null Mon 24 Dec 07:41:24 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-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2obn-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2obn-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.2-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-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.2-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 07:41:29 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/2obn-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2obn-3.2-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 948 and 0 Target number of residues in the AU: 948 Target solvent content: 0.6204 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 61.60 21957 reflections ( 99.70 % complete ) and 0 restraints for refining 12468 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3045 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2351 (Rfree = 0.000) for 12468 atoms. Found 60 (111 requested) and removed 116 (55 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 12684 seeds are put forward NCS extension: 0 residues added, 12684 seeds are put forward Round 1: 605 peptides, 112 chains. Longest chain 16 peptides. Score 0.373 Round 2: 755 peptides, 113 chains. Longest chain 27 peptides. Score 0.532 Round 3: 821 peptides, 116 chains. Longest chain 32 peptides. Score 0.582 Round 4: 848 peptides, 107 chains. Longest chain 26 peptides. Score 0.638 Round 5: 855 peptides, 113 chains. Longest chain 22 peptides. Score 0.622 Taking the results from Round 4 Chains 117, Residues 741, Estimated correctness of the model 50.9 % 14 chains (94 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22184 restraints for refining 10193 atoms. 19085 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2342 (Rfree = 0.000) for 10193 atoms. Found 66 (91 requested) and removed 71 (45 requested) atoms. Cycle 2: After refmac, R = 0.2184 (Rfree = 0.000) for 10081 atoms. Found 35 (91 requested) and removed 53 (45 requested) atoms. Cycle 3: After refmac, R = 0.2121 (Rfree = 0.000) for 10005 atoms. Found 26 (90 requested) and removed 48 (45 requested) atoms. Cycle 4: After refmac, R = 0.2082 (Rfree = 0.000) for 9944 atoms. Found 39 (89 requested) and removed 50 (44 requested) atoms. Cycle 5: After refmac, R = 0.2014 (Rfree = 0.000) for 9910 atoms. Found 23 (89 requested) and removed 49 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 10201 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 10218 seeds are put forward Round 1: 768 peptides, 117 chains. Longest chain 21 peptides. Score 0.528 Round 2: 849 peptides, 113 chains. Longest chain 26 peptides. Score 0.617 Round 3: 859 peptides, 112 chains. Longest chain 27 peptides. Score 0.629 Round 4: 852 peptides, 106 chains. Longest chain 24 peptides. Score 0.645 Round 5: 877 peptides, 102 chains. Longest chain 28 peptides. Score 0.678 Taking the results from Round 5 Chains 111, Residues 775, Estimated correctness of the model 60.4 % 14 chains (125 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 21685 restraints for refining 10195 atoms. 18315 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2291 (Rfree = 0.000) for 10195 atoms. Found 68 (91 requested) and removed 83 (45 requested) atoms. Cycle 7: After refmac, R = 0.2126 (Rfree = 0.000) for 10130 atoms. Found 32 (91 requested) and removed 56 (45 requested) atoms. Cycle 8: After refmac, R = 0.2075 (Rfree = 0.000) for 10054 atoms. Found 34 (90 requested) and removed 51 (45 requested) atoms. Cycle 9: After refmac, R = 0.2015 (Rfree = 0.000) for 10009 atoms. Found 31 (90 requested) and removed 48 (45 requested) atoms. Cycle 10: After refmac, R = 0.1959 (Rfree = 0.000) for 9964 atoms. Found 25 (89 requested) and removed 47 (44 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 10248 seeds are put forward NCS extension: 29 residues added (10 deleted due to clashes), 10277 seeds are put forward Round 1: 750 peptides, 116 chains. Longest chain 21 peptides. Score 0.514 Round 2: 820 peptides, 111 chains. Longest chain 21 peptides. Score 0.600 Round 3: 858 peptides, 110 chains. Longest chain 21 peptides. Score 0.636 Round 4: 871 peptides, 106 chains. Longest chain 27 peptides. Score 0.660 Round 5: 852 peptides, 105 chains. Longest chain 29 peptides. Score 0.649 Taking the results from Round 4 Chains 112, Residues 765, Estimated correctness of the model 56.2 % 14 chains (153 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 21411 restraints for refining 10195 atoms. 17966 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2400 (Rfree = 0.000) for 10195 atoms. Found 86 (91 requested) and removed 79 (45 requested) atoms. Cycle 12: After refmac, R = 0.2128 (Rfree = 0.000) for 10185 atoms. Found 32 (91 requested) and removed 48 (45 requested) atoms. Cycle 13: After refmac, R = 0.2037 (Rfree = 0.000) for 10148 atoms. Found 25 (91 requested) and removed 45 (45 requested) atoms. Cycle 14: After refmac, R = 0.1985 (Rfree = 0.000) for 10116 atoms. Found 14 (90 requested) and removed 45 (45 requested) atoms. Cycle 15: After refmac, R = 0.1939 (Rfree = 0.000) for 10070 atoms. Found 16 (90 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.45 Search for helices and strands: 0 residues in 0 chains, 10330 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 10348 seeds are put forward Round 1: 708 peptides, 111 chains. Longest chain 18 peptides. Score 0.493 Round 2: 800 peptides, 105 chains. Longest chain 27 peptides. Score 0.606 Round 3: 822 peptides, 106 chains. Longest chain 27 peptides. Score 0.621 Round 4: 807 peptides, 101 chains. Longest chain 27 peptides. Score 0.627 Round 5: 828 peptides, 105 chains. Longest chain 24 peptides. Score 0.630 Taking the results from Round 5 Chains 112, Residues 723, Estimated correctness of the model 48.9 % 12 chains (109 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22002 restraints for refining 10196 atoms. 18873 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2293 (Rfree = 0.000) for 10196 atoms. Found 74 (91 requested) and removed 70 (45 requested) atoms. Cycle 17: After refmac, R = 0.2008 (Rfree = 0.000) for 10172 atoms. Found 35 (91 requested) and removed 49 (45 requested) atoms. Cycle 18: After refmac, R = 0.1923 (Rfree = 0.000) for 10143 atoms. Found 21 (91 requested) and removed 45 (45 requested) atoms. Cycle 19: After refmac, R = 0.1894 (Rfree = 0.000) for 10110 atoms. Found 15 (90 requested) and removed 45 (45 requested) atoms. Cycle 20: After refmac, R = 0.1860 (Rfree = 0.000) for 10069 atoms. Found 22 (90 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 10372 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 10392 seeds are put forward Round 1: 719 peptides, 119 chains. Longest chain 17 peptides. Score 0.469 Round 2: 791 peptides, 115 chains. Longest chain 20 peptides. Score 0.558 Round 3: 796 peptides, 112 chains. Longest chain 20 peptides. Score 0.575 Round 4: 775 peptides, 104 chains. Longest chain 24 peptides. Score 0.588 Round 5: 794 peptides, 109 chains. Longest chain 27 peptides. Score 0.585 Taking the results from Round 4 Chains 106, Residues 671, Estimated correctness of the model 37.8 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 23198 restraints for refining 10196 atoms. 20510 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2148 (Rfree = 0.000) for 10196 atoms. Found 49 (91 requested) and removed 54 (45 requested) atoms. Cycle 22: After refmac, R = 0.2017 (Rfree = 0.000) for 10168 atoms. Found 28 (91 requested) and removed 51 (45 requested) atoms. Cycle 23: After refmac, R = 0.1921 (Rfree = 0.000) for 10136 atoms. Found 23 (91 requested) and removed 47 (45 requested) atoms. Cycle 24: After refmac, R = 0.1836 (Rfree = 0.000) for 10108 atoms. Found 18 (90 requested) and removed 45 (45 requested) atoms. Cycle 25: After refmac, R = 0.1798 (Rfree = 0.000) for 10073 atoms. Found 20 (90 requested) and removed 46 (45 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 10343 seeds are put forward NCS extension: 36 residues added (7 deleted due to clashes), 10379 seeds are put forward Round 1: 666 peptides, 114 chains. Longest chain 13 peptides. Score 0.434 Round 2: 752 peptides, 106 chains. Longest chain 24 peptides. Score 0.559 Round 3: 747 peptides, 101 chains. Longest chain 20 peptides. Score 0.575 Round 4: 749 peptides, 104 chains. Longest chain 20 peptides. Score 0.564 Round 5: 761 peptides, 104 chains. Longest chain 20 peptides. Score 0.575 Taking the results from Round 5 Chains 108, Residues 657, Estimated correctness of the model 34.1 % 8 chains (70 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 22665 restraints for refining 10196 atoms. 19903 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2158 (Rfree = 0.000) for 10196 atoms. Found 68 (91 requested) and removed 57 (45 requested) atoms. Cycle 27: After refmac, R = 0.1985 (Rfree = 0.000) for 10189 atoms. Found 17 (91 requested) and removed 47 (45 requested) atoms. Cycle 28: After refmac, R = 0.1941 (Rfree = 0.000) for 10144 atoms. Found 16 (91 requested) and removed 45 (45 requested) atoms. Cycle 29: After refmac, R = 0.1909 (Rfree = 0.000) for 10108 atoms. Found 11 (90 requested) and removed 45 (45 requested) atoms. Cycle 30: After refmac, R = 0.1861 (Rfree = 0.000) for 10072 atoms. Found 12 (90 requested) and removed 46 (45 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.45 Search for helices and strands: 0 residues in 0 chains, 10335 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 10356 seeds are put forward Round 1: 607 peptides, 109 chains. Longest chain 16 peptides. Score 0.391 Round 2: 691 peptides, 99 chains. Longest chain 35 peptides. Score 0.530 Round 3: 687 peptides, 99 chains. Longest chain 22 peptides. Score 0.526 Round 4: 699 peptides, 98 chains. Longest chain 20 peptides. Score 0.542 Round 5: 711 peptides, 99 chains. Longest chain 24 peptides. Score 0.549 Taking the results from Round 5 Chains 104, Residues 612, Estimated correctness of the model 26.6 % 8 chains (64 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 23060 restraints for refining 10195 atoms. 20517 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2067 (Rfree = 0.000) for 10195 atoms. Found 53 (91 requested) and removed 60 (45 requested) atoms. Cycle 32: After refmac, R = 0.1958 (Rfree = 0.000) for 10161 atoms. Found 35 (91 requested) and removed 49 (45 requested) atoms. Cycle 33: After refmac, R = 0.1900 (Rfree = 0.000) for 10135 atoms. Found 19 (91 requested) and removed 46 (45 requested) atoms. Cycle 34: After refmac, R = 0.1870 (Rfree = 0.000) for 10100 atoms. Found 20 (90 requested) and removed 46 (45 requested) atoms. Cycle 35: After refmac, R = 0.1838 (Rfree = 0.000) for 10067 atoms. Found 18 (90 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 10282 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 10301 seeds are put forward Round 1: 592 peptides, 108 chains. Longest chain 15 peptides. Score 0.378 Round 2: 632 peptides, 92 chains. Longest chain 30 peptides. Score 0.501 Round 3: 630 peptides, 94 chains. Longest chain 18 peptides. Score 0.490 Round 4: 673 peptides, 97 chains. Longest chain 20 peptides. Score 0.520 Round 5: 645 peptides, 93 chains. Longest chain 20 peptides. Score 0.510 Taking the results from Round 4 Chains 98, Residues 576, Estimated correctness of the model 17.7 % 7 chains (36 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 23369 restraints for refining 10195 atoms. 21071 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1996 (Rfree = 0.000) for 10195 atoms. Found 57 (91 requested) and removed 51 (45 requested) atoms. Cycle 37: After refmac, R = 0.1920 (Rfree = 0.000) for 10192 atoms. Found 25 (91 requested) and removed 45 (45 requested) atoms. Cycle 38: After refmac, R = 0.1880 (Rfree = 0.000) for 10160 atoms. Found 26 (91 requested) and removed 45 (45 requested) atoms. Cycle 39: After refmac, R = 0.1873 (Rfree = 0.000) for 10138 atoms. Found 18 (91 requested) and removed 46 (45 requested) atoms. Cycle 40: After refmac, R = 0.1856 (Rfree = 0.000) for 10108 atoms. Found 17 (90 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.45 Search for helices and strands: 0 residues in 0 chains, 10416 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 10443 seeds are put forward Round 1: 562 peptides, 107 chains. Longest chain 18 peptides. Score 0.346 Round 2: 604 peptides, 100 chains. Longest chain 14 peptides. Score 0.432 Round 3: 634 peptides, 99 chains. Longest chain 19 peptides. Score 0.470 Round 4: 616 peptides, 98 chains. Longest chain 19 peptides. Score 0.455 Round 5: 583 peptides, 92 chains. Longest chain 16 peptides. Score 0.448 Taking the results from Round 3 Chains 99, Residues 535, Estimated correctness of the model 1.4 % 9 chains (42 residues) have been docked in sequence ------------------------------------------------------ 21957 reflections ( 99.70 % complete ) and 23526 restraints for refining 10195 atoms. 21395 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1907 (Rfree = 0.000) for 10195 atoms. Found 52 (91 requested) and removed 48 (45 requested) atoms. Cycle 42: After refmac, R = 0.1892 (Rfree = 0.000) for 10176 atoms. Found 34 (91 requested) and removed 47 (45 requested) atoms. Cycle 43: After refmac, R = 0.1752 (Rfree = 0.000) for 10156 atoms. Found 18 (91 requested) and removed 45 (45 requested) atoms. Cycle 44: After refmac, R = 0.1845 (Rfree = 0.000) for 10127 atoms. Found 64 (90 requested) and removed 47 (45 requested) atoms. Cycle 45: After refmac, R = 0.1797 (Rfree = 0.000) for 10130 atoms. Found 29 (91 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 10413 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 10439 seeds are put forward Round 1: 505 peptides, 98 chains. Longest chain 15 peptides. Score 0.323 Round 2: 576 peptides, 98 chains. Longest chain 13 peptides. Score 0.410 Round 3: 591 peptides, 90 chains. Longest chain 15 peptides. Score 0.466 Round 4: 564 peptides, 87 chains. Longest chain 15 peptides. Score 0.451 Round 5: 565 peptides, 89 chains. Longest chain 16 peptides. Score 0.442 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 91, Residues 501, Estimated correctness of the model 0.0 % 9 chains (49 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2obn-3_warpNtrace.pdb as input Building loops using Loopy2018 91 chains (501 residues) following loop building 9 chains (49 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21957 reflections ( 99.70 % complete ) and 23683 restraints for refining 10196 atoms. 21653 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1826 (Rfree = 0.000) for 10196 atoms. Found 0 (91 requested) and removed 39 (45 requested) atoms. Cycle 47: After refmac, R = 0.1822 (Rfree = 0.000) for 10151 atoms. Found 0 (91 requested) and removed 11 (45 requested) atoms. Cycle 48: After refmac, R = 0.1794 (Rfree = 0.000) for 10135 atoms. Found 0 (91 requested) and removed 19 (45 requested) atoms. Cycle 49: After refmac, R = 0.1778 (Rfree = 0.000) for 10113 atoms. Found 0 (90 requested) and removed 17 (45 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:20:53 GMT 2018 Job finished. TimeTaking 99.48 Used memory is bytes: 9785008