Mon 24 Dec 01:04:11 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-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/2ifx-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-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 ============================================================ Mon 24 Dec 01:04:15 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-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 180 and 0 Target number of residues in the AU: 180 Target solvent content: 0.6331 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-3.2-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: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-3.2-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 3.201 Wilson plot Bfac: 67.97 4280 reflections ( 99.07 % complete ) and 0 restraints for refining 2022 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3139 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2717 (Rfree = 0.000) for 2022 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 2047 seeds are put forward NCS extension: 0 residues added, 2047 seeds are put forward Round 1: 112 peptides, 21 chains. Longest chain 11 peptides. Score 0.357 Round 2: 129 peptides, 15 chains. Longest chain 16 peptides. Score 0.594 Round 3: 146 peptides, 18 chains. Longest chain 18 peptides. Score 0.609 Round 4: 151 peptides, 18 chains. Longest chain 21 peptides. Score 0.630 Round 5: 154 peptides, 16 chains. Longest chain 23 peptides. Score 0.679 Taking the results from Round 5 Chains 16, Residues 138, Estimated correctness of the model 60.6 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3454 restraints for refining 1665 atoms. 2859 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2618 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 2: After refmac, R = 0.2582 (Rfree = 0.000) for 1646 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 3: After refmac, R = 0.2885 (Rfree = 0.000) for 1637 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 4: After refmac, R = 0.3071 (Rfree = 0.000) for 1619 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 5: After refmac, R = 0.2407 (Rfree = 0.000) for 1600 atoms. Found 12 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 1656 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1676 seeds are put forward Round 1: 134 peptides, 19 chains. Longest chain 17 peptides. Score 0.531 Round 2: 147 peptides, 19 chains. Longest chain 18 peptides. Score 0.593 Round 3: 145 peptides, 18 chains. Longest chain 22 peptides. Score 0.604 Round 4: 149 peptides, 17 chains. Longest chain 19 peptides. Score 0.641 Round 5: 144 peptides, 19 chains. Longest chain 12 peptides. Score 0.579 Taking the results from Round 4 Chains 17, Residues 132, Estimated correctness of the model 51.6 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3487 restraints for refining 1639 atoms. 2912 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2522 (Rfree = 0.000) for 1639 atoms. Found 9 (14 requested) and removed 19 (7 requested) atoms. Cycle 7: After refmac, R = 0.2332 (Rfree = 0.000) for 1623 atoms. Found 9 (14 requested) and removed 15 (7 requested) atoms. Cycle 8: After refmac, R = 0.2786 (Rfree = 0.000) for 1611 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 9: After refmac, R = 0.2261 (Rfree = 0.000) for 1601 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.2262 (Rfree = 0.000) for 1590 atoms. Found 6 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.02 Search for helices and strands: 0 residues in 0 chains, 1635 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1648 seeds are put forward Round 1: 129 peptides, 21 chains. Longest chain 12 peptides. Score 0.458 Round 2: 139 peptides, 16 chains. Longest chain 21 peptides. Score 0.618 Round 3: 134 peptides, 14 chains. Longest chain 21 peptides. Score 0.636 Round 4: 126 peptides, 14 chains. Longest chain 17 peptides. Score 0.601 Round 5: 138 peptides, 13 chains. Longest chain 18 peptides. Score 0.672 Taking the results from Round 5 Chains 13, Residues 125, Estimated correctness of the model 59.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3456 restraints for refining 1665 atoms. 2905 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2809 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 40 (7 requested) atoms. Cycle 12: After refmac, R = 0.2907 (Rfree = 0.000) for 1633 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 13: After refmac, R = 0.2131 (Rfree = 0.000) for 1615 atoms. Found 9 (14 requested) and removed 19 (7 requested) atoms. Cycle 14: After refmac, R = 0.2670 (Rfree = 0.000) for 1602 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 15: After refmac, R = 0.2417 (Rfree = 0.000) for 1597 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 3.02 Search for helices and strands: 0 residues in 0 chains, 1640 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1658 seeds are put forward Round 1: 126 peptides, 18 chains. Longest chain 14 peptides. Score 0.512 Round 2: 149 peptides, 19 chains. Longest chain 20 peptides. Score 0.602 Round 3: 150 peptides, 18 chains. Longest chain 20 peptides. Score 0.626 Round 4: 147 peptides, 17 chains. Longest chain 17 peptides. Score 0.633 Round 5: 141 peptides, 17 chains. Longest chain 18 peptides. Score 0.607 Taking the results from Round 4 Chains 17, Residues 130, Estimated correctness of the model 49.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3581 restraints for refining 1665 atoms. 3078 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2804 (Rfree = 0.000) for 1665 atoms. Found 8 (14 requested) and removed 62 (7 requested) atoms. Cycle 17: After refmac, R = 0.3006 (Rfree = 0.000) for 1607 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 18: After refmac, R = 0.2588 (Rfree = 0.000) for 1593 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 19: After refmac, R = 0.2809 (Rfree = 0.000) for 1586 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 20: After refmac, R = 0.2608 (Rfree = 0.000) for 1582 atoms. Found 14 (14 requested) and removed 36 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.03 Search for helices and strands: 0 residues in 0 chains, 1653 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1670 seeds are put forward Round 1: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.341 Round 2: 111 peptides, 17 chains. Longest chain 13 peptides. Score 0.454 Round 3: 129 peptides, 18 chains. Longest chain 14 peptides. Score 0.528 Round 4: 136 peptides, 18 chains. Longest chain 16 peptides. Score 0.563 Round 5: 137 peptides, 17 chains. Longest chain 17 peptides. Score 0.589 Taking the results from Round 5 Chains 17, Residues 120, Estimated correctness of the model 38.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3540 restraints for refining 1665 atoms. 3077 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2449 (Rfree = 0.000) for 1665 atoms. Found 6 (14 requested) and removed 51 (7 requested) atoms. Cycle 22: After refmac, R = 0.2261 (Rfree = 0.000) for 1615 atoms. Found 7 (14 requested) and removed 11 (7 requested) atoms. Cycle 23: After refmac, R = 0.2259 (Rfree = 0.000) for 1609 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. Cycle 24: After refmac, R = 0.2198 (Rfree = 0.000) for 1604 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.2013 (Rfree = 0.000) for 1597 atoms. Found 6 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 1648 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 1669 seeds are put forward Round 1: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.391 Round 2: 126 peptides, 19 chains. Longest chain 14 peptides. Score 0.489 Round 3: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.371 Round 4: 125 peptides, 21 chains. Longest chain 14 peptides. Score 0.435 Round 5: 125 peptides, 19 chains. Longest chain 16 peptides. Score 0.483 Taking the results from Round 2 Chains 19, Residues 107, Estimated correctness of the model 7.6 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3585 restraints for refining 1646 atoms. 3161 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2309 (Rfree = 0.000) for 1646 atoms. Found 9 (14 requested) and removed 12 (7 requested) atoms. Cycle 27: After refmac, R = 0.2117 (Rfree = 0.000) for 1641 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.2003 (Rfree = 0.000) for 1636 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.1908 (Rfree = 0.000) for 1628 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1830 (Rfree = 0.000) for 1625 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 1661 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1676 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 9 peptides. Score 0.324 Round 2: 118 peptides, 20 chains. Longest chain 13 peptides. Score 0.419 Round 3: 120 peptides, 20 chains. Longest chain 12 peptides. Score 0.431 Round 4: 118 peptides, 19 chains. Longest chain 13 peptides. Score 0.444 Round 5: 125 peptides, 21 chains. Longest chain 13 peptides. Score 0.435 Taking the results from Round 4 Chains 19, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3769 restraints for refining 1665 atoms. 3392 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2247 (Rfree = 0.000) for 1665 atoms. Found 8 (14 requested) and removed 22 (7 requested) atoms. Cycle 32: After refmac, R = 0.2134 (Rfree = 0.000) for 1651 atoms. Found 10 (14 requested) and removed 18 (7 requested) atoms. Cycle 33: After refmac, R = 0.2177 (Rfree = 0.000) for 1640 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 34: After refmac, R = 0.1926 (Rfree = 0.000) for 1634 atoms. Found 10 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1883 (Rfree = 0.000) for 1635 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 1696 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 1707 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 9 peptides. Score 0.283 Round 2: 111 peptides, 21 chains. Longest chain 13 peptides. Score 0.351 Round 3: 107 peptides, 19 chains. Longest chain 12 peptides. Score 0.379 Round 4: 107 peptides, 20 chains. Longest chain 9 peptides. Score 0.352 Round 5: 114 peptides, 21 chains. Longest chain 10 peptides. Score 0.369 Taking the results from Round 3 Chains 19, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3661 restraints for refining 1665 atoms. 3328 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2665 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 37: After refmac, R = 0.2138 (Rfree = 0.000) for 1659 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 38: After refmac, R = 0.1871 (Rfree = 0.000) for 1658 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 39: After refmac, R = 0.2389 (Rfree = 0.000) for 1661 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 40: After refmac, R = 0.1732 (Rfree = 0.000) for 1656 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 1706 seeds are put forward NCS extension: 0 residues added, 1706 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 2: 95 peptides, 16 chains. Longest chain 13 peptides. Score 0.385 Round 3: 107 peptides, 17 chains. Longest chain 13 peptides. Score 0.431 Round 4: 98 peptides, 15 chains. Longest chain 16 peptides. Score 0.430 Round 5: 88 peptides, 13 chains. Longest chain 16 peptides. Score 0.424 Taking the results from Round 3 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3632 restraints for refining 1665 atoms. 3289 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1922 (Rfree = 0.000) for 1665 atoms. Found 10 (14 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.1985 (Rfree = 0.000) for 1662 atoms. Found 12 (14 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.2586 (Rfree = 0.000) for 1661 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 44: After refmac, R = 0.1839 (Rfree = 0.000) for 1656 atoms. Found 10 (14 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1667 (Rfree = 0.000) for 1653 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.01 Search for helices and strands: 0 residues in 0 chains, 1693 seeds are put forward NCS extension: 0 residues added, 1693 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 6 peptides. Score 0.241 Round 2: 92 peptides, 15 chains. Longest chain 11 peptides. Score 0.394 Round 3: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.400 Round 4: 87 peptides, 14 chains. Longest chain 12 peptides. Score 0.390 Round 5: 84 peptides, 14 chains. Longest chain 9 peptides. Score 0.371 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 78, 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. 4280 reflections ( 99.07 % complete ) and 3695 restraints for refining 1665 atoms. 3398 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1825 (Rfree = 0.000) for 1665 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1999 (Rfree = 0.000) for 1656 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1762 (Rfree = 0.000) for 1645 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2274 (Rfree = 0.000) for 1637 atoms. TimeTaking 24.13