Mon 24 Dec 07:58:53 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 2ifx-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-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/2ifx-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-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 07:58:58 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/2ifx-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-4.0-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 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-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: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-4.0-parrot-noncs.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 2026 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3270 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2544 (Rfree = 0.000) for 2026 atoms. Found 7 (9 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 2051 seeds are put forward NCS extension: 0 residues added, 2051 seeds are put forward Round 1: 94 peptides, 14 chains. Longest chain 10 peptides. Score 0.433 Round 2: 100 peptides, 13 chains. Longest chain 15 peptides. Score 0.493 Round 3: 109 peptides, 14 chains. Longest chain 21 peptides. Score 0.517 Round 4: 119 peptides, 14 chains. Longest chain 14 peptides. Score 0.568 Round 5: 114 peptides, 14 chains. Longest chain 20 peptides. Score 0.543 Taking the results from Round 4 Chains 14, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3889 restraints for refining 1646 atoms. 3483 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2338 (Rfree = 0.000) for 1646 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 2: After refmac, R = 0.2190 (Rfree = 0.000) for 1620 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 3: After refmac, R = 0.2169 (Rfree = 0.000) for 1603 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 4: After refmac, R = 0.2244 (Rfree = 0.000) for 1594 atoms. Found 2 (7 requested) and removed 8 (3 requested) atoms. Cycle 5: After refmac, R = 0.2265 (Rfree = 0.000) for 1578 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 1631 seeds are put forward NCS extension: 0 residues added, 1631 seeds are put forward Round 1: 103 peptides, 17 chains. Longest chain 20 peptides. Score 0.407 Round 2: 117 peptides, 18 chains. Longest chain 21 peptides. Score 0.464 Round 3: 118 peptides, 17 chains. Longest chain 12 peptides. Score 0.493 Round 4: 111 peptides, 11 chains. Longest chain 22 peptides. Score 0.597 Round 5: 115 peptides, 16 chains. Longest chain 12 peptides. Score 0.501 Taking the results from Round 4 Chains 11, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3582 restraints for refining 1597 atoms. 3193 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2073 (Rfree = 0.000) for 1597 atoms. Found 6 (7 requested) and removed 18 (3 requested) atoms. Cycle 7: After refmac, R = 0.1898 (Rfree = 0.000) for 1564 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 8: After refmac, R = 0.1961 (Rfree = 0.000) for 1554 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.1808 (Rfree = 0.000) for 1551 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.1815 (Rfree = 0.000) for 1549 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 1597 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 1635 seeds are put forward Round 1: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.389 Round 2: 124 peptides, 16 chains. Longest chain 15 peptides. Score 0.548 Round 3: 127 peptides, 15 chains. Longest chain 20 peptides. Score 0.585 Round 4: 103 peptides, 12 chains. Longest chain 20 peptides. Score 0.534 Round 5: 121 peptides, 16 chains. Longest chain 20 peptides. Score 0.533 Taking the results from Round 3 Chains 15, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3615 restraints for refining 1616 atoms. 3182 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2078 (Rfree = 0.000) for 1616 atoms. Found 4 (7 requested) and removed 13 (3 requested) atoms. Cycle 12: After refmac, R = 0.1967 (Rfree = 0.000) for 1604 atoms. Found 2 (7 requested) and removed 15 (3 requested) atoms. Cycle 13: After refmac, R = 0.2021 (Rfree = 0.000) for 1588 atoms. Found 2 (7 requested) and removed 8 (3 requested) atoms. Cycle 14: After refmac, R = 0.2172 (Rfree = 0.000) for 1578 atoms. Found 2 (7 requested) and removed 9 (3 requested) atoms. Cycle 15: After refmac, R = 0.2256 (Rfree = 0.000) for 1570 atoms. Found 3 (7 requested) and removed 12 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 1632 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 1668 seeds are put forward Round 1: 97 peptides, 16 chains. Longest chain 12 peptides. Score 0.397 Round 2: 112 peptides, 17 chains. Longest chain 11 peptides. Score 0.460 Round 3: 104 peptides, 14 chains. Longest chain 12 peptides. Score 0.490 Round 4: 109 peptides, 17 chains. Longest chain 10 peptides. Score 0.443 Round 5: 118 peptides, 18 chains. Longest chain 12 peptides. Score 0.469 Taking the results from Round 3 Chains 14, Residues 90, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3680 restraints for refining 1647 atoms. 3289 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2059 (Rfree = 0.000) for 1647 atoms. Found 1 (7 requested) and removed 12 (3 requested) atoms. Cycle 17: After refmac, R = 0.1938 (Rfree = 0.000) for 1633 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2407 (Rfree = 0.000) for 1618 atoms. Found 7 (7 requested) and removed 20 (3 requested) atoms. Cycle 19: After refmac, R = 0.1848 (Rfree = 0.000) for 1591 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.1690 (Rfree = 0.000) for 1584 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 1632 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 1642 seeds are put forward Round 1: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.357 Round 2: 106 peptides, 17 chains. Longest chain 12 peptides. Score 0.425 Round 3: 105 peptides, 16 chains. Longest chain 14 peptides. Score 0.445 Round 4: 114 peptides, 18 chains. Longest chain 10 peptides. Score 0.446 Round 5: 108 peptides, 18 chains. Longest chain 12 peptides. Score 0.411 Taking the results from Round 4 Chains 18, Residues 96, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3653 restraints for refining 1647 atoms. 3251 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1881 (Rfree = 0.000) for 1647 atoms. Found 4 (7 requested) and removed 18 (3 requested) atoms. Cycle 22: After refmac, R = 0.1907 (Rfree = 0.000) for 1625 atoms. Found 4 (7 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.1672 (Rfree = 0.000) for 1619 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.1687 (Rfree = 0.000) for 1611 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.1523 (Rfree = 0.000) for 1605 atoms. Found 0 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 1651 seeds are put forward NCS extension: 0 residues added, 1651 seeds are put forward Round 1: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.308 Round 2: 89 peptides, 15 chains. Longest chain 14 peptides. Score 0.375 Round 3: 99 peptides, 18 chains. Longest chain 11 peptides. Score 0.356 Round 4: 104 peptides, 16 chains. Longest chain 14 peptides. Score 0.439 Round 5: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 4 Chains 16, Residues 88, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3611 restraints for refining 1647 atoms. 3197 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1761 (Rfree = 0.000) for 1647 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.1706 (Rfree = 0.000) for 1639 atoms. Found 4 (7 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.1682 (Rfree = 0.000) for 1622 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 29: After refmac, R = 0.1451 (Rfree = 0.000) for 1611 atoms. Found 0 (7 requested) and removed 6 (3 requested) atoms. Cycle 30: After refmac, R = 0.1471 (Rfree = 0.000) for 1593 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 1642 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1659 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 8 peptides. Score 0.226 Round 2: 85 peptides, 17 chains. Longest chain 9 peptides. Score 0.291 Round 3: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.351 Round 4: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.343 Round 5: 95 peptides, 16 chains. Longest chain 10 peptides. Score 0.385 Taking the results from Round 5 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3753 restraints for refining 1619 atoms. 3453 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1717 (Rfree = 0.000) for 1619 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 32: After refmac, R = 0.1614 (Rfree = 0.000) for 1596 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.1832 (Rfree = 0.000) for 1591 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.1518 (Rfree = 0.000) for 1583 atoms. Found 3 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1441 (Rfree = 0.000) for 1576 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 1628 seeds are put forward NCS extension: 0 residues added, 1628 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 9 peptides. Score 0.293 Round 2: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.328 Round 3: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.385 Round 4: 107 peptides, 18 chains. Longest chain 14 peptides. Score 0.405 Round 5: 113 peptides, 19 chains. Longest chain 10 peptides. Score 0.415 Taking the results from Round 5 Chains 19, Residues 94, 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 1606 atoms. 3374 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1766 (Rfree = 0.000) for 1606 atoms. Found 2 (7 requested) and removed 10 (3 requested) atoms. Cycle 37: After refmac, R = 0.1564 (Rfree = 0.000) for 1594 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 38: After refmac, R = 0.1501 (Rfree = 0.000) for 1586 atoms. Found 1 (7 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.1566 (Rfree = 0.000) for 1579 atoms. Found 2 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.1496 (Rfree = 0.000) for 1570 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.56 Search for helices and strands: 0 residues in 0 chains, 1619 seeds are put forward NCS extension: 0 residues added, 1619 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.293 Round 2: 106 peptides, 17 chains. Longest chain 15 peptides. Score 0.425 Round 3: 114 peptides, 19 chains. Longest chain 17 peptides. Score 0.421 Round 4: 115 peptides, 17 chains. Longest chain 15 peptides. Score 0.477 Round 5: 110 peptides, 16 chains. Longest chain 15 peptides. Score 0.474 Taking the results from Round 4 Chains 17, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2192 reflections ( 98.43 % complete ) and 3634 restraints for refining 1603 atoms. 3259 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1831 (Rfree = 0.000) for 1603 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 42: After refmac, R = 0.1776 (Rfree = 0.000) for 1593 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.1635 (Rfree = 0.000) for 1590 atoms. Found 3 (7 requested) and removed 11 (3 requested) atoms. Cycle 44: After refmac, R = 0.1858 (Rfree = 0.000) for 1577 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.1552 (Rfree = 0.000) for 1575 atoms. Found 1 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 1615 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1633 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.265 Round 2: 87 peptides, 16 chains. Longest chain 8 peptides. Score 0.333 Round 3: 88 peptides, 15 chains. Longest chain 14 peptides. Score 0.368 Round 4: 90 peptides, 14 chains. Longest chain 9 peptides. Score 0.409 Round 5: 99 peptides, 15 chains. Longest chain 14 peptides. Score 0.436 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 84, 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 3729 restraints for refining 1607 atoms. 3408 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1716 (Rfree = 0.000) for 1607 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1587 (Rfree = 0.000) for 1597 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1540 (Rfree = 0.000) for 1593 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1521 (Rfree = 0.000) for 1586 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Writing output files ... TimeTaking 24.73