Sun 23 Dec 22:22:46 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 2ajr-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-3.4-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/2ajr-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-3.4-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 ============================================================ Sun 23 Dec 22:22:54 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/2ajr-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-3.4-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 575 and 0 Target number of residues in the AU: 575 Target solvent content: 0.6276 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 662 Adjusted target solvent content: 0.57 Input MTZ file: 2ajr-3.4-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: 92 Cell parameters: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 5296 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: 29.168 3.400 Wilson plot Bfac: 65.12 12126 reflections ( 99.61 % complete ) and 0 restraints for refining 5897 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3586 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3486 (Rfree = 0.000) for 5897 atoms. Found 44 (44 requested) and removed 77 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 5951 seeds are put forward NCS extension: 0 residues added, 5951 seeds are put forward Round 1: 235 peptides, 45 chains. Longest chain 11 peptides. Score 0.299 Round 2: 303 peptides, 51 chains. Longest chain 15 peptides. Score 0.387 Round 3: 344 peptides, 54 chains. Longest chain 18 peptides. Score 0.441 Round 4: 364 peptides, 57 chains. Longest chain 22 peptides. Score 0.453 Round 5: 370 peptides, 50 chains. Longest chain 21 peptides. Score 0.518 Taking the results from Round 5 Chains 53, Residues 320, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10494 restraints for refining 4815 atoms. 9152 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2919 (Rfree = 0.000) for 4815 atoms. Found 36 (36 requested) and removed 42 (18 requested) atoms. Cycle 2: After refmac, R = 0.2757 (Rfree = 0.000) for 4741 atoms. Found 21 (36 requested) and removed 34 (18 requested) atoms. Cycle 3: After refmac, R = 0.2630 (Rfree = 0.000) for 4698 atoms. Found 20 (35 requested) and removed 31 (17 requested) atoms. Cycle 4: After refmac, R = 0.2537 (Rfree = 0.000) for 4664 atoms. Found 19 (35 requested) and removed 21 (17 requested) atoms. Cycle 5: After refmac, R = 0.2487 (Rfree = 0.000) for 4644 atoms. Found 12 (35 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 4810 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 4835 seeds are put forward Round 1: 346 peptides, 57 chains. Longest chain 17 peptides. Score 0.420 Round 2: 356 peptides, 49 chains. Longest chain 21 peptides. Score 0.502 Round 3: 384 peptides, 55 chains. Longest chain 20 peptides. Score 0.504 Round 4: 384 peptides, 54 chains. Longest chain 23 peptides. Score 0.511 Round 5: 402 peptides, 53 chains. Longest chain 31 peptides. Score 0.548 Taking the results from Round 5 Chains 56, Residues 349, Estimated correctness of the model 10.8 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10173 restraints for refining 4815 atoms. 8712 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2727 (Rfree = 0.000) for 4815 atoms. Found 36 (36 requested) and removed 48 (18 requested) atoms. Cycle 7: After refmac, R = 0.2578 (Rfree = 0.000) for 4767 atoms. Found 31 (36 requested) and removed 33 (18 requested) atoms. Cycle 8: After refmac, R = 0.2491 (Rfree = 0.000) for 4740 atoms. Found 18 (35 requested) and removed 27 (17 requested) atoms. Cycle 9: After refmac, R = 0.2390 (Rfree = 0.000) for 4714 atoms. Found 21 (35 requested) and removed 22 (17 requested) atoms. Cycle 10: After refmac, R = 0.2371 (Rfree = 0.000) for 4699 atoms. Found 13 (35 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 4846 seeds are put forward NCS extension: 44 residues added (3 deleted due to clashes), 4890 seeds are put forward Round 1: 348 peptides, 52 chains. Longest chain 27 peptides. Score 0.464 Round 2: 355 peptides, 48 chains. Longest chain 19 peptides. Score 0.508 Round 3: 349 peptides, 47 chains. Longest chain 28 peptides. Score 0.505 Round 4: 346 peptides, 46 chains. Longest chain 19 peptides. Score 0.508 Round 5: 359 peptides, 43 chains. Longest chain 20 peptides. Score 0.552 Taking the results from Round 5 Chains 43, Residues 316, Estimated correctness of the model 12.2 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10701 restraints for refining 4815 atoms. 9444 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2678 (Rfree = 0.000) for 4815 atoms. Found 30 (36 requested) and removed 30 (18 requested) atoms. Cycle 12: After refmac, R = 0.2613 (Rfree = 0.000) for 4802 atoms. Found 29 (36 requested) and removed 27 (18 requested) atoms. Cycle 13: After refmac, R = 0.2497 (Rfree = 0.000) for 4786 atoms. Found 21 (36 requested) and removed 28 (18 requested) atoms. Cycle 14: After refmac, R = 0.2419 (Rfree = 0.000) for 4767 atoms. Found 19 (36 requested) and removed 23 (18 requested) atoms. Cycle 15: After refmac, R = 0.2374 (Rfree = 0.000) for 4758 atoms. Found 25 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 4957 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4979 seeds are put forward Round 1: 335 peptides, 56 chains. Longest chain 17 peptides. Score 0.407 Round 2: 377 peptides, 52 chains. Longest chain 22 peptides. Score 0.514 Round 3: 370 peptides, 44 chains. Longest chain 24 peptides. Score 0.562 Round 4: 364 peptides, 46 chains. Longest chain 19 peptides. Score 0.538 Round 5: 350 peptides, 47 chains. Longest chain 18 peptides. Score 0.507 Taking the results from Round 3 Chains 45, Residues 326, Estimated correctness of the model 15.8 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10135 restraints for refining 4815 atoms. 8700 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2778 (Rfree = 0.000) for 4815 atoms. Found 36 (36 requested) and removed 33 (18 requested) atoms. Cycle 17: After refmac, R = 0.2567 (Rfree = 0.000) for 4786 atoms. Found 36 (36 requested) and removed 28 (18 requested) atoms. Cycle 18: After refmac, R = 0.2480 (Rfree = 0.000) for 4772 atoms. Found 32 (36 requested) and removed 26 (18 requested) atoms. Cycle 19: After refmac, R = 0.2408 (Rfree = 0.000) for 4762 atoms. Found 20 (36 requested) and removed 25 (18 requested) atoms. Cycle 20: After refmac, R = 0.2360 (Rfree = 0.000) for 4747 atoms. Found 21 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 4871 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4888 seeds are put forward Round 1: 309 peptides, 51 chains. Longest chain 15 peptides. Score 0.399 Round 2: 350 peptides, 51 chains. Longest chain 19 peptides. Score 0.476 Round 3: 356 peptides, 45 chains. Longest chain 17 peptides. Score 0.532 Round 4: 344 peptides, 52 chains. Longest chain 15 peptides. Score 0.457 Round 5: 367 peptides, 49 chains. Longest chain 17 peptides. Score 0.520 Taking the results from Round 3 Chains 46, Residues 311, Estimated correctness of the model 4.9 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10310 restraints for refining 4815 atoms. 9026 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2613 (Rfree = 0.000) for 4815 atoms. Found 31 (36 requested) and removed 26 (18 requested) atoms. Cycle 22: After refmac, R = 0.2445 (Rfree = 0.000) for 4788 atoms. Found 25 (36 requested) and removed 29 (18 requested) atoms. Cycle 23: After refmac, R = 0.2376 (Rfree = 0.000) for 4772 atoms. Found 20 (36 requested) and removed 23 (18 requested) atoms. Cycle 24: After refmac, R = 0.2253 (Rfree = 0.000) for 4762 atoms. Found 8 (36 requested) and removed 24 (18 requested) atoms. Cycle 25: After refmac, R = 0.2259 (Rfree = 0.000) for 4736 atoms. Found 17 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 4871 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 4896 seeds are put forward Round 1: 322 peptides, 53 chains. Longest chain 16 peptides. Score 0.407 Round 2: 357 peptides, 48 chains. Longest chain 23 peptides. Score 0.511 Round 3: 354 peptides, 42 chains. Longest chain 22 peptides. Score 0.551 Round 4: 346 peptides, 44 chains. Longest chain 23 peptides. Score 0.523 Round 5: 360 peptides, 43 chains. Longest chain 26 peptides. Score 0.553 Taking the results from Round 5 Chains 45, Residues 317, Estimated correctness of the model 12.6 % 6 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10150 restraints for refining 4814 atoms. 8793 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2551 (Rfree = 0.000) for 4814 atoms. Found 36 (36 requested) and removed 31 (18 requested) atoms. Cycle 27: After refmac, R = 0.2359 (Rfree = 0.000) for 4793 atoms. Found 17 (36 requested) and removed 23 (18 requested) atoms. Cycle 28: After refmac, R = 0.2340 (Rfree = 0.000) for 4775 atoms. Found 23 (36 requested) and removed 21 (18 requested) atoms. Cycle 29: After refmac, R = 0.2304 (Rfree = 0.000) for 4772 atoms. Found 18 (36 requested) and removed 20 (18 requested) atoms. Cycle 30: After refmac, R = 0.2270 (Rfree = 0.000) for 4764 atoms. Found 12 (36 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 4879 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 4900 seeds are put forward Round 1: 323 peptides, 51 chains. Longest chain 16 peptides. Score 0.426 Round 2: 346 peptides, 45 chains. Longest chain 23 peptides. Score 0.515 Round 3: 358 peptides, 51 chains. Longest chain 17 peptides. Score 0.490 Round 4: 381 peptides, 45 chains. Longest chain 23 peptides. Score 0.572 Round 5: 367 peptides, 51 chains. Longest chain 22 peptides. Score 0.505 Taking the results from Round 4 Chains 50, Residues 336, Estimated correctness of the model 19.3 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 9998 restraints for refining 4814 atoms. 8559 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2508 (Rfree = 0.000) for 4814 atoms. Found 30 (36 requested) and removed 38 (18 requested) atoms. Cycle 32: After refmac, R = 0.2374 (Rfree = 0.000) for 4782 atoms. Found 9 (36 requested) and removed 21 (18 requested) atoms. Cycle 33: After refmac, R = 0.2322 (Rfree = 0.000) for 4761 atoms. Found 10 (36 requested) and removed 23 (18 requested) atoms. Cycle 34: After refmac, R = 0.2264 (Rfree = 0.000) for 4744 atoms. Found 10 (35 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.2231 (Rfree = 0.000) for 4731 atoms. Found 7 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.00 Search for helices and strands: 0 residues in 0 chains, 4866 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 4891 seeds are put forward Round 1: 306 peptides, 50 chains. Longest chain 16 peptides. Score 0.402 Round 2: 362 peptides, 48 chains. Longest chain 25 peptides. Score 0.519 Round 3: 381 peptides, 49 chains. Longest chain 26 peptides. Score 0.543 Round 4: 360 peptides, 49 chains. Longest chain 27 peptides. Score 0.508 Round 5: 369 peptides, 51 chains. Longest chain 20 peptides. Score 0.508 Taking the results from Round 3 Chains 51, Residues 332, Estimated correctness of the model 9.0 % 5 chains (26 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12126 reflections ( 99.61 % complete ) and 10127 restraints for refining 4815 atoms. 8783 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2553 (Rfree = 0.000) for 4815 atoms. Found 27 (36 requested) and removed 24 (18 requested) atoms. Cycle 37: After refmac, R = 0.2388 (Rfree = 0.000) for 4813 atoms. Found 20 (36 requested) and removed 23 (18 requested) atoms. Cycle 38: After refmac, R = 0.2298 (Rfree = 0.000) for 4809 atoms. Found 12 (36 requested) and removed 20 (18 requested) atoms. Cycle 39: After refmac, R = 0.2280 (Rfree = 0.000) for 4796 atoms. Found 18 (36 requested) and removed 19 (18 requested) atoms. Cycle 40: After refmac, R = 0.2286 (Rfree = 0.000) for 4791 atoms. Found 17 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 4910 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 4947 seeds are put forward Round 1: 311 peptides, 56 chains. Longest chain 13 peptides. Score 0.360 Round 2: 340 peptides, 52 chains. Longest chain 18 peptides. Score 0.450 Round 3: 330 peptides, 45 chains. Longest chain 16 peptides. Score 0.488 Round 4: 344 peptides, 49 chains. Longest chain 26 peptides. Score 0.481 Round 5: 337 peptides, 50 chains. Longest chain 21 peptides. Score 0.460 Taking the results from Round 3 Chains 45, Residues 285, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 12126 reflections ( 99.61 % complete ) and 10596 restraints for refining 4814 atoms. 9439 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2469 (Rfree = 0.000) for 4814 atoms. Found 21 (36 requested) and removed 23 (18 requested) atoms. Cycle 42: After refmac, R = 0.2287 (Rfree = 0.000) for 4801 atoms. Found 15 (36 requested) and removed 20 (18 requested) atoms. Cycle 43: After refmac, R = 0.2239 (Rfree = 0.000) for 4787 atoms. Found 13 (36 requested) and removed 21 (18 requested) atoms. Cycle 44: After refmac, R = 0.2243 (Rfree = 0.000) for 4772 atoms. Found 12 (36 requested) and removed 19 (18 requested) atoms. Cycle 45: After refmac, R = 0.2224 (Rfree = 0.000) for 4762 atoms. Found 14 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 4852 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4867 seeds are put forward Round 1: 272 peptides, 51 chains. Longest chain 14 peptides. Score 0.324 Round 2: 297 peptides, 43 chains. Longest chain 15 peptides. Score 0.444 Round 3: 319 peptides, 48 chains. Longest chain 15 peptides. Score 0.444 Round 4: 313 peptides, 41 chains. Longest chain 16 peptides. Score 0.490 Round 5: 306 peptides, 42 chains. Longest chain 23 peptides. Score 0.469 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 272, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2ajr-3_warpNtrace.pdb as input Building loops using Loopy2018 42 chains (272 residues) following loop building 3 chains (17 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 12126 reflections ( 99.61 % complete ) and 10726 restraints for refining 4815 atoms. 9631 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2400 (Rfree = 0.000) for 4815 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2345 (Rfree = 0.000) for 4782 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2284 (Rfree = 0.000) for 4757 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2224 (Rfree = 0.000) for 4728 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Writing output files ... TimeTaking 71.55