Sun 23 Dec 23:49:31 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-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 23:49:36 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-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 168 and 0 Target number of residues in the AU: 168 Target solvent content: 0.6575 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-4.0-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-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1824 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: 28.919 4.001 Wilson plot Bfac: 82.96 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2192 reflections ( 98.43 % complete ) and 0 restraints for refining 2016 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3188 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2689 (Rfree = 0.000) for 2016 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.56 Search for helices and strands: 0 residues in 0 chains, 2052 seeds are put forward NCS extension: 0 residues added, 2052 seeds are put forward Round 1: 94 peptides, 17 chains. Longest chain 12 peptides. Score 0.351 Round 2: 112 peptides, 15 chains. Longest chain 14 peptides. Score 0.509 Round 3: 115 peptides, 13 chains. Longest chain 21 peptides. Score 0.571 Round 4: 124 peptides, 14 chains. Longest chain 22 peptides. Score 0.592 Round 5: 112 peptides, 11 chains. Longest chain 20 peptides. Score 0.602 Taking the results from Round 5 Chains 11, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3850 restraints for refining 1646 atoms. 3457 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2453 (Rfree = 0.000) for 1646 atoms. Found 4 (7 requested) and removed 10 (3 requested) atoms. Cycle 2: After refmac, R = 0.2131 (Rfree = 0.000) for 1625 atoms. Found 0 (7 requested) and removed 9 (3 requested) atoms. Cycle 3: After refmac, R = 0.2249 (Rfree = 0.000) for 1611 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 4: After refmac, R = 0.2140 (Rfree = 0.000) for 1602 atoms. Found 1 (7 requested) and removed 9 (3 requested) atoms. Cycle 5: After refmac, R = 0.2004 (Rfree = 0.000) for 1590 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 1655 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1682 seeds are put forward Round 1: 93 peptides, 17 chains. Longest chain 9 peptides. Score 0.345 Round 2: 106 peptides, 14 chains. Longest chain 15 peptides. Score 0.501 Round 3: 109 peptides, 15 chains. Longest chain 15 peptides. Score 0.493 Round 4: 109 peptides, 15 chains. Longest chain 15 peptides. Score 0.493 Round 5: 97 peptides, 16 chains. Longest chain 13 peptides. Score 0.397 Taking the results from Round 2 Chains 15, Residues 92, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3737 restraints for refining 1647 atoms. 3328 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2166 (Rfree = 0.000) for 1647 atoms. Found 2 (7 requested) and removed 15 (3 requested) atoms. Cycle 7: After refmac, R = 0.2049 (Rfree = 0.000) for 1618 atoms. Found 0 (7 requested) and removed 10 (3 requested) atoms. Cycle 8: After refmac, R = 0.1946 (Rfree = 0.000) for 1598 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.1925 (Rfree = 0.000) for 1584 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.1859 (Rfree = 0.000) for 1577 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 1622 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 1639 seeds are put forward Round 1: 94 peptides, 16 chains. Longest chain 13 peptides. Score 0.379 Round 2: 109 peptides, 17 chains. Longest chain 13 peptides. Score 0.443 Round 3: 107 peptides, 14 chains. Longest chain 12 peptides. Score 0.507 Round 4: 110 peptides, 12 chains. Longest chain 15 peptides. Score 0.570 Round 5: 111 peptides, 16 chains. Longest chain 16 peptides. Score 0.479 Taking the results from Round 4 Chains 14, Residues 98, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3490 restraints for refining 1647 atoms. 3047 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1985 (Rfree = 0.000) for 1647 atoms. Found 3 (7 requested) and removed 19 (3 requested) atoms. Cycle 12: After refmac, R = 0.1858 (Rfree = 0.000) for 1620 atoms. Found 2 (7 requested) and removed 8 (3 requested) atoms. Cycle 13: After refmac, R = 0.1908 (Rfree = 0.000) for 1609 atoms. Found 2 (7 requested) and removed 13 (3 requested) atoms. Cycle 14: After refmac, R = 0.1781 (Rfree = 0.000) for 1592 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 15: After refmac, R = 0.2010 (Rfree = 0.000) for 1582 atoms. Found 2 (7 requested) and removed 15 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 1620 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1638 seeds are put forward Round 1: 83 peptides, 15 chains. Longest chain 9 peptides. Score 0.336 Round 2: 109 peptides, 15 chains. Longest chain 13 peptides. Score 0.493 Round 3: 105 peptides, 13 chains. Longest chain 19 peptides. Score 0.521 Round 4: 106 peptides, 16 chains. Longest chain 12 peptides. Score 0.451 Round 5: 112 peptides, 16 chains. Longest chain 17 peptides. Score 0.485 Taking the results from Round 3 Chains 13, Residues 92, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3681 restraints for refining 1647 atoms. 3307 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2086 (Rfree = 0.000) for 1647 atoms. Found 2 (7 requested) and removed 12 (3 requested) atoms. Cycle 17: After refmac, R = 0.1867 (Rfree = 0.000) for 1627 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.1800 (Rfree = 0.000) for 1617 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.1671 (Rfree = 0.000) for 1609 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.1663 (Rfree = 0.000) for 1604 atoms. Found 1 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.56 Search for helices and strands: 0 residues in 0 chains, 1645 seeds are put forward NCS extension: 40 residues added (1 deleted due to clashes), 1685 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 9 peptides. Score 0.307 Round 2: 114 peptides, 17 chains. Longest chain 13 peptides. Score 0.471 Round 3: 104 peptides, 13 chains. Longest chain 26 peptides. Score 0.515 Round 4: 107 peptides, 15 chains. Longest chain 16 peptides. Score 0.482 Round 5: 109 peptides, 17 chains. Longest chain 11 peptides. Score 0.443 Taking the results from Round 3 Chains 13, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3731 restraints for refining 1644 atoms. 3380 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1955 (Rfree = 0.000) for 1644 atoms. Found 1 (7 requested) and removed 15 (3 requested) atoms. Cycle 22: After refmac, R = 0.1774 (Rfree = 0.000) for 1619 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 23: After refmac, R = 0.1720 (Rfree = 0.000) for 1613 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.1532 (Rfree = 0.000) for 1608 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1937 (Rfree = 0.000) for 1604 atoms. Found 3 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.55 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: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.312 Round 2: 94 peptides, 16 chains. Longest chain 11 peptides. Score 0.379 Round 3: 101 peptides, 16 chains. Longest chain 12 peptides. Score 0.422 Round 4: 112 peptides, 18 chains. Longest chain 12 peptides. Score 0.435 Round 5: 115 peptides, 18 chains. Longest chain 12 peptides. Score 0.452 Taking the results from Round 5 Chains 18, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3746 restraints for refining 1647 atoms. 3376 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2087 (Rfree = 0.000) for 1647 atoms. Found 5 (7 requested) and removed 10 (3 requested) atoms. Cycle 27: After refmac, R = 0.1816 (Rfree = 0.000) for 1636 atoms. Found 1 (7 requested) and removed 9 (3 requested) atoms. Cycle 28: After refmac, R = 0.1707 (Rfree = 0.000) for 1628 atoms. Found 2 (7 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.1604 (Rfree = 0.000) for 1626 atoms. Found 1 (7 requested) and removed 6 (3 requested) atoms. Cycle 30: After refmac, R = 0.1609 (Rfree = 0.000) for 1620 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 1667 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1683 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.291 Round 2: 97 peptides, 18 chains. Longest chain 11 peptides. Score 0.343 Round 3: 103 peptides, 17 chains. Longest chain 10 peptides. Score 0.407 Round 4: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.364 Round 5: 105 peptides, 15 chains. Longest chain 20 peptides. Score 0.471 Taking the results from Round 5 Chains 15, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3825 restraints for refining 1646 atoms. 3480 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1938 (Rfree = 0.000) for 1646 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.1976 (Rfree = 0.000) for 1632 atoms. Found 5 (7 requested) and removed 11 (3 requested) atoms. Cycle 33: After refmac, R = 0.1873 (Rfree = 0.000) for 1623 atoms. Found 1 (7 requested) and removed 8 (3 requested) atoms. Cycle 34: After refmac, R = 0.1774 (Rfree = 0.000) for 1609 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.1766 (Rfree = 0.000) for 1606 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 1647 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 1676 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 8 peptides. Score 0.269 Round 2: 103 peptides, 17 chains. Longest chain 9 peptides. Score 0.407 Round 3: 107 peptides, 17 chains. Longest chain 10 peptides. Score 0.431 Round 4: 117 peptides, 19 chains. Longest chain 9 peptides. Score 0.439 Round 5: 123 peptides, 19 chains. Longest chain 13 peptides. Score 0.472 Taking the results from Round 5 Chains 20, Residues 104, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3689 restraints for refining 1647 atoms. 3252 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2017 (Rfree = 0.000) for 1647 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 37: After refmac, R = 0.2015 (Rfree = 0.000) for 1632 atoms. Found 4 (7 requested) and removed 14 (3 requested) atoms. Cycle 38: After refmac, R = 0.1920 (Rfree = 0.000) for 1615 atoms. Found 3 (7 requested) and removed 8 (3 requested) atoms. Cycle 39: After refmac, R = 0.1829 (Rfree = 0.000) for 1607 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 40: After refmac, R = 0.1812 (Rfree = 0.000) for 1598 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.53 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: 81 peptides, 18 chains. Longest chain 7 peptides. Score 0.234 Round 2: 89 peptides, 16 chains. Longest chain 12 peptides. Score 0.347 Round 3: 90 peptides, 17 chains. Longest chain 8 peptides. Score 0.325 Round 4: 99 peptides, 16 chains. Longest chain 10 peptides. Score 0.410 Round 5: 98 peptides, 16 chains. Longest chain 9 peptides. Score 0.404 Taking the results from Round 4 Chains 16, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3833 restraints for refining 1647 atoms. 3517 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2295 (Rfree = 0.000) for 1647 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.1962 (Rfree = 0.000) for 1645 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 43: After refmac, R = 0.1736 (Rfree = 0.000) for 1641 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.1696 (Rfree = 0.000) for 1639 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.1590 (Rfree = 0.000) for 1635 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 1670 seeds are put forward NCS extension: 0 residues added, 1670 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 7 peptides. Score 0.244 Round 2: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.293 Round 3: 89 peptides, 16 chains. Longest chain 10 peptides. Score 0.347 Round 4: 78 peptides, 13 chains. Longest chain 10 peptides. Score 0.361 Round 5: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 65, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2192 reflections ( 98.43 % complete ) and 3947 restraints for refining 1647 atoms. 3700 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2096 (Rfree = 0.000) for 1647 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1723 (Rfree = 0.000) for 1636 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1690 (Rfree = 0.000) for 1631 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1566 (Rfree = 0.000) for 1626 atoms. TimeTaking 22.95