null Mon 24 Dec 07:28:23 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-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ifx-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.2-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-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.2-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 07:28:28 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-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ifx-3.2-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 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-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-3.2-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 3.201 Wilson plot Bfac: 67.97 4280 reflections ( 99.07 % complete ) and 0 restraints for refining 2032 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3156 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2799 (Rfree = 0.000) for 2032 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward NCS extension: 0 residues added, 2054 seeds are put forward Round 1: 111 peptides, 16 chains. Longest chain 14 peptides. Score 0.479 Round 2: 141 peptides, 20 chains. Longest chain 17 peptides. Score 0.544 Round 3: 138 peptides, 18 chains. Longest chain 16 peptides. Score 0.572 Round 4: 148 peptides, 18 chains. Longest chain 16 peptides. Score 0.618 Round 5: 141 peptides, 14 chains. Longest chain 18 peptides. Score 0.665 Taking the results from Round 5 Chains 15, Residues 127, Estimated correctness of the model 57.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3374 restraints for refining 1665 atoms. 2793 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2748 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 2: After refmac, R = 0.2859 (Rfree = 0.000) for 1635 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 3: After refmac, R = 0.2478 (Rfree = 0.000) for 1625 atoms. Found 11 (14 requested) and removed 15 (7 requested) atoms. Cycle 4: After refmac, R = 0.2737 (Rfree = 0.000) for 1613 atoms. Found 11 (14 requested) and removed 18 (7 requested) atoms. Cycle 5: After refmac, R = 0.2245 (Rfree = 0.000) for 1603 atoms. Found 4 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.03 Search for helices and strands: 0 residues in 0 chains, 1674 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1692 seeds are put forward Round 1: 124 peptides, 19 chains. Longest chain 13 peptides. Score 0.478 Round 2: 145 peptides, 20 chains. Longest chain 18 peptides. Score 0.563 Round 3: 141 peptides, 18 chains. Longest chain 17 peptides. Score 0.586 Round 4: 146 peptides, 19 chains. Longest chain 16 peptides. Score 0.589 Round 5: 140 peptides, 18 chains. Longest chain 18 peptides. Score 0.582 Taking the results from Round 4 Chains 21, Residues 127, Estimated correctness of the model 38.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3324 restraints for refining 1665 atoms. 2729 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2862 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 43 (7 requested) atoms. Cycle 7: After refmac, R = 0.2710 (Rfree = 0.000) for 1625 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 8: After refmac, R = 0.2274 (Rfree = 0.000) for 1611 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 9: After refmac, R = 0.1956 (Rfree = 0.000) for 1604 atoms. Found 10 (14 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.1899 (Rfree = 0.000) for 1605 atoms. Found 3 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 1653 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 1673 seeds are put forward Round 1: 128 peptides, 20 chains. Longest chain 17 peptides. Score 0.476 Round 2: 132 peptides, 15 chains. Longest chain 18 peptides. Score 0.607 Round 3: 127 peptides, 14 chains. Longest chain 17 peptides. Score 0.606 Round 4: 130 peptides, 14 chains. Longest chain 18 peptides. Score 0.619 Round 5: 130 peptides, 14 chains. Longest chain 17 peptides. Score 0.619 Taking the results from Round 5 Chains 15, Residues 116, Estimated correctness of the model 46.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3600 restraints for refining 1665 atoms. 3090 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2422 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 12: After refmac, R = 0.2254 (Rfree = 0.000) for 1663 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 13: After refmac, R = 0.2209 (Rfree = 0.000) for 1661 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. Cycle 14: After refmac, R = 0.2150 (Rfree = 0.000) for 1661 atoms. Found 13 (14 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.2618 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 1697 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 1718 seeds are put forward Round 1: 112 peptides, 17 chains. Longest chain 14 peptides. Score 0.460 Round 2: 132 peptides, 17 chains. Longest chain 18 peptides. Score 0.565 Round 3: 129 peptides, 15 chains. Longest chain 15 peptides. Score 0.594 Round 4: 130 peptides, 14 chains. Longest chain 22 peptides. Score 0.619 Round 5: 131 peptides, 15 chains. Longest chain 15 peptides. Score 0.603 Taking the results from Round 4 Chains 16, Residues 116, Estimated correctness of the model 46.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3445 restraints for refining 1665 atoms. 2924 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2550 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 17: After refmac, R = 0.2654 (Rfree = 0.000) for 1642 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 18: After refmac, R = 0.2262 (Rfree = 0.000) for 1630 atoms. Found 12 (14 requested) and removed 13 (7 requested) atoms. Cycle 19: After refmac, R = 0.2127 (Rfree = 0.000) for 1623 atoms. Found 13 (14 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.2085 (Rfree = 0.000) for 1625 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.02 Search for helices and strands: 0 residues in 0 chains, 1683 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1710 seeds are put forward Round 1: 101 peptides, 17 chains. Longest chain 10 peptides. Score 0.395 Round 2: 114 peptides, 18 chains. Longest chain 12 peptides. Score 0.446 Round 3: 123 peptides, 18 chains. Longest chain 13 peptides. Score 0.496 Round 4: 133 peptides, 16 chains. Longest chain 16 peptides. Score 0.591 Round 5: 126 peptides, 16 chains. Longest chain 15 peptides. Score 0.558 Taking the results from Round 4 Chains 16, Residues 117, Estimated correctness of the model 38.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3664 restraints for refining 1665 atoms. 3212 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2349 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 22: After refmac, R = 0.2004 (Rfree = 0.000) for 1661 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.1959 (Rfree = 0.000) for 1661 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.2354 (Rfree = 0.000) for 1657 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 25: After refmac, R = 0.1795 (Rfree = 0.000) for 1658 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 1711 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1725 seeds are put forward Round 1: 110 peptides, 16 chains. Longest chain 14 peptides. Score 0.474 Round 2: 116 peptides, 14 chains. Longest chain 15 peptides. Score 0.553 Round 3: 117 peptides, 12 chains. Longest chain 17 peptides. Score 0.603 Round 4: 115 peptides, 13 chains. Longest chain 15 peptides. Score 0.571 Round 5: 117 peptides, 13 chains. Longest chain 16 peptides. Score 0.581 Taking the results from Round 3 Chains 12, Residues 105, Estimated correctness of the model 41.8 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3564 restraints for refining 1665 atoms. 3113 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2216 (Rfree = 0.000) for 1665 atoms. Found 10 (14 requested) and removed 17 (7 requested) atoms. Cycle 27: After refmac, R = 0.1977 (Rfree = 0.000) for 1658 atoms. Found 10 (14 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.1957 (Rfree = 0.000) for 1660 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.1859 (Rfree = 0.000) for 1656 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1819 (Rfree = 0.000) for 1655 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 1695 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1710 seeds are put forward Round 1: 113 peptides, 17 chains. Longest chain 18 peptides. Score 0.466 Round 2: 119 peptides, 15 chains. Longest chain 14 peptides. Score 0.546 Round 3: 125 peptides, 17 chains. Longest chain 15 peptides. Score 0.530 Round 4: 117 peptides, 17 chains. Longest chain 14 peptides. Score 0.488 Round 5: 128 peptides, 14 chains. Longest chain 16 peptides. Score 0.610 Taking the results from Round 5 Chains 14, Residues 114, Estimated correctness of the model 43.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3694 restraints for refining 1664 atoms. 3252 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2068 (Rfree = 0.000) for 1664 atoms. Found 13 (14 requested) and removed 16 (7 requested) atoms. Cycle 32: After refmac, R = 0.1882 (Rfree = 0.000) for 1661 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 33: After refmac, R = 0.1889 (Rfree = 0.000) for 1654 atoms. Found 11 (14 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1871 (Rfree = 0.000) for 1656 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1833 (Rfree = 0.000) for 1653 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 1699 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1720 seeds are put forward Round 1: 111 peptides, 14 chains. Longest chain 15 peptides. Score 0.528 Round 2: 111 peptides, 16 chains. Longest chain 15 peptides. Score 0.479 Round 3: 112 peptides, 15 chains. Longest chain 17 peptides. Score 0.509 Round 4: 119 peptides, 16 chains. Longest chain 15 peptides. Score 0.522 Round 5: 134 peptides, 18 chains. Longest chain 15 peptides. Score 0.553 Taking the results from Round 5 Chains 18, Residues 116, Estimated correctness of the model 27.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3697 restraints for refining 1665 atoms. 3251 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2224 (Rfree = 0.000) for 1665 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 37: After refmac, R = 0.2028 (Rfree = 0.000) for 1664 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. Cycle 38: After refmac, R = 0.1904 (Rfree = 0.000) for 1658 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1841 (Rfree = 0.000) for 1654 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1793 (Rfree = 0.000) for 1648 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 1693 seeds are put forward NCS extension: 16 residues added (7 deleted due to clashes), 1709 seeds are put forward Round 1: 97 peptides, 14 chains. Longest chain 12 peptides. Score 0.451 Round 2: 110 peptides, 14 chains. Longest chain 14 peptides. Score 0.523 Round 3: 107 peptides, 11 chains. Longest chain 15 peptides. Score 0.578 Round 4: 131 peptides, 16 chains. Longest chain 25 peptides. Score 0.582 Round 5: 109 peptides, 14 chains. Longest chain 13 peptides. Score 0.517 Taking the results from Round 4 Chains 16, Residues 115, Estimated correctness of the model 36.1 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3604 restraints for refining 1665 atoms. 3135 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2200 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.2459 (Rfree = 0.000) for 1666 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 43: After refmac, R = 0.2271 (Rfree = 0.000) for 1668 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1854 (Rfree = 0.000) for 1672 atoms. Found 11 (15 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.2104 (Rfree = 0.000) for 1674 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.02 Search for helices and strands: 0 residues in 0 chains, 1725 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1738 seeds are put forward Round 1: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.391 Round 2: 110 peptides, 15 chains. Longest chain 15 peptides. Score 0.498 Round 3: 110 peptides, 15 chains. Longest chain 14 peptides. Score 0.498 Round 4: 116 peptides, 16 chains. Longest chain 14 peptides. Score 0.507 Round 5: 103 peptides, 13 chains. Longest chain 12 peptides. Score 0.510 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 90, Estimated correctness of the model 14.5 % 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 3756 restraints for refining 1665 atoms. 3409 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1860 (Rfree = 0.000) for 1665 atoms. Found 0 (14 requested) and removed 4 (7 requested) atoms. Cycle 47: After refmac, R = 0.2658 (Rfree = 0.000) for 1660 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1811 (Rfree = 0.000) for 1652 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1639 (Rfree = 0.000) for 1645 atoms. Found 0 (14 requested) and removed 3 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:53:20 GMT 2018 Job finished. TimeTaking 24.94 Used memory is bytes: 10517936