0.504 Taking the results from Round 5 Chains 36, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8066 restraints for refining 3415 atoms. 7238 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2709 (Rfree = 0.000) for 3415 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Cycle 2: After refmac, R = 0.2533 (Rfree = 0.000) for 3337 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. Cycle 3: After refmac, R = 0.2311 (Rfree = 0.000) for 3299 atoms. Found 18 (18 requested) and removed 38 (9 requested) atoms. Cycle 4: After refmac, R = 0.2369 (Rfree = 0.000) for 3260 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 5: After refmac, R = 0.2031 (Rfree = 0.000) for 3239 atoms. Found 9 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3379 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3395 seeds are put forward Round 1: 206 peptides, 41 chains. Longest chain 11 peptides. Score 0.309 Round 2: 245 peptides, 40 chains. Longest chain 16 peptides. Score 0.438 Round 3: 250 peptides, 38 chains. Longest chain 12 peptides. Score 0.475 Round 4: 247 peptides, 35 chains. Longest chain 22 peptides. Score 0.502 Round 5: 253 peptides, 39 chains. Longest chain 12 peptides. Score 0.472 Taking the results from Round 4 Chains 35, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7796 restraints for refining 3352 atoms. 6983 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2198 (Rfree = 0.000) for 3352 atoms. Found 8 (18 requested) and removed 26 (9 requested) atoms. Cycle 7: After refmac, R = 0.2224 (Rfree = 0.000) for 3311 atoms. Found 18 (18 requested) and removed 38 (9 requested) atoms. Cycle 8: After refmac, R = 0.2131 (Rfree = 0.000) for 3279 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 9: After refmac, R = 0.2119 (Rfree = 0.000) for 3266 atoms. Found 13 (18 requested) and removed 20 (9 requested) atoms. Cycle 10: After refmac, R = 0.2085 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 3378 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3400 seeds are put forward Round 1: 226 peptides, 41 chains. Longest chain 12 peptides. Score 0.371 Round 2: 235 peptides, 41 chains. Longest chain 12 peptides. Score 0.397 Round 3: 216 peptides, 34 chains. Longest chain 15 peptides. Score 0.430 Round 4: 223 peptides, 34 chains. Longest chain 16 peptides. Score 0.450 Round 5: 229 peptides, 37 chains. Longest chain 15 peptides. Score 0.430 Taking the results from Round 4 Chains 34, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8089 restraints for refining 3415 atoms. 7367 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2665 (Rfree = 0.000) for 3415 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 12: After refmac, R = 0.2409 (Rfree = 0.000) for 3386 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 13: After refmac, R = 0.2172 (Rfree = 0.000) for 3362 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 14: After refmac, R = 0.1810 (Rfree = 0.000) for 3357 atoms. Found 8 (18 requested) and removed 19 (9 requested) atoms. Cycle 15: After refmac, R = 0.1704 (Rfree = 0.000) for 3339 atoms. Found 3 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 3457 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3476 seeds are put forward Round 1: 206 peptides, 40 chains. Longest chain 13 peptides. Score 0.322 Round 2: 219 peptides, 36 chains. Longest chain 15 peptides. Score 0.414 Round 3: 227 peptides, 35 chains. Longest chain 14 peptides. Score 0.449 Round 4: 230 peptides, 33 chains. Longest chain 15 peptides. Score 0.481 Round 5: 235 peptides, 36 chains. Longest chain 13 peptides. Score 0.459 Taking the results from Round 4 Chains 33, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8136 restraints for refining 3415 atoms. 7381 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2534 (Rfree = 0.000) for 3415 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 17: After refmac, R = 0.2325 (Rfree = 0.000) for 3395 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 18: After refmac, R = 0.2201 (Rfree = 0.000) for 3380 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 19: After refmac, R = 0.2224 (Rfree = 0.000) for 3367 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 20: After refmac, R = 0.1839 (Rfree = 0.000) for 3356 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 3483 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3507 seeds are put forward Round 1: 190 peptides, 37 chains. Longest chain 13 peptides. Score 0.312 Round 2: 217 peptides, 30 chains. Longest chain 18 peptides. Score 0.482 Round 3: 222 peptides, 32 chains. Longest chain 15 peptides. Score 0.472 Round 4: 223 peptides, 34 chains. Longest chain 14 peptides. Score 0.450 Round 5: 221 peptides, 32 chains. Longest chain 19 peptides. Score 0.469 Taking the results from Round 2 Chains 30, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8030 restraints for refining 3415 atoms. 7312 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2286 (Rfree = 0.000) for 3415 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 22: After refmac, R = 0.2278 (Rfree = 0.000) for 3401 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 23: After refmac, R = 0.2129 (Rfree = 0.000) for 3389 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 24: After refmac, R = 0.2163 (Rfree = 0.000) for 3379 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 25: After refmac, R = 0.1700 (Rfree = 0.000) for 3373 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3501 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3522 seeds are put forward Round 1: 187 peptides, 34 chains. Longest chain 11 peptides. Score 0.343 Round 2: 228 peptides, 35 chains. Longest chain 14 peptides. Score 0.452 Round 3: 229 peptides, 35 chains. Longest chain 13 peptides. Score 0.454 Round 4: 212 peptides, 33 chains. Longest chain 14 peptides. Score 0.431 Round 5: 208 peptides, 34 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 3 Chains 35, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7945 restraints for refining 3414 atoms. 7204 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2413 (Rfree = 0.000) for 3414 atoms. Found 18 (18 requested) and removed 36 (9 requested) atoms. Cycle 27: After refmac, R = 0.2251 (Rfree = 0.000) for 3374 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 28: After refmac, R = 0.2181 (Rfree = 0.000) for 3355 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 29: After refmac, R = 0.1734 (Rfree = 0.000) for 3343 atoms. Found 5 (18 requested) and removed 16 (9 requested) atoms. Cycle 30: After refmac, R = 0.1659 (Rfree = 0.000) for 3326 atoms. Found 3 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 3417 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3430 seeds are put forward Round 1: 178 peptides, 39 chains. Longest chain 11 peptides. Score 0.244 Round 2: 205 peptides, 35 chains. Longest chain 13 peptides. Score 0.385 Round 3: 220 peptides, 34 chains. Longest chain 18 peptides. Score 0.442 Round 4: 211 peptides, 30 chains. Longest chain 15 peptides. Score 0.466 Round 5: 203 peptides, 28 chains. Longest chain 13 peptides. Score 0.469 Taking the results from Round 5 Chains 28, Residues 175, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8012 restraints for refining 3415 atoms. 7313 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2355 (Rfree = 0.000) for 3415 atoms. Found 18 (18 requested) and removed 41 (9 requested) atoms. Cycle 32: After refmac, R = 0.2207 (Rfree = 0.000) for 3382 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 33: After refmac, R = 0.1818 (Rfree = 0.000) for 3362 atoms. Found 6 (18 requested) and removed 17 (9 requested) atoms. Cycle 34: After refmac, R = 0.1776 (Rfree = 0.000) for 3343 atoms. Found 7 (18 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.1758 (Rfree = 0.000) for 3337 atoms. Found 6 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 3447 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3458 seeds are put forward Round 1: 169 peptides, 35 chains. Longest chain 14 peptides. Score 0.270 Round 2: 195 peptides, 31 chains. Longest chain 15 peptides. Score 0.408 Round 3: 190 peptides, 28 chains. Longest chain 16 peptides. Score 0.432 Round 4: 208 peptides, 30 chains. Longest chain 15 peptides. Score 0.458 Round 5: 204 peptides, 30 chains. Longest chain 15 peptides. Score 0.447 Taking the results from Round 4 Chains 30, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8003 restraints for refining 3410 atoms. 7321 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2260 (Rfree = 0.000) for 3410 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 37: After refmac, R = 0.2062 (Rfree = 0.000) for 3398 atoms. Found 14 (18 requested) and removed 21 (9 requested) atoms. Cycle 38: After refmac, R = 0.2046 (Rfree = 0.000) for 3381 atoms. Found 16 (18 requested) and removed 14 (9 requested) atoms. Cycle 39: After refmac, R = 0.1685 (Rfree = 0.000) for 3377 atoms. Found 1 (18 requested) and removed 13 (9 requested) atoms. Cycle 40: After refmac, R = 0.1603 (Rfree = 0.000) for 3357 atoms. Found 0 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 3465 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3488 seeds are put forward Round 1: 167 peptides, 37 chains. Longest chain 7 peptides. Score 0.235 Round 2: 194 peptides, 34 chains. Longest chain 13 peptides. Score 0.365 Round 3: 205 peptides, 35 chains. Longest chain 11 peptides. Score 0.385 Round 4: 211 peptides, 36 chains. Longest chain 10 peptides. Score 0.390 Round 5: 209 peptides, 32 chains. Longest chain 17 peptides. Score 0.435 Taking the results from Round 5 Chains 32, Residues 177, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8011 restraints for refining 3415 atoms. 7309 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2491 (Rfree = 0.000) for 3415 atoms. Found 12 (18 requested) and removed 192 (9 requested) atoms. Cycle 42: After refmac, R = 0.2268 (Rfree = 0.000) for 3227 atoms. Found 14 (17 requested) and removed 77 (8 requested) atoms. Cycle 43: After refmac, R = 0.2189 (Rfree = 0.000) for 3161 atoms. Found 15 (17 requested) and removed 41 (8 requested) atoms. Cycle 44: After refmac, R = 0.2299 (Rfree = 0.000) for 3129 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 45: After refmac, R = 0.1959 (Rfree = 0.000) for 3118 atoms. Found 13 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 3250 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3274 seeds are put forward Round 1: 147 peptides, 31 chains. Longest chain 9 peptides. Score 0.252 Round 2: 162 peptides, 30 chains. Longest chain 15 peptides. Score 0.318 Round 3: 159 peptides, 28 chains. Longest chain 11 peptides. Score 0.337 Round 4: 172 peptides, 31 chains. Longest chain 10 peptides. Score 0.337 Round 5: 158 peptides, 27 chains. Longest chain 11 peptides. Score 0.348 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, 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 2fea-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5507 reflections ( 98.22 % complete ) and 7642 restraints for refining 3252 atoms. 7145 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2162 (Rfree = 0.000) for 3252 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2177 (Rfree = 0.000) for 3231 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2095 (Rfree = 0.000) for 3217 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2285 (Rfree = 0.000) for 3205 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:21:16 GMT 2018 Job finished. TimeTaking 41.91 Used memory is bytes: 5763840