null Sun 23 Dec 23:43:18 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2nlv-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nlv-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nlv-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.2-parrot-mrncs ############### 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 ============================================================ Sun 23 Dec 23:43:23 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/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nlv-3.2-parrot-mrncs/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 155 and 0 Target number of residues in the AU: 155 Target solvent content: 0.6190 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 224 Adjusted target solvent content: 0.45 Input MTZ file: 2nlv-3.2-parrot-mrncs.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: 46.793 37.359 63.476 90.000 97.240 90.000 Input sequence file: 2nlv-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1792 target number of atoms Had to go as low as 0.70 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: 29.104 3.200 Wilson plot Bfac: 60.11 3736 reflections ( 99.84 % complete ) and 0 restraints for refining 1984 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3494 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2914 (Rfree = 0.000) for 1984 atoms. Found 13 (17 requested) and removed 24 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 2009 seeds are put forward NCS extension: 0 residues added, 2009 seeds are put forward Round 1: 93 peptides, 20 chains. Longest chain 12 peptides. Score 0.274 Round 2: 121 peptides, 19 chains. Longest chain 16 peptides. Score 0.504 Round 3: 130 peptides, 20 chains. Longest chain 22 peptides. Score 0.532 Round 4: 121 peptides, 20 chains. Longest chain 14 peptides. Score 0.476 Round 5: 121 peptides, 18 chains. Longest chain 14 peptides. Score 0.531 Taking the results from Round 3 Chains 20, Residues 110, Estimated correctness of the model 21.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3616 restraints for refining 1636 atoms. 3196 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2411 (Rfree = 0.000) for 1636 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. Cycle 2: After refmac, R = 0.2354 (Rfree = 0.000) for 1626 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 3: After refmac, R = 0.2365 (Rfree = 0.000) for 1624 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 4: After refmac, R = 0.2106 (Rfree = 0.000) for 1614 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2246 (Rfree = 0.000) for 1608 atoms. Found 1 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.31 Search for helices and strands: 0 residues in 0 chains, 1667 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 1693 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 7 peptides. Score 0.316 Round 2: 116 peptides, 22 chains. Longest chain 9 peptides. Score 0.385 Round 3: 114 peptides, 21 chains. Longest chain 11 peptides. Score 0.400 Round 4: 117 peptides, 20 chains. Longest chain 12 peptides. Score 0.450 Round 5: 123 peptides, 19 chains. Longest chain 10 peptides. Score 0.516 Taking the results from Round 5 Chains 19, Residues 104, Estimated correctness of the model 16.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3741 restraints for refining 1635 atoms. 3344 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2373 (Rfree = 0.000) for 1635 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 7: After refmac, R = 0.2215 (Rfree = 0.000) for 1624 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 8: After refmac, R = 0.2182 (Rfree = 0.000) for 1617 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 9: After refmac, R = 0.2133 (Rfree = 0.000) for 1610 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 10: After refmac, R = 0.2165 (Rfree = 0.000) for 1604 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 1649 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 1660 seeds are put forward Round 1: 125 peptides, 21 chains. Longest chain 9 peptides. Score 0.475 Round 2: 143 peptides, 22 chains. Longest chain 18 peptides. Score 0.558 Round 3: 132 peptides, 19 chains. Longest chain 26 peptides. Score 0.569 Round 4: 135 peptides, 17 chains. Longest chain 26 peptides. Score 0.632 Round 5: 123 peptides, 17 chains. Longest chain 23 peptides. Score 0.568 Taking the results from Round 4 Chains 18, Residues 118, Estimated correctness of the model 49.4 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3473 restraints for refining 1636 atoms. 2940 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2354 (Rfree = 0.000) for 1636 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 12: After refmac, R = 0.2336 (Rfree = 0.000) for 1626 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 13: After refmac, R = 0.3094 (Rfree = 0.000) for 1614 atoms. Found 13 (14 requested) and removed 17 (7 requested) atoms. Cycle 14: After refmac, R = 0.2283 (Rfree = 0.000) for 1603 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.2709 (Rfree = 0.000) for 1592 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 1655 seeds are put forward NCS extension: 27 residues added (8 deleted due to clashes), 1682 seeds are put forward Round 1: 106 peptides, 19 chains. Longest chain 10 peptides. Score 0.404 Round 2: 129 peptides, 20 chains. Longest chain 13 peptides. Score 0.526 Round 3: 122 peptides, 16 chains. Longest chain 15 peptides. Score 0.587 Round 4: 117 peptides, 17 chains. Longest chain 17 peptides. Score 0.533 Round 5: 106 peptides, 16 chains. Longest chain 13 peptides. Score 0.492 Taking the results from Round 3 Chains 16, Residues 106, Estimated correctness of the model 37.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3643 restraints for refining 1636 atoms. 3235 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2298 (Rfree = 0.000) for 1636 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 17: After refmac, R = 0.2112 (Rfree = 0.000) for 1634 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 18: After refmac, R = 0.2091 (Rfree = 0.000) for 1629 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.2044 (Rfree = 0.000) for 1620 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1914 (Rfree = 0.000) for 1614 atoms. Found 1 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 1650 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1670 seeds are put forward Round 1: 99 peptides, 15 chains. Longest chain 10 peptides. Score 0.474 Round 2: 112 peptides, 18 chains. Longest chain 13 peptides. Score 0.474 Round 3: 122 peptides, 18 chains. Longest chain 12 peptides. Score 0.537 Round 4: 112 peptides, 14 chains. Longest chain 29 peptides. Score 0.582 Round 5: 115 peptides, 16 chains. Longest chain 18 peptides. Score 0.547 Taking the results from Round 4 Chains 14, Residues 98, Estimated correctness of the model 36.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3638 restraints for refining 1636 atoms. 3260 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2117 (Rfree = 0.000) for 1636 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. Cycle 22: After refmac, R = 0.1963 (Rfree = 0.000) for 1633 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.1988 (Rfree = 0.000) for 1628 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.1861 (Rfree = 0.000) for 1624 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1799 (Rfree = 0.000) for 1620 atoms. Found 2 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 1654 seeds are put forward NCS extension: 35 residues added (6 deleted due to clashes), 1689 seeds are put forward Round 1: 114 peptides, 21 chains. Longest chain 9 peptides. Score 0.400 Round 2: 133 peptides, 20 chains. Longest chain 13 peptides. Score 0.550 Round 3: 123 peptides, 20 chains. Longest chain 14 peptides. Score 0.489 Round 4: 125 peptides, 17 chains. Longest chain 13 peptides. Score 0.579 Round 5: 126 peptides, 18 chains. Longest chain 12 peptides. Score 0.560 Taking the results from Round 4 Chains 17, Residues 108, Estimated correctness of the model 35.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3541 restraints for refining 1635 atoms. 3126 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2040 (Rfree = 0.000) for 1635 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.2015 (Rfree = 0.000) for 1636 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 28: After refmac, R = 0.1977 (Rfree = 0.000) for 1630 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.1891 (Rfree = 0.000) for 1627 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1838 (Rfree = 0.000) for 1624 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 1656 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1670 seeds are put forward Round 1: 97 peptides, 20 chains. Longest chain 8 peptides. Score 0.305 Round 2: 116 peptides, 19 chains. Longest chain 10 peptides. Score 0.472 Round 3: 113 peptides, 19 chains. Longest chain 12 peptides. Score 0.452 Round 4: 127 peptides, 21 chains. Longest chain 10 peptides. Score 0.487 Round 5: 106 peptides, 18 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 4 Chains 21, Residues 106, Estimated correctness of the model 7.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3611 restraints for refining 1635 atoms. 3208 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2034 (Rfree = 0.000) for 1635 atoms. Found 11 (14 requested) and removed 8 (7 requested) atoms. Cycle 32: After refmac, R = 0.1904 (Rfree = 0.000) for 1636 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.1888 (Rfree = 0.000) for 1631 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1771 (Rfree = 0.000) for 1625 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1811 (Rfree = 0.000) for 1617 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 1646 seeds are put forward NCS extension: 0 residues added, 1646 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 10 peptides. Score 0.297 Round 2: 90 peptides, 14 chains. Longest chain 17 peptides. Score 0.443 Round 3: 90 peptides, 14 chains. Longest chain 15 peptides. Score 0.443 Round 4: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.368 Round 5: 86 peptides, 15 chains. Longest chain 13 peptides. Score 0.383 Taking the results from Round 3 Chains 14, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3760 restraints for refining 1636 atoms. 3470 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1872 (Rfree = 0.000) for 1636 atoms. Found 12 (14 requested) and removed 7 (7 requested) atoms. Cycle 37: After refmac, R = 0.1830 (Rfree = 0.000) for 1640 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.1788 (Rfree = 0.000) for 1638 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1875 (Rfree = 0.000) for 1630 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1785 (Rfree = 0.000) for 1630 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 1681 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 1698 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 7 peptides. Score 0.281 Round 2: 98 peptides, 16 chains. Longest chain 14 peptides. Score 0.438 Round 3: 99 peptides, 15 chains. Longest chain 14 peptides. Score 0.474 Round 4: 92 peptides, 13 chains. Longest chain 17 peptides. Score 0.487 Round 5: 90 peptides, 14 chains. Longest chain 15 peptides. Score 0.443 Taking the results from Round 4 Chains 13, Residues 79, Estimated correctness of the model 7.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3736 reflections ( 99.84 % complete ) and 3661 restraints for refining 1636 atoms. 3358 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1928 (Rfree = 0.000) for 1636 atoms. Found 8 (14 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.1902 (Rfree = 0.000) for 1634 atoms. Found 9 (14 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.1964 (Rfree = 0.000) for 1635 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1904 (Rfree = 0.000) for 1636 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1826 (Rfree = 0.000) for 1637 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 1670 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 1696 seeds are put forward Round 1: 76 peptides, 13 chains. Longest chain 10 peptides. Score 0.373 Round 2: 82 peptides, 13 chains. Longest chain 10 peptides. Score 0.417 Round 3: 74 peptides, 11 chains. Longest chain 13 peptides. Score 0.424 Round 4: 79 peptides, 12 chains. Longest chain 10 peptides. Score 0.428 Round 5: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.421 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2nlv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3736 reflections ( 99.84 % complete ) and 3734 restraints for refining 1635 atoms. 3478 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1974 (Rfree = 0.000) for 1635 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1957 (Rfree = 0.000) for 1628 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1831 (Rfree = 0.000) for 1621 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1784 (Rfree = 0.000) for 1614 atoms. Found 0 (14 requested) and removed 6 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:09:59 GMT 2018 Job finished. TimeTaking 26.7 Used memory is bytes: 21309984