Mon 24 Dec 00:15:40 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 2ifx-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.6-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/2ifx-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.6-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 ============================================================ Mon 24 Dec 00:15:44 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/2ifx-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.6-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 172 and 0 Target number of residues in the AU: 172 Target solvent content: 0.6494 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.54 Input MTZ file: 2ifx-3.6-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: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.65 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: 28.919 3.601 Wilson plot Bfac: 77.07 2994 reflections ( 98.75 % complete ) and 0 restraints for refining 2019 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3195 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3175 (Rfree = 0.000) for 2019 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 2044 seeds are put forward NCS extension: 0 residues added, 2044 seeds are put forward Round 1: 102 peptides, 18 chains. Longest chain 10 peptides. Score 0.374 Round 2: 125 peptides, 17 chains. Longest chain 14 peptides. Score 0.530 Round 3: 130 peptides, 19 chains. Longest chain 15 peptides. Score 0.510 Round 4: 122 peptides, 14 chains. Longest chain 16 peptides. Score 0.583 Round 5: 138 peptides, 17 chains. Longest chain 14 peptides. Score 0.593 Taking the results from Round 5 Chains 17, Residues 121, Estimated correctness of the model 11.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3701 restraints for refining 1653 atoms. 3234 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2773 (Rfree = 0.000) for 1653 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 2: After refmac, R = 0.2417 (Rfree = 0.000) for 1612 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 3: After refmac, R = 0.2308 (Rfree = 0.000) for 1593 atoms. Found 6 (10 requested) and removed 11 (5 requested) atoms. Cycle 4: After refmac, R = 0.2239 (Rfree = 0.000) for 1581 atoms. Found 3 (10 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.2174 (Rfree = 0.000) for 1573 atoms. Found 1 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 1614 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1630 seeds are put forward Round 1: 119 peptides, 19 chains. Longest chain 12 peptides. Score 0.450 Round 2: 123 peptides, 19 chains. Longest chain 15 peptides. Score 0.472 Round 3: 126 peptides, 19 chains. Longest chain 14 peptides. Score 0.489 Round 4: 136 peptides, 17 chains. Longest chain 18 peptides. Score 0.584 Round 5: 127 peptides, 15 chains. Longest chain 19 peptides. Score 0.585 Taking the results from Round 5 Chains 15, Residues 112, Estimated correctness of the model 8.6 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3691 restraints for refining 1651 atoms. 3238 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2365 (Rfree = 0.000) for 1651 atoms. Found 9 (10 requested) and removed 21 (5 requested) atoms. Cycle 7: After refmac, R = 0.2162 (Rfree = 0.000) for 1626 atoms. Found 5 (10 requested) and removed 11 (5 requested) atoms. Cycle 8: After refmac, R = 0.2172 (Rfree = 0.000) for 1618 atoms. Found 4 (10 requested) and removed 20 (5 requested) atoms. Cycle 9: After refmac, R = 0.2149 (Rfree = 0.000) for 1599 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 10: After refmac, R = 0.1910 (Rfree = 0.000) for 1597 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 1660 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1673 seeds are put forward Round 1: 110 peptides, 20 chains. Longest chain 9 peptides. Score 0.371 Round 2: 121 peptides, 16 chains. Longest chain 16 peptides. Score 0.533 Round 3: 128 peptides, 15 chains. Longest chain 15 peptides. Score 0.589 Round 4: 125 peptides, 17 chains. Longest chain 16 peptides. Score 0.530 Round 5: 126 peptides, 16 chains. Longest chain 15 peptides. Score 0.558 Taking the results from Round 3 Chains 15, Residues 113, Estimated correctness of the model 10.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3595 restraints for refining 1618 atoms. 3158 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2126 (Rfree = 0.000) for 1618 atoms. Found 6 (10 requested) and removed 15 (5 requested) atoms. Cycle 12: After refmac, R = 0.2147 (Rfree = 0.000) for 1601 atoms. Found 4 (10 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2043 (Rfree = 0.000) for 1589 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2691 (Rfree = 0.000) for 1588 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 15: After refmac, R = 0.2206 (Rfree = 0.000) for 1573 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 1622 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1635 seeds are put forward Round 1: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.357 Round 2: 116 peptides, 15 chains. Longest chain 14 peptides. Score 0.530 Round 3: 129 peptides, 19 chains. Longest chain 12 peptides. Score 0.505 Round 4: 115 peptides, 16 chains. Longest chain 13 peptides. Score 0.501 Round 5: 120 peptides, 16 chains. Longest chain 12 peptides. Score 0.528 Taking the results from Round 2 Chains 15, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3550 restraints for refining 1576 atoms. 3161 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2110 (Rfree = 0.000) for 1576 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 17: After refmac, R = 0.1985 (Rfree = 0.000) for 1570 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.2074 (Rfree = 0.000) for 1563 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.1567 (Rfree = 0.000) for 1557 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.1511 (Rfree = 0.000) for 1547 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 1598 seeds are put forward NCS extension: 0 residues added, 1598 seeds are put forward Round 1: 104 peptides, 19 chains. Longest chain 11 peptides. Score 0.360 Round 2: 123 peptides, 15 chains. Longest chain 18 peptides. Score 0.565 Round 3: 122 peptides, 15 chains. Longest chain 24 peptides. Score 0.560 Round 4: 116 peptides, 15 chains. Longest chain 18 peptides. Score 0.530 Round 5: 124 peptides, 12 chains. Longest chain 26 peptides. Score 0.634 Taking the results from Round 5 Chains 12, Residues 112, Estimated correctness of the model 27.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3521 restraints for refining 1614 atoms. 3085 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2080 (Rfree = 0.000) for 1614 atoms. Found 9 (10 requested) and removed 13 (5 requested) atoms. Cycle 22: After refmac, R = 0.2197 (Rfree = 0.000) for 1605 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 23: After refmac, R = 0.1955 (Rfree = 0.000) for 1596 atoms. Found 8 (10 requested) and removed 14 (5 requested) atoms. Cycle 24: After refmac, R = 0.1908 (Rfree = 0.000) for 1588 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1835 (Rfree = 0.000) for 1590 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 1647 seeds are put forward NCS extension: 0 residues added, 1647 seeds are put forward Round 1: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.360 Round 2: 121 peptides, 16 chains. Longest chain 13 peptides. Score 0.533 Round 3: 116 peptides, 14 chains. Longest chain 16 peptides. Score 0.553 Round 4: 121 peptides, 14 chains. Longest chain 23 peptides. Score 0.578 Round 5: 121 peptides, 14 chains. Longest chain 24 peptides. Score 0.578 Taking the results from Round 5 Chains 14, Residues 107, Estimated correctness of the model 5.8 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3683 restraints for refining 1654 atoms. 3250 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1955 (Rfree = 0.000) for 1654 atoms. Found 7 (10 requested) and removed 14 (5 requested) atoms. Cycle 27: After refmac, R = 0.1944 (Rfree = 0.000) for 1641 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 28: After refmac, R = 0.2033 (Rfree = 0.000) for 1636 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.1974 (Rfree = 0.000) for 1637 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.2070 (Rfree = 0.000) for 1634 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 1692 seeds are put forward NCS extension: 41 residues added (1 deleted due to clashes), 1733 seeds are put forward Round 1: 115 peptides, 23 chains. Longest chain 10 peptides. Score 0.323 Round 2: 115 peptides, 18 chains. Longest chain 12 peptides. Score 0.452 Round 3: 124 peptides, 19 chains. Longest chain 12 peptides. Score 0.478 Round 4: 125 peptides, 20 chains. Longest chain 13 peptides. Score 0.459 Round 5: 126 peptides, 18 chains. Longest chain 13 peptides. Score 0.512 Taking the results from Round 5 Chains 18, Residues 108, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3654 restraints for refining 1652 atoms. 3225 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2169 (Rfree = 0.000) for 1652 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. Cycle 32: After refmac, R = 0.2233 (Rfree = 0.000) for 1646 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 33: After refmac, R = 0.1920 (Rfree = 0.000) for 1634 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.1919 (Rfree = 0.000) for 1631 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 35: After refmac, R = 0.1725 (Rfree = 0.000) for 1627 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 1700 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1714 seeds are put forward Round 1: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.347 Round 2: 102 peptides, 16 chains. Longest chain 14 peptides. Score 0.428 Round 3: 106 peptides, 17 chains. Longest chain 14 peptides. Score 0.425 Round 4: 110 peptides, 15 chains. Longest chain 19 peptides. Score 0.498 Round 5: 103 peptides, 15 chains. Longest chain 19 peptides. Score 0.459 Taking the results from Round 4 Chains 15, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3643 restraints for refining 1652 atoms. 3278 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2032 (Rfree = 0.000) for 1652 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 37: After refmac, R = 0.2012 (Rfree = 0.000) for 1644 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 38: After refmac, R = 0.1989 (Rfree = 0.000) for 1636 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.1989 (Rfree = 0.000) for 1635 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 40: After refmac, R = 0.1715 (Rfree = 0.000) for 1629 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1677 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 1700 seeds are put forward Round 1: 82 peptides, 16 chains. Longest chain 13 peptides. Score 0.300 Round 2: 97 peptides, 16 chains. Longest chain 13 peptides. Score 0.397 Round 3: 103 peptides, 15 chains. Longest chain 14 peptides. Score 0.459 Round 4: 101 peptides, 15 chains. Longest chain 15 peptides. Score 0.448 Round 5: 104 peptides, 18 chains. Longest chain 9 peptides. Score 0.387 Taking the results from Round 3 Chains 15, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3780 restraints for refining 1654 atoms. 3443 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1858 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 42: After refmac, R = 0.1797 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.1839 (Rfree = 0.000) for 1652 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.1997 (Rfree = 0.000) for 1653 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.1717 (Rfree = 0.000) for 1652 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 1692 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1713 seeds are put forward Round 1: 80 peptides, 15 chains. Longest chain 10 peptides. Score 0.315 Round 2: 92 peptides, 15 chains. Longest chain 10 peptides. Score 0.394 Round 3: 95 peptides, 16 chains. Longest chain 11 peptides. Score 0.385 Round 4: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.353 Round 5: 97 peptides, 15 chains. Longest chain 11 peptides. Score 0.424 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 82, 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 2ifx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2994 reflections ( 98.75 % complete ) and 3773 restraints for refining 1654 atoms. 3460 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1881 (Rfree = 0.000) for 1654 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2026 (Rfree = 0.000) for 1648 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1821 (Rfree = 0.000) for 1641 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1980 (Rfree = 0.000) for 1634 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 24.03