Sun 23 Dec 23:54:42 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ifx-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.4-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 23:54:46 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.4-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 176 and 0 Target number of residues in the AU: 176 Target solvent content: 0.6412 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-3.4-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-3.4-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 3.401 Wilson plot Bfac: 72.01 3571 reflections ( 98.92 % complete ) and 0 restraints for refining 2038 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3089 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2834 (Rfree = 0.000) for 2038 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 2070 seeds are put forward NCS extension: 0 residues added, 2070 seeds are put forward Round 1: 107 peptides, 18 chains. Longest chain 12 peptides. Score 0.405 Round 2: 124 peptides, 18 chains. Longest chain 15 peptides. Score 0.502 Round 3: 152 peptides, 17 chains. Longest chain 22 peptides. Score 0.653 Round 4: 149 peptides, 17 chains. Longest chain 15 peptides. Score 0.641 Round 5: 157 peptides, 15 chains. Longest chain 22 peptides. Score 0.707 Taking the results from Round 5 Chains 19, Residues 142, Estimated correctness of the model 59.6 % 3 chains (33 residues) have been docked in sequence Building loops using Loopy2018 19 chains (142 residues) following loop building 3 chains (33 residues) in sequence following loop building ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3217 restraints for refining 1658 atoms. 2540 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2634 (Rfree = 0.000) for 1658 atoms. Found 10 (12 requested) and removed 22 (6 requested) atoms. Cycle 2: After refmac, R = 0.2275 (Rfree = 0.000) for 1620 atoms. Found 5 (12 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.2126 (Rfree = 0.000) for 1588 atoms. Found 2 (12 requested) and removed 12 (6 requested) atoms. Cycle 4: After refmac, R = 0.2016 (Rfree = 0.000) for 1571 atoms. Found 1 (10 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2012 (Rfree = 0.000) for 1560 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 1620 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 1650 seeds are put forward Round 1: 142 peptides, 20 chains. Longest chain 14 peptides. Score 0.549 Round 2: 151 peptides, 18 chains. Longest chain 21 peptides. Score 0.630 Round 3: 143 peptides, 14 chains. Longest chain 21 peptides. Score 0.673 Round 4: 151 peptides, 18 chains. Longest chain 27 peptides. Score 0.630 Round 5: 144 peptides, 16 chains. Longest chain 22 peptides. Score 0.639 Taking the results from Round 3 Chains 16, Residues 129, Estimated correctness of the model 50.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3578 restraints for refining 1658 atoms. 3041 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2282 (Rfree = 0.000) for 1658 atoms. Found 6 (11 requested) and removed 11 (6 requested) atoms. Cycle 7: After refmac, R = 0.2144 (Rfree = 0.000) for 1650 atoms. Found 6 (11 requested) and removed 11 (6 requested) atoms. Cycle 8: After refmac, R = 0.2521 (Rfree = 0.000) for 1640 atoms. Found 11 (11 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.2071 (Rfree = 0.000) for 1633 atoms. Found 5 (11 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2399 (Rfree = 0.000) for 1622 atoms. Found 11 (11 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 1680 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1697 seeds are put forward Round 1: 135 peptides, 19 chains. Longest chain 19 peptides. Score 0.536 Round 2: 148 peptides, 17 chains. Longest chain 17 peptides. Score 0.637 Round 3: 148 peptides, 17 chains. Longest chain 16 peptides. Score 0.637 Round 4: 147 peptides, 16 chains. Longest chain 29 peptides. Score 0.652 Round 5: 144 peptides, 18 chains. Longest chain 20 peptides. Score 0.600 Taking the results from Round 4 Chains 16, Residues 131, Estimated correctness of the model 44.7 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3571 restraints for refining 1658 atoms. 3035 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2247 (Rfree = 0.000) for 1658 atoms. Found 4 (11 requested) and removed 12 (6 requested) atoms. Cycle 12: After refmac, R = 0.2084 (Rfree = 0.000) for 1645 atoms. Found 3 (11 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2078 (Rfree = 0.000) for 1637 atoms. Found 6 (11 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.1987 (Rfree = 0.000) for 1635 atoms. Found 3 (11 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.1979 (Rfree = 0.000) for 1626 atoms. Found 4 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 1678 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 1718 seeds are put forward Round 1: 132 peptides, 17 chains. Longest chain 19 peptides. Score 0.565 Round 2: 141 peptides, 18 chains. Longest chain 25 peptides. Score 0.586 Round 3: 149 peptides, 16 chains. Longest chain 17 peptides. Score 0.660 Round 4: 137 peptides, 14 chains. Longest chain 32 peptides. Score 0.649 Round 5: 137 peptides, 17 chains. Longest chain 19 peptides. Score 0.589 Taking the results from Round 3 Chains 16, Residues 133, Estimated correctness of the model 47.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3665 restraints for refining 1657 atoms. 3149 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2098 (Rfree = 0.000) for 1657 atoms. Found 4 (11 requested) and removed 14 (6 requested) atoms. Cycle 17: After refmac, R = 0.2374 (Rfree = 0.000) for 1645 atoms. Found 10 (11 requested) and removed 11 (6 requested) atoms. Cycle 18: After refmac, R = 0.1992 (Rfree = 0.000) for 1635 atoms. Found 4 (11 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1887 (Rfree = 0.000) for 1631 atoms. Found 4 (11 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.1804 (Rfree = 0.000) for 1625 atoms. Found 2 (11 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 1664 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1686 seeds are put forward Round 1: 121 peptides, 19 chains. Longest chain 23 peptides. Score 0.461 Round 2: 142 peptides, 18 chains. Longest chain 25 peptides. Score 0.591 Round 3: 137 peptides, 18 chains. Longest chain 17 peptides. Score 0.567 Round 4: 137 peptides, 14 chains. Longest chain 23 peptides. Score 0.649 Round 5: 122 peptides, 18 chains. Longest chain 19 peptides. Score 0.491 Taking the results from Round 4 Chains 14, Residues 123, Estimated correctness of the model 43.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3657 restraints for refining 1658 atoms. 3179 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2083 (Rfree = 0.000) for 1658 atoms. Found 8 (11 requested) and removed 8 (6 requested) atoms. Cycle 22: After refmac, R = 0.2063 (Rfree = 0.000) for 1657 atoms. Found 7 (11 requested) and removed 8 (6 requested) atoms. Cycle 23: After refmac, R = 0.1949 (Rfree = 0.000) for 1655 atoms. Found 4 (11 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.1921 (Rfree = 0.000) for 1651 atoms. Found 2 (11 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1995 (Rfree = 0.000) for 1646 atoms. Found 5 (11 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1684 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 1709 seeds are put forward Round 1: 111 peptides, 17 chains. Longest chain 24 peptides. Score 0.454 Round 2: 119 peptides, 16 chains. Longest chain 25 peptides. Score 0.522 Round 3: 121 peptides, 17 chains. Longest chain 19 peptides. Score 0.509 Round 4: 125 peptides, 16 chains. Longest chain 25 peptides. Score 0.553 Round 5: 119 peptides, 16 chains. Longest chain 20 peptides. Score 0.522 Taking the results from Round 4 Chains 16, Residues 109, Estimated correctness of the model 12.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3755 restraints for refining 1658 atoms. 3335 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2213 (Rfree = 0.000) for 1658 atoms. Found 7 (11 requested) and removed 55 (6 requested) atoms. Cycle 27: After refmac, R = 0.2077 (Rfree = 0.000) for 1606 atoms. Found 7 (11 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.1970 (Rfree = 0.000) for 1604 atoms. Found 3 (11 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.1919 (Rfree = 0.000) for 1596 atoms. Found 7 (11 requested) and removed 8 (6 requested) atoms. Cycle 30: After refmac, R = 0.1918 (Rfree = 0.000) for 1595 atoms. Found 4 (11 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 1631 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 1658 seeds are put forward Round 1: 110 peptides, 18 chains. Longest chain 19 peptides. Score 0.423 Round 2: 102 peptides, 13 chains. Longest chain 22 peptides. Score 0.504 Round 3: 116 peptides, 15 chains. Longest chain 26 peptides. Score 0.530 Round 4: 106 peptides, 14 chains. Longest chain 15 peptides. Score 0.501 Round 5: 120 peptides, 17 chains. Longest chain 22 peptides. Score 0.504 Taking the results from Round 3 Chains 16, Residues 101, Estimated correctness of the model 4.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3470 restraints for refining 1658 atoms. 3028 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2274 (Rfree = 0.000) for 1658 atoms. Found 10 (11 requested) and removed 18 (6 requested) atoms. Cycle 32: After refmac, R = 0.2624 (Rfree = 0.000) for 1646 atoms. Found 11 (11 requested) and removed 15 (6 requested) atoms. Cycle 33: After refmac, R = 0.2039 (Rfree = 0.000) for 1638 atoms. Found 5 (11 requested) and removed 12 (6 requested) atoms. Cycle 34: After refmac, R = 0.2076 (Rfree = 0.000) for 1630 atoms. Found 6 (11 requested) and removed 12 (6 requested) atoms. Cycle 35: After refmac, R = 0.2050 (Rfree = 0.000) for 1622 atoms. Found 4 (11 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 1671 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1695 seeds are put forward Round 1: 94 peptides, 16 chains. Longest chain 19 peptides. Score 0.379 Round 2: 108 peptides, 15 chains. Longest chain 20 peptides. Score 0.488 Round 3: 121 peptides, 17 chains. Longest chain 21 peptides. Score 0.509 Round 4: 110 peptides, 14 chains. Longest chain 16 peptides. Score 0.523 Round 5: 120 peptides, 16 chains. Longest chain 21 peptides. Score 0.528 Taking the results from Round 5 Chains 16, Residues 104, Estimated correctness of the model 3.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3667 restraints for refining 1658 atoms. 3267 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2070 (Rfree = 0.000) for 1658 atoms. Found 9 (11 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.1780 (Rfree = 0.000) for 1654 atoms. Found 0 (11 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2248 (Rfree = 0.000) for 1645 atoms. Found 11 (11 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.1782 (Rfree = 0.000) for 1647 atoms. Found 5 (11 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.2046 (Rfree = 0.000) for 1641 atoms. Found 11 (11 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 1699 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 1728 seeds are put forward Round 1: 85 peptides, 14 chains. Longest chain 21 peptides. Score 0.377 Round 2: 108 peptides, 16 chains. Longest chain 21 peptides. Score 0.462 Round 3: 112 peptides, 15 chains. Longest chain 22 peptides. Score 0.509 Round 4: 126 peptides, 20 chains. Longest chain 22 peptides. Score 0.465 Round 5: 122 peptides, 17 chains. Longest chain 22 peptides. Score 0.515 Taking the results from Round 5 Chains 19, Residues 105, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3567 restraints for refining 1657 atoms. 3140 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2071 (Rfree = 0.000) for 1657 atoms. Found 2 (11 requested) and removed 11 (6 requested) atoms. Cycle 42: After refmac, R = 0.1855 (Rfree = 0.000) for 1645 atoms. Found 2 (11 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.1782 (Rfree = 0.000) for 1638 atoms. Found 1 (11 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.1763 (Rfree = 0.000) for 1632 atoms. Found 8 (11 requested) and removed 8 (6 requested) atoms. Cycle 45: After refmac, R = 0.1632 (Rfree = 0.000) for 1631 atoms. Found 1 (11 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 1676 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 1700 seeds are put forward Round 1: 77 peptides, 12 chains. Longest chain 20 peptides. Score 0.383 Round 2: 104 peptides, 14 chains. Longest chain 22 peptides. Score 0.490 Round 3: 101 peptides, 13 chains. Longest chain 22 peptides. Score 0.499 Round 4: 97 peptides, 13 chains. Longest chain 12 peptides. Score 0.477 Round 5: 94 peptides, 12 chains. Longest chain 14 peptides. Score 0.486 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 88, 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. 3571 reflections ( 98.92 % complete ) and 3755 restraints for refining 1658 atoms. 3416 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1781 (Rfree = 0.000) for 1658 atoms. Found 0 (11 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1718 (Rfree = 0.000) for 1651 atoms. Found 0 (11 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2611 (Rfree = 0.000) for 1644 atoms. Found 0 (11 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1645 (Rfree = 0.000) for 1638 atoms. TimeTaking 24.97