Mon 24 Dec 07:58:50 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.4-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 07:58:54 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.4-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 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-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-3.4-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 3.401 Wilson plot Bfac: 72.01 3571 reflections ( 98.92 % complete ) and 0 restraints for refining 2024 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3150 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3179 (Rfree = 0.000) for 2024 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 2053 seeds are put forward NCS extension: 0 residues added, 2053 seeds are put forward Round 1: 97 peptides, 18 chains. Longest chain 13 peptides. Score 0.343 Round 2: 123 peptides, 16 chains. Longest chain 17 peptides. Score 0.543 Round 3: 127 peptides, 18 chains. Longest chain 18 peptides. Score 0.518 Round 4: 125 peptides, 17 chains. Longest chain 18 peptides. Score 0.530 Round 5: 146 peptides, 15 chains. Longest chain 18 peptides. Score 0.666 Taking the results from Round 5 Chains 15, Residues 131, Estimated correctness of the model 48.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3585 restraints for refining 1657 atoms. 3076 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2558 (Rfree = 0.000) for 1657 atoms. Found 5 (12 requested) and removed 20 (6 requested) atoms. Cycle 2: After refmac, R = 0.2504 (Rfree = 0.000) for 1626 atoms. Found 7 (12 requested) and removed 14 (6 requested) atoms. Cycle 3: After refmac, R = 0.2540 (Rfree = 0.000) for 1604 atoms. Found 10 (12 requested) and removed 19 (6 requested) atoms. Cycle 4: After refmac, R = 0.2265 (Rfree = 0.000) for 1585 atoms. Found 5 (12 requested) and removed 13 (6 requested) atoms. Cycle 5: After refmac, R = 0.2177 (Rfree = 0.000) for 1570 atoms. Found 5 (11 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 1635 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1650 seeds are put forward Round 1: 123 peptides, 18 chains. Longest chain 18 peptides. Score 0.496 Round 2: 141 peptides, 15 chains. Longest chain 18 peptides. Score 0.646 Round 3: 154 peptides, 19 chains. Longest chain 18 peptides. Score 0.624 Round 4: 140 peptides, 16 chains. Longest chain 23 peptides. Score 0.622 Round 5: 148 peptides, 16 chains. Longest chain 35 peptides. Score 0.656 Taking the results from Round 5 Chains 16, Residues 132, Estimated correctness of the model 45.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3657 restraints for refining 1636 atoms. 3145 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2269 (Rfree = 0.000) for 1636 atoms. Found 8 (12 requested) and removed 19 (6 requested) atoms. Cycle 7: After refmac, R = 0.2180 (Rfree = 0.000) for 1616 atoms. Found 8 (12 requested) and removed 12 (6 requested) atoms. Cycle 8: After refmac, R = 0.2029 (Rfree = 0.000) for 1610 atoms. Found 6 (12 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.2112 (Rfree = 0.000) for 1601 atoms. Found 9 (12 requested) and removed 13 (6 requested) atoms. Cycle 10: After refmac, R = 0.2152 (Rfree = 0.000) for 1593 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 1664 seeds are put forward NCS extension: 48 residues added (6 deleted due to clashes), 1712 seeds are put forward Round 1: 126 peptides, 21 chains. Longest chain 12 peptides. Score 0.441 Round 2: 147 peptides, 19 chains. Longest chain 16 peptides. Score 0.593 Round 3: 147 peptides, 17 chains. Longest chain 16 peptides. Score 0.633 Round 4: 153 peptides, 20 chains. Longest chain 17 peptides. Score 0.600 Round 5: 153 peptides, 17 chains. Longest chain 17 peptides. Score 0.657 Taking the results from Round 5 Chains 17, Residues 136, Estimated correctness of the model 46.1 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3495 restraints for refining 1658 atoms. 2908 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2296 (Rfree = 0.000) for 1658 atoms. Found 11 (12 requested) and removed 14 (6 requested) atoms. Cycle 12: After refmac, R = 0.2075 (Rfree = 0.000) for 1651 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.2277 (Rfree = 0.000) for 1645 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.1978 (Rfree = 0.000) for 1639 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.1909 (Rfree = 0.000) for 1630 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 1681 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1696 seeds are put forward Round 1: 130 peptides, 18 chains. Longest chain 19 peptides. Score 0.533 Round 2: 140 peptides, 16 chains. Longest chain 19 peptides. Score 0.622 Round 3: 143 peptides, 17 chains. Longest chain 19 peptides. Score 0.616 Round 4: 141 peptides, 17 chains. Longest chain 16 peptides. Score 0.607 Round 5: 136 peptides, 18 chains. Longest chain 18 peptides. Score 0.563 Taking the results from Round 2 Chains 16, Residues 124, Estimated correctness of the model 35.6 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3515 restraints for refining 1658 atoms. 2983 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2179 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 17: After refmac, R = 0.2512 (Rfree = 0.000) for 1651 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 18: After refmac, R = 0.2140 (Rfree = 0.000) for 1643 atoms. Found 11 (12 requested) and removed 15 (6 requested) atoms. Cycle 19: After refmac, R = 0.2130 (Rfree = 0.000) for 1633 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.2034 (Rfree = 0.000) for 1633 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 1686 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 1712 seeds are put forward Round 1: 125 peptides, 18 chains. Longest chain 17 peptides. Score 0.507 Round 2: 135 peptides, 20 chains. Longest chain 15 peptides. Score 0.513 Round 3: 143 peptides, 17 chains. Longest chain 17 peptides. Score 0.616 Round 4: 141 peptides, 17 chains. Longest chain 18 peptides. Score 0.607 Round 5: 136 peptides, 18 chains. Longest chain 14 peptides. Score 0.563 Taking the results from Round 3 Chains 17, Residues 126, Estimated correctness of the model 33.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3576 restraints for refining 1648 atoms. 3089 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2121 (Rfree = 0.000) for 1648 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 22: After refmac, R = 0.2103 (Rfree = 0.000) for 1645 atoms. Found 8 (12 requested) and removed 11 (6 requested) atoms. Cycle 23: After refmac, R = 0.2044 (Rfree = 0.000) for 1641 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.2072 (Rfree = 0.000) for 1637 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.1963 (Rfree = 0.000) for 1635 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 1672 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1692 seeds are put forward Round 1: 126 peptides, 19 chains. Longest chain 12 peptides. Score 0.489 Round 2: 135 peptides, 14 chains. Longest chain 18 peptides. Score 0.641 Round 3: 140 peptides, 16 chains. Longest chain 19 peptides. Score 0.622 Round 4: 141 peptides, 17 chains. Longest chain 17 peptides. Score 0.607 Round 5: 145 peptides, 17 chains. Longest chain 18 peptides. Score 0.624 Taking the results from Round 2 Chains 14, Residues 121, Estimated correctness of the model 41.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3555 restraints for refining 1643 atoms. 3085 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2015 (Rfree = 0.000) for 1643 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 27: After refmac, R = 0.1999 (Rfree = 0.000) for 1640 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2451 (Rfree = 0.000) for 1632 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.1831 (Rfree = 0.000) for 1635 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.2406 (Rfree = 0.000) for 1627 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 1671 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1689 seeds are put forward Round 1: 119 peptides, 19 chains. Longest chain 9 peptides. Score 0.450 Round 2: 139 peptides, 19 chains. Longest chain 19 peptides. Score 0.556 Round 3: 140 peptides, 20 chains. Longest chain 13 peptides. Score 0.539 Round 4: 152 peptides, 18 chains. Longest chain 17 peptides. Score 0.635 Round 5: 139 peptides, 17 chains. Longest chain 18 peptides. Score 0.598 Taking the results from Round 4 Chains 18, Residues 134, Estimated correctness of the model 39.6 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3333 restraints for refining 1658 atoms. 2756 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2120 (Rfree = 0.000) for 1658 atoms. Found 9 (12 requested) and removed 35 (6 requested) atoms. Cycle 32: After refmac, R = 0.1928 (Rfree = 0.000) for 1627 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.1897 (Rfree = 0.000) for 1626 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1795 (Rfree = 0.000) for 1623 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1825 (Rfree = 0.000) for 1617 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1652 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1673 seeds are put forward Round 1: 119 peptides, 17 chains. Longest chain 12 peptides. Score 0.499 Round 2: 136 peptides, 20 chains. Longest chain 14 peptides. Score 0.518 Round 3: 142 peptides, 19 chains. Longest chain 19 peptides. Score 0.570 Round 4: 134 peptides, 18 chains. Longest chain 14 peptides. Score 0.553 Round 5: 143 peptides, 17 chains. Longest chain 20 peptides. Score 0.616 Taking the results from Round 5 Chains 19, Residues 126, Estimated correctness of the model 33.7 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3365 restraints for refining 1658 atoms. 2821 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2192 (Rfree = 0.000) for 1658 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 37: After refmac, R = 0.1977 (Rfree = 0.000) for 1653 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.2405 (Rfree = 0.000) for 1645 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 39: After refmac, R = 0.2120 (Rfree = 0.000) for 1638 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.1955 (Rfree = 0.000) for 1639 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 1665 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 1680 seeds are put forward Round 1: 110 peptides, 19 chains. Longest chain 11 peptides. Score 0.397 Round 2: 125 peptides, 16 chains. Longest chain 27 peptides. Score 0.553 Round 3: 129 peptides, 17 chains. Longest chain 15 peptides. Score 0.550 Round 4: 128 peptides, 18 chains. Longest chain 15 peptides. Score 0.523 Round 5: 123 peptides, 17 chains. Longest chain 16 peptides. Score 0.520 Taking the results from Round 2 Chains 16, Residues 109, Estimated correctness of the model 12.5 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3227 restraints for refining 1658 atoms. 2681 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2167 (Rfree = 0.000) for 1658 atoms. Found 7 (12 requested) and removed 14 (6 requested) atoms. Cycle 42: After refmac, R = 0.2302 (Rfree = 0.000) for 1644 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 43: After refmac, R = 0.2212 (Rfree = 0.000) for 1638 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 44: After refmac, R = 0.1856 (Rfree = 0.000) for 1635 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.1634 (Rfree = 0.000) for 1634 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 1674 seeds are put forward NCS extension: 35 residues added (4 deleted due to clashes), 1709 seeds are put forward Round 1: 102 peptides, 17 chains. Longest chain 17 peptides. Score 0.401 Round 2: 122 peptides, 18 chains. Longest chain 11 peptides. Score 0.491 Round 3: 129 peptides, 17 chains. Longest chain 17 peptides. Score 0.550 Round 4: 127 peptides, 15 chains. Longest chain 16 peptides. Score 0.585 Round 5: 133 peptides, 18 chains. Longest chain 16 peptides. Score 0.548 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 112, Estimated correctness of the model 23.6 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 7 % 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 3457 restraints for refining 1657 atoms. 3001 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1765 (Rfree = 0.000) for 1657 atoms. Found 0 (12 requested) and removed 5 (6 requested) atoms. Cycle 47: After refmac, R = 0.1665 (Rfree = 0.000) for 1648 atoms. Found 0 (12 requested) and removed 2 (6 requested) atoms. Cycle 48: After refmac, R = 0.1598 (Rfree = 0.000) for 1646 atoms. Found 0 (12 requested) and removed 1 (6 requested) atoms. Cycle 49: After refmac, R = 0.2102 (Rfree = 0.000) for 1644 atoms. TimeTaking 24.23