Mon 24 Dec 07:29:23 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.6-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 07:29:28 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.6-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 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-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-3.6-parrot-noncs.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 2029 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3232 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3233 (Rfree = 0.000) for 2029 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 2060 seeds are put forward NCS extension: 0 residues added, 2060 seeds are put forward Round 1: 95 peptides, 17 chains. Longest chain 15 peptides. Score 0.357 Round 2: 110 peptides, 17 chains. Longest chain 15 peptides. Score 0.449 Round 3: 129 peptides, 19 chains. Longest chain 15 peptides. Score 0.505 Round 4: 130 peptides, 18 chains. Longest chain 15 peptides. Score 0.533 Round 5: 131 peptides, 14 chains. Longest chain 17 peptides. Score 0.624 Taking the results from Round 5 Chains 14, Residues 117, Estimated correctness of the model 23.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3747 restraints for refining 1654 atoms. 3293 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2383 (Rfree = 0.000) for 1654 atoms. Found 7 (10 requested) and removed 15 (5 requested) atoms. Cycle 2: After refmac, R = 0.2663 (Rfree = 0.000) for 1612 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 3: After refmac, R = 0.2439 (Rfree = 0.000) for 1600 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 4: After refmac, R = 0.2457 (Rfree = 0.000) for 1584 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 5: After refmac, R = 0.2382 (Rfree = 0.000) for 1570 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.30 Search for helices and strands: 0 residues in 0 chains, 1651 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1668 seeds are put forward Round 1: 110 peptides, 18 chains. Longest chain 13 peptides. Score 0.423 Round 2: 115 peptides, 17 chains. Longest chain 13 peptides. Score 0.477 Round 3: 115 peptides, 16 chains. Longest chain 16 peptides. Score 0.501 Round 4: 128 peptides, 16 chains. Longest chain 17 peptides. Score 0.568 Round 5: 125 peptides, 16 chains. Longest chain 17 peptides. Score 0.553 Taking the results from Round 4 Chains 16, Residues 112, Estimated correctness of the model 1.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3663 restraints for refining 1623 atoms. 3231 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2403 (Rfree = 0.000) for 1623 atoms. Found 3 (10 requested) and removed 18 (5 requested) atoms. Cycle 7: After refmac, R = 0.2489 (Rfree = 0.000) for 1601 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 8: After refmac, R = 0.2714 (Rfree = 0.000) for 1586 atoms. Found 10 (10 requested) and removed 25 (5 requested) atoms. Cycle 9: After refmac, R = 0.2487 (Rfree = 0.000) for 1561 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.2347 (Rfree = 0.000) for 1553 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 1623 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1645 seeds are put forward Round 1: 98 peptides, 18 chains. Longest chain 11 peptides. Score 0.349 Round 2: 107 peptides, 16 chains. Longest chain 14 peptides. Score 0.457 Round 3: 112 peptides, 17 chains. Longest chain 12 peptides. Score 0.460 Round 4: 126 peptides, 18 chains. Longest chain 13 peptides. Score 0.512 Round 5: 128 peptides, 17 chains. Longest chain 15 peptides. Score 0.545 Taking the results from Round 5 Chains 17, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3718 restraints for refining 1636 atoms. 3291 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2385 (Rfree = 0.000) for 1636 atoms. Found 5 (10 requested) and removed 19 (5 requested) atoms. Cycle 12: After refmac, R = 0.2205 (Rfree = 0.000) for 1608 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 13: After refmac, R = 0.2196 (Rfree = 0.000) for 1602 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2541 (Rfree = 0.000) for 1594 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 15: After refmac, R = 0.2780 (Rfree = 0.000) for 1585 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.30 Search for helices and strands: 0 residues in 0 chains, 1621 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1635 seeds are put forward Round 1: 107 peptides, 20 chains. Longest chain 9 peptides. Score 0.352 Round 2: 118 peptides, 19 chains. Longest chain 15 peptides. Score 0.444 Round 3: 119 peptides, 19 chains. Longest chain 11 peptides. Score 0.450 Round 4: 128 peptides, 18 chains. Longest chain 12 peptides. Score 0.523 Round 5: 132 peptides, 18 chains. Longest chain 12 peptides. Score 0.543 Taking the results from Round 5 Chains 18, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3738 restraints for refining 1654 atoms. 3300 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2599 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 17: After refmac, R = 0.2319 (Rfree = 0.000) for 1631 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.2331 (Rfree = 0.000) for 1623 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 19: After refmac, R = 0.2202 (Rfree = 0.000) for 1612 atoms. Found 8 (10 requested) and removed 14 (5 requested) atoms. Cycle 20: After refmac, R = 0.2232 (Rfree = 0.000) for 1602 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 1667 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1682 seeds are put forward Round 1: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.320 Round 2: 108 peptides, 18 chains. Longest chain 9 peptides. Score 0.411 Round 3: 118 peptides, 18 chains. Longest chain 13 peptides. Score 0.469 Round 4: 115 peptides, 18 chains. Longest chain 15 peptides. Score 0.452 Round 5: 122 peptides, 20 chains. Longest chain 14 peptides. Score 0.442 Taking the results from Round 3 Chains 18, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3833 restraints for refining 1654 atoms. 3451 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2347 (Rfree = 0.000) for 1654 atoms. Found 7 (10 requested) and removed 17 (5 requested) atoms. Cycle 22: After refmac, R = 0.2514 (Rfree = 0.000) for 1639 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.2420 (Rfree = 0.000) for 1637 atoms. Found 8 (10 requested) and removed 13 (5 requested) atoms. Cycle 24: After refmac, R = 0.2174 (Rfree = 0.000) for 1628 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2009 (Rfree = 0.000) for 1623 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 1677 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1696 seeds are put forward Round 1: 92 peptides, 17 chains. Longest chain 8 peptides. Score 0.338 Round 2: 109 peptides, 17 chains. Longest chain 11 peptides. Score 0.443 Round 3: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.417 Round 4: 112 peptides, 17 chains. Longest chain 11 peptides. Score 0.460 Round 5: 103 peptides, 16 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 4 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3826 restraints for refining 1654 atoms. 3463 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2452 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 27: After refmac, R = 0.2350 (Rfree = 0.000) for 1643 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.1972 (Rfree = 0.000) for 1638 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.1993 (Rfree = 0.000) for 1632 atoms. Found 5 (10 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.1819 (Rfree = 0.000) for 1626 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 1668 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1671 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 8 peptides. Score 0.267 Round 2: 113 peptides, 20 chains. Longest chain 14 peptides. Score 0.389 Round 3: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.413 Round 4: 111 peptides, 16 chains. Longest chain 11 peptides. Score 0.479 Round 5: 111 peptides, 17 chains. Longest chain 16 peptides. Score 0.454 Taking the results from Round 4 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3609 restraints for refining 1654 atoms. 3206 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2163 (Rfree = 0.000) for 1654 atoms. Found 4 (10 requested) and removed 10 (5 requested) atoms. Cycle 32: After refmac, R = 0.2218 (Rfree = 0.000) for 1641 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.2302 (Rfree = 0.000) for 1640 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2184 (Rfree = 0.000) for 1636 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 35: After refmac, R = 0.2426 (Rfree = 0.000) for 1635 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 1677 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1683 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 9 peptides. Score 0.259 Round 2: 78 peptides, 14 chains. Longest chain 10 peptides. Score 0.331 Round 3: 85 peptides, 13 chains. Longest chain 11 peptides. Score 0.405 Round 4: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.377 Round 5: 96 peptides, 14 chains. Longest chain 15 peptides. Score 0.445 Taking the results from Round 5 Chains 14, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3808 restraints for refining 1654 atoms. 3494 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2551 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 37: After refmac, R = 0.2414 (Rfree = 0.000) for 1641 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 38: After refmac, R = 0.1861 (Rfree = 0.000) for 1635 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1733 (Rfree = 0.000) for 1628 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.1713 (Rfree = 0.000) for 1623 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 1646 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1664 seeds are put forward Round 1: 76 peptides, 18 chains. Longest chain 5 peptides. Score 0.197 Round 2: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.349 Round 3: 90 peptides, 16 chains. Longest chain 11 peptides. Score 0.353 Round 4: 91 peptides, 14 chains. Longest chain 13 peptides. Score 0.415 Round 5: 92 peptides, 14 chains. Longest chain 18 peptides. Score 0.421 Taking the results from Round 5 Chains 16, Residues 78, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3584 restraints for refining 1654 atoms. 3224 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2008 (Rfree = 0.000) for 1654 atoms. Found 8 (10 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.2061 (Rfree = 0.000) for 1640 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2836 (Rfree = 0.000) for 1629 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 44: After refmac, R = 0.2365 (Rfree = 0.000) for 1618 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.1897 (Rfree = 0.000) for 1610 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 1637 seeds are put forward NCS extension: 0 residues added, 1637 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.272 Round 2: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.323 Round 3: 107 peptides, 19 chains. Longest chain 14 peptides. Score 0.379 Round 4: 95 peptides, 17 chains. Longest chain 12 peptides. Score 0.357 Round 5: 98 peptides, 15 chains. Longest chain 17 peptides. Score 0.430 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 83, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 11 % 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 3332 restraints for refining 1576 atoms. 2982 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1978 (Rfree = 0.000) for 1576 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2351 (Rfree = 0.000) for 1564 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2105 (Rfree = 0.000) for 1547 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2050 (Rfree = 0.000) for 1536 atoms. TimeTaking 24.9