Sun 23 Dec 23:46:05 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 2p7i-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-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/2p7i-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-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 23:46:09 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/2p7i-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-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 337 and 0 Target number of residues in the AU: 337 Target solvent content: 0.6663 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4000 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: 94.045 3.800 Wilson plot Bfac: 89.21 5722 reflections ( 99.65 % complete ) and 0 restraints for refining 4431 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3378 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3212 (Rfree = 0.000) for 4431 atoms. Found 12 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.67 Search for helices and strands: 0 residues in 0 chains, 4512 seeds are put forward NCS extension: 0 residues added, 4512 seeds are put forward Round 1: 188 peptides, 37 chains. Longest chain 12 peptides. Score 0.306 Round 2: 256 peptides, 39 chains. Longest chain 18 peptides. Score 0.481 Round 3: 279 peptides, 35 chains. Longest chain 22 peptides. Score 0.582 Round 4: 297 peptides, 37 chains. Longest chain 20 peptides. Score 0.602 Round 5: 284 peptides, 37 chains. Longest chain 19 peptides. Score 0.573 Taking the results from Round 4 Chains 38, Residues 260, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8123 restraints for refining 3615 atoms. 7079 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2523 (Rfree = 0.000) for 3615 atoms. Found 5 (19 requested) and removed 13 (9 requested) atoms. Cycle 2: After refmac, R = 0.2503 (Rfree = 0.000) for 3525 atoms. Found 6 (19 requested) and removed 17 (9 requested) atoms. Cycle 3: After refmac, R = 0.2352 (Rfree = 0.000) for 3492 atoms. Found 5 (19 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2028 (Rfree = 0.000) for 3470 atoms. Found 2 (19 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.1950 (Rfree = 0.000) for 3450 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.73 Search for helices and strands: 0 residues in 0 chains, 3586 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3601 seeds are put forward Round 1: 229 peptides, 42 chains. Longest chain 9 peptides. Score 0.368 Round 2: 266 peptides, 36 chains. Longest chain 16 peptides. Score 0.541 Round 3: 275 peptides, 34 chains. Longest chain 18 peptides. Score 0.583 Round 4: 272 peptides, 37 chains. Longest chain 21 peptides. Score 0.544 Round 5: 291 peptides, 33 chains. Longest chain 21 peptides. Score 0.628 Taking the results from Round 5 Chains 34, Residues 258, Estimated correctness of the model 11.5 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8034 restraints for refining 3616 atoms. 6966 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2457 (Rfree = 0.000) for 3616 atoms. Found 6 (19 requested) and removed 25 (9 requested) atoms. Cycle 7: After refmac, R = 0.2311 (Rfree = 0.000) for 3571 atoms. Found 12 (19 requested) and removed 14 (9 requested) atoms. Cycle 8: After refmac, R = 0.2212 (Rfree = 0.000) for 3554 atoms. Found 3 (19 requested) and removed 17 (9 requested) atoms. Cycle 9: After refmac, R = 0.2197 (Rfree = 0.000) for 3531 atoms. Found 5 (19 requested) and removed 13 (9 requested) atoms. Cycle 10: After refmac, R = 0.2179 (Rfree = 0.000) for 3513 atoms. Found 2 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.71 Search for helices and strands: 0 residues in 0 chains, 3607 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3627 seeds are put forward Round 1: 228 peptides, 44 chains. Longest chain 14 peptides. Score 0.339 Round 2: 249 peptides, 37 chains. Longest chain 18 peptides. Score 0.486 Round 3: 250 peptides, 36 chains. Longest chain 17 peptides. Score 0.500 Round 4: 265 peptides, 33 chains. Longest chain 20 peptides. Score 0.571 Round 5: 265 peptides, 35 chains. Longest chain 20 peptides. Score 0.549 Taking the results from Round 4 Chains 34, Residues 232, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8367 restraints for refining 3616 atoms. 7436 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2317 (Rfree = 0.000) for 3616 atoms. Found 13 (19 requested) and removed 17 (9 requested) atoms. Cycle 12: After refmac, R = 0.2251 (Rfree = 0.000) for 3602 atoms. Found 10 (19 requested) and removed 17 (9 requested) atoms. Cycle 13: After refmac, R = 0.2183 (Rfree = 0.000) for 3585 atoms. Found 5 (19 requested) and removed 18 (9 requested) atoms. Cycle 14: After refmac, R = 0.2188 (Rfree = 0.000) for 3564 atoms. Found 2 (19 requested) and removed 13 (9 requested) atoms. Cycle 15: After refmac, R = 0.2168 (Rfree = 0.000) for 3546 atoms. Found 10 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.69 Search for helices and strands: 0 residues in 0 chains, 3653 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3667 seeds are put forward Round 1: 201 peptides, 35 chains. Longest chain 15 peptides. Score 0.374 Round 2: 233 peptides, 35 chains. Longest chain 19 peptides. Score 0.467 Round 3: 243 peptides, 37 chains. Longest chain 17 peptides. Score 0.470 Round 4: 250 peptides, 34 chains. Longest chain 17 peptides. Score 0.523 Round 5: 264 peptides, 36 chains. Longest chain 17 peptides. Score 0.536 Taking the results from Round 5 Chains 38, Residues 228, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8268 restraints for refining 3617 atoms. 7329 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2421 (Rfree = 0.000) for 3617 atoms. Found 7 (19 requested) and removed 18 (9 requested) atoms. Cycle 17: After refmac, R = 0.2310 (Rfree = 0.000) for 3576 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 18: After refmac, R = 0.2164 (Rfree = 0.000) for 3557 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. Cycle 19: After refmac, R = 0.2091 (Rfree = 0.000) for 3538 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2048 (Rfree = 0.000) for 3521 atoms. Found 6 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.63 Search for helices and strands: 0 residues in 0 chains, 3645 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3665 seeds are put forward Round 1: 197 peptides, 39 chains. Longest chain 9 peptides. Score 0.308 Round 2: 255 peptides, 45 chains. Longest chain 12 peptides. Score 0.407 Round 3: 254 peptides, 40 chains. Longest chain 15 peptides. Score 0.464 Round 4: 245 peptides, 37 chains. Longest chain 19 peptides. Score 0.476 Round 5: 222 peptides, 35 chains. Longest chain 12 peptides. Score 0.436 Taking the results from Round 4 Chains 39, Residues 208, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8181 restraints for refining 3618 atoms. 7284 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2234 (Rfree = 0.000) for 3618 atoms. Found 5 (19 requested) and removed 17 (9 requested) atoms. Cycle 22: After refmac, R = 0.2180 (Rfree = 0.000) for 3580 atoms. Found 6 (19 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.2078 (Rfree = 0.000) for 3557 atoms. Found 9 (19 requested) and removed 16 (9 requested) atoms. Cycle 24: After refmac, R = 0.1953 (Rfree = 0.000) for 3546 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.2026 (Rfree = 0.000) for 3531 atoms. Found 4 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.67 Search for helices and strands: 0 residues in 0 chains, 3653 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3667 seeds are put forward Round 1: 185 peptides, 37 chains. Longest chain 11 peptides. Score 0.296 Round 2: 238 peptides, 41 chains. Longest chain 11 peptides. Score 0.407 Round 3: 245 peptides, 43 chains. Longest chain 12 peptides. Score 0.403 Round 4: 233 peptides, 39 chains. Longest chain 12 peptides. Score 0.418 Round 5: 241 peptides, 38 chains. Longest chain 13 peptides. Score 0.453 Taking the results from Round 5 Chains 38, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8716 restraints for refining 3617 atoms. 7942 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2394 (Rfree = 0.000) for 3617 atoms. Found 17 (19 requested) and removed 18 (9 requested) atoms. Cycle 27: After refmac, R = 0.2229 (Rfree = 0.000) for 3599 atoms. Found 18 (19 requested) and removed 12 (9 requested) atoms. Cycle 28: After refmac, R = 0.2377 (Rfree = 0.000) for 3588 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 29: After refmac, R = 0.2218 (Rfree = 0.000) for 3578 atoms. Found 14 (19 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.2409 (Rfree = 0.000) for 3568 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.67 Search for helices and strands: 0 residues in 0 chains, 3711 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3726 seeds are put forward Round 1: 188 peptides, 38 chains. Longest chain 9 peptides. Score 0.292 Round 2: 219 peptides, 40 chains. Longest chain 10 peptides. Score 0.364 Round 3: 206 peptides, 35 chains. Longest chain 11 peptides. Score 0.389 Round 4: 198 peptides, 33 chains. Longest chain 12 peptides. Score 0.392 Round 5: 212 peptides, 35 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 5 Chains 35, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8694 restraints for refining 3617 atoms. 8021 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2379 (Rfree = 0.000) for 3617 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 32: After refmac, R = 0.2313 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 33: After refmac, R = 0.2334 (Rfree = 0.000) for 3580 atoms. Found 16 (19 requested) and removed 16 (9 requested) atoms. Cycle 34: After refmac, R = 0.2355 (Rfree = 0.000) for 3566 atoms. Found 12 (19 requested) and removed 15 (9 requested) atoms. Cycle 35: After refmac, R = 0.2312 (Rfree = 0.000) for 3545 atoms. Found 11 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.69 Search for helices and strands: 0 residues in 0 chains, 3685 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3701 seeds are put forward Round 1: 174 peptides, 35 chains. Longest chain 10 peptides. Score 0.288 Round 2: 197 peptides, 36 chains. Longest chain 12 peptides. Score 0.349 Round 3: 197 peptides, 32 chains. Longest chain 21 peptides. Score 0.402 Round 4: 205 peptides, 36 chains. Longest chain 12 peptides. Score 0.373 Round 5: 194 peptides, 34 chains. Longest chain 14 peptides. Score 0.366 Taking the results from Round 3 Chains 32, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8245 restraints for refining 3539 atoms. 7617 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2366 (Rfree = 0.000) for 3539 atoms. Found 5 (19 requested) and removed 22 (9 requested) atoms. Cycle 37: After refmac, R = 0.2361 (Rfree = 0.000) for 3511 atoms. Found 12 (19 requested) and removed 14 (9 requested) atoms. Cycle 38: After refmac, R = 0.2243 (Rfree = 0.000) for 3491 atoms. Found 11 (19 requested) and removed 16 (9 requested) atoms. Cycle 39: After refmac, R = 0.2299 (Rfree = 0.000) for 3481 atoms. Found 17 (19 requested) and removed 16 (9 requested) atoms. Cycle 40: After refmac, R = 0.2207 (Rfree = 0.000) for 3472 atoms. Found 11 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.68 Search for helices and strands: 0 residues in 0 chains, 3600 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 3635 seeds are put forward Round 1: 150 peptides, 32 chains. Longest chain 8 peptides. Score 0.249 Round 2: 187 peptides, 33 chains. Longest chain 13 peptides. Score 0.358 Round 3: 195 peptides, 35 chains. Longest chain 12 peptides. Score 0.356 Round 4: 201 peptides, 33 chains. Longest chain 16 peptides. Score 0.401 Round 5: 188 peptides, 30 chains. Longest chain 14 peptides. Score 0.401 Taking the results from Round 5 Chains 30, Residues 158, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8037 restraints for refining 3520 atoms. 7406 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2414 (Rfree = 0.000) for 3520 atoms. Found 9 (19 requested) and removed 40 (9 requested) atoms. Cycle 42: After refmac, R = 0.2265 (Rfree = 0.000) for 3475 atoms. Found 15 (19 requested) and removed 16 (9 requested) atoms. Cycle 43: After refmac, R = 0.2351 (Rfree = 0.000) for 3463 atoms. Found 13 (19 requested) and removed 13 (9 requested) atoms. Cycle 44: After refmac, R = 0.2231 (Rfree = 0.000) for 3448 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 45: After refmac, R = 0.1855 (Rfree = 0.000) for 3452 atoms. Found 3 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.69 Search for helices and strands: 0 residues in 0 chains, 3579 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3594 seeds are put forward Round 1: 137 peptides, 31 chains. Longest chain 7 peptides. Score 0.217 Round 2: 172 peptides, 34 chains. Longest chain 10 peptides. Score 0.295 Round 3: 188 peptides, 35 chains. Longest chain 12 peptides. Score 0.334 Round 4: 179 peptides, 33 chains. Longest chain 15 peptides. Score 0.332 Round 5: 188 peptides, 34 chains. Longest chain 15 peptides. Score 0.347 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 154, 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 2p7i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5722 reflections ( 99.65 % complete ) and 8364 restraints for refining 3566 atoms. 7782 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2412 (Rfree = 0.000) for 3566 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2351 (Rfree = 0.000) for 3541 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2136 (Rfree = 0.000) for 3520 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2587 (Rfree = 0.000) for 3504 atoms. TimeTaking 45.75