Mon 24 Dec 00:39:01 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 2ii1-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.8-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/2ii1-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.8-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 00:39:06 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/2ii1-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.8-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 748 and 0 Target number of residues in the AU: 748 Target solvent content: 0.6354 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-3.8-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: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9632 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: 91.283 3.800 Wilson plot Bfac: 69.22 9674 reflections ( 91.17 % complete ) and 0 restraints for refining 10641 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3215 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3025 (Rfree = 0.000) for 10641 atoms. Found 58 (58 requested) and removed 185 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.94 Search for helices and strands: 0 residues in 0 chains, 10627 seeds are put forward NCS extension: 0 residues added, 10627 seeds are put forward Round 1: 288 peptides, 67 chains. Longest chain 8 peptides. Score 0.204 Round 2: 388 peptides, 83 chains. Longest chain 9 peptides. Score 0.263 Round 3: 432 peptides, 84 chains. Longest chain 14 peptides. Score 0.326 Round 4: 430 peptides, 80 chains. Longest chain 12 peptides. Score 0.349 Round 5: 426 peptides, 79 chains. Longest chain 15 peptides. Score 0.350 Taking the results from Round 5 Chains 79, Residues 347, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21333 restraints for refining 8710 atoms. 19993 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2294 (Rfree = 0.000) for 8710 atoms. Found 42 (47 requested) and removed 66 (23 requested) atoms. Cycle 2: After refmac, R = 0.2201 (Rfree = 0.000) for 8594 atoms. Found 26 (47 requested) and removed 64 (23 requested) atoms. Cycle 3: After refmac, R = 0.2047 (Rfree = 0.000) for 8520 atoms. Found 31 (47 requested) and removed 52 (23 requested) atoms. Cycle 4: After refmac, R = 0.1886 (Rfree = 0.000) for 8461 atoms. Found 18 (46 requested) and removed 46 (23 requested) atoms. Cycle 5: After refmac, R = 0.1966 (Rfree = 0.000) for 8418 atoms. Found 46 (46 requested) and removed 42 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.89 Search for helices and strands: 0 residues in 0 chains, 8615 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 8637 seeds are put forward Round 1: 339 peptides, 74 chains. Longest chain 9 peptides. Score 0.243 Round 2: 395 peptides, 76 chains. Longest chain 11 peptides. Score 0.321 Round 3: 409 peptides, 73 chains. Longest chain 12 peptides. Score 0.363 Round 4: 437 peptides, 75 chains. Longest chain 14 peptides. Score 0.392 Round 5: 441 peptides, 79 chains. Longest chain 14 peptides. Score 0.372 Taking the results from Round 4 Chains 76, Residues 362, Estimated correctness of the model 0.0 % 9 chains (60 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 19753 restraints for refining 8381 atoms. 18229 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1909 (Rfree = 0.000) for 8381 atoms. Found 25 (46 requested) and removed 55 (23 requested) atoms. Cycle 7: After refmac, R = 0.1815 (Rfree = 0.000) for 8314 atoms. Found 32 (45 requested) and removed 47 (22 requested) atoms. Cycle 8: After refmac, R = 0.1417 (Rfree = 0.000) for 8272 atoms. Found 11 (45 requested) and removed 31 (22 requested) atoms. Cycle 9: After refmac, R = 0.1500 (Rfree = 0.000) for 8239 atoms. Found 12 (45 requested) and removed 25 (22 requested) atoms. Cycle 10: After refmac, R = 0.1685 (Rfree = 0.000) for 8219 atoms. Found 21 (45 requested) and removed 39 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 8362 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8379 seeds are put forward Round 1: 392 peptides, 83 chains. Longest chain 8 peptides. Score 0.269 Round 2: 441 peptides, 86 chains. Longest chain 10 peptides. Score 0.327 Round 3: 457 peptides, 81 chains. Longest chain 15 peptides. Score 0.383 Round 4: 468 peptides, 82 chains. Longest chain 16 peptides. Score 0.393 Round 5: 462 peptides, 79 chains. Longest chain 19 peptides. Score 0.403 Taking the results from Round 5 Chains 80, Residues 383, Estimated correctness of the model 0.0 % 10 chains (65 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 20662 restraints for refining 8673 atoms. 19057 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1828 (Rfree = 0.000) for 8673 atoms. Found 29 (47 requested) and removed 79 (23 requested) atoms. Cycle 12: After refmac, R = 0.1843 (Rfree = 0.000) for 8587 atoms. Found 46 (47 requested) and removed 71 (23 requested) atoms. Cycle 13: After refmac, R = 0.1607 (Rfree = 0.000) for 8537 atoms. Found 29 (47 requested) and removed 52 (23 requested) atoms. Cycle 14: After refmac, R = 0.1301 (Rfree = 0.000) for 8499 atoms. Found 6 (46 requested) and removed 28 (23 requested) atoms. Cycle 15: After refmac, R = 0.1287 (Rfree = 0.000) for 8468 atoms. Found 10 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.89 Search for helices and strands: 0 residues in 0 chains, 8654 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 8675 seeds are put forward Round 1: 410 peptides, 91 chains. Longest chain 8 peptides. Score 0.245 Round 2: 482 peptides, 92 chains. Longest chain 11 peptides. Score 0.351 Round 3: 489 peptides, 90 chains. Longest chain 13 peptides. Score 0.374 Round 4: 497 peptides, 86 chains. Longest chain 19 peptides. Score 0.410 Round 5: 515 peptides, 88 chains. Longest chain 15 peptides. Score 0.423 Taking the results from Round 5 Chains 89, Residues 427, Estimated correctness of the model 0.0 % 6 chains (37 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 20638 restraints for refining 8712 atoms. 18922 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1739 (Rfree = 0.000) for 8712 atoms. Found 38 (47 requested) and removed 40 (23 requested) atoms. Cycle 17: After refmac, R = 0.1650 (Rfree = 0.000) for 8670 atoms. Found 34 (47 requested) and removed 46 (23 requested) atoms. Cycle 18: After refmac, R = 0.1542 (Rfree = 0.000) for 8631 atoms. Found 31 (47 requested) and removed 41 (23 requested) atoms. Cycle 19: After refmac, R = 0.1465 (Rfree = 0.000) for 8606 atoms. Found 31 (47 requested) and removed 37 (23 requested) atoms. Cycle 20: After refmac, R = 0.1532 (Rfree = 0.000) for 8591 atoms. Found 42 (47 requested) and removed 42 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.86 Search for helices and strands: 0 residues in 0 chains, 8775 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 8794 seeds are put forward Round 1: 356 peptides, 79 chains. Longest chain 7 peptides. Score 0.237 Round 2: 425 peptides, 83 chains. Longest chain 13 peptides. Score 0.322 Round 3: 418 peptides, 77 chains. Longest chain 13 peptides. Score 0.350 Round 4: 433 peptides, 75 chains. Longest chain 13 peptides. Score 0.386 Round 5: 441 peptides, 79 chains. Longest chain 15 peptides. Score 0.372 Taking the results from Round 4 Chains 75, Residues 358, Estimated correctness of the model 0.0 % 11 chains (50 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 20930 restraints for refining 8711 atoms. 19451 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1608 (Rfree = 0.000) for 8711 atoms. Found 27 (47 requested) and removed 37 (23 requested) atoms. Cycle 22: After refmac, R = 0.1657 (Rfree = 0.000) for 8660 atoms. Found 47 (47 requested) and removed 35 (23 requested) atoms. Cycle 23: After refmac, R = 0.1557 (Rfree = 0.000) for 8656 atoms. Found 41 (47 requested) and removed 29 (23 requested) atoms. Cycle 24: After refmac, R = 0.1484 (Rfree = 0.000) for 8651 atoms. Found 42 (47 requested) and removed 30 (23 requested) atoms. Cycle 25: After refmac, R = 0.1486 (Rfree = 0.000) for 8644 atoms. Found 38 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.88 Search for helices and strands: 0 residues in 0 chains, 8844 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 8856 seeds are put forward Round 1: 373 peptides, 78 chains. Longest chain 11 peptides. Score 0.272 Round 2: 444 peptides, 83 chains. Longest chain 12 peptides. Score 0.351 Round 3: 440 peptides, 79 chains. Longest chain 15 peptides. Score 0.371 Round 4: 420 peptides, 74 chains. Longest chain 11 peptides. Score 0.373 Round 5: 424 peptides, 76 chains. Longest chain 13 peptides. Score 0.366 Taking the results from Round 4 Chains 74, Residues 346, Estimated correctness of the model 0.0 % 7 chains (37 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9674 reflections ( 91.17 % complete ) and 21124 restraints for refining 8708 atoms. 19733 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1656 (Rfree = 0.000) for 8708 atoms. Found 43 (47 requested) and removed 41 (23 requested) atoms. Cycle 27: After refmac, R = 0.1600 (Rfree = 0.000) for 8683 atoms. Found 44 (47 requested) and removed 36 (23 requested) atoms. Cycle 28: After refmac, R = 0.1468 (Rfree = 0.000) for 8672 atoms. Found 28 (47 requested) and removed 29 (23 requested) atoms. Cycle 29: After refmac, R = 0.1208 (Rfree = 0.000) for 8662 atoms. Found 13 (47 requested) and removed 26 (23 requested) atoms. Cycle 30: After refmac, R = 0.1138 (Rfree = 0.000) for 8637 atoms. Found 8 (47 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.88 Search for helices and strands: 0 residues in 0 chains, 8788 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8802 seeds are put forward Round 1: 329 peptides, 76 chains. Longest chain 8 peptides. Score 0.212 Round 2: 365 peptides, 71 chains. Longest chain 9 peptides. Score 0.307 Round 3: 374 peptides, 69 chains. Longest chain 11 peptides. Score 0.335 Round 4: 388 peptides, 71 chains. Longest chain 11 peptides. Score 0.344 Round 5: 390 peptides, 69 chains. Longest chain 13 peptides. Score 0.360 Taking the results from Round 5 Chains 70, Residues 321, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21253 restraints for refining 8712 atoms. 19984 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1565 (Rfree = 0.000) for 8712 atoms. Found 40 (47 requested) and removed 34 (23 requested) atoms. Cycle 32: After refmac, R = 0.1637 (Rfree = 0.000) for 8704 atoms. Found 47 (47 requested) and removed 28 (23 requested) atoms. Cycle 33: After refmac, R = 0.1529 (Rfree = 0.000) for 8710 atoms. Found 43 (47 requested) and removed 30 (23 requested) atoms. Cycle 34: After refmac, R = 0.1198 (Rfree = 0.000) for 8715 atoms. Found 9 (47 requested) and removed 25 (23 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1167 (Rfree = 0.000) for 8694 atoms. Found 9 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 8862 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8874 seeds are put forward Round 1: 328 peptides, 73 chains. Longest chain 7 peptides. Score 0.231 Round 2: 341 peptides, 69 chains. Longest chain 10 peptides. Score 0.282 Round 3: 373 peptides, 71 chains. Longest chain 11 peptides. Score 0.320 Round 4: 385 peptides, 75 chains. Longest chain 11 peptides. Score 0.312 Round 5: 363 peptides, 67 chains. Longest chain 12 peptides. Score 0.332 Taking the results from Round 5 Chains 67, Residues 296, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21572 restraints for refining 8711 atoms. 20407 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1554 (Rfree = 0.000) for 8711 atoms. Found 38 (47 requested) and removed 30 (23 requested) atoms. Cycle 37: After refmac, R = 0.1604 (Rfree = 0.000) for 8699 atoms. Found 47 (47 requested) and removed 29 (23 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1582 (Rfree = 0.000) for 8707 atoms. Found 47 (47 requested) and removed 36 (23 requested) atoms. Cycle 39: After refmac, R = 0.1099 (Rfree = 0.000) for 8705 atoms. Found 18 (47 requested) and removed 28 (23 requested) atoms. Cycle 40: After refmac, R = 0.1028 (Rfree = 0.000) for 8688 atoms. Found 6 (47 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.87 Search for helices and strands: 0 residues in 0 chains, 8847 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 8858 seeds are put forward Round 1: 272 peptides, 63 chains. Longest chain 7 peptides. Score 0.205 Round 2: 326 peptides, 68 chains. Longest chain 8 peptides. Score 0.264 Round 3: 300 peptides, 58 chains. Longest chain 12 peptides. Score 0.292 Round 4: 338 peptides, 66 chains. Longest chain 10 peptides. Score 0.298 Round 5: 332 peptides, 66 chains. Longest chain 9 peptides. Score 0.288 Taking the results from Round 4 Chains 66, Residues 272, Estimated correctness of the model 0.0 % 10 chains (41 residues) have been docked in sequence ------------------------------------------------------ 9674 reflections ( 91.17 % complete ) and 21250 restraints for refining 8712 atoms. 20132 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1521 (Rfree = 0.000) for 8712 atoms. Found 44 (47 requested) and removed 35 (23 requested) atoms. Cycle 42: After refmac, R = 0.1539 (Rfree = 0.000) for 8700 atoms. Found 37 (47 requested) and removed 38 (23 requested) atoms. Cycle 43: After refmac, R = 0.1518 (Rfree = 0.000) for 8680 atoms. Found 47 (47 requested) and removed 35 (23 requested) atoms. Cycle 44: After refmac, R = 0.1512 (Rfree = 0.000) for 8675 atoms. Found 47 (47 requested) and removed 31 (23 requested) atoms. Cycle 45: After refmac, R = 0.1497 (Rfree = 0.000) for 8676 atoms. Found 47 (47 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.84 Search for helices and strands: 0 residues in 0 chains, 8900 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 8910 seeds are put forward Round 1: 223 peptides, 53 chains. Longest chain 7 peptides. Score 0.189 Round 2: 276 peptides, 57 chains. Longest chain 9 peptides. Score 0.257 Round 3: 287 peptides, 55 chains. Longest chain 10 peptides. Score 0.292 Round 4: 290 peptides, 57 chains. Longest chain 10 peptides. Score 0.282 Round 5: 272 peptides, 52 chains. Longest chain 9 peptides. Score 0.288 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 232, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 55 chains (232 residues) following loop building 2 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9674 reflections ( 91.17 % complete ) and 21367 restraints for refining 8559 atoms. 20471 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1472 (Rfree = 0.000) for 8559 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.1479 (Rfree = 0.000) for 8518 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.1355 (Rfree = 0.000) for 8489 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1090 (Rfree = 0.000) for 8460 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Writing output files ... TimeTaking 84.18