null Mon 24 Dec 07:58:47 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fea-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fea-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-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 07:58:51 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-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 377 and 0 Target number of residues in the AU: 377 Target solvent content: 0.6295 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 66.13 7649 reflections ( 98.32 % complete ) and 0 restraints for refining 4159 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3251 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3370 (Rfree = 0.000) for 4159 atoms. Found 31 (31 requested) and removed 63 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 4234 seeds are put forward NCS extension: 0 residues added, 4234 seeds are put forward Round 1: 153 peptides, 33 chains. Longest chain 8 peptides. Score 0.244 Round 2: 228 peptides, 40 chains. Longest chain 13 peptides. Score 0.389 Round 3: 262 peptides, 45 chains. Longest chain 13 peptides. Score 0.425 Round 4: 251 peptides, 38 chains. Longest chain 16 peptides. Score 0.478 Round 5: 259 peptides, 35 chains. Longest chain 23 peptides. Score 0.533 Taking the results from Round 5 Chains 35, Residues 224, Estimated correctness of the model 5.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7759 restraints for refining 3432 atoms. 6898 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2815 (Rfree = 0.000) for 3432 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 2: After refmac, R = 0.2560 (Rfree = 0.000) for 3385 atoms. Found 23 (25 requested) and removed 21 (12 requested) atoms. Cycle 3: After refmac, R = 0.2451 (Rfree = 0.000) for 3364 atoms. Found 22 (25 requested) and removed 18 (12 requested) atoms. Cycle 4: After refmac, R = 0.2359 (Rfree = 0.000) for 3361 atoms. Found 16 (25 requested) and removed 21 (12 requested) atoms. Cycle 5: After refmac, R = 0.2278 (Rfree = 0.000) for 3346 atoms. Found 18 (25 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 3492 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 3523 seeds are put forward Round 1: 225 peptides, 40 chains. Longest chain 15 peptides. Score 0.381 Round 2: 267 peptides, 39 chains. Longest chain 17 peptides. Score 0.508 Round 3: 263 peptides, 36 chains. Longest chain 24 peptides. Score 0.531 Round 4: 288 peptides, 38 chains. Longest chain 25 peptides. Score 0.570 Round 5: 275 peptides, 38 chains. Longest chain 21 peptides. Score 0.539 Taking the results from Round 4 Chains 39, Residues 250, Estimated correctness of the model 18.6 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7632 restraints for refining 3433 atoms. 6629 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2597 (Rfree = 0.000) for 3433 atoms. Found 15 (25 requested) and removed 23 (12 requested) atoms. Cycle 7: After refmac, R = 0.2431 (Rfree = 0.000) for 3404 atoms. Found 15 (25 requested) and removed 20 (12 requested) atoms. Cycle 8: After refmac, R = 0.2398 (Rfree = 0.000) for 3387 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 9: After refmac, R = 0.2239 (Rfree = 0.000) for 3388 atoms. Found 15 (25 requested) and removed 17 (12 requested) atoms. Cycle 10: After refmac, R = 0.2186 (Rfree = 0.000) for 3382 atoms. Found 10 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3511 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 3536 seeds are put forward Round 1: 265 peptides, 46 chains. Longest chain 11 peptides. Score 0.422 Round 2: 276 peptides, 40 chains. Longest chain 15 peptides. Score 0.520 Round 3: 280 peptides, 36 chains. Longest chain 22 peptides. Score 0.572 Round 4: 285 peptides, 37 chains. Longest chain 22 peptides. Score 0.573 Round 5: 291 peptides, 37 chains. Longest chain 21 peptides. Score 0.587 Taking the results from Round 5 Chains 37, Residues 254, Estimated correctness of the model 24.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7637 restraints for refining 3432 atoms. 6658 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2333 (Rfree = 0.000) for 3432 atoms. Found 16 (25 requested) and removed 20 (12 requested) atoms. Cycle 12: After refmac, R = 0.2158 (Rfree = 0.000) for 3416 atoms. Found 13 (25 requested) and removed 13 (12 requested) atoms. Cycle 13: After refmac, R = 0.2085 (Rfree = 0.000) for 3413 atoms. Found 6 (25 requested) and removed 14 (12 requested) atoms. Cycle 14: After refmac, R = 0.2114 (Rfree = 0.000) for 3392 atoms. Found 13 (25 requested) and removed 15 (12 requested) atoms. Cycle 15: After refmac, R = 0.2105 (Rfree = 0.000) for 3387 atoms. Found 10 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 3528 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 3561 seeds are put forward Round 1: 252 peptides, 44 chains. Longest chain 11 peptides. Score 0.409 Round 2: 290 peptides, 39 chains. Longest chain 19 peptides. Score 0.564 Round 3: 269 peptides, 39 chains. Longest chain 15 peptides. Score 0.513 Round 4: 281 peptides, 38 chains. Longest chain 20 peptides. Score 0.553 Round 5: 291 peptides, 36 chains. Longest chain 25 peptides. Score 0.597 Taking the results from Round 5 Chains 37, Residues 255, Estimated correctness of the model 27.7 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7402 restraints for refining 3433 atoms. 6332 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2407 (Rfree = 0.000) for 3433 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 17: After refmac, R = 0.2227 (Rfree = 0.000) for 3418 atoms. Found 21 (25 requested) and removed 14 (12 requested) atoms. Cycle 18: After refmac, R = 0.2172 (Rfree = 0.000) for 3417 atoms. Found 19 (25 requested) and removed 19 (12 requested) atoms. Cycle 19: After refmac, R = 0.2090 (Rfree = 0.000) for 3410 atoms. Found 10 (25 requested) and removed 20 (12 requested) atoms. Cycle 20: After refmac, R = 0.2050 (Rfree = 0.000) for 3393 atoms. Found 15 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 3519 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 3544 seeds are put forward Round 1: 211 peptides, 39 chains. Longest chain 12 peptides. Score 0.351 Round 2: 260 peptides, 39 chains. Longest chain 17 peptides. Score 0.490 Round 3: 273 peptides, 40 chains. Longest chain 23 peptides. Score 0.512 Round 4: 253 peptides, 34 chains. Longest chain 19 peptides. Score 0.529 Round 5: 261 peptides, 34 chains. Longest chain 17 peptides. Score 0.548 Taking the results from Round 5 Chains 35, Residues 227, Estimated correctness of the model 10.8 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7625 restraints for refining 3433 atoms. 6698 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2352 (Rfree = 0.000) for 3433 atoms. Found 19 (25 requested) and removed 19 (12 requested) atoms. Cycle 22: After refmac, R = 0.2287 (Rfree = 0.000) for 3426 atoms. Found 22 (25 requested) and removed 16 (12 requested) atoms. Cycle 23: After refmac, R = 0.2170 (Rfree = 0.000) for 3424 atoms. Found 16 (25 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.2099 (Rfree = 0.000) for 3419 atoms. Found 13 (25 requested) and removed 19 (12 requested) atoms. Cycle 25: After refmac, R = 0.2083 (Rfree = 0.000) for 3410 atoms. Found 11 (25 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 3513 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3537 seeds are put forward Round 1: 224 peptides, 41 chains. Longest chain 15 peptides. Score 0.365 Round 2: 276 peptides, 45 chains. Longest chain 16 peptides. Score 0.464 Round 3: 273 peptides, 44 chains. Longest chain 15 peptides. Score 0.467 Round 4: 274 peptides, 42 chains. Longest chain 16 peptides. Score 0.492 Round 5: 268 peptides, 41 chains. Longest chain 19 peptides. Score 0.488 Taking the results from Round 4 Chains 42, Residues 232, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7723 restraints for refining 3433 atoms. 6813 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2191 (Rfree = 0.000) for 3433 atoms. Found 20 (25 requested) and removed 16 (12 requested) atoms. Cycle 27: After refmac, R = 0.2116 (Rfree = 0.000) for 3425 atoms. Found 15 (25 requested) and removed 14 (12 requested) atoms. Cycle 28: After refmac, R = 0.2057 (Rfree = 0.000) for 3421 atoms. Found 12 (25 requested) and removed 15 (12 requested) atoms. Cycle 29: After refmac, R = 0.2205 (Rfree = 0.000) for 3415 atoms. Found 25 (25 requested) and removed 14 (12 requested) atoms. Cycle 30: After refmac, R = 0.1988 (Rfree = 0.000) for 3422 atoms. Found 15 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 3572 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3585 seeds are put forward Round 1: 226 peptides, 42 chains. Longest chain 13 peptides. Score 0.358 Round 2: 245 peptides, 36 chains. Longest chain 16 peptides. Score 0.486 Round 3: 262 peptides, 39 chains. Longest chain 21 peptides. Score 0.495 Round 4: 256 peptides, 34 chains. Longest chain 20 peptides. Score 0.536 Round 5: 266 peptides, 37 chains. Longest chain 19 peptides. Score 0.528 Taking the results from Round 4 Chains 35, Residues 222, Estimated correctness of the model 6.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7780 restraints for refining 3433 atoms. 6889 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2284 (Rfree = 0.000) for 3433 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 32: After refmac, R = 0.2140 (Rfree = 0.000) for 3433 atoms. Found 20 (25 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.2034 (Rfree = 0.000) for 3436 atoms. Found 18 (25 requested) and removed 16 (12 requested) atoms. Cycle 34: After refmac, R = 0.1985 (Rfree = 0.000) for 3434 atoms. Found 16 (25 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1894 (Rfree = 0.000) for 3433 atoms. Found 13 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 3548 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3571 seeds are put forward Round 1: 235 peptides, 45 chains. Longest chain 12 peptides. Score 0.347 Round 2: 260 peptides, 38 chains. Longest chain 22 peptides. Score 0.502 Round 3: 246 peptides, 36 chains. Longest chain 21 peptides. Score 0.488 Round 4: 265 peptides, 37 chains. Longest chain 15 peptides. Score 0.525 Round 5: 259 peptides, 34 chains. Longest chain 23 peptides. Score 0.544 Taking the results from Round 5 Chains 34, Residues 225, Estimated correctness of the model 9.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7873 restraints for refining 3431 atoms. 7007 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2165 (Rfree = 0.000) for 3431 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 37: After refmac, R = 0.2006 (Rfree = 0.000) for 3436 atoms. Found 12 (25 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.1947 (Rfree = 0.000) for 3428 atoms. Found 16 (25 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.1875 (Rfree = 0.000) for 3427 atoms. Found 15 (25 requested) and removed 16 (12 requested) atoms. Cycle 40: After refmac, R = 0.1795 (Rfree = 0.000) for 3419 atoms. Found 13 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 3575 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3598 seeds are put forward Round 1: 192 peptides, 35 chains. Longest chain 24 peptides. Score 0.345 Round 2: 228 peptides, 37 chains. Longest chain 24 peptides. Score 0.427 Round 3: 234 peptides, 36 chains. Longest chain 20 peptides. Score 0.456 Round 4: 225 peptides, 33 chains. Longest chain 14 peptides. Score 0.468 Round 5: 226 peptides, 35 chains. Longest chain 15 peptides. Score 0.446 Taking the results from Round 4 Chains 33, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 8046 restraints for refining 3433 atoms. 7311 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2112 (Rfree = 0.000) for 3433 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 42: After refmac, R = 0.1863 (Rfree = 0.000) for 3438 atoms. Found 15 (25 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.1845 (Rfree = 0.000) for 3435 atoms. Found 14 (25 requested) and removed 16 (12 requested) atoms. Cycle 44: After refmac, R = 0.1773 (Rfree = 0.000) for 3429 atoms. Found 16 (25 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.1757 (Rfree = 0.000) for 3425 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.03 Search for helices and strands: 0 residues in 0 chains, 3525 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3538 seeds are put forward Round 1: 193 peptides, 36 chains. Longest chain 10 peptides. Score 0.335 Round 2: 218 peptides, 33 chains. Longest chain 15 peptides. Score 0.448 Round 3: 212 peptides, 31 chains. Longest chain 15 peptides. Score 0.456 Round 4: 223 peptides, 33 chains. Longest chain 15 peptides. Score 0.462 Round 5: 228 peptides, 34 chains. Longest chain 15 peptides. Score 0.464 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 194, 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. 7649 reflections ( 98.32 % complete ) and 7959 restraints for refining 3433 atoms. 7217 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1943 (Rfree = 0.000) for 3433 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1869 (Rfree = 0.000) for 3414 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1874 (Rfree = 0.000) for 3400 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1798 (Rfree = 0.000) for 3385 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:36:22 GMT 2018 Job finished. TimeTaking 37.59 Used memory is bytes: 10220024