null Mon 24 Dec 07:27:53 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 2obn-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2obn-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2obn-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-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/2obn-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-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 07:27:58 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/2obn-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-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 907 and 0 Target number of residues in the AU: 907 Target solvent content: 0.6368 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-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: 4 Cell parameters: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 11168 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: 73.214 3.400 Wilson plot Bfac: 70.07 18320 reflections ( 99.66 % complete ) and 0 restraints for refining 12332 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3069 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2522 (Rfree = 0.000) for 12332 atoms. Found 68 (93 requested) and removed 101 (46 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 12539 seeds are put forward NCS extension: 0 residues added, 12539 seeds are put forward Round 1: 531 peptides, 105 chains. Longest chain 12 peptides. Score 0.318 Round 2: 695 peptides, 112 chains. Longest chain 23 peptides. Score 0.475 Round 3: 729 peptides, 103 chains. Longest chain 20 peptides. Score 0.550 Round 4: 737 peptides, 99 chains. Longest chain 19 peptides. Score 0.574 Round 5: 783 peptides, 107 chains. Longest chain 22 peptides. Score 0.583 Taking the results from Round 5 Chains 112, Residues 676, Estimated correctness of the model 23.0 % 18 chains (147 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22079 restraints for refining 10150 atoms. 19057 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2258 (Rfree = 0.000) for 10150 atoms. Found 45 (76 requested) and removed 73 (38 requested) atoms. Cycle 2: After refmac, R = 0.2181 (Rfree = 0.000) for 10009 atoms. Found 41 (76 requested) and removed 56 (38 requested) atoms. Cycle 3: After refmac, R = 0.2017 (Rfree = 0.000) for 9947 atoms. Found 39 (75 requested) and removed 47 (37 requested) atoms. Cycle 4: After refmac, R = 0.1923 (Rfree = 0.000) for 9904 atoms. Found 26 (75 requested) and removed 42 (37 requested) atoms. Cycle 5: After refmac, R = 0.1829 (Rfree = 0.000) for 9860 atoms. Found 27 (74 requested) and removed 39 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.61 Search for helices and strands: 0 residues in 0 chains, 10188 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 10213 seeds are put forward Round 1: 629 peptides, 110 chains. Longest chain 22 peptides. Score 0.411 Round 2: 690 peptides, 103 chains. Longest chain 19 peptides. Score 0.511 Round 3: 725 peptides, 106 chains. Longest chain 21 peptides. Score 0.533 Round 4: 740 peptides, 101 chains. Longest chain 20 peptides. Score 0.568 Round 5: 743 peptides, 99 chains. Longest chain 22 peptides. Score 0.579 Taking the results from Round 5 Chains 105, Residues 644, Estimated correctness of the model 21.7 % 8 chains (64 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23078 restraints for refining 10154 atoms. 20441 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2072 (Rfree = 0.000) for 10154 atoms. Found 58 (76 requested) and removed 58 (38 requested) atoms. Cycle 7: After refmac, R = 0.1950 (Rfree = 0.000) for 10092 atoms. Found 36 (76 requested) and removed 46 (38 requested) atoms. Cycle 8: After refmac, R = 0.1826 (Rfree = 0.000) for 10052 atoms. Found 21 (76 requested) and removed 42 (38 requested) atoms. Cycle 9: After refmac, R = 0.1751 (Rfree = 0.000) for 10012 atoms. Found 19 (75 requested) and removed 43 (37 requested) atoms. Cycle 10: After refmac, R = 0.1696 (Rfree = 0.000) for 9973 atoms. Found 11 (75 requested) and removed 40 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 10286 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 10300 seeds are put forward Round 1: 649 peptides, 117 chains. Longest chain 20 peptides. Score 0.400 Round 2: 700 peptides, 102 chains. Longest chain 17 peptides. Score 0.525 Round 3: 741 peptides, 108 chains. Longest chain 21 peptides. Score 0.540 Round 4: 744 peptides, 109 chains. Longest chain 22 peptides. Score 0.539 Round 5: 744 peptides, 101 chains. Longest chain 20 peptides. Score 0.572 Taking the results from Round 5 Chains 105, Residues 643, Estimated correctness of the model 19.3 % 14 chains (96 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 22525 restraints for refining 10154 atoms. 19788 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2031 (Rfree = 0.000) for 10154 atoms. Found 49 (76 requested) and removed 52 (38 requested) atoms. Cycle 12: After refmac, R = 0.1948 (Rfree = 0.000) for 10110 atoms. Found 34 (76 requested) and removed 46 (38 requested) atoms. Cycle 13: After refmac, R = 0.1833 (Rfree = 0.000) for 10075 atoms. Found 32 (76 requested) and removed 43 (38 requested) atoms. Cycle 14: After refmac, R = 0.1747 (Rfree = 0.000) for 10040 atoms. Found 21 (75 requested) and removed 39 (37 requested) atoms. Cycle 15: After refmac, R = 0.1690 (Rfree = 0.000) for 10008 atoms. Found 18 (75 requested) and removed 38 (37 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 10310 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 10334 seeds are put forward Round 1: 631 peptides, 112 chains. Longest chain 18 peptides. Score 0.404 Round 2: 700 peptides, 106 chains. Longest chain 18 peptides. Score 0.508 Round 3: 730 peptides, 107 chains. Longest chain 22 peptides. Score 0.533 Round 4: 710 peptides, 99 chains. Longest chain 23 peptides. Score 0.548 Round 5: 726 peptides, 107 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 4 Chains 100, Residues 611, Estimated correctness of the model 10.8 % 7 chains (35 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23085 restraints for refining 10154 atoms. 20668 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1902 (Rfree = 0.000) for 10154 atoms. Found 50 (76 requested) and removed 44 (38 requested) atoms. Cycle 17: After refmac, R = 0.1819 (Rfree = 0.000) for 10143 atoms. Found 21 (76 requested) and removed 43 (38 requested) atoms. Cycle 18: After refmac, R = 0.1722 (Rfree = 0.000) for 10101 atoms. Found 25 (76 requested) and removed 41 (38 requested) atoms. Cycle 19: After refmac, R = 0.1671 (Rfree = 0.000) for 10071 atoms. Found 25 (76 requested) and removed 39 (38 requested) atoms. Cycle 20: After refmac, R = 0.1592 (Rfree = 0.000) for 10044 atoms. Found 25 (75 requested) and removed 37 (37 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 10352 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 10372 seeds are put forward Round 1: 593 peptides, 105 chains. Longest chain 16 peptides. Score 0.394 Round 2: 677 peptides, 106 chains. Longest chain 14 peptides. Score 0.484 Round 3: 667 peptides, 96 chains. Longest chain 21 peptides. Score 0.519 Round 4: 669 peptides, 98 chains. Longest chain 24 peptides. Score 0.512 Round 5: 669 peptides, 96 chains. Longest chain 17 peptides. Score 0.521 Taking the results from Round 5 Chains 98, Residues 573, Estimated correctness of the model 0.8 % 6 chains (36 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23580 restraints for refining 10153 atoms. 21286 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1954 (Rfree = 0.000) for 10153 atoms. Found 51 (76 requested) and removed 46 (38 requested) atoms. Cycle 22: After refmac, R = 0.1831 (Rfree = 0.000) for 10131 atoms. Found 33 (76 requested) and removed 41 (38 requested) atoms. Cycle 23: After refmac, R = 0.1705 (Rfree = 0.000) for 10104 atoms. Found 19 (76 requested) and removed 41 (38 requested) atoms. Cycle 24: After refmac, R = 0.1661 (Rfree = 0.000) for 10062 atoms. Found 23 (76 requested) and removed 42 (38 requested) atoms. Cycle 25: After refmac, R = 0.1621 (Rfree = 0.000) for 10033 atoms. Found 23 (75 requested) and removed 40 (37 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 10360 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 10379 seeds are put forward Round 1: 594 peptides, 112 chains. Longest chain 13 peptides. Score 0.360 Round 2: 653 peptides, 110 chains. Longest chain 19 peptides. Score 0.439 Round 3: 636 peptides, 102 chains. Longest chain 20 peptides. Score 0.458 Round 4: 646 peptides, 98 chains. Longest chain 25 peptides. Score 0.488 Round 5: 662 peptides, 104 chains. Longest chain 20 peptides. Score 0.477 Taking the results from Round 4 Chains 102, Residues 548, Estimated correctness of the model 0.0 % 11 chains (71 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23150 restraints for refining 10152 atoms. 20840 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1888 (Rfree = 0.000) for 10152 atoms. Found 50 (76 requested) and removed 48 (38 requested) atoms. Cycle 27: After refmac, R = 0.1751 (Rfree = 0.000) for 10126 atoms. Found 21 (76 requested) and removed 42 (38 requested) atoms. Cycle 28: After refmac, R = 0.1702 (Rfree = 0.000) for 10089 atoms. Found 26 (76 requested) and removed 40 (38 requested) atoms. Cycle 29: After refmac, R = 0.1674 (Rfree = 0.000) for 10062 atoms. Found 31 (76 requested) and removed 40 (38 requested) atoms. Cycle 30: After refmac, R = 0.1603 (Rfree = 0.000) for 10037 atoms. Found 18 (75 requested) and removed 38 (37 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.62 Search for helices and strands: 0 residues in 0 chains, 10321 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 10337 seeds are put forward Round 1: 564 peptides, 111 chains. Longest chain 12 peptides. Score 0.328 Round 2: 619 peptides, 105 chains. Longest chain 14 peptides. Score 0.425 Round 3: 656 peptides, 105 chains. Longest chain 17 peptides. Score 0.466 Round 4: 672 peptides, 113 chains. Longest chain 16 peptides. Score 0.446 Round 5: 644 peptides, 103 chains. Longest chain 20 peptides. Score 0.462 Taking the results from Round 3 Chains 107, Residues 551, Estimated correctness of the model 0.0 % 13 chains (80 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23142 restraints for refining 10154 atoms. 20846 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1853 (Rfree = 0.000) for 10154 atoms. Found 46 (76 requested) and removed 50 (38 requested) atoms. Cycle 32: After refmac, R = 0.1735 (Rfree = 0.000) for 10105 atoms. Found 46 (76 requested) and removed 42 (38 requested) atoms. Cycle 33: After refmac, R = 0.1666 (Rfree = 0.000) for 10093 atoms. Found 30 (76 requested) and removed 42 (38 requested) atoms. Cycle 34: After refmac, R = 0.1586 (Rfree = 0.000) for 10066 atoms. Found 26 (76 requested) and removed 40 (38 requested) atoms. Cycle 35: After refmac, R = 0.1572 (Rfree = 0.000) for 10034 atoms. Found 34 (75 requested) and removed 41 (37 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 10323 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 10348 seeds are put forward Round 1: 464 peptides, 95 chains. Longest chain 10 peptides. Score 0.285 Round 2: 554 peptides, 91 chains. Longest chain 19 peptides. Score 0.419 Round 3: 567 peptides, 100 chains. Longest chain 13 peptides. Score 0.389 Round 4: 561 peptides, 89 chains. Longest chain 15 peptides. Score 0.438 Round 5: 561 peptides, 90 chains. Longest chain 14 peptides. Score 0.433 Taking the results from Round 4 Chains 91, Residues 472, Estimated correctness of the model 0.0 % 5 chains (40 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23891 restraints for refining 10153 atoms. 21974 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1728 (Rfree = 0.000) for 10153 atoms. Found 53 (76 requested) and removed 43 (38 requested) atoms. Cycle 37: After refmac, R = 0.1598 (Rfree = 0.000) for 10134 atoms. Found 30 (76 requested) and removed 42 (38 requested) atoms. Cycle 38: After refmac, R = 0.1560 (Rfree = 0.000) for 10100 atoms. Found 44 (76 requested) and removed 40 (38 requested) atoms. Cycle 39: After refmac, R = 0.1471 (Rfree = 0.000) for 10093 atoms. Found 23 (76 requested) and removed 39 (38 requested) atoms. Cycle 40: After refmac, R = 0.1474 (Rfree = 0.000) for 10067 atoms. Found 39 (76 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.59 Search for helices and strands: 0 residues in 0 chains, 10332 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 10351 seeds are put forward Round 1: 439 peptides, 95 chains. Longest chain 8 peptides. Score 0.251 Round 2: 495 peptides, 86 chains. Longest chain 13 peptides. Score 0.375 Round 3: 532 peptides, 92 chains. Longest chain 14 peptides. Score 0.388 Round 4: 540 peptides, 83 chains. Longest chain 19 peptides. Score 0.444 Round 5: 558 peptides, 88 chains. Longest chain 16 peptides. Score 0.439 Taking the results from Round 4 Chains 85, Residues 457, Estimated correctness of the model 0.0 % 8 chains (63 residues) have been docked in sequence ------------------------------------------------------ 18320 reflections ( 99.66 % complete ) and 23387 restraints for refining 10154 atoms. 21408 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1681 (Rfree = 0.000) for 10154 atoms. Found 54 (76 requested) and removed 43 (38 requested) atoms. Cycle 42: After refmac, R = 0.1624 (Rfree = 0.000) for 10142 atoms. Found 35 (76 requested) and removed 42 (38 requested) atoms. Cycle 43: After refmac, R = 0.1492 (Rfree = 0.000) for 10120 atoms. Found 22 (76 requested) and removed 39 (38 requested) atoms. Cycle 44: After refmac, R = 0.1474 (Rfree = 0.000) for 10088 atoms. Found 24 (76 requested) and removed 41 (38 requested) atoms. Cycle 45: After refmac, R = 0.1426 (Rfree = 0.000) for 10062 atoms. Found 24 (76 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.60 Search for helices and strands: 0 residues in 0 chains, 10319 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 10351 seeds are put forward Round 1: 428 peptides, 88 chains. Longest chain 12 peptides. Score 0.276 Round 2: 499 peptides, 90 chains. Longest chain 14 peptides. Score 0.358 Round 3: 480 peptides, 80 chains. Longest chain 13 peptides. Score 0.388 Round 4: 484 peptides, 80 chains. Longest chain 14 peptides. Score 0.393 Round 5: 482 peptides, 81 chains. Longest chain 15 peptides. Score 0.385 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 404, Estimated correctness of the model 0.0 % 5 chains (20 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 80 chains (404 residues) following loop building 5 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18320 reflections ( 99.66 % complete ) and 24813 restraints for refining 10154 atoms. 23248 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1609 (Rfree = 0.000) for 10154 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 47: After refmac, R = 0.1589 (Rfree = 0.000) for 10100 atoms. Found 0 (76 requested) and removed 38 (38 requested) atoms. Cycle 48: After refmac, R = 0.1568 (Rfree = 0.000) for 10052 atoms. Found 0 (75 requested) and removed 37 (37 requested) atoms. Cycle 49: After refmac, R = 0.1536 (Rfree = 0.000) for 10006 atoms. Found 0 (75 requested) and removed 37 (37 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:11:59 GMT 2018 Job finished. TimeTaking 104.1 Used memory is bytes: 22366800