null Mon 24 Dec 07:56:29 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2obn-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2obn-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2obn-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-parrot-noncs ############### 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 07:56:34 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/noncs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-4.0-parrot-noncs/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 807 and 0 Target number of residues in the AU: 807 Target solvent content: 0.6768 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-4.0-parrot-noncs.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: 4 Cell parameters: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 11168 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: 73.214 4.000 Wilson plot Bfac: 98.12 11286 reflections ( 99.58 % complete ) and 0 restraints for refining 12313 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3215 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2935 (Rfree = 0.000) for 12313 atoms. Found 58 (58 requested) and removed 103 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.85 4.17 Search for helices and strands: 0 residues in 0 chains, 12471 seeds are put forward NCS extension: 0 residues added, 12471 seeds are put forward Round 1: 378 peptides, 81 chains. Longest chain 9 peptides. Score 0.248 Round 2: 513 peptides, 93 chains. Longest chain 15 peptides. Score 0.360 Round 3: 572 peptides, 98 chains. Longest chain 12 peptides. Score 0.405 Round 4: 591 peptides, 95 chains. Longest chain 13 peptides. Score 0.442 Round 5: 594 peptides, 96 chains. Longest chain 17 peptides. Score 0.440 Taking the results from Round 4 Chains 95, Residues 496, Estimated correctness of the model 0.0 % 8 chains (44 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 24248 restraints for refining 10083 atoms. 22249 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2293 (Rfree = 0.000) for 10083 atoms. Found 29 (47 requested) and removed 52 (23 requested) atoms. Cycle 2: After refmac, R = 0.2337 (Rfree = 0.000) for 9895 atoms. Found 37 (47 requested) and removed 61 (23 requested) atoms. Cycle 3: After refmac, R = 0.1861 (Rfree = 0.000) for 9758 atoms. Found 19 (46 requested) and removed 35 (23 requested) atoms. Cycle 4: After refmac, R = 0.1698 (Rfree = 0.000) for 9677 atoms. Found 11 (46 requested) and removed 31 (23 requested) atoms. Cycle 5: After refmac, R = 0.1713 (Rfree = 0.000) for 9628 atoms. Found 13 (45 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.88 4.20 Search for helices and strands: 0 residues in 0 chains, 9940 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 9953 seeds are put forward Round 1: 452 peptides, 91 chains. Longest chain 14 peptides. Score 0.292 Round 2: 553 peptides, 93 chains. Longest chain 15 peptides. Score 0.408 Round 3: 575 peptides, 91 chains. Longest chain 16 peptides. Score 0.444 Round 4: 593 peptides, 95 chains. Longest chain 18 peptides. Score 0.444 Round 5: 601 peptides, 89 chains. Longest chain 24 peptides. Score 0.482 Taking the results from Round 5 Chains 90, Residues 512, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22248 restraints for refining 9485 atoms. 20158 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2099 (Rfree = 0.000) for 9485 atoms. Found 24 (45 requested) and removed 62 (22 requested) atoms. Cycle 7: After refmac, R = 0.2074 (Rfree = 0.000) for 9350 atoms. Found 28 (44 requested) and removed 69 (22 requested) atoms. Cycle 8: After refmac, R = 0.1857 (Rfree = 0.000) for 9271 atoms. Found 39 (44 requested) and removed 50 (22 requested) atoms. Cycle 9: After refmac, R = 0.1776 (Rfree = 0.000) for 9232 atoms. Found 33 (43 requested) and removed 31 (21 requested) atoms. Cycle 10: After refmac, R = 0.1718 (Rfree = 0.000) for 9201 atoms. Found 39 (43 requested) and removed 35 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 4.16 Search for helices and strands: 0 residues in 0 chains, 9513 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 9529 seeds are put forward Round 1: 490 peptides, 94 chains. Longest chain 12 peptides. Score 0.325 Round 2: 614 peptides, 99 chains. Longest chain 18 peptides. Score 0.448 Round 3: 631 peptides, 98 chains. Longest chain 14 peptides. Score 0.472 Round 4: 605 peptides, 92 chains. Longest chain 19 peptides. Score 0.472 Round 5: 637 peptides, 97 chains. Longest chain 19 peptides. Score 0.483 Taking the results from Round 5 Chains 97, Residues 540, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22348 restraints for refining 9622 atoms. 20285 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1807 (Rfree = 0.000) for 9622 atoms. Found 24 (45 requested) and removed 69 (22 requested) atoms. Cycle 12: After refmac, R = 0.1881 (Rfree = 0.000) for 9481 atoms. Found 45 (45 requested) and removed 71 (22 requested) atoms. Cycle 13: After refmac, R = 0.1848 (Rfree = 0.000) for 9400 atoms. Found 40 (44 requested) and removed 44 (22 requested) atoms. Cycle 14: After refmac, R = 0.1715 (Rfree = 0.000) for 9353 atoms. Found 38 (44 requested) and removed 43 (22 requested) atoms. Cycle 15: After refmac, R = 0.1835 (Rfree = 0.000) for 9309 atoms. Found 44 (44 requested) and removed 41 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.88 4.20 Search for helices and strands: 0 residues in 0 chains, 9643 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 9661 seeds are put forward Round 1: 431 peptides, 90 chains. Longest chain 11 peptides. Score 0.269 Round 2: 506 peptides, 94 chains. Longest chain 12 peptides. Score 0.345 Round 3: 533 peptides, 95 chains. Longest chain 12 peptides. Score 0.374 Round 4: 551 peptides, 94 chains. Longest chain 16 peptides. Score 0.401 Round 5: 562 peptides, 87 chains. Longest chain 17 peptides. Score 0.449 Taking the results from Round 5 Chains 89, Residues 475, Estimated correctness of the model 0.0 % 7 chains (50 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 21588 restraints for refining 9444 atoms. 19604 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2028 (Rfree = 0.000) for 9444 atoms. Found 37 (44 requested) and removed 87 (22 requested) atoms. Cycle 17: After refmac, R = 0.1827 (Rfree = 0.000) for 9332 atoms. Found 44 (44 requested) and removed 48 (22 requested) atoms. Cycle 18: After refmac, R = 0.1788 (Rfree = 0.000) for 9296 atoms. Found 44 (44 requested) and removed 44 (22 requested) atoms. Cycle 19: After refmac, R = 0.1338 (Rfree = 0.000) for 9252 atoms. Found 9 (44 requested) and removed 30 (22 requested) atoms. Cycle 20: After refmac, R = 0.1285 (Rfree = 0.000) for 9211 atoms. Found 14 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.88 4.20 Search for helices and strands: 0 residues in 0 chains, 9447 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 9461 seeds are put forward Round 1: 458 peptides, 94 chains. Longest chain 13 peptides. Score 0.283 Round 2: 500 peptides, 87 chains. Longest chain 13 peptides. Score 0.375 Round 3: 543 peptides, 93 chains. Longest chain 13 peptides. Score 0.396 Round 4: 536 peptides, 91 chains. Longest chain 15 peptides. Score 0.398 Round 5: 525 peptides, 86 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 5 Chains 86, Residues 439, Estimated correctness of the model 0.0 % 7 chains (41 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 21593 restraints for refining 9377 atoms. 19775 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1875 (Rfree = 0.000) for 9377 atoms. Found 26 (44 requested) and removed 50 (22 requested) atoms. Cycle 22: After refmac, R = 0.1902 (Rfree = 0.000) for 9299 atoms. Found 39 (44 requested) and removed 46 (22 requested) atoms. Cycle 23: After refmac, R = 0.1853 (Rfree = 0.000) for 9259 atoms. Found 35 (44 requested) and removed 48 (22 requested) atoms. Cycle 24: After refmac, R = 0.1430 (Rfree = 0.000) for 9226 atoms. Found 12 (43 requested) and removed 32 (21 requested) atoms. Cycle 25: After refmac, R = 0.1326 (Rfree = 0.000) for 9188 atoms. Found 5 (43 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 4.17 Search for helices and strands: 0 residues in 0 chains, 9441 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 9461 seeds are put forward Round 1: 447 peptides, 89 chains. Longest chain 11 peptides. Score 0.296 Round 2: 498 peptides, 85 chains. Longest chain 11 peptides. Score 0.384 Round 3: 509 peptides, 89 chains. Longest chain 13 peptides. Score 0.376 Round 4: 521 peptides, 88 chains. Longest chain 17 peptides. Score 0.396 Round 5: 521 peptides, 90 chains. Longest chain 13 peptides. Score 0.385 Taking the results from Round 4 Chains 89, Residues 433, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22440 restraints for refining 9455 atoms. 20760 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1878 (Rfree = 0.000) for 9455 atoms. Found 36 (44 requested) and removed 56 (22 requested) atoms. Cycle 27: After refmac, R = 0.1801 (Rfree = 0.000) for 9385 atoms. Found 43 (44 requested) and removed 44 (22 requested) atoms. Cycle 28: After refmac, R = 0.1407 (Rfree = 0.000) for 9353 atoms. Found 10 (44 requested) and removed 32 (22 requested) atoms. Cycle 29: After refmac, R = 0.1320 (Rfree = 0.000) for 9305 atoms. Found 8 (44 requested) and removed 33 (22 requested) atoms. Cycle 30: After refmac, R = 0.1340 (Rfree = 0.000) for 9269 atoms. Found 8 (44 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.89 4.22 Search for helices and strands: 0 residues in 0 chains, 9512 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 9529 seeds are put forward Round 1: 425 peptides, 93 chains. Longest chain 8 peptides. Score 0.244 Round 2: 500 peptides, 92 chains. Longest chain 13 peptides. Score 0.349 Round 3: 491 peptides, 88 chains. Longest chain 12 peptides. Score 0.359 Round 4: 517 peptides, 90 chains. Longest chain 12 peptides. Score 0.380 Round 5: 506 peptides, 88 chains. Longest chain 12 peptides. Score 0.378 Taking the results from Round 4 Chains 90, Residues 427, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22447 restraints for refining 9499 atoms. 20794 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2048 (Rfree = 0.000) for 9499 atoms. Found 45 (45 requested) and removed 66 (22 requested) atoms. Cycle 32: After refmac, R = 0.1927 (Rfree = 0.000) for 9435 atoms. Found 45 (45 requested) and removed 54 (22 requested) atoms. Cycle 33: After refmac, R = 0.1800 (Rfree = 0.000) for 9386 atoms. Found 44 (44 requested) and removed 41 (22 requested) atoms. Cycle 34: After refmac, R = 0.1412 (Rfree = 0.000) for 9364 atoms. Found 17 (44 requested) and removed 30 (22 requested) atoms. Cycle 35: After refmac, R = 0.1349 (Rfree = 0.000) for 9329 atoms. Found 9 (44 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.87 4.19 Search for helices and strands: 0 residues in 0 chains, 9554 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 9568 seeds are put forward Round 1: 392 peptides, 83 chains. Longest chain 10 peptides. Score 0.256 Round 2: 444 peptides, 84 chains. Longest chain 17 peptides. Score 0.321 Round 3: 447 peptides, 81 chains. Longest chain 15 peptides. Score 0.341 Round 4: 465 peptides, 80 chains. Longest chain 16 peptides. Score 0.370 Round 5: 463 peptides, 80 chains. Longest chain 16 peptides. Score 0.367 Taking the results from Round 4 Chains 81, Residues 385, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22035 restraints for refining 9372 atoms. 20525 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1982 (Rfree = 0.000) for 9372 atoms. Found 44 (44 requested) and removed 65 (22 requested) atoms. Cycle 37: After refmac, R = 0.1972 (Rfree = 0.000) for 9312 atoms. Found 44 (44 requested) and removed 41 (22 requested) atoms. Cycle 38: After refmac, R = 0.1863 (Rfree = 0.000) for 9280 atoms. Found 40 (44 requested) and removed 42 (22 requested) atoms. Cycle 39: After refmac, R = 0.1370 (Rfree = 0.000) for 9260 atoms. Found 8 (44 requested) and removed 27 (22 requested) atoms. Cycle 40: After refmac, R = 0.1306 (Rfree = 0.000) for 9234 atoms. Found 7 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.85 4.17 Search for helices and strands: 0 residues in 0 chains, 9495 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 9511 seeds are put forward Round 1: 389 peptides, 89 chains. Longest chain 9 peptides. Score 0.216 Round 2: 424 peptides, 82 chains. Longest chain 13 peptides. Score 0.305 Round 3: 434 peptides, 83 chains. Longest chain 14 peptides. Score 0.313 Round 4: 438 peptides, 83 chains. Longest chain 13 peptides. Score 0.318 Round 5: 418 peptides, 75 chains. Longest chain 17 peptides. Score 0.337 Taking the results from Round 5 Chains 75, Residues 343, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11286 reflections ( 99.58 % complete ) and 22234 restraints for refining 9336 atoms. 20937 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2220 (Rfree = 0.000) for 9336 atoms. Found 44 (44 requested) and removed 267 (22 requested) atoms. Cycle 42: After refmac, R = 0.1811 (Rfree = 0.000) for 9087 atoms. Found 43 (43 requested) and removed 39 (21 requested) atoms. Cycle 43: After refmac, R = 0.1762 (Rfree = 0.000) for 9066 atoms. Found 43 (43 requested) and removed 32 (21 requested) atoms. Cycle 44: After refmac, R = 0.1810 (Rfree = 0.000) for 9057 atoms. Found 43 (43 requested) and removed 28 (21 requested) atoms. Cycle 45: After refmac, R = 0.1739 (Rfree = 0.000) for 9061 atoms. Found 43 (43 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 4.15 Search for helices and strands: 0 residues in 0 chains, 9327 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 9357 seeds are put forward Round 1: 331 peptides, 76 chains. Longest chain 7 peptides. Score 0.209 Round 2: 408 peptides, 84 chains. Longest chain 10 peptides. Score 0.272 Round 3: 407 peptides, 79 chains. Longest chain 12 peptides. Score 0.300 Round 4: 389 peptides, 76 chains. Longest chain 11 peptides. Score 0.293 Round 5: 374 peptides, 70 chains. Longest chain 10 peptides. Score 0.308 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 304, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2obn-4_warpNtrace.pdb as input Building loops using Loopy2018 70 chains (304 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11286 reflections ( 99.58 % complete ) and 21677 restraints for refining 9152 atoms. 20514 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1877 (Rfree = 0.000) for 9152 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.1918 (Rfree = 0.000) for 9104 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.1798 (Rfree = 0.000) for 9065 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.1674 (Rfree = 0.000) for 9033 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:34:37 GMT 2018 Job finished. TimeTaking 98.13 Used memory is bytes: 10984744