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 1vll-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vll-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vll-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-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/1vll-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-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 ============================================================ Tue 25 Dec 19:28:06 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/1vll-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-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 426 and 0 Target number of residues in the AU: 426 Target solvent content: 0.6761 Checking the provided sequence file Detected sequence length: 334 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 668 Adjusted target solvent content: 0.49 Input MTZ file: 1vll-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: 19 Cell parameters: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 5344 target number of atoms Had to go as low as 0.70 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: 76.441 3.400 Wilson plot Bfac: 97.07 10325 reflections ( 99.97 % complete ) and 0 restraints for refining 5969 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3589 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2929 (Rfree = 0.000) for 5969 atoms. Found 45 (45 requested) and removed 35 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 6112 seeds are put forward NCS extension: 0 residues added, 6112 seeds are put forward Round 1: 297 peptides, 53 chains. Longest chain 20 peptides. Score 0.382 Round 2: 352 peptides, 51 chains. Longest chain 19 peptides. Score 0.516 Round 3: 377 peptides, 49 chains. Longest chain 22 peptides. Score 0.579 Round 4: 388 peptides, 51 chains. Longest chain 22 peptides. Score 0.582 Round 5: 388 peptides, 47 chains. Longest chain 32 peptides. Score 0.613 Taking the results from Round 5 Chains 52, Residues 341, Estimated correctness of the model 32.9 % 6 chains (56 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10751 restraints for refining 4854 atoms. 9247 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2724 (Rfree = 0.000) for 4854 atoms. Found 19 (36 requested) and removed 38 (18 requested) atoms. Cycle 2: After refmac, R = 0.2498 (Rfree = 0.000) for 4795 atoms. Found 4 (36 requested) and removed 31 (18 requested) atoms. Cycle 3: After refmac, R = 0.2489 (Rfree = 0.000) for 4743 atoms. Found 6 (36 requested) and removed 30 (18 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2463 (Rfree = 0.000) for 4709 atoms. Found 4 (35 requested) and removed 18 (17 requested) atoms. Cycle 5: After refmac, R = 0.2440 (Rfree = 0.000) for 4680 atoms. Found 2 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 4824 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4842 seeds are put forward Round 1: 321 peptides, 51 chains. Longest chain 12 peptides. Score 0.454 Round 2: 387 peptides, 46 chains. Longest chain 21 peptides. Score 0.618 Round 3: 399 peptides, 51 chains. Longest chain 21 peptides. Score 0.601 Round 4: 397 peptides, 46 chains. Longest chain 24 peptides. Score 0.634 Round 5: 391 peptides, 47 chains. Longest chain 26 peptides. Score 0.617 Taking the results from Round 4 Chains 52, Residues 351, Estimated correctness of the model 39.4 % 6 chains (60 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10394 restraints for refining 4859 atoms. 8833 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2630 (Rfree = 0.000) for 4859 atoms. Found 15 (36 requested) and removed 34 (18 requested) atoms. Cycle 7: After refmac, R = 0.2502 (Rfree = 0.000) for 4810 atoms. Found 8 (36 requested) and removed 29 (18 requested) atoms. Cycle 8: After refmac, R = 0.2468 (Rfree = 0.000) for 4776 atoms. Found 4 (36 requested) and removed 23 (18 requested) atoms. Cycle 9: After refmac, R = 0.2442 (Rfree = 0.000) for 4743 atoms. Found 6 (35 requested) and removed 25 (17 requested) atoms. Cycle 10: After refmac, R = 0.2382 (Rfree = 0.000) for 4716 atoms. Found 5 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 4872 seeds are put forward NCS extension: 28 residues added (5 deleted due to clashes), 4900 seeds are put forward Round 1: 342 peptides, 55 chains. Longest chain 16 peptides. Score 0.461 Round 2: 369 peptides, 44 chains. Longest chain 33 peptides. Score 0.604 Round 3: 366 peptides, 48 chains. Longest chain 26 peptides. Score 0.567 Round 4: 375 peptides, 45 chains. Longest chain 21 peptides. Score 0.606 Round 5: 383 peptides, 41 chains. Longest chain 30 peptides. Score 0.648 Taking the results from Round 5 Chains 45, Residues 342, Estimated correctness of the model 43.6 % 4 chains (52 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10616 restraints for refining 4859 atoms. 9115 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2489 (Rfree = 0.000) for 4859 atoms. Found 29 (36 requested) and removed 42 (18 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2279 (Rfree = 0.000) for 4820 atoms. Found 9 (36 requested) and removed 31 (18 requested) atoms. Cycle 13: After refmac, R = 0.2222 (Rfree = 0.000) for 4784 atoms. Found 5 (36 requested) and removed 20 (18 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2182 (Rfree = 0.000) for 4761 atoms. Found 5 (36 requested) and removed 19 (18 requested) atoms. Cycle 15: After refmac, R = 0.2129 (Rfree = 0.000) for 4743 atoms. Found 4 (35 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 4890 seeds are put forward NCS extension: 53 residues added (3 deleted due to clashes), 4943 seeds are put forward Round 1: 324 peptides, 59 chains. Longest chain 12 peptides. Score 0.385 Round 2: 345 peptides, 46 chains. Longest chain 21 peptides. Score 0.545 Round 3: 352 peptides, 46 chains. Longest chain 29 peptides. Score 0.558 Round 4: 356 peptides, 45 chains. Longest chain 25 peptides. Score 0.574 Round 5: 338 peptides, 43 chains. Longest chain 31 peptides. Score 0.557 Taking the results from Round 4 Chains 49, Residues 311, Estimated correctness of the model 20.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11165 restraints for refining 4858 atoms. 9893 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2307 (Rfree = 0.000) for 4858 atoms. Found 5 (36 requested) and removed 29 (18 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2282 (Rfree = 0.000) for 4815 atoms. Found 6 (36 requested) and removed 25 (18 requested) atoms. Cycle 18: After refmac, R = 0.2160 (Rfree = 0.000) for 4781 atoms. Found 4 (36 requested) and removed 19 (18 requested) atoms. Cycle 19: After refmac, R = 0.2169 (Rfree = 0.000) for 4759 atoms. Found 9 (35 requested) and removed 23 (17 requested) atoms. Cycle 20: After refmac, R = 0.2129 (Rfree = 0.000) for 4743 atoms. Found 8 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 4890 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4914 seeds are put forward Round 1: 278 peptides, 45 chains. Longest chain 12 peptides. Score 0.417 Round 2: 322 peptides, 45 chains. Longest chain 16 peptides. Score 0.510 Round 3: 338 peptides, 50 chains. Longest chain 20 peptides. Score 0.498 Round 4: 340 peptides, 49 chains. Longest chain 13 peptides. Score 0.510 Round 5: 339 peptides, 48 chains. Longest chain 17 peptides. Score 0.517 Taking the results from Round 5 Chains 49, Residues 291, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10325 reflections ( 99.97 % complete ) and 11247 restraints for refining 4857 atoms. 10064 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2447 (Rfree = 0.000) for 4857 atoms. Found 25 (36 requested) and removed 27 (18 requested) atoms. Cycle 22: After refmac, R = 0.2299 (Rfree = 0.000) for 4831 atoms. Found 4 (36 requested) and removed 25 (18 requested) atoms. Cycle 23: After refmac, R = 0.2271 (Rfree = 0.000) for 4804 atoms. Found 6 (36 requested) and removed 25 (18 requested) atoms. Cycle 24: After refmac, R = 0.2240 (Rfree = 0.000) for 4775 atoms. Found 10 (36 requested) and removed 24 (18 requested) atoms. Cycle 25: After refmac, R = 0.2181 (Rfree = 0.000) for 4756 atoms. Found 9 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 4955 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4973 seeds are put forward Round 1: 274 peptides, 52 chains. Longest chain 12 peptides. Score 0.338 Round 2: 316 peptides, 52 chains. Longest chain 12 peptides. Score 0.434 Round 3: 305 peptides, 46 chains. Longest chain 13 peptides. Score 0.466 Round 4: 312 peptides, 47 chains. Longest chain 13 peptides. Score 0.472 Round 5: 320 peptides, 48 chains. Longest chain 15 peptides. Score 0.479 Taking the results from Round 5 Chains 50, Residues 272, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11207 restraints for refining 4858 atoms. 10063 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2371 (Rfree = 0.000) for 4858 atoms. Found 17 (36 requested) and removed 35 (18 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2399 (Rfree = 0.000) for 4826 atoms. Found 2 (36 requested) and removed 25 (18 requested) atoms. Cycle 28: After refmac, R = 0.2383 (Rfree = 0.000) for 4796 atoms. Found 4 (36 requested) and removed 26 (18 requested) atoms. Cycle 29: After refmac, R = 0.2364 (Rfree = 0.000) for 4766 atoms. Found 9 (36 requested) and removed 23 (18 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2781 (Rfree = 0.000) for 4748 atoms. Found 31 (35 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 4892 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4906 seeds are put forward Round 1: 253 peptides, 47 chains. Longest chain 13 peptides. Score 0.339 Round 2: 275 peptides, 43 chains. Longest chain 17 peptides. Score 0.430 Round 3: 298 peptides, 46 chains. Longest chain 16 peptides. Score 0.451 Round 4: 296 peptides, 42 chains. Longest chain 19 peptides. Score 0.484 Round 5: 310 peptides, 46 chains. Longest chain 17 peptides. Score 0.477 Taking the results from Round 4 Chains 44, Residues 254, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10325 reflections ( 99.97 % complete ) and 11172 restraints for refining 4858 atoms. 10134 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2340 (Rfree = 0.000) for 4858 atoms. Found 15 (36 requested) and removed 23 (18 requested) atoms. Cycle 32: After refmac, R = 0.2286 (Rfree = 0.000) for 4832 atoms. Found 4 (36 requested) and removed 25 (18 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2295 (Rfree = 0.000) for 4806 atoms. Found 4 (36 requested) and removed 34 (18 requested) atoms. Cycle 34: After refmac, R = 0.2204 (Rfree = 0.000) for 4770 atoms. Found 8 (36 requested) and removed 24 (18 requested) atoms. Cycle 35: After refmac, R = 0.2144 (Rfree = 0.000) for 4751 atoms. Found 3 (35 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 4894 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4912 seeds are put forward Round 1: 234 peptides, 47 chains. Longest chain 10 peptides. Score 0.292 Round 2: 282 peptides, 49 chains. Longest chain 12 peptides. Score 0.387 Round 3: 291 peptides, 49 chains. Longest chain 13 peptides. Score 0.407 Round 4: 302 peptides, 44 chains. Longest chain 15 peptides. Score 0.478 Round 5: 299 peptides, 47 chains. Longest chain 18 peptides. Score 0.444 Taking the results from Round 4 Chains 45, Residues 258, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11105 restraints for refining 4859 atoms. 10031 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2192 (Rfree = 0.000) for 4859 atoms. Found 10 (36 requested) and removed 24 (18 requested) atoms. Cycle 37: After refmac, R = 0.2146 (Rfree = 0.000) for 4827 atoms. Found 6 (36 requested) and removed 21 (18 requested) atoms. Cycle 38: After refmac, R = 0.2075 (Rfree = 0.000) for 4805 atoms. Found 6 (36 requested) and removed 23 (18 requested) atoms. Cycle 39: After refmac, R = 0.2070 (Rfree = 0.000) for 4772 atoms. Found 10 (36 requested) and removed 22 (18 requested) atoms. Cycle 40: After refmac, R = 0.1999 (Rfree = 0.000) for 4754 atoms. Found 10 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 4919 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4935 seeds are put forward Round 1: 222 peptides, 43 chains. Longest chain 10 peptides. Score 0.304 Round 2: 245 peptides, 40 chains. Longest chain 13 peptides. Score 0.392 Round 3: 272 peptides, 39 chains. Longest chain 14 peptides. Score 0.462 Round 4: 260 peptides, 37 chains. Longest chain 14 peptides. Score 0.456 Round 5: 258 peptides, 39 chains. Longest chain 15 peptides. Score 0.432 Taking the results from Round 3 Chains 39, Residues 233, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11354 restraints for refining 4854 atoms. 10461 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2102 (Rfree = 0.000) for 4854 atoms. Found 6 (36 requested) and removed 36 (18 requested) atoms. Cycle 42: After refmac, R = 0.2071 (Rfree = 0.000) for 4816 atoms. Found 10 (36 requested) and removed 25 (18 requested) atoms. Cycle 43: After refmac, R = 0.2080 (Rfree = 0.000) for 4799 atoms. Found 9 (36 requested) and removed 23 (18 requested) atoms. Cycle 44: After refmac, R = 0.2002 (Rfree = 0.000) for 4780 atoms. Found 9 (36 requested) and removed 23 (18 requested) atoms. Cycle 45: After refmac, R = 0.1975 (Rfree = 0.000) for 4761 atoms. Found 8 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 4914 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4926 seeds are put forward Round 1: 215 peptides, 40 chains. Longest chain 11 peptides. Score 0.319 Round 2: 250 peptides, 41 chains. Longest chain 13 peptides. Score 0.393 Round 3: 249 peptides, 40 chains. Longest chain 12 peptides. Score 0.401 Round 4: 247 peptides, 40 chains. Longest chain 13 peptides. Score 0.397 Round 5: 256 peptides, 39 chains. Longest chain 13 peptides. Score 0.427 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 217, Estimated correctness of the model 0.0 % 5 chains (30 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input Building loops using Loopy2018 40 chains (217 residues) following loop building 5 chains (30 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10325 reflections ( 99.97 % complete ) and 11352 restraints for refining 4859 atoms. 10422 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2195 (Rfree = 0.000) for 4859 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2104 (Rfree = 0.000) for 4829 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2073 (Rfree = 0.000) for 4806 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1999 (Rfree = 0.000) for 4782 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... TimeTaking 75.9