Sun 23 Dec 23:45:32 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.4-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 ============================================================ Sun 23 Dec 23:45:37 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.4-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 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-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-3.4-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 3.400 Wilson plot Bfac: 97.07 10325 reflections ( 99.97 % complete ) and 0 restraints for refining 5887 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3503 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2928 (Rfree = 0.000) for 5887 atoms. Found 38 (44 requested) and removed 37 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.76 Search for helices and strands: 0 residues in 0 chains, 6031 seeds are put forward NCS extension: 0 residues added, 6031 seeds are put forward Round 1: 323 peptides, 58 chains. Longest chain 10 peptides. Score 0.392 Round 2: 344 peptides, 54 chains. Longest chain 17 peptides. Score 0.474 Round 3: 395 peptides, 52 chains. Longest chain 25 peptides. Score 0.587 Round 4: 387 peptides, 46 chains. Longest chain 22 peptides. Score 0.618 Round 5: 395 peptides, 48 chains. Longest chain 18 peptides. Score 0.617 Taking the results from Round 4 Chains 52, Residues 341, Estimated correctness of the model 34.4 % 8 chains (66 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10585 restraints for refining 4859 atoms. 9069 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2840 (Rfree = 0.000) for 4859 atoms. Found 10 (36 requested) and removed 26 (18 requested) atoms. Cycle 2: After refmac, R = 0.2645 (Rfree = 0.000) for 4774 atoms. Found 8 (36 requested) and removed 29 (18 requested) atoms. Cycle 3: After refmac, R = 0.2484 (Rfree = 0.000) for 4733 atoms. Found 1 (35 requested) and removed 22 (17 requested) atoms. Cycle 4: After refmac, R = 0.2480 (Rfree = 0.000) for 4704 atoms. Found 3 (35 requested) and removed 22 (17 requested) atoms. Cycle 5: After refmac, R = 0.2462 (Rfree = 0.000) for 4679 atoms. Found 3 (35 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 4836 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4856 seeds are put forward Round 1: 341 peptides, 53 chains. Longest chain 15 peptides. Score 0.477 Round 2: 365 peptides, 48 chains. Longest chain 21 peptides. Score 0.565 Round 3: 367 peptides, 46 chains. Longest chain 24 peptides. Score 0.585 Round 4: 370 peptides, 44 chains. Longest chain 28 peptides. Score 0.605 Round 5: 345 peptides, 44 chains. Longest chain 22 peptides. Score 0.562 Taking the results from Round 4 Chains 52, Residues 326, Estimated correctness of the model 30.3 % 8 chains (89 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10385 restraints for refining 4859 atoms. 8822 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2620 (Rfree = 0.000) for 4859 atoms. Found 14 (36 requested) and removed 44 (18 requested) atoms. Cycle 7: After refmac, R = 0.2483 (Rfree = 0.000) for 4791 atoms. Found 4 (36 requested) and removed 26 (18 requested) atoms. Cycle 8: After refmac, R = 0.2462 (Rfree = 0.000) for 4750 atoms. Found 7 (36 requested) and removed 31 (18 requested) atoms. Cycle 9: After refmac, R = 0.2374 (Rfree = 0.000) for 4712 atoms. Found 4 (35 requested) and removed 21 (17 requested) atoms. Cycle 10: After refmac, R = 0.2325 (Rfree = 0.000) for 4688 atoms. Found 3 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 4829 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 4851 seeds are put forward Round 1: 317 peptides, 54 chains. Longest chain 14 peptides. Score 0.417 Round 2: 372 peptides, 47 chains. Longest chain 24 peptides. Score 0.586 Round 3: 389 peptides, 48 chains. Longest chain 23 peptides. Score 0.607 Round 4: 378 peptides, 45 chains. Longest chain 27 peptides. Score 0.611 Round 5: 375 peptides, 47 chains. Longest chain 18 peptides. Score 0.591 Taking the results from Round 4 Chains 50, Residues 333, Estimated correctness of the model 32.2 % 6 chains (57 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10674 restraints for refining 4859 atoms. 9203 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2527 (Rfree = 0.000) for 4859 atoms. Found 29 (36 requested) and removed 39 (18 requested) atoms. Cycle 12: After refmac, R = 0.2401 (Rfree = 0.000) for 4819 atoms. Found 17 (36 requested) and removed 32 (18 requested) atoms. Cycle 13: After refmac, R = 0.2307 (Rfree = 0.000) for 4797 atoms. Found 10 (36 requested) and removed 24 (18 requested) atoms. Cycle 14: After refmac, R = 0.2277 (Rfree = 0.000) for 4777 atoms. Found 11 (36 requested) and removed 24 (18 requested) atoms. Cycle 15: After refmac, R = 0.2234 (Rfree = 0.000) for 4757 atoms. Found 9 (35 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 4886 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4907 seeds are put forward Round 1: 283 peptides, 51 chains. Longest chain 13 peptides. Score 0.369 Round 2: 327 peptides, 50 chains. Longest chain 14 peptides. Score 0.475 Round 3: 335 peptides, 49 chains. Longest chain 14 peptides. Score 0.500 Round 4: 342 peptides, 47 chains. Longest chain 22 peptides. Score 0.531 Round 5: 327 peptides, 44 chains. Longest chain 16 peptides. Score 0.528 Taking the results from Round 4 Chains 49, Residues 295, Estimated correctness of the model 4.6 % 5 chains (55 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10936 restraints for refining 4859 atoms. 9621 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2519 (Rfree = 0.000) for 4859 atoms. Found 21 (36 requested) and removed 36 (18 requested) atoms. Cycle 17: After refmac, R = 0.2440 (Rfree = 0.000) for 4826 atoms. Found 15 (36 requested) and removed 26 (18 requested) atoms. Cycle 18: After refmac, R = 0.2361 (Rfree = 0.000) for 4803 atoms. Found 9 (36 requested) and removed 26 (18 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2360 (Rfree = 0.000) for 4773 atoms. Found 12 (36 requested) and removed 26 (18 requested) atoms. Cycle 20: After refmac, R = 0.2296 (Rfree = 0.000) for 4744 atoms. Found 10 (35 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 4901 seeds are put forward NCS extension: 41 residues added (1 deleted due to clashes), 4942 seeds are put forward Round 1: 289 peptides, 55 chains. Longest chain 10 peptides. Score 0.343 Round 2: 320 peptides, 52 chains. Longest chain 13 peptides. Score 0.442 Round 3: 323 peptides, 46 chains. Longest chain 15 peptides. Score 0.503 Round 4: 360 peptides, 52 chains. Longest chain 16 peptides. Score 0.523 Round 5: 349 peptides, 52 chains. Longest chain 15 peptides. Score 0.502 Taking the results from Round 4 Chains 53, Residues 308, Estimated correctness of the model 1.6 % 6 chains (42 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10829 restraints for refining 4858 atoms. 9522 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2447 (Rfree = 0.000) for 4858 atoms. Found 11 (36 requested) and removed 39 (18 requested) atoms. Cycle 22: After refmac, R = 0.2373 (Rfree = 0.000) for 4812 atoms. Found 3 (36 requested) and removed 36 (18 requested) atoms. Cycle 23: After refmac, R = 0.2354 (Rfree = 0.000) for 4766 atoms. Found 6 (36 requested) and removed 32 (18 requested) atoms. Cycle 24: After refmac, R = 0.2308 (Rfree = 0.000) for 4730 atoms. Found 8 (35 requested) and removed 31 (17 requested) atoms. Cycle 25: After refmac, R = 0.2026 (Rfree = 0.000) for 4699 atoms. Found 1 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 4865 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4879 seeds are put forward Round 1: 278 peptides, 51 chains. Longest chain 14 peptides. Score 0.358 Round 2: 307 peptides, 50 chains. Longest chain 14 peptides. Score 0.433 Round 3: 318 peptides, 46 chains. Longest chain 16 peptides. Score 0.493 Round 4: 304 peptides, 46 chains. Longest chain 17 peptides. Score 0.464 Round 5: 336 peptides, 51 chains. Longest chain 16 peptides. Score 0.485 Taking the results from Round 3 Chains 48, Residues 272, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11141 restraints for refining 4853 atoms. 9992 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2342 (Rfree = 0.000) for 4853 atoms. Found 5 (36 requested) and removed 36 (18 requested) atoms. Cycle 27: After refmac, R = 0.2384 (Rfree = 0.000) for 4800 atoms. Found 11 (36 requested) and removed 35 (18 requested) atoms. Cycle 28: After refmac, R = 0.2319 (Rfree = 0.000) for 4765 atoms. Found 2 (36 requested) and removed 30 (18 requested) atoms. Cycle 29: After refmac, R = 0.2294 (Rfree = 0.000) for 4728 atoms. Found 6 (35 requested) and removed 26 (17 requested) atoms. Cycle 30: After refmac, R = 0.2332 (Rfree = 0.000) for 4698 atoms. Found 3 (35 requested) and removed 34 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 4840 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4853 seeds are put forward Round 1: 229 peptides, 44 chains. Longest chain 12 peptides. Score 0.311 Round 2: 262 peptides, 44 chains. Longest chain 14 peptides. Score 0.391 Round 3: 290 peptides, 48 chains. Longest chain 15 peptides. Score 0.415 Round 4: 287 peptides, 44 chains. Longest chain 14 peptides. Score 0.447 Round 5: 286 peptides, 43 chains. Longest chain 16 peptides. Score 0.454 Taking the results from Round 5 Chains 43, Residues 243, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11435 restraints for refining 4858 atoms. 10446 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2447 (Rfree = 0.000) for 4858 atoms. Found 7 (36 requested) and removed 53 (18 requested) atoms. Cycle 32: After refmac, R = 0.2398 (Rfree = 0.000) for 4797 atoms. Found 4 (36 requested) and removed 32 (18 requested) atoms. Cycle 33: After refmac, R = 0.2306 (Rfree = 0.000) for 4758 atoms. Found 5 (36 requested) and removed 28 (18 requested) atoms. Cycle 34: After refmac, R = 0.2028 (Rfree = 0.000) for 4726 atoms. Found 3 (35 requested) and removed 19 (17 requested) atoms. Cycle 35: After refmac, R = 0.1984 (Rfree = 0.000) for 4706 atoms. Found 0 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.76 Search for helices and strands: 0 residues in 0 chains, 4859 seeds are put forward NCS extension: 0 residues added, 4859 seeds are put forward Round 1: 240 peptides, 47 chains. Longest chain 9 peptides. Score 0.307 Round 2: 282 peptides, 44 chains. Longest chain 18 peptides. Score 0.436 Round 3: 284 peptides, 45 chains. Longest chain 19 peptides. Score 0.431 Round 4: 285 peptides, 45 chains. Longest chain 16 peptides. Score 0.433 Round 5: 276 peptides, 41 chains. Longest chain 15 peptides. Score 0.452 Taking the results from Round 5 Chains 43, Residues 235, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11383 restraints for refining 4857 atoms. 10422 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2341 (Rfree = 0.000) for 4857 atoms. Found 20 (36 requested) and removed 29 (18 requested) atoms. Cycle 37: After refmac, R = 0.2278 (Rfree = 0.000) for 4837 atoms. Found 11 (36 requested) and removed 38 (18 requested) atoms. Cycle 38: After refmac, R = 0.2268 (Rfree = 0.000) for 4801 atoms. Found 9 (36 requested) and removed 23 (18 requested) atoms. Cycle 39: After refmac, R = 0.2164 (Rfree = 0.000) for 4779 atoms. Found 7 (36 requested) and removed 24 (18 requested) atoms. Cycle 40: After refmac, R = 0.2164 (Rfree = 0.000) for 4754 atoms. Found 9 (35 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 4883 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4899 seeds are put forward Round 1: 228 peptides, 46 chains. Longest chain 8 peptides. Score 0.287 Round 2: 250 peptides, 43 chains. Longest chain 14 peptides. Score 0.373 Round 3: 251 peptides, 38 chains. Longest chain 18 peptides. Score 0.426 Round 4: 266 peptides, 42 chains. Longest chain 19 peptides. Score 0.420 Round 5: 270 peptides, 42 chains. Longest chain 15 peptides. Score 0.429 Taking the results from Round 5 Chains 42, Residues 228, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11406 restraints for refining 4859 atoms. 10489 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2366 (Rfree = 0.000) for 4859 atoms. Found 7 (36 requested) and removed 35 (18 requested) atoms. Cycle 42: After refmac, R = 0.2382 (Rfree = 0.000) for 4814 atoms. Found 9 (36 requested) and removed 34 (18 requested) atoms. Cycle 43: After refmac, R = 0.2352 (Rfree = 0.000) for 4777 atoms. Found 8 (36 requested) and removed 24 (18 requested) atoms. Cycle 44: After refmac, R = 0.2237 (Rfree = 0.000) for 4757 atoms. Found 15 (35 requested) and removed 24 (17 requested) atoms. Cycle 45: After refmac, R = 0.1992 (Rfree = 0.000) for 4742 atoms. Found 2 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 4891 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4907 seeds are put forward Round 1: 202 peptides, 43 chains. Longest chain 7 peptides. Score 0.252 Round 2: 232 peptides, 42 chains. Longest chain 11 peptides. Score 0.340 Round 3: 255 peptides, 42 chains. Longest chain 12 peptides. Score 0.395 Round 4: 245 peptides, 42 chains. Longest chain 14 peptides. Score 0.371 Round 5: 251 peptides, 43 chains. Longest chain 13 peptides. Score 0.375 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 213, 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 1vll-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10325 reflections ( 99.97 % complete ) and 11312 restraints for refining 4859 atoms. 10502 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2350 (Rfree = 0.000) for 4859 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2324 (Rfree = 0.000) for 4834 atoms. Found 0 (36 requested) and removed 15 (18 requested) atoms. Cycle 48: After refmac, R = 0.2350 (Rfree = 0.000) for 4818 atoms. Found 0 (36 requested) and removed 16 (18 requested) atoms. Cycle 49: After refmac, R = 0.2132 (Rfree = 0.000) for 4798 atoms. TimeTaking 60