Mon 24 Dec 07:26:56 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 2ii1-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-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/2ii1-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-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 07:27:01 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/2ii1-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-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 774 and 0 Target number of residues in the AU: 774 Target solvent content: 0.6227 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: 2ii1-3.4-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: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 9632 target number of atoms Had to go as low as 0.60 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 3.400 Wilson plot Bfac: 62.70 13485 reflections ( 91.19 % complete ) and 0 restraints for refining 10668 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3257 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2765 (Rfree = 0.000) for 10668 atoms. Found 56 (80 requested) and removed 146 (40 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 10660 seeds are put forward NCS extension: 0 residues added, 10660 seeds are put forward Round 1: 280 peptides, 64 chains. Longest chain 10 peptides. Score 0.212 Round 2: 340 peptides, 71 chains. Longest chain 9 peptides. Score 0.266 Round 3: 372 peptides, 74 chains. Longest chain 15 peptides. Score 0.298 Round 4: 409 peptides, 82 chains. Longest chain 11 peptides. Score 0.303 Round 5: 398 peptides, 76 chains. Longest chain 16 peptides. Score 0.326 Taking the results from Round 5 Chains 76, Residues 322, Estimated correctness of the model 0.0 % 13 chains (54 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20667 restraints for refining 8757 atoms. 19335 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2434 (Rfree = 0.000) for 8757 atoms. Found 40 (66 requested) and removed 66 (33 requested) atoms. Cycle 2: After refmac, R = 0.2288 (Rfree = 0.000) for 8672 atoms. Found 49 (65 requested) and removed 48 (32 requested) atoms. Cycle 3: After refmac, R = 0.2209 (Rfree = 0.000) for 8635 atoms. Found 32 (65 requested) and removed 42 (32 requested) atoms. Cycle 4: After refmac, R = 0.2141 (Rfree = 0.000) for 8594 atoms. Found 37 (65 requested) and removed 43 (32 requested) atoms. Cycle 5: After refmac, R = 0.2045 (Rfree = 0.000) for 8560 atoms. Found 33 (64 requested) and removed 44 (32 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.54 Search for helices and strands: 0 residues in 0 chains, 8713 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 8738 seeds are put forward Round 1: 336 peptides, 77 chains. Longest chain 6 peptides. Score 0.217 Round 2: 418 peptides, 83 chains. Longest chain 10 peptides. Score 0.311 Round 3: 406 peptides, 80 chains. Longest chain 12 peptides. Score 0.312 Round 4: 383 peptides, 72 chains. Longest chain 10 peptides. Score 0.329 Round 5: 404 peptides, 75 chains. Longest chain 12 peptides. Score 0.342 Taking the results from Round 5 Chains 76, Residues 329, Estimated correctness of the model 0.0 % 9 chains (47 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 19505 restraints for refining 8357 atoms. 18157 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2068 (Rfree = 0.000) for 8357 atoms. Found 38 (63 requested) and removed 53 (31 requested) atoms. Cycle 7: After refmac, R = 0.1917 (Rfree = 0.000) for 8303 atoms. Found 33 (62 requested) and removed 42 (31 requested) atoms. Cycle 8: After refmac, R = 0.1855 (Rfree = 0.000) for 8268 atoms. Found 31 (62 requested) and removed 39 (31 requested) atoms. Cycle 9: After refmac, R = 0.1821 (Rfree = 0.000) for 8242 atoms. Found 31 (62 requested) and removed 36 (31 requested) atoms. Cycle 10: After refmac, R = 0.1558 (Rfree = 0.000) for 8230 atoms. Found 14 (62 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.57 Search for helices and strands: 0 residues in 0 chains, 8365 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 8376 seeds are put forward Round 1: 377 peptides, 82 chains. Longest chain 7 peptides. Score 0.251 Round 2: 435 peptides, 84 chains. Longest chain 10 peptides. Score 0.331 Round 3: 449 peptides, 82 chains. Longest chain 11 peptides. Score 0.365 Round 4: 468 peptides, 84 chains. Longest chain 13 peptides. Score 0.380 Round 5: 454 peptides, 78 chains. Longest chain 21 peptides. Score 0.398 Taking the results from Round 5 Chains 78, Residues 376, Estimated correctness of the model 0.0 % 6 chains (19 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20000 restraints for refining 8472 atoms. 18540 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1952 (Rfree = 0.000) for 8472 atoms. Found 47 (63 requested) and removed 59 (31 requested) atoms. Cycle 12: After refmac, R = 0.1982 (Rfree = 0.000) for 8424 atoms. Found 58 (63 requested) and removed 46 (31 requested) atoms. Cycle 13: After refmac, R = 0.1907 (Rfree = 0.000) for 8414 atoms. Found 34 (63 requested) and removed 40 (31 requested) atoms. Cycle 14: After refmac, R = 0.1810 (Rfree = 0.000) for 8398 atoms. Found 37 (63 requested) and removed 49 (31 requested) atoms. Cycle 15: After refmac, R = 0.1519 (Rfree = 0.000) for 8371 atoms. Found 17 (63 requested) and removed 36 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.54 Search for helices and strands: 0 residues in 0 chains, 8528 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 8552 seeds are put forward Round 1: 363 peptides, 80 chains. Longest chain 7 peptides. Score 0.242 Round 2: 404 peptides, 75 chains. Longest chain 12 peptides. Score 0.342 Round 3: 423 peptides, 73 chains. Longest chain 17 peptides. Score 0.384 Round 4: 430 peptides, 77 chains. Longest chain 14 peptides. Score 0.369 Round 5: 436 peptides, 76 chains. Longest chain 15 peptides. Score 0.384 Taking the results from Round 5 Chains 77, Residues 360, Estimated correctness of the model 0.0 % 15 chains (69 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 19359 restraints for refining 8511 atoms. 17832 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1973 (Rfree = 0.000) for 8511 atoms. Found 41 (64 requested) and removed 59 (32 requested) atoms. Cycle 17: After refmac, R = 0.1795 (Rfree = 0.000) for 8465 atoms. Found 30 (64 requested) and removed 38 (32 requested) atoms. Cycle 18: After refmac, R = 0.1757 (Rfree = 0.000) for 8445 atoms. Found 29 (63 requested) and removed 38 (31 requested) atoms. Cycle 19: After refmac, R = 0.1692 (Rfree = 0.000) for 8421 atoms. Found 35 (63 requested) and removed 33 (31 requested) atoms. Cycle 20: After refmac, R = 0.1709 (Rfree = 0.000) for 8410 atoms. Found 31 (63 requested) and removed 39 (31 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.54 Search for helices and strands: 0 residues in 0 chains, 8556 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 8567 seeds are put forward Round 1: 411 peptides, 90 chains. Longest chain 11 peptides. Score 0.253 Round 2: 462 peptides, 90 chains. Longest chain 12 peptides. Score 0.333 Round 3: 480 peptides, 88 chains. Longest chain 13 peptides. Score 0.373 Round 4: 503 peptides, 91 chains. Longest chain 11 peptides. Score 0.388 Round 5: 480 peptides, 81 chains. Longest chain 11 peptides. Score 0.416 Taking the results from Round 5 Chains 81, Residues 399, Estimated correctness of the model 0.0 % 13 chains (64 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20004 restraints for refining 8698 atoms. 18324 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2050 (Rfree = 0.000) for 8698 atoms. Found 43 (65 requested) and removed 61 (32 requested) atoms. Cycle 22: After refmac, R = 0.1916 (Rfree = 0.000) for 8661 atoms. Found 40 (65 requested) and removed 34 (32 requested) atoms. Cycle 23: After refmac, R = 0.1914 (Rfree = 0.000) for 8645 atoms. Found 49 (65 requested) and removed 38 (32 requested) atoms. Cycle 24: After refmac, R = 0.1855 (Rfree = 0.000) for 8638 atoms. Found 45 (65 requested) and removed 39 (32 requested) atoms. Cycle 25: After refmac, R = 0.1908 (Rfree = 0.000) for 8617 atoms. Found 36 (65 requested) and removed 41 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 8728 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 8740 seeds are put forward Round 1: 381 peptides, 83 chains. Longest chain 8 peptides. Score 0.251 Round 2: 459 peptides, 89 chains. Longest chain 10 peptides. Score 0.335 Round 3: 440 peptides, 80 chains. Longest chain 11 peptides. Score 0.364 Round 4: 443 peptides, 83 chains. Longest chain 16 peptides. Score 0.350 Round 5: 436 peptides, 78 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 5 Chains 78, Residues 358, Estimated correctness of the model 0.0 % 7 chains (30 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20508 restraints for refining 8682 atoms. 19085 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2010 (Rfree = 0.000) for 8682 atoms. Found 46 (65 requested) and removed 61 (32 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1875 (Rfree = 0.000) for 8645 atoms. Found 41 (65 requested) and removed 42 (32 requested) atoms. Cycle 28: After refmac, R = 0.1862 (Rfree = 0.000) for 8627 atoms. Found 32 (65 requested) and removed 39 (32 requested) atoms. Cycle 29: After refmac, R = 0.1852 (Rfree = 0.000) for 8608 atoms. Found 42 (65 requested) and removed 43 (32 requested) atoms. Cycle 30: After refmac, R = 0.1835 (Rfree = 0.000) for 8598 atoms. Found 44 (64 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 3.52 Search for helices and strands: 0 residues in 0 chains, 8733 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8750 seeds are put forward Round 1: 420 peptides, 89 chains. Longest chain 9 peptides. Score 0.274 Round 2: 423 peptides, 76 chains. Longest chain 16 peptides. Score 0.365 Round 3: 419 peptides, 77 chains. Longest chain 11 peptides. Score 0.352 Round 4: 395 peptides, 71 chains. Longest chain 11 peptides. Score 0.355 Round 5: 420 peptides, 74 chains. Longest chain 19 peptides. Score 0.373 Taking the results from Round 5 Chains 74, Residues 346, Estimated correctness of the model 0.0 % 6 chains (29 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20578 restraints for refining 8758 atoms. 19201 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1988 (Rfree = 0.000) for 8758 atoms. Found 47 (66 requested) and removed 47 (33 requested) atoms. Cycle 32: After refmac, R = 0.1954 (Rfree = 0.000) for 8734 atoms. Found 64 (66 requested) and removed 40 (33 requested) atoms. Cycle 33: After refmac, R = 0.1904 (Rfree = 0.000) for 8738 atoms. Found 64 (66 requested) and removed 38 (33 requested) atoms. Cycle 34: After refmac, R = 0.1878 (Rfree = 0.000) for 8743 atoms. Found 50 (66 requested) and removed 40 (33 requested) atoms. Cycle 35: After refmac, R = 0.1805 (Rfree = 0.000) for 8738 atoms. Found 51 (66 requested) and removed 42 (33 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 3.54 Search for helices and strands: 0 residues in 0 chains, 8880 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 8899 seeds are put forward Round 1: 325 peptides, 75 chains. Longest chain 7 peptides. Score 0.212 Round 2: 378 peptides, 75 chains. Longest chain 12 peptides. Score 0.301 Round 3: 376 peptides, 73 chains. Longest chain 12 peptides. Score 0.311 Round 4: 366 peptides, 67 chains. Longest chain 13 peptides. Score 0.336 Round 5: 392 peptides, 73 chains. Longest chain 13 peptides. Score 0.337 Taking the results from Round 5 Chains 73, Residues 319, Estimated correctness of the model 0.0 % 9 chains (35 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20725 restraints for refining 8757 atoms. 19446 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1828 (Rfree = 0.000) for 8757 atoms. Found 40 (66 requested) and removed 38 (33 requested) atoms. Cycle 37: After refmac, R = 0.1794 (Rfree = 0.000) for 8745 atoms. Found 50 (66 requested) and removed 41 (33 requested) atoms. Cycle 38: After refmac, R = 0.1783 (Rfree = 0.000) for 8740 atoms. Found 39 (66 requested) and removed 36 (33 requested) atoms. Cycle 39: After refmac, R = 0.1735 (Rfree = 0.000) for 8731 atoms. Found 50 (66 requested) and removed 42 (33 requested) atoms. Cycle 40: After refmac, R = 0.1720 (Rfree = 0.000) for 8723 atoms. Found 50 (65 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 3.53 Search for helices and strands: 0 residues in 0 chains, 8900 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 8913 seeds are put forward Round 1: 294 peptides, 67 chains. Longest chain 8 peptides. Score 0.215 Round 2: 315 peptides, 65 chains. Longest chain 8 peptides. Score 0.267 Round 3: 329 peptides, 65 chains. Longest chain 11 peptides. Score 0.290 Round 4: 319 peptides, 58 chains. Longest chain 14 peptides. Score 0.323 Round 5: 307 peptides, 59 chains. Longest chain 10 peptides. Score 0.296 Taking the results from Round 4 Chains 58, Residues 261, Estimated correctness of the model 0.0 % 9 chains (51 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20941 restraints for refining 8758 atoms. 19843 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1768 (Rfree = 0.000) for 8758 atoms. Found 39 (66 requested) and removed 41 (33 requested) atoms. Cycle 42: After refmac, R = 0.1698 (Rfree = 0.000) for 8743 atoms. Found 48 (66 requested) and removed 39 (33 requested) atoms. Cycle 43: After refmac, R = 0.1717 (Rfree = 0.000) for 8746 atoms. Found 34 (66 requested) and removed 40 (33 requested) atoms. Cycle 44: After refmac, R = 0.1420 (Rfree = 0.000) for 8726 atoms. Found 16 (65 requested) and removed 36 (32 requested) atoms. Cycle 45: After refmac, R = 0.1346 (Rfree = 0.000) for 8701 atoms. Found 12 (65 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.53 Search for helices and strands: 0 residues in 0 chains, 8791 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8806 seeds are put forward Round 1: 311 peptides, 72 chains. Longest chain 7 peptides. Score 0.209 Round 2: 347 peptides, 70 chains. Longest chain 14 peptides. Score 0.285 Round 3: 350 peptides, 69 chains. Longest chain 14 peptides. Score 0.297 Round 4: 359 peptides, 66 chains. Longest chain 17 peptides. Score 0.332 Round 5: 352 peptides, 69 chains. Longest chain 9 peptides. Score 0.300 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 67, Residues 293, Estimated correctness of the model 0.0 % 8 chains (38 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 67 chains (293 residues) following loop building 8 chains (38 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13485 reflections ( 91.19 % complete ) and 20303 restraints for refining 8736 atoms. 19109 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1671 (Rfree = 0.000) for 8736 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1596 (Rfree = 0.000) for 8696 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.1590 (Rfree = 0.000) for 8658 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.1548 (Rfree = 0.000) for 8617 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Writing output files ... TimeTaking 90.9