Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fno-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fno-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fno-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:07 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/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-hancs/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 392 and 0 Target number of residues in the AU: 392 Target solvent content: 0.6387 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-3.6-parrot-hancs.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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3968 target number of atoms Had to go as low as 0.80 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: 106.006 3.600 Wilson plot Bfac: 71.28 6884 reflections ( 99.21 % complete ) and 0 restraints for refining 4365 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3267 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3477 (Rfree = 0.000) for 4365 atoms. Found 27 (27 requested) and removed 58 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 4439 seeds are put forward NCS extension: 0 residues added, 4439 seeds are put forward Round 1: 151 peptides, 32 chains. Longest chain 8 peptides. Score 0.248 Round 2: 196 peptides, 35 chains. Longest chain 10 peptides. Score 0.349 Round 3: 228 peptides, 41 chains. Longest chain 11 peptides. Score 0.367 Round 4: 244 peptides, 38 chains. Longest chain 15 peptides. Score 0.446 Round 5: 252 peptides, 42 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 4 Chains 39, Residues 206, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8184 restraints for refining 3597 atoms. 7368 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2789 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 2: After refmac, R = 0.2446 (Rfree = 0.000) for 3548 atoms. Found 18 (23 requested) and removed 23 (11 requested) atoms. Cycle 3: After refmac, R = 0.2336 (Rfree = 0.000) for 3520 atoms. Found 18 (22 requested) and removed 22 (11 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2230 (Rfree = 0.000) for 3502 atoms. Found 7 (22 requested) and removed 17 (11 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2198 (Rfree = 0.000) for 3483 atoms. Found 9 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 3629 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 3647 seeds are put forward Round 1: 254 peptides, 48 chains. Longest chain 11 peptides. Score 0.356 Round 2: 276 peptides, 40 chains. Longest chain 16 peptides. Score 0.504 Round 3: 280 peptides, 41 chains. Longest chain 22 peptides. Score 0.503 Round 4: 292 peptides, 42 chains. Longest chain 26 peptides. Score 0.521 Round 5: 289 peptides, 42 chains. Longest chain 15 peptides. Score 0.514 Taking the results from Round 4 Chains 45, Residues 250, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 7944 restraints for refining 3596 atoms. 6916 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2453 (Rfree = 0.000) for 3596 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2444 (Rfree = 0.000) for 3563 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 8: After refmac, R = 0.2483 (Rfree = 0.000) for 3542 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2359 (Rfree = 0.000) for 3522 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 10: After refmac, R = 0.2085 (Rfree = 0.000) for 3509 atoms. Found 14 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 3676 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3694 seeds are put forward Round 1: 235 peptides, 45 chains. Longest chain 10 peptides. Score 0.338 Round 2: 270 peptides, 44 chains. Longest chain 18 peptides. Score 0.446 Round 3: 277 peptides, 38 chains. Longest chain 14 peptides. Score 0.527 Round 4: 274 peptides, 37 chains. Longest chain 18 peptides. Score 0.531 Round 5: 284 peptides, 40 chains. Longest chain 16 peptides. Score 0.523 Taking the results from Round 4 Chains 39, Residues 237, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8012 restraints for refining 3596 atoms. 7081 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2518 (Rfree = 0.000) for 3596 atoms. Found 23 (23 requested) and removed 38 (11 requested) atoms. Cycle 12: After refmac, R = 0.2368 (Rfree = 0.000) for 3552 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2405 (Rfree = 0.000) for 3526 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 14: After refmac, R = 0.2398 (Rfree = 0.000) for 3519 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2461 (Rfree = 0.000) for 3510 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3667 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3697 seeds are put forward Round 1: 231 peptides, 42 chains. Longest chain 13 peptides. Score 0.363 Round 2: 281 peptides, 40 chains. Longest chain 15 peptides. Score 0.516 Round 3: 285 peptides, 37 chains. Longest chain 17 peptides. Score 0.556 Round 4: 286 peptides, 37 chains. Longest chain 24 peptides. Score 0.558 Round 5: 281 peptides, 38 chains. Longest chain 23 peptides. Score 0.537 Taking the results from Round 4 Chains 37, Residues 249, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6884 reflections ( 99.21 % complete ) and 7897 restraints for refining 3597 atoms. 6900 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2410 (Rfree = 0.000) for 3597 atoms. Found 22 (23 requested) and removed 22 (11 requested) atoms. Cycle 17: After refmac, R = 0.2256 (Rfree = 0.000) for 3577 atoms. Found 13 (23 requested) and removed 16 (11 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2239 (Rfree = 0.000) for 3565 atoms. Found 12 (22 requested) and removed 16 (11 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2109 (Rfree = 0.000) for 3556 atoms. Found 10 (22 requested) and removed 17 (11 requested) atoms. Cycle 20: After refmac, R = 0.2056 (Rfree = 0.000) for 3546 atoms. Found 5 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 3727 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 3759 seeds are put forward Round 1: 234 peptides, 43 chains. Longest chain 14 peptides. Score 0.360 Round 2: 260 peptides, 41 chains. Longest chain 20 peptides. Score 0.453 Round 3: 292 peptides, 44 chains. Longest chain 18 peptides. Score 0.500 Round 4: 272 peptides, 40 chains. Longest chain 16 peptides. Score 0.494 Round 5: 273 peptides, 36 chains. Longest chain 20 peptides. Score 0.539 Taking the results from Round 5 Chains 36, Residues 237, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8093 restraints for refining 3596 atoms. 7181 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2334 (Rfree = 0.000) for 3596 atoms. Found 17 (23 requested) and removed 14 (11 requested) atoms. Cycle 22: After refmac, R = 0.2130 (Rfree = 0.000) for 3578 atoms. Found 9 (23 requested) and removed 14 (11 requested) atoms. Cycle 23: After refmac, R = 0.2046 (Rfree = 0.000) for 3562 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.2005 (Rfree = 0.000) for 3553 atoms. Found 8 (22 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.1995 (Rfree = 0.000) for 3544 atoms. Found 7 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 3663 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3691 seeds are put forward Round 1: 214 peptides, 44 chains. Longest chain 8 peptides. Score 0.288 Round 2: 242 peptides, 38 chains. Longest chain 19 peptides. Score 0.441 Round 3: 268 peptides, 44 chains. Longest chain 17 peptides. Score 0.440 Round 4: 269 peptides, 42 chains. Longest chain 17 peptides. Score 0.465 Round 5: 274 peptides, 45 chains. Longest chain 22 peptides. Score 0.445 Taking the results from Round 4 Chains 42, Residues 227, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8270 restraints for refining 3597 atoms. 7404 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2371 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 27: After refmac, R = 0.2145 (Rfree = 0.000) for 3591 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.2106 (Rfree = 0.000) for 3578 atoms. Found 17 (22 requested) and removed 15 (11 requested) atoms. Cycle 29: After refmac, R = 0.2005 (Rfree = 0.000) for 3577 atoms. Found 9 (22 requested) and removed 16 (11 requested) atoms. Cycle 30: After refmac, R = 0.2035 (Rfree = 0.000) for 3570 atoms. Found 10 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 3738 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 3759 seeds are put forward Round 1: 231 peptides, 42 chains. Longest chain 14 peptides. Score 0.363 Round 2: 244 peptides, 39 chains. Longest chain 14 peptides. Score 0.435 Round 3: 241 peptides, 38 chains. Longest chain 20 peptides. Score 0.438 Round 4: 252 peptides, 33 chains. Longest chain 24 peptides. Score 0.522 Round 5: 232 peptides, 37 chains. Longest chain 17 peptides. Score 0.426 Taking the results from Round 4 Chains 34, Residues 219, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8086 restraints for refining 3597 atoms. 7178 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2329 (Rfree = 0.000) for 3597 atoms. Found 18 (23 requested) and removed 23 (11 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2433 (Rfree = 0.000) for 3583 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 33: After refmac, R = 0.2056 (Rfree = 0.000) for 3572 atoms. Found 8 (22 requested) and removed 15 (11 requested) atoms. Cycle 34: After refmac, R = 0.2009 (Rfree = 0.000) for 3556 atoms. Found 6 (22 requested) and removed 18 (11 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1926 (Rfree = 0.000) for 3534 atoms. Found 5 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 3673 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3695 seeds are put forward Round 1: 237 peptides, 46 chains. Longest chain 14 peptides. Score 0.332 Round 2: 255 peptides, 44 chains. Longest chain 16 peptides. Score 0.406 Round 3: 248 peptides, 39 chains. Longest chain 17 peptides. Score 0.445 Round 4: 245 peptides, 43 chains. Longest chain 15 peptides. Score 0.390 Round 5: 257 peptides, 42 chains. Longest chain 14 peptides. Score 0.434 Taking the results from Round 3 Chains 40, Residues 209, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8268 restraints for refining 3597 atoms. 7422 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2351 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 37: After refmac, R = 0.2453 (Rfree = 0.000) for 3585 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 38: After refmac, R = 0.2247 (Rfree = 0.000) for 3585 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 39: After refmac, R = 0.2439 (Rfree = 0.000) for 3587 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 40: After refmac, R = 0.2272 (Rfree = 0.000) for 3588 atoms. Found 23 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3734 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3745 seeds are put forward Round 1: 196 peptides, 40 chains. Longest chain 12 peptides. Score 0.285 Round 2: 209 peptides, 37 chains. Longest chain 12 peptides. Score 0.362 Round 3: 201 peptides, 35 chains. Longest chain 15 peptides. Score 0.364 Round 4: 209 peptides, 33 chains. Longest chain 18 peptides. Score 0.411 Round 5: 207 peptides, 35 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 4 Chains 33, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8473 restraints for refining 3597 atoms. 7802 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2486 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 42: After refmac, R = 0.2208 (Rfree = 0.000) for 3586 atoms. Found 20 (23 requested) and removed 15 (11 requested) atoms. Cycle 43: After refmac, R = 0.2088 (Rfree = 0.000) for 3585 atoms. Found 12 (23 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2275 (Rfree = 0.000) for 3575 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 45: After refmac, R = 0.2008 (Rfree = 0.000) for 3578 atoms. Found 11 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3713 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3729 seeds are put forward Round 1: 180 peptides, 39 chains. Longest chain 9 peptides. Score 0.247 Round 2: 227 peptides, 42 chains. Longest chain 11 peptides. Score 0.352 Round 3: 229 peptides, 39 chains. Longest chain 12 peptides. Score 0.394 Round 4: 227 peptides, 38 chains. Longest chain 14 peptides. Score 0.400 Round 5: 232 peptides, 39 chains. Longest chain 14 peptides. Score 0.402 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 193, 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 2fno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6884 reflections ( 99.21 % complete ) and 8539 restraints for refining 3597 atoms. 7806 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2336 (Rfree = 0.000) for 3597 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2200 (Rfree = 0.000) for 3582 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2137 (Rfree = 0.000) for 3568 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2106 (Rfree = 0.000) for 3554 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 64.97