null Mon 24 Dec 07:28:10 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 2ii1-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.6-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/2ii1-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.6-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 07:28:14 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/2ii1-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.6-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 757 and 0 Target number of residues in the AU: 757 Target solvent content: 0.6310 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: 2ii1-3.6-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: 2ii1-3.6-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 3.600 Wilson plot Bfac: 66.82 11359 reflections ( 91.15 % complete ) and 0 restraints for refining 10640 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3324 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2789 (Rfree = 0.000) for 10640 atoms. Found 53 (68 requested) and removed 186 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 10599 seeds are put forward NCS extension: 0 residues added, 10599 seeds are put forward Round 1: 267 peptides, 62 chains. Longest chain 7 peptides. Score 0.203 Round 2: 341 peptides, 71 chains. Longest chain 8 peptides. Score 0.268 Round 3: 361 peptides, 71 chains. Longest chain 14 peptides. Score 0.301 Round 4: 374 peptides, 71 chains. Longest chain 12 peptides. Score 0.322 Round 5: 376 peptides, 68 chains. Longest chain 19 peptides. Score 0.345 Taking the results from Round 5 Chains 68, Residues 308, Estimated correctness of the model 0.0 % 9 chains (42 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21188 restraints for refining 8730 atoms. 19928 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2048 (Rfree = 0.000) for 8730 atoms. Found 26 (56 requested) and removed 58 (28 requested) atoms. Cycle 2: After refmac, R = 0.2018 (Rfree = 0.000) for 8628 atoms. Found 25 (55 requested) and removed 40 (27 requested) atoms. Cycle 3: After refmac, R = 0.1963 (Rfree = 0.000) for 8582 atoms. Found 34 (55 requested) and removed 42 (27 requested) atoms. Cycle 4: After refmac, R = 0.1656 (Rfree = 0.000) for 8551 atoms. Found 14 (55 requested) and removed 37 (27 requested) atoms. Cycle 5: After refmac, R = 0.1703 (Rfree = 0.000) for 8515 atoms. Found 13 (54 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.78 Search for helices and strands: 0 residues in 0 chains, 8650 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 8682 seeds are put forward Round 1: 392 peptides, 80 chains. Longest chain 9 peptides. Score 0.290 Round 2: 409 peptides, 74 chains. Longest chain 15 peptides. Score 0.356 Round 3: 436 peptides, 77 chains. Longest chain 14 peptides. Score 0.378 Round 4: 447 peptides, 80 chains. Longest chain 14 peptides. Score 0.375 Round 5: 424 peptides, 75 chains. Longest chain 15 peptides. Score 0.372 Taking the results from Round 3 Chains 78, Residues 359, Estimated correctness of the model 0.0 % 5 chains (32 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20895 restraints for refining 8647 atoms. 19452 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1923 (Rfree = 0.000) for 8647 atoms. Found 47 (55 requested) and removed 61 (27 requested) atoms. Cycle 7: After refmac, R = 0.1811 (Rfree = 0.000) for 8603 atoms. Found 31 (55 requested) and removed 49 (27 requested) atoms. Cycle 8: After refmac, R = 0.1764 (Rfree = 0.000) for 8562 atoms. Found 32 (55 requested) and removed 47 (27 requested) atoms. Cycle 9: After refmac, R = 0.1673 (Rfree = 0.000) for 8536 atoms. Found 20 (54 requested) and removed 41 (27 requested) atoms. Cycle 10: After refmac, R = 0.1431 (Rfree = 0.000) for 8505 atoms. Found 6 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 8659 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 8677 seeds are put forward Round 1: 345 peptides, 73 chains. Longest chain 9 peptides. Score 0.260 Round 2: 394 peptides, 77 chains. Longest chain 10 peptides. Score 0.313 Round 3: 405 peptides, 72 chains. Longest chain 12 peptides. Score 0.363 Round 4: 426 peptides, 76 chains. Longest chain 13 peptides. Score 0.369 Round 5: 421 peptides, 76 chains. Longest chain 12 peptides. Score 0.361 Taking the results from Round 4 Chains 78, Residues 350, Estimated correctness of the model 0.0 % 8 chains (46 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21082 restraints for refining 8730 atoms. 19650 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1723 (Rfree = 0.000) for 8730 atoms. Found 29 (56 requested) and removed 44 (28 requested) atoms. Cycle 12: After refmac, R = 0.1736 (Rfree = 0.000) for 8668 atoms. Found 32 (55 requested) and removed 36 (27 requested) atoms. Cycle 13: After refmac, R = 0.1734 (Rfree = 0.000) for 8640 atoms. Found 28 (55 requested) and removed 38 (27 requested) atoms. Cycle 14: After refmac, R = 0.1685 (Rfree = 0.000) for 8618 atoms. Found 40 (55 requested) and removed 38 (27 requested) atoms. Cycle 15: After refmac, R = 0.1360 (Rfree = 0.000) for 8609 atoms. Found 13 (55 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.76 Search for helices and strands: 0 residues in 0 chains, 8787 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 8807 seeds are put forward Round 1: 364 peptides, 76 chains. Longest chain 11 peptides. Score 0.271 Round 2: 406 peptides, 71 chains. Longest chain 15 peptides. Score 0.371 Round 3: 413 peptides, 76 chains. Longest chain 11 peptides. Score 0.349 Round 4: 406 peptides, 70 chains. Longest chain 11 peptides. Score 0.378 Round 5: 410 peptides, 66 chains. Longest chain 16 peptides. Score 0.410 Taking the results from Round 5 Chains 67, Residues 344, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21244 restraints for refining 8729 atoms. 19883 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1677 (Rfree = 0.000) for 8729 atoms. Found 34 (56 requested) and removed 38 (28 requested) atoms. Cycle 17: After refmac, R = 0.1752 (Rfree = 0.000) for 8701 atoms. Found 54 (55 requested) and removed 36 (27 requested) atoms. Cycle 18: After refmac, R = 0.1632 (Rfree = 0.000) for 8699 atoms. Found 42 (55 requested) and removed 34 (27 requested) atoms. Cycle 19: After refmac, R = 0.1244 (Rfree = 0.000) for 8686 atoms. Found 8 (55 requested) and removed 31 (27 requested) atoms. Cycle 20: After refmac, R = 0.1183 (Rfree = 0.000) for 8653 atoms. Found 8 (55 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.77 Search for helices and strands: 0 residues in 0 chains, 8787 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 8803 seeds are put forward Round 1: 388 peptides, 82 chains. Longest chain 10 peptides. Score 0.270 Round 2: 429 peptides, 77 chains. Longest chain 13 peptides. Score 0.367 Round 3: 427 peptides, 74 chains. Longest chain 16 peptides. Score 0.383 Round 4: 425 peptides, 76 chains. Longest chain 12 peptides. Score 0.368 Round 5: 421 peptides, 74 chains. Longest chain 15 peptides. Score 0.374 Taking the results from Round 3 Chains 75, Residues 353, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21207 restraints for refining 8731 atoms. 19824 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1561 (Rfree = 0.000) for 8731 atoms. Found 22 (56 requested) and removed 42 (28 requested) atoms. Cycle 22: After refmac, R = 0.1588 (Rfree = 0.000) for 8697 atoms. Found 33 (55 requested) and removed 34 (27 requested) atoms. Cycle 23: After refmac, R = 0.1596 (Rfree = 0.000) for 8685 atoms. Found 33 (55 requested) and removed 33 (27 requested) atoms. Cycle 24: After refmac, R = 0.1490 (Rfree = 0.000) for 8675 atoms. Found 37 (55 requested) and removed 30 (27 requested) atoms. Cycle 25: After refmac, R = 0.1213 (Rfree = 0.000) for 8672 atoms. Found 8 (55 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.74 Search for helices and strands: 0 residues in 0 chains, 8802 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8816 seeds are put forward Round 1: 361 peptides, 75 chains. Longest chain 11 peptides. Score 0.273 Round 2: 368 peptides, 70 chains. Longest chain 13 peptides. Score 0.319 Round 3: 378 peptides, 70 chains. Longest chain 13 peptides. Score 0.335 Round 4: 388 peptides, 70 chains. Longest chain 13 peptides. Score 0.350 Round 5: 385 peptides, 68 chains. Longest chain 12 peptides. Score 0.359 Taking the results from Round 5 Chains 68, Residues 317, Estimated correctness of the model 0.0 % 8 chains (47 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21336 restraints for refining 8730 atoms. 20033 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1551 (Rfree = 0.000) for 8730 atoms. Found 27 (56 requested) and removed 36 (28 requested) atoms. Cycle 27: After refmac, R = 0.1497 (Rfree = 0.000) for 8710 atoms. Found 24 (55 requested) and removed 27 (27 requested) atoms. Cycle 28: After refmac, R = 0.1609 (Rfree = 0.000) for 8698 atoms. Found 35 (55 requested) and removed 36 (27 requested) atoms. Cycle 29: After refmac, R = 0.1557 (Rfree = 0.000) for 8687 atoms. Found 27 (55 requested) and removed 33 (27 requested) atoms. Cycle 30: After refmac, R = 0.1597 (Rfree = 0.000) for 8670 atoms. Found 51 (55 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.73 Search for helices and strands: 0 residues in 0 chains, 8873 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 8891 seeds are put forward Round 1: 302 peptides, 68 chains. Longest chain 7 peptides. Score 0.222 Round 2: 326 peptides, 64 chains. Longest chain 12 peptides. Score 0.292 Round 3: 335 peptides, 65 chains. Longest chain 8 peptides. Score 0.300 Round 4: 349 peptides, 66 chains. Longest chain 12 peptides. Score 0.316 Round 5: 346 peptides, 64 chains. Longest chain 13 peptides. Score 0.325 Taking the results from Round 5 Chains 64, Residues 282, Estimated correctness of the model 0.0 % 5 chains (24 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21763 restraints for refining 8731 atoms. 20649 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1735 (Rfree = 0.000) for 8731 atoms. Found 24 (56 requested) and removed 95 (28 requested) atoms. Cycle 32: After refmac, R = 0.1645 (Rfree = 0.000) for 8639 atoms. Found 47 (55 requested) and removed 32 (27 requested) atoms. Cycle 33: After refmac, R = 0.1245 (Rfree = 0.000) for 8636 atoms. Found 19 (55 requested) and removed 30 (27 requested) atoms. Cycle 34: After refmac, R = 0.1182 (Rfree = 0.000) for 8622 atoms. Found 5 (55 requested) and removed 27 (27 requested) atoms. Cycle 35: After refmac, R = 0.1182 (Rfree = 0.000) for 8598 atoms. Found 8 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.74 Search for helices and strands: 0 residues in 0 chains, 8751 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8766 seeds are put forward Round 1: 347 peptides, 79 chains. Longest chain 9 peptides. Score 0.222 Round 2: 377 peptides, 74 chains. Longest chain 11 peptides. Score 0.306 Round 3: 386 peptides, 74 chains. Longest chain 14 peptides. Score 0.321 Round 4: 399 peptides, 75 chains. Longest chain 12 peptides. Score 0.334 Round 5: 386 peptides, 72 chains. Longest chain 14 peptides. Score 0.334 Taking the results from Round 5 Chains 72, Residues 314, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21498 restraints for refining 8731 atoms. 20289 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1536 (Rfree = 0.000) for 8731 atoms. Found 30 (56 requested) and removed 33 (28 requested) atoms. Cycle 37: After refmac, R = 0.1570 (Rfree = 0.000) for 8707 atoms. Found 45 (55 requested) and removed 32 (27 requested) atoms. Cycle 38: After refmac, R = 0.1229 (Rfree = 0.000) for 8711 atoms. Found 13 (55 requested) and removed 30 (27 requested) atoms. Cycle 39: After refmac, R = 0.1190 (Rfree = 0.000) for 8685 atoms. Found 13 (55 requested) and removed 27 (27 requested) atoms. Cycle 40: After refmac, R = 0.1184 (Rfree = 0.000) for 8667 atoms. Found 11 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 8814 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 8828 seeds are put forward Round 1: 308 peptides, 67 chains. Longest chain 9 peptides. Score 0.240 Round 2: 340 peptides, 66 chains. Longest chain 11 peptides. Score 0.301 Round 3: 327 peptides, 61 chains. Longest chain 13 peptides. Score 0.315 Round 4: 335 peptides, 63 chains. Longest chain 12 peptides. Score 0.314 Round 5: 343 peptides, 61 chains. Longest chain 12 peptides. Score 0.341 Taking the results from Round 5 Chains 61, Residues 282, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21500 restraints for refining 8731 atoms. 20387 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1544 (Rfree = 0.000) for 8731 atoms. Found 38 (56 requested) and removed 29 (28 requested) atoms. Cycle 42: After refmac, R = 0.1478 (Rfree = 0.000) for 8724 atoms. Found 44 (56 requested) and removed 32 (28 requested) atoms. Cycle 43: After refmac, R = 0.1251 (Rfree = 0.000) for 8725 atoms. Found 11 (56 requested) and removed 30 (28 requested) atoms. Cycle 44: After refmac, R = 0.1249 (Rfree = 0.000) for 8698 atoms. Found 14 (55 requested) and removed 29 (27 requested) atoms. Cycle 45: After refmac, R = 0.1247 (Rfree = 0.000) for 8681 atoms. Found 18 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.77 Search for helices and strands: 0 residues in 0 chains, 8813 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 8831 seeds are put forward Round 1: 330 peptides, 72 chains. Longest chain 9 peptides. Score 0.242 Round 2: 348 peptides, 69 chains. Longest chain 12 peptides. Score 0.293 Round 3: 359 peptides, 66 chains. Longest chain 14 peptides. Score 0.332 Round 4: 370 peptides, 68 chains. Longest chain 13 peptides. Score 0.336 Round 5: 370 peptides, 60 chains. Longest chain 15 peptides. Score 0.390 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 310, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 60 chains (310 residues) following loop building 6 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11359 reflections ( 91.15 % complete ) and 21414 restraints for refining 8731 atoms. 20164 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1501 (Rfree = 0.000) for 8731 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.1290 (Rfree = 0.000) for 8682 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1285 (Rfree = 0.000) for 8646 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1246 (Rfree = 0.000) for 8616 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:58:54 GMT 2018 Job finished. TimeTaking 90.75 Used memory is bytes: 15523152