null Mon 24 Dec 07:33:25 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 2pbl-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-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/2pbl-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-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 07:33:29 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/2pbl-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-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 635 and 0 Target number of residues in the AU: 635 Target solvent content: 0.6597 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-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: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 8384 target number of atoms Had to go as low as 0.75 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: 87.858 4.000 Wilson plot Bfac: 84.56 8486 reflections ( 98.79 % complete ) and 0 restraints for refining 9290 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3705 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4155 (Rfree = 0.000) for 9290 atoms. Found 44 (44 requested) and removed 101 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 9402 seeds are put forward NCS extension: 0 residues added, 9402 seeds are put forward Round 1: 236 peptides, 52 chains. Longest chain 8 peptides. Score 0.226 Round 2: 337 peptides, 66 chains. Longest chain 14 peptides. Score 0.306 Round 3: 365 peptides, 68 chains. Longest chain 14 peptides. Score 0.339 Round 4: 393 peptides, 67 chains. Longest chain 14 peptides. Score 0.393 Round 5: 415 peptides, 74 chains. Longest chain 14 peptides. Score 0.380 Taking the results from Round 4 Chains 67, Residues 326, Estimated correctness of the model 0.0 % 13 chains (78 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 17756 restraints for refining 7567 atoms. 16318 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3721 (Rfree = 0.000) for 7567 atoms. Found 35 (35 requested) and removed 88 (17 requested) atoms. Cycle 2: After refmac, R = 0.3596 (Rfree = 0.000) for 7313 atoms. Found 35 (35 requested) and removed 59 (17 requested) atoms. Cycle 3: After refmac, R = 0.3512 (Rfree = 0.000) for 7173 atoms. Found 34 (34 requested) and removed 56 (17 requested) atoms. Cycle 4: After refmac, R = 0.3506 (Rfree = 0.000) for 7048 atoms. Found 33 (33 requested) and removed 48 (16 requested) atoms. Cycle 5: After refmac, R = 0.3485 (Rfree = 0.000) for 6979 atoms. Found 33 (33 requested) and removed 47 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 7186 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 7201 seeds are put forward Round 1: 337 peptides, 70 chains. Longest chain 8 peptides. Score 0.275 Round 2: 408 peptides, 67 chains. Longest chain 14 peptides. Score 0.417 Round 3: 394 peptides, 62 chains. Longest chain 15 peptides. Score 0.429 Round 4: 412 peptides, 70 chains. Longest chain 15 peptides. Score 0.403 Round 5: 406 peptides, 67 chains. Longest chain 18 peptides. Score 0.414 Taking the results from Round 3 Chains 63, Residues 332, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15441 restraints for refining 6752 atoms. 14081 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3209 (Rfree = 0.000) for 6752 atoms. Found 32 (32 requested) and removed 66 (16 requested) atoms. Cycle 7: After refmac, R = 0.3087 (Rfree = 0.000) for 6622 atoms. Found 31 (31 requested) and removed 49 (15 requested) atoms. Cycle 8: After refmac, R = 0.2992 (Rfree = 0.000) for 6543 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 9: After refmac, R = 0.3011 (Rfree = 0.000) for 6500 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 10: After refmac, R = 0.2878 (Rfree = 0.000) for 6458 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 6670 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 6684 seeds are put forward Round 1: 401 peptides, 77 chains. Longest chain 11 peptides. Score 0.336 Round 2: 452 peptides, 77 chains. Longest chain 15 peptides. Score 0.418 Round 3: 447 peptides, 72 chains. Longest chain 17 peptides. Score 0.443 Round 4: 458 peptides, 72 chains. Longest chain 17 peptides. Score 0.460 Round 5: 459 peptides, 69 chains. Longest chain 13 peptides. Score 0.481 Taking the results from Round 5 Chains 70, Residues 390, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15643 restraints for refining 6925 atoms. 14062 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3363 (Rfree = 0.000) for 6925 atoms. Found 32 (32 requested) and removed 92 (16 requested) atoms. Cycle 12: After refmac, R = 0.3096 (Rfree = 0.000) for 6754 atoms. Found 32 (32 requested) and removed 51 (16 requested) atoms. Cycle 13: After refmac, R = 0.2851 (Rfree = 0.000) for 6660 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 14: After refmac, R = 0.2199 (Rfree = 0.000) for 6579 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 15: After refmac, R = 0.2526 (Rfree = 0.000) for 6541 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 6747 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 6759 seeds are put forward Round 1: 353 peptides, 66 chains. Longest chain 14 peptides. Score 0.334 Round 2: 413 peptides, 64 chains. Longest chain 23 peptides. Score 0.445 Round 3: 410 peptides, 64 chains. Longest chain 20 peptides. Score 0.440 Round 4: 413 peptides, 63 chains. Longest chain 14 peptides. Score 0.452 Round 5: 436 peptides, 68 chains. Longest chain 15 peptides. Score 0.453 Taking the results from Round 5 Chains 68, Residues 368, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15179 restraints for refining 6768 atoms. 13702 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2939 (Rfree = 0.000) for 6768 atoms. Found 32 (32 requested) and removed 78 (16 requested) atoms. Cycle 17: After refmac, R = 0.2899 (Rfree = 0.000) for 6640 atoms. Found 31 (31 requested) and removed 47 (15 requested) atoms. Cycle 18: After refmac, R = 0.2112 (Rfree = 0.000) for 6568 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 19: After refmac, R = 0.2595 (Rfree = 0.000) for 6540 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 20: After refmac, R = 0.2610 (Rfree = 0.000) for 6514 atoms. Found 31 (31 requested) and removed 38 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.93 Search for helices and strands: 0 residues in 0 chains, 6718 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6733 seeds are put forward Round 1: 316 peptides, 65 chains. Longest chain 9 peptides. Score 0.275 Round 2: 375 peptides, 65 chains. Longest chain 17 peptides. Score 0.378 Round 3: 388 peptides, 62 chains. Longest chain 25 peptides. Score 0.420 Round 4: 405 peptides, 68 chains. Longest chain 16 peptides. Score 0.405 Round 5: 412 peptides, 66 chains. Longest chain 17 peptides. Score 0.430 Taking the results from Round 5 Chains 66, Residues 346, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15676 restraints for refining 6871 atoms. 14291 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2852 (Rfree = 0.000) for 6871 atoms. Found 32 (32 requested) and removed 78 (16 requested) atoms. Cycle 22: After refmac, R = 0.2636 (Rfree = 0.000) for 6759 atoms. Found 32 (32 requested) and removed 47 (16 requested) atoms. Cycle 23: After refmac, R = 0.2624 (Rfree = 0.000) for 6702 atoms. Found 32 (32 requested) and removed 43 (16 requested) atoms. Cycle 24: After refmac, R = 0.2484 (Rfree = 0.000) for 6650 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 25: After refmac, R = 0.2598 (Rfree = 0.000) for 6617 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 6825 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6846 seeds are put forward Round 1: 352 peptides, 70 chains. Longest chain 10 peptides. Score 0.302 Round 2: 382 peptides, 67 chains. Longest chain 15 peptides. Score 0.375 Round 3: 415 peptides, 66 chains. Longest chain 18 peptides. Score 0.435 Round 4: 402 peptides, 68 chains. Longest chain 13 peptides. Score 0.401 Round 5: 404 peptides, 71 chains. Longest chain 14 peptides. Score 0.383 Taking the results from Round 3 Chains 68, Residues 349, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15195 restraints for refining 6865 atoms. 13731 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2751 (Rfree = 0.000) for 6865 atoms. Found 32 (32 requested) and removed 78 (16 requested) atoms. Cycle 27: After refmac, R = 0.2670 (Rfree = 0.000) for 6756 atoms. Found 32 (32 requested) and removed 41 (16 requested) atoms. Cycle 28: After refmac, R = 0.2716 (Rfree = 0.000) for 6711 atoms. Found 32 (32 requested) and removed 43 (16 requested) atoms. Cycle 29: After refmac, R = 0.2722 (Rfree = 0.000) for 6665 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 30: After refmac, R = 0.2767 (Rfree = 0.000) for 6638 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 6863 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 6877 seeds are put forward Round 1: 306 peptides, 65 chains. Longest chain 10 peptides. Score 0.257 Round 2: 363 peptides, 69 chains. Longest chain 10 peptides. Score 0.329 Round 3: 377 peptides, 67 chains. Longest chain 12 peptides. Score 0.367 Round 4: 381 peptides, 66 chains. Longest chain 12 peptides. Score 0.381 Round 5: 366 peptides, 60 chains. Longest chain 17 peptides. Score 0.399 Taking the results from Round 5 Chains 63, Residues 306, Estimated correctness of the model 0.0 % 7 chains (49 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15771 restraints for refining 6959 atoms. 14458 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3076 (Rfree = 0.000) for 6959 atoms. Found 33 (33 requested) and removed 81 (16 requested) atoms. Cycle 32: After refmac, R = 0.2922 (Rfree = 0.000) for 6847 atoms. Found 32 (32 requested) and removed 43 (16 requested) atoms. Cycle 33: After refmac, R = 0.2797 (Rfree = 0.000) for 6788 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 34: After refmac, R = 0.2827 (Rfree = 0.000) for 6738 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 35: After refmac, R = 0.2727 (Rfree = 0.000) for 6692 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 6911 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 6934 seeds are put forward Round 1: 288 peptides, 62 chains. Longest chain 10 peptides. Score 0.246 Round 2: 330 peptides, 63 chains. Longest chain 10 peptides. Score 0.316 Round 3: 340 peptides, 61 chains. Longest chain 13 peptides. Score 0.348 Round 4: 345 peptides, 60 chains. Longest chain 12 peptides. Score 0.364 Round 5: 349 peptides, 62 chains. Longest chain 12 peptides. Score 0.356 Taking the results from Round 4 Chains 60, Residues 285, Estimated correctness of the model 0.0 % 6 chains (27 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 15387 restraints for refining 6731 atoms. 14244 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3097 (Rfree = 0.000) for 6731 atoms. Found 31 (31 requested) and removed 76 (15 requested) atoms. Cycle 37: After refmac, R = 0.3028 (Rfree = 0.000) for 6631 atoms. Found 31 (31 requested) and removed 46 (15 requested) atoms. Cycle 38: After refmac, R = 0.2931 (Rfree = 0.000) for 6574 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 39: After refmac, R = 0.2044 (Rfree = 0.000) for 6539 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. Cycle 40: After refmac, R = 0.1812 (Rfree = 0.000) for 6506 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 6763 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6780 seeds are put forward Round 1: 224 peptides, 51 chains. Longest chain 7 peptides. Score 0.210 Round 2: 287 peptides, 56 chains. Longest chain 11 peptides. Score 0.292 Round 3: 270 peptides, 53 chains. Longest chain 13 peptides. Score 0.284 Round 4: 283 peptides, 56 chains. Longest chain 10 peptides. Score 0.285 Round 5: 305 peptides, 57 chains. Longest chain 11 peptides. Score 0.317 Taking the results from Round 5 Chains 58, Residues 248, Estimated correctness of the model 0.0 % 8 chains (36 residues) have been docked in sequence ------------------------------------------------------ 8486 reflections ( 98.79 % complete ) and 14688 restraints for refining 6512 atoms. 13669 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2904 (Rfree = 0.000) for 6512 atoms. Found 30 (30 requested) and removed 70 (15 requested) atoms. Cycle 42: After refmac, R = 0.2834 (Rfree = 0.000) for 6435 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 43: After refmac, R = 0.2725 (Rfree = 0.000) for 6392 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 44: After refmac, R = 0.2741 (Rfree = 0.000) for 6365 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 45: After refmac, R = 0.1951 (Rfree = 0.000) for 6338 atoms. Found 30 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 4.02 Search for helices and strands: 0 residues in 0 chains, 6556 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 6568 seeds are put forward Round 1: 222 peptides, 50 chains. Longest chain 9 peptides. Score 0.214 Round 2: 266 peptides, 57 chains. Longest chain 9 peptides. Score 0.244 Round 3: 292 peptides, 56 chains. Longest chain 11 peptides. Score 0.301 Round 4: 275 peptides, 52 chains. Longest chain 10 peptides. Score 0.302 Round 5: 261 peptides, 48 chains. Longest chain 13 peptides. Score 0.308 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 213, Estimated correctness of the model 0.0 % 6 chains (29 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2pbl-4_warpNtrace.pdb as input Building loops using Loopy2018 50 chains (213 residues) following loop building 6 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8486 reflections ( 98.79 % complete ) and 14419 restraints for refining 6322 atoms. 13546 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2949 (Rfree = 0.000) for 6322 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2865 (Rfree = 0.000) for 6286 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2926 (Rfree = 0.000) for 6251 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2865 (Rfree = 0.000) for 6212 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:44:17 GMT 2018 Job finished. TimeTaking 70.88 Used memory is bytes: 4103312