null Mon 24 Dec 01:13:26 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 2go7-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2go7-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2go7-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-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/2go7-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-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 01:13:31 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/2go7-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-4.0-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 753 and 0 Target number of residues in the AU: 753 Target solvent content: 0.6678 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 828 Adjusted target solvent content: 0.63 Input MTZ file: 2go7-4.0-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: 169 Cell parameters: 155.000 155.000 88.440 90.000 90.000 120.000 Input sequence file: 2go7-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6624 target number of atoms Had to go as low as 1.10 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: 134.234 4.001 Wilson plot Bfac: 90.68 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 10348 reflections ( 99.71 % complete ) and 0 restraints for refining 7374 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3521 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3424 (Rfree = 0.000) for 7374 atoms. Found 35 (35 requested) and removed 341 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.16 Search for helices and strands: 0 residues in 0 chains, 7117 seeds are put forward NCS extension: 0 residues added, 7117 seeds are put forward Round 1: 247 peptides, 54 chains. Longest chain 9 peptides. Score 0.224 Round 2: 347 peptides, 67 chains. Longest chain 11 peptides. Score 0.296 Round 3: 388 peptides, 66 chains. Longest chain 11 peptides. Score 0.363 Round 4: 406 peptides, 68 chains. Longest chain 15 peptides. Score 0.375 Round 5: 395 peptides, 64 chains. Longest chain 15 peptides. Score 0.385 Taking the results from Round 5 Chains 64, Residues 331, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13961 restraints for refining 5964 atoms. 12666 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3000 (Rfree = 0.000) for 5964 atoms. Found 28 (28 requested) and removed 132 (14 requested) atoms. Cycle 2: After refmac, R = 0.2648 (Rfree = 0.000) for 5753 atoms. Found 27 (27 requested) and removed 114 (13 requested) atoms. Cycle 3: After refmac, R = 0.2551 (Rfree = 0.000) for 5611 atoms. Found 26 (26 requested) and removed 59 (13 requested) atoms. Cycle 4: After refmac, R = 0.2482 (Rfree = 0.000) for 5531 atoms. Found 26 (26 requested) and removed 51 (13 requested) atoms. Cycle 5: After refmac, R = 0.2367 (Rfree = 0.000) for 5464 atoms. Found 26 (26 requested) and removed 38 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.15 Search for helices and strands: 0 residues in 0 chains, 5726 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5742 seeds are put forward Round 1: 410 peptides, 67 chains. Longest chain 14 peptides. Score 0.387 Round 2: 466 peptides, 62 chains. Longest chain 21 peptides. Score 0.488 Round 3: 470 peptides, 68 chains. Longest chain 18 peptides. Score 0.459 Round 4: 452 peptides, 55 chains. Longest chain 19 peptides. Score 0.509 Round 5: 461 peptides, 54 chains. Longest chain 30 peptides. Score 0.525 Taking the results from Round 5 Chains 56, Residues 407, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13499 restraints for refining 5982 atoms. 11881 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2718 (Rfree = 0.000) for 5982 atoms. Found 28 (28 requested) and removed 100 (14 requested) atoms. Cycle 7: After refmac, R = 0.2462 (Rfree = 0.000) for 5803 atoms. Found 28 (28 requested) and removed 163 (14 requested) atoms. Cycle 8: After refmac, R = 0.2466 (Rfree = 0.000) for 5596 atoms. Found 26 (26 requested) and removed 94 (13 requested) atoms. Cycle 9: After refmac, R = 0.2301 (Rfree = 0.000) for 5473 atoms. Found 26 (26 requested) and removed 38 (13 requested) atoms. Cycle 10: After refmac, R = 0.1970 (Rfree = 0.000) for 5415 atoms. Found 10 (25 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.17 Search for helices and strands: 0 residues in 0 chains, 5621 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5639 seeds are put forward Round 1: 401 peptides, 64 chains. Longest chain 15 peptides. Score 0.393 Round 2: 451 peptides, 64 chains. Longest chain 19 peptides. Score 0.458 Round 3: 452 peptides, 57 chains. Longest chain 22 peptides. Score 0.498 Round 4: 465 peptides, 60 chains. Longest chain 27 peptides. Score 0.497 Round 5: 456 peptides, 58 chains. Longest chain 27 peptides. Score 0.498 Taking the results from Round 5 Chains 62, Residues 398, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13112 restraints for refining 5950 atoms. 11492 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2649 (Rfree = 0.000) for 5950 atoms. Found 28 (28 requested) and removed 107 (14 requested) atoms. Cycle 12: After refmac, R = 0.2504 (Rfree = 0.000) for 5780 atoms. Found 27 (27 requested) and removed 66 (13 requested) atoms. Cycle 13: After refmac, R = 0.2373 (Rfree = 0.000) for 5682 atoms. Found 27 (27 requested) and removed 60 (13 requested) atoms. Cycle 14: After refmac, R = 0.2045 (Rfree = 0.000) for 5609 atoms. Found 15 (26 requested) and removed 33 (13 requested) atoms. Cycle 15: After refmac, R = 0.2152 (Rfree = 0.000) for 5560 atoms. Found 26 (26 requested) and removed 179 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.16 Search for helices and strands: 0 residues in 0 chains, 5624 seeds are put forward NCS extension: 32 residues added (4 deleted due to clashes), 5656 seeds are put forward Round 1: 418 peptides, 68 chains. Longest chain 15 peptides. Score 0.392 Round 2: 453 peptides, 66 chains. Longest chain 15 peptides. Score 0.449 Round 3: 461 peptides, 62 chains. Longest chain 18 peptides. Score 0.482 Round 4: 455 peptides, 62 chains. Longest chain 23 peptides. Score 0.474 Round 5: 478 peptides, 62 chains. Longest chain 18 peptides. Score 0.502 Taking the results from Round 5 Chains 64, Residues 416, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 12469 restraints for refining 5855 atoms. 10792 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2466 (Rfree = 0.000) for 5855 atoms. Found 27 (27 requested) and removed 51 (13 requested) atoms. Cycle 17: After refmac, R = 0.2238 (Rfree = 0.000) for 5741 atoms. Found 27 (27 requested) and removed 55 (13 requested) atoms. Cycle 18: After refmac, R = 0.2205 (Rfree = 0.000) for 5670 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 19: After refmac, R = 0.2274 (Rfree = 0.000) for 5619 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. Cycle 20: After refmac, R = 0.2108 (Rfree = 0.000) for 5588 atoms. Found 26 (26 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.17 Search for helices and strands: 0 residues in 0 chains, 5924 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5941 seeds are put forward Round 1: 374 peptides, 67 chains. Longest chain 15 peptides. Score 0.336 Round 2: 417 peptides, 60 chains. Longest chain 20 peptides. Score 0.438 Round 3: 430 peptides, 62 chains. Longest chain 14 peptides. Score 0.443 Round 4: 432 peptides, 61 chains. Longest chain 18 peptides. Score 0.451 Round 5: 425 peptides, 62 chains. Longest chain 16 peptides. Score 0.437 Taking the results from Round 4 Chains 61, Residues 371, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13360 restraints for refining 5981 atoms. 11937 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2402 (Rfree = 0.000) for 5981 atoms. Found 28 (28 requested) and removed 54 (14 requested) atoms. Cycle 22: After refmac, R = 0.2207 (Rfree = 0.000) for 5906 atoms. Found 28 (28 requested) and removed 48 (14 requested) atoms. Cycle 23: After refmac, R = 0.2181 (Rfree = 0.000) for 5850 atoms. Found 27 (27 requested) and removed 45 (13 requested) atoms. Cycle 24: After refmac, R = 0.2074 (Rfree = 0.000) for 5810 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 25: After refmac, R = 0.2002 (Rfree = 0.000) for 5785 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 3.18 Search for helices and strands: 0 residues in 0 chains, 6098 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 6124 seeds are put forward Round 1: 392 peptides, 74 chains. Longest chain 17 peptides. Score 0.319 Round 2: 422 peptides, 60 chains. Longest chain 18 peptides. Score 0.444 Round 3: 397 peptides, 54 chains. Longest chain 21 peptides. Score 0.447 Round 4: 414 peptides, 58 chains. Longest chain 19 peptides. Score 0.446 Round 5: 401 peptides, 54 chains. Longest chain 20 peptides. Score 0.452 Taking the results from Round 5 Chains 55, Residues 347, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13711 restraints for refining 5980 atoms. 12350 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2511 (Rfree = 0.000) for 5980 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 27: After refmac, R = 0.2281 (Rfree = 0.000) for 5920 atoms. Found 28 (28 requested) and removed 31 (14 requested) atoms. Cycle 28: After refmac, R = 0.2273 (Rfree = 0.000) for 5894 atoms. Found 28 (28 requested) and removed 31 (14 requested) atoms. Cycle 29: After refmac, R = 0.2152 (Rfree = 0.000) for 5861 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 30: After refmac, R = 0.2088 (Rfree = 0.000) for 5847 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.85 3.22 Search for helices and strands: 0 residues in 0 chains, 6114 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 6152 seeds are put forward Round 1: 360 peptides, 70 chains. Longest chain 11 peptides. Score 0.297 Round 2: 406 peptides, 66 chains. Longest chain 14 peptides. Score 0.388 Round 3: 409 peptides, 63 chains. Longest chain 16 peptides. Score 0.410 Round 4: 404 peptides, 62 chains. Longest chain 16 peptides. Score 0.409 Round 5: 431 peptides, 63 chains. Longest chain 19 peptides. Score 0.439 Taking the results from Round 5 Chains 63, Residues 368, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13692 restraints for refining 5981 atoms. 12283 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2497 (Rfree = 0.000) for 5981 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 32: After refmac, R = 0.2282 (Rfree = 0.000) for 5926 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. Cycle 33: After refmac, R = 0.2183 (Rfree = 0.000) for 5881 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. Cycle 34: After refmac, R = 0.2140 (Rfree = 0.000) for 5868 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 35: After refmac, R = 0.2095 (Rfree = 0.000) for 5857 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.17 Search for helices and strands: 0 residues in 0 chains, 6180 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6200 seeds are put forward Round 1: 358 peptides, 67 chains. Longest chain 13 peptides. Score 0.313 Round 2: 380 peptides, 56 chains. Longest chain 14 peptides. Score 0.413 Round 3: 394 peptides, 58 chains. Longest chain 21 peptides. Score 0.420 Round 4: 386 peptides, 56 chains. Longest chain 15 peptides. Score 0.421 Round 5: 388 peptides, 56 chains. Longest chain 16 peptides. Score 0.424 Taking the results from Round 5 Chains 56, Residues 332, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13879 restraints for refining 5981 atoms. 12607 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2345 (Rfree = 0.000) for 5981 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 37: After refmac, R = 0.2274 (Rfree = 0.000) for 5946 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 38: After refmac, R = 0.2240 (Rfree = 0.000) for 5919 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 39: After refmac, R = 0.2164 (Rfree = 0.000) for 5899 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 40: After refmac, R = 0.2119 (Rfree = 0.000) for 5883 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 3.17 Search for helices and strands: 0 residues in 0 chains, 6111 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6127 seeds are put forward Round 1: 315 peptides, 63 chains. Longest chain 9 peptides. Score 0.273 Round 2: 343 peptides, 56 chains. Longest chain 15 peptides. Score 0.362 Round 3: 381 peptides, 58 chains. Longest chain 17 peptides. Score 0.402 Round 4: 365 peptides, 57 chains. Longest chain 15 peptides. Score 0.386 Round 5: 379 peptides, 55 chains. Longest chain 17 peptides. Score 0.418 Taking the results from Round 5 Chains 55, Residues 324, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10348 reflections ( 99.71 % complete ) and 13970 restraints for refining 5981 atoms. 12729 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2283 (Rfree = 0.000) for 5981 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 42: After refmac, R = 0.2321 (Rfree = 0.000) for 5938 atoms. Found 28 (28 requested) and removed 33 (14 requested) atoms. Cycle 43: After refmac, R = 0.2202 (Rfree = 0.000) for 5901 atoms. Found 28 (28 requested) and removed 42 (14 requested) atoms. Cycle 44: After refmac, R = 0.2093 (Rfree = 0.000) for 5871 atoms. Found 27 (27 requested) and removed 67 (13 requested) atoms. Cycle 45: After refmac, R = 0.2078 (Rfree = 0.000) for 5820 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.16 Search for helices and strands: 0 residues in 0 chains, 6042 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6065 seeds are put forward Round 1: 297 peptides, 62 chains. Longest chain 11 peptides. Score 0.251 Round 2: 346 peptides, 57 chains. Longest chain 24 peptides. Score 0.359 Round 3: 336 peptides, 52 chains. Longest chain 21 peptides. Score 0.377 Round 4: 352 peptides, 60 chains. Longest chain 23 peptides. Score 0.349 Round 5: 350 peptides, 52 chains. Longest chain 23 peptides. Score 0.397 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 52, Residues 298, 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 2go7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10348 reflections ( 99.71 % complete ) and 13929 restraints for refining 5982 atoms. 12789 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2330 (Rfree = 0.000) for 5982 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2331 (Rfree = 0.000) for 5934 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2119 (Rfree = 0.000) for 5898 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2231 (Rfree = 0.000) for 5867 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:19:58 GMT 2018 Job finished. TimeTaking 66.53 Used memory is bytes: 14717656