null Mon 24 Dec 07:43:38 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fea-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fea-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-3.6-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 07:43:42 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-3.6-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 363 and 0 Target number of residues in the AU: 363 Target solvent content: 0.6433 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-3.6-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-3.6-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 3.601 Wilson plot Bfac: 73.95 6451 reflections ( 98.28 % complete ) and 0 restraints for refining 4158 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3302 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3073 (Rfree = 0.000) for 4158 atoms. Found 26 (26 requested) and removed 86 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 4170 seeds are put forward NCS extension: 0 residues added, 4170 seeds are put forward Round 1: 204 peptides, 41 chains. Longest chain 9 peptides. Score 0.303 Round 2: 243 peptides, 39 chains. Longest chain 20 peptides. Score 0.445 Round 3: 250 peptides, 37 chains. Longest chain 14 peptides. Score 0.487 Round 4: 252 peptides, 39 chains. Longest chain 22 peptides. Score 0.469 Round 5: 252 peptides, 34 chains. Longest chain 24 peptides. Score 0.526 Taking the results from Round 5 Chains 34, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7866 restraints for refining 3422 atoms. 7028 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2461 (Rfree = 0.000) for 3422 atoms. Found 21 (21 requested) and removed 73 (10 requested) atoms. Cycle 2: After refmac, R = 0.2236 (Rfree = 0.000) for 3338 atoms. Found 11 (21 requested) and removed 21 (10 requested) atoms. Cycle 3: After refmac, R = 0.2130 (Rfree = 0.000) for 3310 atoms. Found 8 (21 requested) and removed 19 (10 requested) atoms. Cycle 4: After refmac, R = 0.2043 (Rfree = 0.000) for 3293 atoms. Found 6 (21 requested) and removed 15 (10 requested) atoms. Cycle 5: After refmac, R = 0.2031 (Rfree = 0.000) for 3274 atoms. Found 10 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3389 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3406 seeds are put forward Round 1: 229 peptides, 40 chains. Longest chain 11 peptides. Score 0.392 Round 2: 241 peptides, 37 chains. Longest chain 15 peptides. Score 0.463 Round 3: 245 peptides, 35 chains. Longest chain 15 peptides. Score 0.497 Round 4: 264 peptides, 38 chains. Longest chain 25 peptides. Score 0.512 Round 5: 264 peptides, 37 chains. Longest chain 16 peptides. Score 0.523 Taking the results from Round 5 Chains 38, Residues 227, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7833 restraints for refining 3423 atoms. 6928 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2461 (Rfree = 0.000) for 3423 atoms. Found 20 (21 requested) and removed 19 (10 requested) atoms. Cycle 7: After refmac, R = 0.2134 (Rfree = 0.000) for 3409 atoms. Found 8 (21 requested) and removed 20 (10 requested) atoms. Cycle 8: After refmac, R = 0.2008 (Rfree = 0.000) for 3393 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.2008 (Rfree = 0.000) for 3375 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.1959 (Rfree = 0.000) for 3363 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3502 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3519 seeds are put forward Round 1: 236 peptides, 41 chains. Longest chain 13 peptides. Score 0.400 Round 2: 261 peptides, 35 chains. Longest chain 15 peptides. Score 0.537 Round 3: 279 peptides, 36 chains. Longest chain 16 peptides. Score 0.570 Round 4: 271 peptides, 36 chains. Longest chain 16 peptides. Score 0.551 Round 5: 281 peptides, 38 chains. Longest chain 25 peptides. Score 0.553 Taking the results from Round 3 Chains 36, Residues 243, Estimated correctness of the model 2.5 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7613 restraints for refining 3422 atoms. 6655 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2401 (Rfree = 0.000) for 3422 atoms. Found 20 (21 requested) and removed 113 (10 requested) atoms. Cycle 12: After refmac, R = 0.2361 (Rfree = 0.000) for 3309 atoms. Found 19 (21 requested) and removed 14 (10 requested) atoms. Cycle 13: After refmac, R = 0.2146 (Rfree = 0.000) for 3306 atoms. Found 7 (21 requested) and removed 14 (10 requested) atoms. Cycle 14: After refmac, R = 0.2085 (Rfree = 0.000) for 3293 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 15: After refmac, R = 0.2071 (Rfree = 0.000) for 3279 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3403 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3423 seeds are put forward Round 1: 236 peptides, 40 chains. Longest chain 17 peptides. Score 0.413 Round 2: 253 peptides, 36 chains. Longest chain 19 peptides. Score 0.506 Round 3: 269 peptides, 35 chains. Longest chain 21 peptides. Score 0.557 Round 4: 256 peptides, 37 chains. Longest chain 17 peptides. Score 0.503 Round 5: 258 peptides, 34 chains. Longest chain 16 peptides. Score 0.541 Taking the results from Round 3 Chains 35, Residues 234, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7723 restraints for refining 3423 atoms. 6822 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2350 (Rfree = 0.000) for 3423 atoms. Found 13 (21 requested) and removed 73 (10 requested) atoms. Cycle 17: After refmac, R = 0.2233 (Rfree = 0.000) for 3337 atoms. Found 16 (21 requested) and removed 21 (10 requested) atoms. Cycle 18: After refmac, R = 0.2209 (Rfree = 0.000) for 3326 atoms. Found 14 (21 requested) and removed 33 (10 requested) atoms. Cycle 19: After refmac, R = 0.2135 (Rfree = 0.000) for 3304 atoms. Found 10 (21 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.2015 (Rfree = 0.000) for 3299 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3422 seeds are put forward NCS extension: 46 residues added (4 deleted due to clashes), 3468 seeds are put forward Round 1: 200 peptides, 36 chains. Longest chain 13 peptides. Score 0.357 Round 2: 248 peptides, 36 chains. Longest chain 17 peptides. Score 0.493 Round 3: 255 peptides, 34 chains. Longest chain 23 peptides. Score 0.534 Round 4: 242 peptides, 31 chains. Longest chain 19 peptides. Score 0.535 Round 5: 245 peptides, 33 chains. Longest chain 15 peptides. Score 0.520 Taking the results from Round 4 Chains 31, Residues 211, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7791 restraints for refining 3423 atoms. 6964 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2300 (Rfree = 0.000) for 3423 atoms. Found 20 (21 requested) and removed 14 (10 requested) atoms. Cycle 22: After refmac, R = 0.2048 (Rfree = 0.000) for 3413 atoms. Found 5 (21 requested) and removed 14 (10 requested) atoms. Cycle 23: After refmac, R = 0.2041 (Rfree = 0.000) for 3396 atoms. Found 7 (21 requested) and removed 18 (10 requested) atoms. Cycle 24: After refmac, R = 0.1964 (Rfree = 0.000) for 3371 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.1939 (Rfree = 0.000) for 3358 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3471 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3493 seeds are put forward Round 1: 212 peptides, 42 chains. Longest chain 11 peptides. Score 0.315 Round 2: 232 peptides, 40 chains. Longest chain 15 peptides. Score 0.401 Round 3: 248 peptides, 40 chains. Longest chain 15 peptides. Score 0.446 Round 4: 243 peptides, 39 chains. Longest chain 14 peptides. Score 0.445 Round 5: 249 peptides, 39 chains. Longest chain 18 peptides. Score 0.461 Taking the results from Round 5 Chains 39, Residues 210, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7797 restraints for refining 3423 atoms. 6962 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2168 (Rfree = 0.000) for 3423 atoms. Found 19 (21 requested) and removed 20 (10 requested) atoms. Cycle 27: After refmac, R = 0.1958 (Rfree = 0.000) for 3409 atoms. Found 9 (21 requested) and removed 16 (10 requested) atoms. Cycle 28: After refmac, R = 0.1903 (Rfree = 0.000) for 3395 atoms. Found 2 (21 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.1892 (Rfree = 0.000) for 3385 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1863 (Rfree = 0.000) for 3373 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3508 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3526 seeds are put forward Round 1: 203 peptides, 41 chains. Longest chain 13 peptides. Score 0.299 Round 2: 232 peptides, 41 chains. Longest chain 14 peptides. Score 0.389 Round 3: 244 peptides, 41 chains. Longest chain 17 peptides. Score 0.423 Round 4: 258 peptides, 42 chains. Longest chain 13 peptides. Score 0.450 Round 5: 229 peptides, 35 chains. Longest chain 16 peptides. Score 0.454 Taking the results from Round 5 Chains 35, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7901 restraints for refining 3423 atoms. 7160 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2172 (Rfree = 0.000) for 3423 atoms. Found 15 (21 requested) and removed 19 (10 requested) atoms. Cycle 32: After refmac, R = 0.2003 (Rfree = 0.000) for 3400 atoms. Found 9 (21 requested) and removed 16 (10 requested) atoms. Cycle 33: After refmac, R = 0.1924 (Rfree = 0.000) for 3391 atoms. Found 8 (21 requested) and removed 14 (10 requested) atoms. Cycle 34: After refmac, R = 0.1659 (Rfree = 0.000) for 3380 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. Cycle 35: After refmac, R = 0.1752 (Rfree = 0.000) for 3366 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 3484 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3512 seeds are put forward Round 1: 177 peptides, 35 chains. Longest chain 10 peptides. Score 0.297 Round 2: 212 peptides, 35 chains. Longest chain 12 peptides. Score 0.406 Round 3: 220 peptides, 35 chains. Longest chain 13 peptides. Score 0.429 Round 4: 211 peptides, 32 chains. Longest chain 15 peptides. Score 0.441 Round 5: 234 peptides, 34 chains. Longest chain 20 peptides. Score 0.480 Taking the results from Round 5 Chains 35, Residues 200, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7700 restraints for refining 3423 atoms. 6896 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2164 (Rfree = 0.000) for 3423 atoms. Found 18 (21 requested) and removed 14 (10 requested) atoms. Cycle 37: After refmac, R = 0.1912 (Rfree = 0.000) for 3411 atoms. Found 9 (21 requested) and removed 16 (10 requested) atoms. Cycle 38: After refmac, R = 0.1888 (Rfree = 0.000) for 3401 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.1873 (Rfree = 0.000) for 3387 atoms. Found 8 (21 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.1839 (Rfree = 0.000) for 3379 atoms. Found 2 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3495 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3511 seeds are put forward Round 1: 219 peptides, 47 chains. Longest chain 9 peptides. Score 0.271 Round 2: 236 peptides, 42 chains. Longest chain 16 peptides. Score 0.388 Round 3: 216 peptides, 38 chains. Longest chain 20 peptides. Score 0.379 Round 4: 221 peptides, 35 chains. Longest chain 20 peptides. Score 0.432 Round 5: 226 peptides, 34 chains. Longest chain 20 peptides. Score 0.458 Taking the results from Round 5 Chains 34, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7915 restraints for refining 3423 atoms. 7181 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2067 (Rfree = 0.000) for 3423 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 42: After refmac, R = 0.1861 (Rfree = 0.000) for 3420 atoms. Found 9 (22 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.1807 (Rfree = 0.000) for 3408 atoms. Found 6 (21 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.1720 (Rfree = 0.000) for 3398 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1678 (Rfree = 0.000) for 3389 atoms. Found 3 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3489 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3507 seeds are put forward Round 1: 173 peptides, 37 chains. Longest chain 14 peptides. Score 0.256 Round 2: 190 peptides, 33 chains. Longest chain 14 peptides. Score 0.366 Round 3: 204 peptides, 34 chains. Longest chain 22 peptides. Score 0.395 Round 4: 209 peptides, 35 chains. Longest chain 23 peptides. Score 0.397 Round 5: 195 peptides, 33 chains. Longest chain 18 peptides. Score 0.381 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 174, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2fea-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (174 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6451 reflections ( 98.28 % complete ) and 8000 restraints for refining 3423 atoms. 7327 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2309 (Rfree = 0.000) for 3423 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1903 (Rfree = 0.000) for 3405 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1857 (Rfree = 0.000) for 3392 atoms. Found 0 (21 requested) and removed 7 (10 requested) atoms. Cycle 49: After refmac, R = 0.1789 (Rfree = 0.000) for 3380 atoms. Found 0 (21 requested) and removed 5 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:21:12 GMT 2018 Job finished. TimeTaking 37.58 Used memory is bytes: 6384776