Sun 23 Dec 23:57:55 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 2fea-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-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/2fea-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-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 23:57:59 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/2fea-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-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 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-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: 4 Cell parameters: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3776 target number of atoms Had to go as low as 0.70 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 4161 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3349 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3184 (Rfree = 0.000) for 4161 atoms. Found 22 (22 requested) and removed 66 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 4218 seeds are put forward NCS extension: 0 residues added, 4218 seeds are put forward Round 1: 174 peptides, 36 chains. Longest chain 8 peptides. Score 0.273 Round 2: 231 peptides, 41 chains. Longest chain 16 peptides. Score 0.386 Round 3: 230 peptides, 38 chains. Longest chain 14 peptides. Score 0.420 Round 4: 240 peptides, 35 chains. Longest chain 16 peptides. Score 0.484 Round 5: 236 peptides, 35 chains. Longest chain 24 peptides. Score 0.473 Taking the results from Round 4 Chains 35, Residues 205, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7899 restraints for refining 3413 atoms. 7099 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2948 (Rfree = 0.000) for 3413 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 2: After refmac, R = 0.2383 (Rfree = 0.000) for 3356 atoms. Found 13 (18 requested) and removed 25 (9 requested) atoms. Cycle 3: After refmac, R = 0.2057 (Rfree = 0.000) for 3321 atoms. Found 9 (18 requested) and removed 15 (9 requested) atoms. Cycle 4: After refmac, R = 0.2135 (Rfree = 0.000) for 3304 atoms. Found 12 (18 requested) and removed 16 (9 requested) atoms. Cycle 5: After refmac, R = 0.2213 (Rfree = 0.000) for 3283 atoms. Found 17 (18 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 3430 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3457 seeds are put forward Round 1: 218 peptides, 43 chains. Longest chain 9 peptides. Score 0.320 Round 2: 256 peptides, 38 chains. Longest chain 17 peptides. Score 0.491 Round 3: 246 peptides, 37 chains. Longest chain 16 peptides. Score 0.476 Round 4: 255 peptides, 37 chains. Longest chain 17 peptides. Score 0.500 Round 5: 245 peptides, 35 chains. Longest chain 17 peptides. Score 0.497 Taking the results from Round 4 Chains 38, Residues 218, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7845 restraints for refining 3411 atoms. 6963 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2436 (Rfree = 0.000) for 3411 atoms. Found 18 (18 requested) and removed 47 (9 requested) atoms. Cycle 7: After refmac, R = 0.2298 (Rfree = 0.000) for 3350 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 8: After refmac, R = 0.2174 (Rfree = 0.000) for 3329 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 9: After refmac, R = 0.2103 (Rfree = 0.000) for 3318 atoms. Found 16 (18 requested) and removed 24 (9 requested) atoms. Cycle 10: After refmac, R = 0.1753 (Rfree = 0.000) for 3304 atoms. Found 5 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 3457 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3475 seeds are put forward Round 1: 216 peptides, 39 chains. Longest chain 12 peptides. Score 0.366 Round 2: 238 peptides, 39 chains. Longest chain 13 peptides. Score 0.431 Round 3: 232 peptides, 35 chains. Longest chain 14 peptides. Score 0.463 Round 4: 227 peptides, 35 chains. Longest chain 13 peptides. Score 0.449 Round 5: 257 peptides, 34 chains. Longest chain 16 peptides. Score 0.539 Taking the results from Round 5 Chains 34, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7797 restraints for refining 3414 atoms. 6939 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2244 (Rfree = 0.000) for 3414 atoms. Found 18 (18 requested) and removed 38 (9 requested) atoms. Cycle 12: After refmac, R = 0.2079 (Rfree = 0.000) for 3368 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 13: After refmac, R = 0.2117 (Rfree = 0.000) for 3347 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 14: After refmac, R = 0.1958 (Rfree = 0.000) for 3331 atoms. Found 12 (18 requested) and removed 18 (9 requested) atoms. Cycle 15: After refmac, R = 0.1884 (Rfree = 0.000) for 3313 atoms. Found 15 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 3457 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3474 seeds are put forward Round 1: 201 peptides, 40 chains. Longest chain 12 peptides. Score 0.307 Round 2: 222 peptides, 33 chains. Longest chain 15 peptides. Score 0.459 Round 3: 229 peptides, 34 chains. Longest chain 17 peptides. Score 0.466 Round 4: 229 peptides, 33 chains. Longest chain 15 peptides. Score 0.478 Round 5: 232 peptides, 32 chains. Longest chain 13 peptides. Score 0.498 Taking the results from Round 5 Chains 32, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8026 restraints for refining 3414 atoms. 7258 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2326 (Rfree = 0.000) for 3414 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 17: After refmac, R = 0.2295 (Rfree = 0.000) for 3386 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 18: After refmac, R = 0.1823 (Rfree = 0.000) for 3364 atoms. Found 6 (18 requested) and removed 37 (9 requested) atoms. Cycle 19: After refmac, R = 0.1670 (Rfree = 0.000) for 3325 atoms. Found 9 (18 requested) and removed 18 (9 requested) atoms. Cycle 20: After refmac, R = 0.1626 (Rfree = 0.000) for 3313 atoms. Found 4 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3438 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3458 seeds are put forward Round 1: 197 peptides, 34 chains. Longest chain 14 peptides. Score 0.374 Round 2: 212 peptides, 34 chains. Longest chain 13 peptides. Score 0.419 Round 3: 210 peptides, 33 chains. Longest chain 21 peptides. Score 0.426 Round 4: 207 peptides, 32 chains. Longest chain 17 peptides. Score 0.430 Round 5: 207 peptides, 33 chains. Longest chain 17 peptides. Score 0.417 Taking the results from Round 4 Chains 32, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8007 restraints for refining 3415 atoms. 7339 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2297 (Rfree = 0.000) for 3415 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 22: After refmac, R = 0.2116 (Rfree = 0.000) for 3393 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 23: After refmac, R = 0.2101 (Rfree = 0.000) for 3386 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 24: After refmac, R = 0.1948 (Rfree = 0.000) for 3373 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 25: After refmac, R = 0.1557 (Rfree = 0.000) for 3371 atoms. Found 1 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 3497 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3517 seeds are put forward Round 1: 182 peptides, 36 chains. Longest chain 9 peptides. Score 0.300 Round 2: 216 peptides, 34 chains. Longest chain 15 peptides. Score 0.430 Round 3: 219 peptides, 33 chains. Longest chain 15 peptides. Score 0.451 Round 4: 224 peptides, 35 chains. Longest chain 16 peptides. Score 0.440 Round 5: 208 peptides, 30 chains. Longest chain 20 peptides. Score 0.458 Taking the results from Round 5 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 8031 restraints for refining 3415 atoms. 7349 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2124 (Rfree = 0.000) for 3415 atoms. Found 15 (18 requested) and removed 14 (9 requested) atoms. Cycle 27: After refmac, R = 0.2141 (Rfree = 0.000) for 3402 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 28: After refmac, R = 0.2200 (Rfree = 0.000) for 3391 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 29: After refmac, R = 0.2133 (Rfree = 0.000) for 3381 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 30: After refmac, R = 0.1721 (Rfree = 0.000) for 3372 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 3470 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3492 seeds are put forward Round 1: 179 peptides, 36 chains. Longest chain 8 peptides. Score 0.290 Round 2: 194 peptides, 34 chains. Longest chain 11 peptides. Score 0.365 Round 3: 203 peptides, 31 chains. Longest chain 13 peptides. Score 0.431 Round 4: 203 peptides, 31 chains. Longest chain 12 peptides. Score 0.431 Round 5: 202 peptides, 31 chains. Longest chain 13 peptides. Score 0.428 Taking the results from Round 4 Chains 31, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8134 restraints for refining 3415 atoms. 7477 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2346 (Rfree = 0.000) for 3415 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 32: After refmac, R = 0.1988 (Rfree = 0.000) for 3407 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 33: After refmac, R = 0.2066 (Rfree = 0.000) for 3393 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 34: After refmac, R = 0.1670 (Rfree = 0.000) for 3379 atoms. Found 2 (18 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.1598 (Rfree = 0.000) for 3362 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3461 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3464 seeds are put forward Round 1: 179 peptides, 35 chains. Longest chain 12 peptides. Score 0.304 Round 2: 209 peptides, 41 chains. Longest chain 8 peptides. Score 0.319 Round 3: 211 peptides, 35 chains. Longest chain 13 peptides. Score 0.403 Round 4: 196 peptides, 35 chains. Longest chain 11 peptides. Score 0.358 Round 5: 204 peptides, 33 chains. Longest chain 14 peptides. Score 0.408 Taking the results from Round 5 Chains 33, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8122 restraints for refining 3415 atoms. 7471 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2334 (Rfree = 0.000) for 3415 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 37: After refmac, R = 0.2272 (Rfree = 0.000) for 3403 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 38: After refmac, R = 0.2088 (Rfree = 0.000) for 3388 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 39: After refmac, R = 0.1782 (Rfree = 0.000) for 3386 atoms. Found 10 (18 requested) and removed 13 (9 requested) atoms. Cycle 40: After refmac, R = 0.1675 (Rfree = 0.000) for 3376 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3480 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3498 seeds are put forward Round 1: 148 peptides, 29 chains. Longest chain 9 peptides. Score 0.286 Round 2: 163 peptides, 25 chains. Longest chain 13 peptides. Score 0.392 Round 3: 164 peptides, 28 chains. Longest chain 11 peptides. Score 0.353 Round 4: 172 peptides, 29 chains. Longest chain 13 peptides. Score 0.364 Round 5: 185 peptides, 30 chains. Longest chain 10 peptides. Score 0.391 Taking the results from Round 2 Chains 25, Residues 138, 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 3366 atoms. 7609 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2229 (Rfree = 0.000) for 3366 atoms. Found 18 (18 requested) and removed 43 (9 requested) atoms. Cycle 42: After refmac, R = 0.2114 (Rfree = 0.000) for 3336 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 43: After refmac, R = 0.2130 (Rfree = 0.000) for 3325 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 44: After refmac, R = 0.2016 (Rfree = 0.000) for 3322 atoms. Found 16 (18 requested) and removed 12 (9 requested) atoms. Cycle 45: After refmac, R = 0.1578 (Rfree = 0.000) for 3322 atoms. Found 3 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 3412 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3426 seeds are put forward Round 1: 166 peptides, 36 chains. Longest chain 7 peptides. Score 0.246 Round 2: 190 peptides, 37 chains. Longest chain 10 peptides. Score 0.312 Round 3: 184 peptides, 33 chains. Longest chain 11 peptides. Score 0.347 Round 4: 191 peptides, 32 chains. Longest chain 14 peptides. Score 0.382 Round 5: 181 peptides, 31 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 159, 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 8082 restraints for refining 3415 atoms. 7478 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2377 (Rfree = 0.000) for 3415 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2174 (Rfree = 0.000) for 3398 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2153 (Rfree = 0.000) for 3382 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2054 (Rfree = 0.000) for 3369 atoms. TimeTaking 34.18