Mon 24 Dec 01:12:53 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 1vl0-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl0-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.4-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/1vl0-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.4-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 ============================================================ Mon 24 Dec 01:12:57 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/1vl0-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl0-3.4-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 737 and 0 Target number of residues in the AU: 737 Target solvent content: 0.6208 Checking the provided sequence file Detected sequence length: 292 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 876 Adjusted target solvent content: 0.55 Input MTZ file: 1vl0-3.4-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: 20 Cell parameters: 106.471 130.661 151.225 90.000 90.000 90.000 Input sequence file: 1vl0-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7008 target number of atoms Had to go as low as 0.80 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: 29.987 3.400 Wilson plot Bfac: 61.68 14719 reflections ( 99.09 % complete ) and 0 restraints for refining 7782 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3801 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3566 (Rfree = 0.000) for 7782 atoms. Found 58 (58 requested) and removed 85 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.15 Search for helices and strands: 0 residues in 0 chains, 7802 seeds are put forward NCS extension: 0 residues added, 7802 seeds are put forward Round 1: 225 peptides, 50 chains. Longest chain 8 peptides. Score 0.219 Round 2: 310 peptides, 65 chains. Longest chain 9 peptides. Score 0.261 Round 3: 334 peptides, 67 chains. Longest chain 10 peptides. Score 0.289 Round 4: 362 peptides, 69 chains. Longest chain 10 peptides. Score 0.322 Round 5: 372 peptides, 69 chains. Longest chain 13 peptides. Score 0.339 Taking the results from Round 5 Chains 70, Residues 303, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 14244 restraints for refining 6370 atoms. 13083 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3148 (Rfree = 0.000) for 6370 atoms. Found 47 (48 requested) and removed 56 (24 requested) atoms. Cycle 2: After refmac, R = 0.2977 (Rfree = 0.000) for 6267 atoms. Found 48 (48 requested) and removed 44 (24 requested) atoms. Cycle 3: After refmac, R = 0.2812 (Rfree = 0.000) for 6230 atoms. Found 45 (47 requested) and removed 36 (23 requested) atoms. Cycle 4: After refmac, R = 0.2781 (Rfree = 0.000) for 6199 atoms. Found 47 (47 requested) and removed 35 (23 requested) atoms. Cycle 5: After refmac, R = 0.2640 (Rfree = 0.000) for 6188 atoms. Found 42 (46 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 6320 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6339 seeds are put forward Round 1: 329 peptides, 68 chains. Longest chain 10 peptides. Score 0.273 Round 2: 374 peptides, 71 chains. Longest chain 11 peptides. Score 0.328 Round 3: 379 peptides, 71 chains. Longest chain 13 peptides. Score 0.336 Round 4: 398 peptides, 71 chains. Longest chain 13 peptides. Score 0.367 Round 5: 405 peptides, 68 chains. Longest chain 15 peptides. Score 0.398 Taking the results from Round 5 Chains 68, Residues 337, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13910 restraints for refining 6372 atoms. 12606 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2921 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 44 (24 requested) atoms. Cycle 7: After refmac, R = 0.2698 (Rfree = 0.000) for 6302 atoms. Found 48 (48 requested) and removed 44 (24 requested) atoms. Cycle 8: After refmac, R = 0.2652 (Rfree = 0.000) for 6265 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2565 (Rfree = 0.000) for 6249 atoms. Found 47 (47 requested) and removed 34 (23 requested) atoms. Cycle 10: After refmac, R = 0.2489 (Rfree = 0.000) for 6248 atoms. Found 47 (47 requested) and removed 36 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 6375 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6388 seeds are put forward Round 1: 348 peptides, 74 chains. Longest chain 12 peptides. Score 0.262 Round 2: 408 peptides, 78 chains. Longest chain 12 peptides. Score 0.335 Round 3: 423 peptides, 79 chains. Longest chain 15 peptides. Score 0.352 Round 4: 435 peptides, 78 chains. Longest chain 14 peptides. Score 0.378 Round 5: 417 peptides, 72 chains. Longest chain 15 peptides. Score 0.390 Taking the results from Round 5 Chains 72, Residues 345, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 14007 restraints for refining 6372 atoms. 12654 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2629 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 43 (24 requested) atoms. Cycle 12: After refmac, R = 0.2558 (Rfree = 0.000) for 6329 atoms. Found 48 (48 requested) and removed 43 (24 requested) atoms. Cycle 13: After refmac, R = 0.2433 (Rfree = 0.000) for 6307 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 14: After refmac, R = 0.2327 (Rfree = 0.000) for 6293 atoms. Found 47 (47 requested) and removed 29 (23 requested) atoms. Cycle 15: After refmac, R = 0.2249 (Rfree = 0.000) for 6286 atoms. Found 45 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 6438 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6457 seeds are put forward Round 1: 374 peptides, 80 chains. Longest chain 8 peptides. Score 0.264 Round 2: 422 peptides, 80 chains. Longest chain 13 peptides. Score 0.344 Round 3: 413 peptides, 72 chains. Longest chain 14 peptides. Score 0.384 Round 4: 431 peptides, 73 chains. Longest chain 14 peptides. Score 0.405 Round 5: 432 peptides, 73 chains. Longest chain 15 peptides. Score 0.406 Taking the results from Round 5 Chains 73, Residues 359, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13812 restraints for refining 6372 atoms. 12418 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2554 (Rfree = 0.000) for 6372 atoms. Found 47 (48 requested) and removed 36 (24 requested) atoms. Cycle 17: After refmac, R = 0.2368 (Rfree = 0.000) for 6341 atoms. Found 44 (48 requested) and removed 39 (24 requested) atoms. Cycle 18: After refmac, R = 0.2274 (Rfree = 0.000) for 6327 atoms. Found 33 (47 requested) and removed 37 (23 requested) atoms. Cycle 19: After refmac, R = 0.2150 (Rfree = 0.000) for 6308 atoms. Found 29 (47 requested) and removed 31 (23 requested) atoms. Cycle 20: After refmac, R = 0.1845 (Rfree = 0.000) for 6292 atoms. Found 14 (47 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.05 Search for helices and strands: 0 residues in 0 chains, 6361 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6375 seeds are put forward Round 1: 377 peptides, 82 chains. Longest chain 9 peptides. Score 0.255 Round 2: 411 peptides, 79 chains. Longest chain 11 peptides. Score 0.333 Round 3: 421 peptides, 74 chains. Longest chain 15 peptides. Score 0.383 Round 4: 431 peptides, 77 chains. Longest chain 12 peptides. Score 0.379 Round 5: 416 peptides, 67 chains. Longest chain 23 peptides. Score 0.422 Taking the results from Round 5 Chains 68, Residues 349, Estimated correctness of the model 0.0 % 7 chains (34 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13463 restraints for refining 6372 atoms. 12035 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2275 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 29 (24 requested) atoms. Cycle 22: After refmac, R = 0.2206 (Rfree = 0.000) for 6360 atoms. Found 42 (48 requested) and removed 29 (24 requested) atoms. Cycle 23: After refmac, R = 0.2123 (Rfree = 0.000) for 6349 atoms. Found 45 (48 requested) and removed 29 (24 requested) atoms. Cycle 24: After refmac, R = 0.1841 (Rfree = 0.000) for 6345 atoms. Found 15 (48 requested) and removed 28 (24 requested) atoms. Cycle 25: After refmac, R = 0.1783 (Rfree = 0.000) for 6323 atoms. Found 10 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 6384 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6401 seeds are put forward Round 1: 397 peptides, 86 chains. Longest chain 8 peptides. Score 0.261 Round 2: 402 peptides, 73 chains. Longest chain 14 peptides. Score 0.360 Round 3: 408 peptides, 70 chains. Longest chain 17 peptides. Score 0.390 Round 4: 391 peptides, 67 chains. Longest chain 11 peptides. Score 0.383 Round 5: 403 peptides, 68 chains. Longest chain 15 peptides. Score 0.395 Taking the results from Round 5 Chains 68, Residues 335, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13947 restraints for refining 6372 atoms. 12655 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2335 (Rfree = 0.000) for 6372 atoms. Found 42 (48 requested) and removed 31 (24 requested) atoms. Cycle 27: After refmac, R = 0.2214 (Rfree = 0.000) for 6358 atoms. Found 48 (48 requested) and removed 32 (24 requested) atoms. Cycle 28: After refmac, R = 0.2215 (Rfree = 0.000) for 6357 atoms. Found 48 (48 requested) and removed 30 (24 requested) atoms. Cycle 29: After refmac, R = 0.2148 (Rfree = 0.000) for 6357 atoms. Found 48 (48 requested) and removed 29 (24 requested) atoms. Cycle 30: After refmac, R = 0.2028 (Rfree = 0.000) for 6363 atoms. Found 34 (48 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 6469 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6491 seeds are put forward Round 1: 354 peptides, 74 chains. Longest chain 11 peptides. Score 0.273 Round 2: 400 peptides, 76 chains. Longest chain 10 peptides. Score 0.336 Round 3: 411 peptides, 72 chains. Longest chain 17 peptides. Score 0.381 Round 4: 402 peptides, 67 chains. Longest chain 13 peptides. Score 0.401 Round 5: 402 peptides, 70 chains. Longest chain 13 peptides. Score 0.380 Taking the results from Round 4 Chains 67, Residues 335, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13915 restraints for refining 6371 atoms. 12613 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2300 (Rfree = 0.000) for 6371 atoms. Found 48 (48 requested) and removed 30 (24 requested) atoms. Cycle 32: After refmac, R = 0.2180 (Rfree = 0.000) for 6365 atoms. Found 48 (48 requested) and removed 29 (24 requested) atoms. Cycle 33: After refmac, R = 0.2089 (Rfree = 0.000) for 6369 atoms. Found 48 (48 requested) and removed 28 (24 requested) atoms. Cycle 34: After refmac, R = 0.2032 (Rfree = 0.000) for 6379 atoms. Found 41 (48 requested) and removed 27 (24 requested) atoms. Cycle 35: After refmac, R = 0.1982 (Rfree = 0.000) for 6377 atoms. Found 31 (48 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.01 Search for helices and strands: 0 residues in 0 chains, 6473 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6492 seeds are put forward Round 1: 309 peptides, 68 chains. Longest chain 8 peptides. Score 0.237 Round 2: 339 peptides, 66 chains. Longest chain 11 peptides. Score 0.305 Round 3: 365 peptides, 64 chains. Longest chain 11 peptides. Score 0.363 Round 4: 368 peptides, 60 chains. Longest chain 11 peptides. Score 0.395 Round 5: 370 peptides, 60 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 5 Chains 60, Residues 310, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13694 restraints for refining 6372 atoms. 12420 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2200 (Rfree = 0.000) for 6372 atoms. Found 48 (48 requested) and removed 31 (24 requested) atoms. Cycle 37: After refmac, R = 0.2113 (Rfree = 0.000) for 6361 atoms. Found 48 (48 requested) and removed 28 (24 requested) atoms. Cycle 38: After refmac, R = 0.2029 (Rfree = 0.000) for 6360 atoms. Found 44 (48 requested) and removed 27 (24 requested) atoms. Cycle 39: After refmac, R = 0.1947 (Rfree = 0.000) for 6364 atoms. Found 34 (48 requested) and removed 26 (24 requested) atoms. Cycle 40: After refmac, R = 0.1892 (Rfree = 0.000) for 6363 atoms. Found 27 (48 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.04 Search for helices and strands: 0 residues in 0 chains, 6424 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6439 seeds are put forward Round 1: 313 peptides, 65 chains. Longest chain 9 peptides. Score 0.267 Round 2: 343 peptides, 60 chains. Longest chain 14 peptides. Score 0.355 Round 3: 365 peptides, 64 chains. Longest chain 12 peptides. Score 0.363 Round 4: 370 peptides, 68 chains. Longest chain 12 peptides. Score 0.343 Round 5: 377 peptides, 68 chains. Longest chain 13 peptides. Score 0.354 Taking the results from Round 3 Chains 64, Residues 301, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 14719 reflections ( 99.09 % complete ) and 13692 restraints for refining 6369 atoms. 12451 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2085 (Rfree = 0.000) for 6369 atoms. Found 36 (48 requested) and removed 35 (24 requested) atoms. Cycle 42: After refmac, R = 0.1999 (Rfree = 0.000) for 6348 atoms. Found 37 (48 requested) and removed 25 (24 requested) atoms. Cycle 43: After refmac, R = 0.1949 (Rfree = 0.000) for 6344 atoms. Found 34 (48 requested) and removed 29 (24 requested) atoms. Cycle 44: After refmac, R = 0.1998 (Rfree = 0.000) for 6336 atoms. Found 35 (47 requested) and removed 27 (23 requested) atoms. Cycle 45: After refmac, R = 0.1828 (Rfree = 0.000) for 6331 atoms. Found 34 (47 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.05 Search for helices and strands: 0 residues in 0 chains, 6376 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 6387 seeds are put forward Round 1: 306 peptides, 63 chains. Longest chain 9 peptides. Score 0.269 Round 2: 324 peptides, 58 chains. Longest chain 10 peptides. Score 0.338 Round 3: 347 peptides, 58 chains. Longest chain 10 peptides. Score 0.376 Round 4: 339 peptides, 58 chains. Longest chain 13 peptides. Score 0.363 Round 5: 329 peptides, 59 chains. Longest chain 9 peptides. Score 0.339 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 289, Estimated correctness of the model 0.0 % 7 chains (37 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vl0-3_warpNtrace.pdb as input Building loops using Loopy2018 58 chains (289 residues) following loop building 7 chains (37 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14719 reflections ( 99.09 % complete ) and 13721 restraints for refining 6372 atoms. 12510 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2037 (Rfree = 0.000) for 6372 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2028 (Rfree = 0.000) for 6331 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.1933 (Rfree = 0.000) for 6302 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1879 (Rfree = 0.000) for 6268 atoms. TimeTaking 62.9