null Mon 24 Dec 08:03:12 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 2it9-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2it9-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2it9-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.6-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/2it9-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.6-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 08:03:16 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/2it9-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-3.6-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 393 and 0 Target number of residues in the AU: 393 Target solvent content: 0.6465 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-3.6-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 4064 target number of atoms Had to go as low as 0.85 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: 67.879 3.600 Wilson plot Bfac: 75.92 7278 reflections ( 98.28 % complete ) and 0 restraints for refining 4502 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3830 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3190 (Rfree = 0.000) for 4502 atoms. Found 28 (28 requested) and removed 61 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 4534 seeds are put forward NCS extension: 0 residues added, 4534 seeds are put forward Round 1: 181 peptides, 35 chains. Longest chain 11 peptides. Score 0.301 Round 2: 237 peptides, 42 chains. Longest chain 11 peptides. Score 0.376 Round 3: 242 peptides, 37 chains. Longest chain 17 peptides. Score 0.447 Round 4: 257 peptides, 38 chains. Longest chain 14 peptides. Score 0.474 Round 5: 264 peptides, 38 chains. Longest chain 14 peptides. Score 0.491 Taking the results from Round 5 Chains 38, Residues 226, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8356 restraints for refining 3684 atoms. 7490 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2545 (Rfree = 0.000) for 3684 atoms. Found 22 (23 requested) and removed 19 (11 requested) atoms. Cycle 2: After refmac, R = 0.2406 (Rfree = 0.000) for 3652 atoms. Found 17 (23 requested) and removed 19 (11 requested) atoms. Cycle 3: After refmac, R = 0.2290 (Rfree = 0.000) for 3636 atoms. Found 11 (23 requested) and removed 22 (11 requested) atoms. Cycle 4: After refmac, R = 0.2289 (Rfree = 0.000) for 3615 atoms. Found 10 (23 requested) and removed 18 (11 requested) atoms. Cycle 5: After refmac, R = 0.2051 (Rfree = 0.000) for 3599 atoms. Found 8 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3717 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 3727 seeds are put forward Round 1: 250 peptides, 47 chains. Longest chain 12 peptides. Score 0.353 Round 2: 260 peptides, 44 chains. Longest chain 13 peptides. Score 0.415 Round 3: 274 peptides, 39 chains. Longest chain 15 peptides. Score 0.504 Round 4: 262 peptides, 36 chains. Longest chain 16 peptides. Score 0.507 Round 5: 269 peptides, 37 chains. Longest chain 15 peptides. Score 0.513 Taking the results from Round 5 Chains 37, Residues 232, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8225 restraints for refining 3684 atoms. 7334 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2537 (Rfree = 0.000) for 3684 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 7: After refmac, R = 0.2382 (Rfree = 0.000) for 3654 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 8: After refmac, R = 0.2242 (Rfree = 0.000) for 3634 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 9: After refmac, R = 0.1858 (Rfree = 0.000) for 3614 atoms. Found 11 (23 requested) and removed 12 (11 requested) atoms. Cycle 10: After refmac, R = 0.1744 (Rfree = 0.000) for 3606 atoms. Found 4 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3730 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3743 seeds are put forward Round 1: 238 peptides, 45 chains. Longest chain 11 peptides. Score 0.343 Round 2: 259 peptides, 40 chains. Longest chain 13 peptides. Score 0.457 Round 3: 264 peptides, 41 chains. Longest chain 12 peptides. Score 0.458 Round 4: 256 peptides, 37 chains. Longest chain 15 peptides. Score 0.482 Round 5: 253 peptides, 35 chains. Longest chain 18 peptides. Score 0.496 Taking the results from Round 5 Chains 35, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8219 restraints for refining 3684 atoms. 7382 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2370 (Rfree = 0.000) for 3684 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 12: After refmac, R = 0.2070 (Rfree = 0.000) for 3662 atoms. Found 10 (23 requested) and removed 20 (11 requested) atoms. Cycle 13: After refmac, R = 0.1946 (Rfree = 0.000) for 3641 atoms. Found 10 (23 requested) and removed 18 (11 requested) atoms. Cycle 14: After refmac, R = 0.1689 (Rfree = 0.000) for 3632 atoms. Found 0 (23 requested) and removed 14 (11 requested) atoms. Cycle 15: After refmac, R = 0.1640 (Rfree = 0.000) for 3612 atoms. Found 3 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 3711 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3732 seeds are put forward Round 1: 216 peptides, 40 chains. Longest chain 10 peptides. Score 0.341 Round 2: 235 peptides, 36 chains. Longest chain 14 peptides. Score 0.441 Round 3: 249 peptides, 36 chains. Longest chain 18 peptides. Score 0.476 Round 4: 261 peptides, 39 chains. Longest chain 15 peptides. Score 0.473 Round 5: 278 peptides, 42 chains. Longest chain 14 peptides. Score 0.482 Taking the results from Round 5 Chains 42, Residues 236, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8153 restraints for refining 3683 atoms. 7251 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2150 (Rfree = 0.000) for 3683 atoms. Found 8 (23 requested) and removed 18 (11 requested) atoms. Cycle 17: After refmac, R = 0.1979 (Rfree = 0.000) for 3659 atoms. Found 6 (23 requested) and removed 14 (11 requested) atoms. Cycle 18: After refmac, R = 0.1886 (Rfree = 0.000) for 3646 atoms. Found 6 (23 requested) and removed 16 (11 requested) atoms. Cycle 19: After refmac, R = 0.1905 (Rfree = 0.000) for 3632 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.1887 (Rfree = 0.000) for 3619 atoms. Found 12 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3735 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3755 seeds are put forward Round 1: 233 peptides, 44 chains. Longest chain 10 peptides. Score 0.341 Round 2: 256 peptides, 39 chains. Longest chain 17 peptides. Score 0.460 Round 3: 253 peptides, 42 chains. Longest chain 13 peptides. Score 0.419 Round 4: 277 peptides, 42 chains. Longest chain 17 peptides. Score 0.479 Round 5: 262 peptides, 40 chains. Longest chain 15 peptides. Score 0.464 Taking the results from Round 4 Chains 42, Residues 235, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8162 restraints for refining 3683 atoms. 7264 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2244 (Rfree = 0.000) for 3683 atoms. Found 15 (23 requested) and removed 17 (11 requested) atoms. Cycle 22: After refmac, R = 0.2090 (Rfree = 0.000) for 3662 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. Cycle 23: After refmac, R = 0.2006 (Rfree = 0.000) for 3645 atoms. Found 12 (23 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.1952 (Rfree = 0.000) for 3642 atoms. Found 8 (23 requested) and removed 13 (11 requested) atoms. Cycle 25: After refmac, R = 0.1880 (Rfree = 0.000) for 3636 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3741 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3761 seeds are put forward Round 1: 228 peptides, 44 chains. Longest chain 11 peptides. Score 0.327 Round 2: 245 peptides, 39 chains. Longest chain 14 peptides. Score 0.432 Round 3: 250 peptides, 41 chains. Longest chain 16 peptides. Score 0.423 Round 4: 254 peptides, 39 chains. Longest chain 18 peptides. Score 0.455 Round 5: 254 peptides, 41 chains. Longest chain 13 peptides. Score 0.433 Taking the results from Round 4 Chains 39, Residues 215, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8184 restraints for refining 3684 atoms. 7327 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2183 (Rfree = 0.000) for 3684 atoms. Found 13 (23 requested) and removed 15 (11 requested) atoms. Cycle 27: After refmac, R = 0.1981 (Rfree = 0.000) for 3671 atoms. Found 6 (23 requested) and removed 15 (11 requested) atoms. Cycle 28: After refmac, R = 0.1928 (Rfree = 0.000) for 3658 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. Cycle 29: After refmac, R = 0.1879 (Rfree = 0.000) for 3645 atoms. Found 1 (23 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.1824 (Rfree = 0.000) for 3629 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3705 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3719 seeds are put forward Round 1: 213 peptides, 40 chains. Longest chain 14 peptides. Score 0.333 Round 2: 246 peptides, 40 chains. Longest chain 14 peptides. Score 0.423 Round 3: 224 peptides, 36 chains. Longest chain 16 peptides. Score 0.412 Round 4: 231 peptides, 40 chains. Longest chain 10 peptides. Score 0.383 Round 5: 216 peptides, 35 chains. Longest chain 12 peptides. Score 0.402 Taking the results from Round 2 Chains 40, Residues 206, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8208 restraints for refining 3684 atoms. 7424 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2150 (Rfree = 0.000) for 3684 atoms. Found 7 (23 requested) and removed 16 (11 requested) atoms. Cycle 32: After refmac, R = 0.2053 (Rfree = 0.000) for 3666 atoms. Found 14 (23 requested) and removed 16 (11 requested) atoms. Cycle 33: After refmac, R = 0.1952 (Rfree = 0.000) for 3660 atoms. Found 1 (23 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1912 (Rfree = 0.000) for 3642 atoms. Found 3 (23 requested) and removed 13 (11 requested) atoms. Cycle 35: After refmac, R = 0.1916 (Rfree = 0.000) for 3630 atoms. Found 8 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3713 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3724 seeds are put forward Round 1: 214 peptides, 41 chains. Longest chain 12 peptides. Score 0.323 Round 2: 235 peptides, 39 chains. Longest chain 12 peptides. Score 0.406 Round 3: 236 peptides, 39 chains. Longest chain 15 peptides. Score 0.409 Round 4: 249 peptides, 39 chains. Longest chain 13 peptides. Score 0.443 Round 5: 249 peptides, 38 chains. Longest chain 14 peptides. Score 0.454 Taking the results from Round 5 Chains 38, Residues 211, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8017 restraints for refining 3683 atoms. 7185 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2096 (Rfree = 0.000) for 3683 atoms. Found 14 (23 requested) and removed 19 (11 requested) atoms. Cycle 37: After refmac, R = 0.1936 (Rfree = 0.000) for 3667 atoms. Found 10 (23 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.1869 (Rfree = 0.000) for 3663 atoms. Found 5 (23 requested) and removed 14 (11 requested) atoms. Cycle 39: After refmac, R = 0.1875 (Rfree = 0.000) for 3649 atoms. Found 11 (23 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.1841 (Rfree = 0.000) for 3647 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3721 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3744 seeds are put forward Round 1: 217 peptides, 44 chains. Longest chain 10 peptides. Score 0.295 Round 2: 233 peptides, 42 chains. Longest chain 11 peptides. Score 0.365 Round 3: 242 peptides, 39 chains. Longest chain 18 peptides. Score 0.424 Round 4: 206 peptides, 36 chains. Longest chain 15 peptides. Score 0.362 Round 5: 219 peptides, 34 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 3 Chains 39, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8179 restraints for refining 3683 atoms. 7406 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2002 (Rfree = 0.000) for 3683 atoms. Found 9 (23 requested) and removed 14 (11 requested) atoms. Cycle 42: After refmac, R = 0.1933 (Rfree = 0.000) for 3668 atoms. Found 10 (23 requested) and removed 14 (11 requested) atoms. Cycle 43: After refmac, R = 0.1888 (Rfree = 0.000) for 3658 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.1794 (Rfree = 0.000) for 3645 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1784 (Rfree = 0.000) for 3636 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3709 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 3738 seeds are put forward Round 1: 183 peptides, 37 chains. Longest chain 8 peptides. Score 0.281 Round 2: 216 peptides, 37 chains. Longest chain 15 peptides. Score 0.378 Round 3: 217 peptides, 37 chains. Longest chain 13 peptides. Score 0.381 Round 4: 200 peptides, 33 chains. Longest chain 17 peptides. Score 0.382 Round 5: 200 peptides, 33 chains. Longest chain 16 peptides. Score 0.382 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 167, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2it9-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (167 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7278 reflections ( 98.28 % complete ) and 8183 restraints for refining 3684 atoms. 7469 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2072 (Rfree = 0.000) for 3684 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2058 (Rfree = 0.000) for 3666 atoms. Found 0 (23 requested) and removed 10 (11 requested) atoms. Cycle 48: After refmac, R = 0.1971 (Rfree = 0.000) for 3649 atoms. Found 0 (23 requested) and removed 10 (11 requested) atoms. Cycle 49: After refmac, R = 0.1957 (Rfree = 0.000) for 3635 atoms. Found 0 (23 requested) and removed 9 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:45:03 GMT 2018 Job finished. TimeTaking 41.86 Used memory is bytes: 8433896