Mon 24 Dec 00:28:53 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 1vll-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.2-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/1vll-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.2-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 ============================================================ Mon 24 Dec 00:28:57 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/1vll-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.2-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 437 and 0 Target number of residues in the AU: 437 Target solvent content: 0.6678 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-3.2-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: 19 Cell parameters: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-3.2-parrot-mrncs.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 3.200 Wilson plot Bfac: 90.38 12307 reflections ( 99.98 % complete ) and 0 restraints for refining 5958 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3470 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2749 (Rfree = 0.000) for 5958 atoms. Found 25 (53 requested) and removed 40 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 6078 seeds are put forward NCS extension: 0 residues added, 6078 seeds are put forward Round 1: 355 peptides, 62 chains. Longest chain 16 peptides. Score 0.425 Round 2: 406 peptides, 53 chains. Longest chain 19 peptides. Score 0.598 Round 3: 404 peptides, 46 chains. Longest chain 22 peptides. Score 0.645 Round 4: 424 peptides, 45 chains. Longest chain 25 peptides. Score 0.681 Round 5: 422 peptides, 48 chains. Longest chain 39 peptides. Score 0.658 Taking the results from Round 4 Chains 51, Residues 379, Estimated correctness of the model 61.0 % 8 chains (86 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10050 restraints for refining 4875 atoms. 8274 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2757 (Rfree = 0.000) for 4875 atoms. Found 35 (43 requested) and removed 41 (21 requested) atoms. Cycle 2: After refmac, R = 0.2643 (Rfree = 0.000) for 4812 atoms. Found 15 (43 requested) and removed 29 (21 requested) atoms. Cycle 3: After refmac, R = 0.2583 (Rfree = 0.000) for 4783 atoms. Found 13 (43 requested) and removed 24 (21 requested) atoms. Cycle 4: After refmac, R = 0.2573 (Rfree = 0.000) for 4760 atoms. Found 13 (42 requested) and removed 28 (21 requested) atoms. Cycle 5: After refmac, R = 0.2545 (Rfree = 0.000) for 4737 atoms. Found 13 (42 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 4904 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 4932 seeds are put forward Round 1: 350 peptides, 56 chains. Longest chain 16 peptides. Score 0.469 Round 2: 394 peptides, 52 chains. Longest chain 28 peptides. Score 0.585 Round 3: 381 peptides, 47 chains. Longest chain 36 peptides. Score 0.601 Round 4: 405 peptides, 50 chains. Longest chain 36 peptides. Score 0.618 Round 5: 428 peptides, 49 chains. Longest chain 27 peptides. Score 0.660 Taking the results from Round 5 Chains 57, Residues 379, Estimated correctness of the model 56.2 % 12 chains (112 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 9830 restraints for refining 4877 atoms. 8012 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2723 (Rfree = 0.000) for 4877 atoms. Found 17 (43 requested) and removed 61 (21 requested) atoms. Cycle 7: After refmac, R = 0.2708 (Rfree = 0.000) for 4792 atoms. Found 16 (43 requested) and removed 44 (21 requested) atoms. Cycle 8: After refmac, R = 0.2585 (Rfree = 0.000) for 4740 atoms. Found 13 (42 requested) and removed 33 (21 requested) atoms. Cycle 9: After refmac, R = 0.2573 (Rfree = 0.000) for 4706 atoms. Found 16 (42 requested) and removed 39 (21 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2230 (Rfree = 0.000) for 4676 atoms. Found 7 (42 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 4819 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4835 seeds are put forward Round 1: 342 peptides, 49 chains. Longest chain 25 peptides. Score 0.514 Round 2: 381 peptides, 50 chains. Longest chain 20 peptides. Score 0.578 Round 3: 383 peptides, 50 chains. Longest chain 20 peptides. Score 0.581 Round 4: 380 peptides, 47 chains. Longest chain 16 peptides. Score 0.599 Round 5: 373 peptides, 45 chains. Longest chain 20 peptides. Score 0.603 Taking the results from Round 5 Chains 50, Residues 328, Estimated correctness of the model 41.9 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10714 restraints for refining 4878 atoms. 9309 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2598 (Rfree = 0.000) for 4878 atoms. Found 25 (43 requested) and removed 43 (21 requested) atoms. Cycle 12: After refmac, R = 0.2365 (Rfree = 0.000) for 4848 atoms. Found 17 (43 requested) and removed 32 (21 requested) atoms. Cycle 13: After refmac, R = 0.2635 (Rfree = 0.000) for 4817 atoms. Found 35 (43 requested) and removed 43 (21 requested) atoms. Cycle 14: After refmac, R = 0.2193 (Rfree = 0.000) for 4794 atoms. Found 17 (43 requested) and removed 32 (21 requested) atoms. Cycle 15: After refmac, R = 0.2076 (Rfree = 0.000) for 4769 atoms. Found 1 (42 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 4906 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4921 seeds are put forward Round 1: 339 peptides, 58 chains. Longest chain 13 peptides. Score 0.428 Round 2: 361 peptides, 50 chains. Longest chain 24 peptides. Score 0.542 Round 3: 357 peptides, 52 chains. Longest chain 22 peptides. Score 0.518 Round 4: 374 peptides, 56 chains. Longest chain 17 peptides. Score 0.517 Round 5: 369 peptides, 51 chains. Longest chain 18 peptides. Score 0.548 Taking the results from Round 5 Chains 51, Residues 318, Estimated correctness of the model 26.3 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 11012 restraints for refining 4878 atoms. 9727 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2416 (Rfree = 0.000) for 4878 atoms. Found 16 (43 requested) and removed 45 (21 requested) atoms. Cycle 17: After refmac, R = 0.2634 (Rfree = 0.000) for 4825 atoms. Found 43 (43 requested) and removed 27 (21 requested) atoms. Cycle 18: After refmac, R = 0.2272 (Rfree = 0.000) for 4826 atoms. Found 8 (43 requested) and removed 33 (21 requested) atoms. Cycle 19: After refmac, R = 0.2083 (Rfree = 0.000) for 4784 atoms. Found 5 (43 requested) and removed 25 (21 requested) atoms. Cycle 20: After refmac, R = 0.2057 (Rfree = 0.000) for 4763 atoms. Found 3 (42 requested) and removed 26 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 4898 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 4916 seeds are put forward Round 1: 303 peptides, 54 chains. Longest chain 21 peptides. Score 0.386 Round 2: 341 peptides, 53 chains. Longest chain 23 peptides. Score 0.477 Round 3: 328 peptides, 48 chains. Longest chain 20 peptides. Score 0.495 Round 4: 327 peptides, 49 chains. Longest chain 19 peptides. Score 0.484 Round 5: 346 peptides, 51 chains. Longest chain 18 peptides. Score 0.505 Taking the results from Round 5 Chains 52, Residues 295, Estimated correctness of the model 12.9 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 11111 restraints for refining 4876 atoms. 9930 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2437 (Rfree = 0.000) for 4876 atoms. Found 17 (43 requested) and removed 25 (21 requested) atoms. Cycle 22: After refmac, R = 0.2343 (Rfree = 0.000) for 4859 atoms. Found 10 (43 requested) and removed 28 (21 requested) atoms. Cycle 23: After refmac, R = 0.2258 (Rfree = 0.000) for 4839 atoms. Found 10 (43 requested) and removed 22 (21 requested) atoms. Cycle 24: After refmac, R = 0.2230 (Rfree = 0.000) for 4820 atoms. Found 4 (43 requested) and removed 21 (21 requested) atoms. Cycle 25: After refmac, R = 0.2212 (Rfree = 0.000) for 4799 atoms. Found 8 (43 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 4917 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4934 seeds are put forward Round 1: 285 peptides, 53 chains. Longest chain 10 peptides. Score 0.354 Round 2: 327 peptides, 48 chains. Longest chain 22 peptides. Score 0.493 Round 3: 342 peptides, 51 chains. Longest chain 22 peptides. Score 0.497 Round 4: 341 peptides, 48 chains. Longest chain 19 peptides. Score 0.521 Round 5: 334 peptides, 48 chains. Longest chain 22 peptides. Score 0.507 Taking the results from Round 4 Chains 48, Residues 293, Estimated correctness of the model 18.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 11294 restraints for refining 4878 atoms. 10149 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2375 (Rfree = 0.000) for 4878 atoms. Found 16 (43 requested) and removed 25 (21 requested) atoms. Cycle 27: After refmac, R = 0.2312 (Rfree = 0.000) for 4852 atoms. Found 19 (43 requested) and removed 22 (21 requested) atoms. Cycle 28: After refmac, R = 0.2264 (Rfree = 0.000) for 4843 atoms. Found 15 (43 requested) and removed 21 (21 requested) atoms. Cycle 29: After refmac, R = 0.2239 (Rfree = 0.000) for 4834 atoms. Found 6 (43 requested) and removed 21 (21 requested) atoms. Cycle 30: After refmac, R = 0.2285 (Rfree = 0.000) for 4818 atoms. Found 18 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 4985 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5010 seeds are put forward Round 1: 268 peptides, 49 chains. Longest chain 12 peptides. Score 0.354 Round 2: 311 peptides, 50 chains. Longest chain 22 peptides. Score 0.442 Round 3: 319 peptides, 50 chains. Longest chain 17 peptides. Score 0.459 Round 4: 321 peptides, 46 chains. Longest chain 22 peptides. Score 0.499 Round 5: 332 peptides, 45 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 5 Chains 49, Residues 287, Estimated correctness of the model 20.5 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10861 restraints for refining 4878 atoms. 9645 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2435 (Rfree = 0.000) for 4878 atoms. Found 11 (43 requested) and removed 28 (21 requested) atoms. Cycle 32: After refmac, R = 0.2362 (Rfree = 0.000) for 4852 atoms. Found 11 (43 requested) and removed 23 (21 requested) atoms. Cycle 33: After refmac, R = 0.2344 (Rfree = 0.000) for 4832 atoms. Found 9 (43 requested) and removed 21 (21 requested) atoms. Cycle 34: After refmac, R = 0.2307 (Rfree = 0.000) for 4817 atoms. Found 10 (43 requested) and removed 21 (21 requested) atoms. Cycle 35: After refmac, R = 0.2253 (Rfree = 0.000) for 4803 atoms. Found 10 (43 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 4954 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4972 seeds are put forward Round 1: 282 peptides, 53 chains. Longest chain 16 peptides. Score 0.347 Round 2: 316 peptides, 48 chains. Longest chain 23 peptides. Score 0.471 Round 3: 329 peptides, 55 chains. Longest chain 16 peptides. Score 0.434 Round 4: 314 peptides, 46 chains. Longest chain 20 peptides. Score 0.485 Round 5: 319 peptides, 50 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 4 Chains 47, Residues 268, Estimated correctness of the model 6.4 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 11333 restraints for refining 4876 atoms. 10264 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2506 (Rfree = 0.000) for 4876 atoms. Found 31 (43 requested) and removed 22 (21 requested) atoms. Cycle 37: After refmac, R = 0.2467 (Rfree = 0.000) for 4879 atoms. Found 17 (43 requested) and removed 22 (21 requested) atoms. Cycle 38: After refmac, R = 0.2477 (Rfree = 0.000) for 4871 atoms. Found 14 (43 requested) and removed 21 (21 requested) atoms. Cycle 39: After refmac, R = 0.2417 (Rfree = 0.000) for 4862 atoms. Found 17 (43 requested) and removed 21 (21 requested) atoms. Cycle 40: After refmac, R = 0.2423 (Rfree = 0.000) for 4857 atoms. Found 15 (43 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.56 Search for helices and strands: 0 residues in 0 chains, 4996 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5009 seeds are put forward Round 1: 246 peptides, 47 chains. Longest chain 10 peptides. Score 0.322 Round 2: 298 peptides, 45 chains. Longest chain 19 peptides. Score 0.461 Round 3: 295 peptides, 44 chains. Longest chain 19 peptides. Score 0.464 Round 4: 284 peptides, 43 chains. Longest chain 19 peptides. Score 0.450 Round 5: 280 peptides, 43 chains. Longest chain 17 peptides. Score 0.441 Taking the results from Round 3 Chains 44, Residues 251, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 11450 restraints for refining 4878 atoms. 10472 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2544 (Rfree = 0.000) for 4878 atoms. Found 24 (43 requested) and removed 25 (21 requested) atoms. Cycle 42: After refmac, R = 0.2512 (Rfree = 0.000) for 4869 atoms. Found 11 (43 requested) and removed 21 (21 requested) atoms. Cycle 43: After refmac, R = 0.2509 (Rfree = 0.000) for 4854 atoms. Found 8 (43 requested) and removed 21 (21 requested) atoms. Cycle 44: After refmac, R = 0.2503 (Rfree = 0.000) for 4838 atoms. Found 11 (43 requested) and removed 22 (21 requested) atoms. Cycle 45: After refmac, R = 0.2510 (Rfree = 0.000) for 4826 atoms. Found 7 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 4948 seeds are put forward NCS extension: 42 residues added (1 deleted due to clashes), 4990 seeds are put forward Round 1: 237 peptides, 46 chains. Longest chain 11 peptides. Score 0.310 Round 2: 279 peptides, 45 chains. Longest chain 14 peptides. Score 0.419 Round 3: 261 peptides, 47 chains. Longest chain 11 peptides. Score 0.358 Round 4: 246 peptides, 41 chains. Longest chain 13 peptides. Score 0.384 Round 5: 260 peptides, 42 chains. Longest chain 19 peptides. Score 0.406 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 234, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input Building loops using Loopy2018 45 chains (234 residues) following loop building 4 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12307 reflections ( 99.98 % complete ) and 11324 restraints for refining 4878 atoms. 10376 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2456 (Rfree = 0.000) for 4878 atoms. Found 0 (43 requested) and removed 14 (21 requested) atoms. Cycle 47: After refmac, R = 0.2444 (Rfree = 0.000) for 4857 atoms. Found 0 (43 requested) and removed 7 (21 requested) atoms. Cycle 48: After refmac, R = 0.2423 (Rfree = 0.000) for 4846 atoms. Found 0 (43 requested) and removed 4 (21 requested) atoms. Cycle 49: After refmac, R = 0.2409 (Rfree = 0.000) for 4840 atoms. TimeTaking 47.27