null Mon 24 Dec 00:51:43 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 2i8d-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-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/2i8d-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-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 00:51:48 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/2i8d-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-4.0-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 194 and 0 Target number of residues in the AU: 194 Target solvent content: 0.6529 Checking the provided sequence file Detected sequence length: 123 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 246 Adjusted target solvent content: 0.56 Input MTZ file: 2i8d-4.0-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: 19 Cell parameters: 47.981 69.366 90.889 90.000 90.000 90.000 Input sequence file: 2i8d-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1968 target number of atoms Had to go as low as 0.85 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: 55.142 4.000 Wilson plot Bfac: 79.92 2744 reflections ( 98.21 % complete ) and 0 restraints for refining 2182 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3509 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3427 (Rfree = 0.000) for 2182 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 2216 seeds are put forward NCS extension: 0 residues added, 2216 seeds are put forward Round 1: 108 peptides, 20 chains. Longest chain 8 peptides. Score 0.341 Round 2: 138 peptides, 19 chains. Longest chain 17 peptides. Score 0.518 Round 3: 147 peptides, 19 chains. Longest chain 19 peptides. Score 0.558 Round 4: 146 peptides, 17 chains. Longest chain 23 peptides. Score 0.592 Round 5: 144 peptides, 20 chains. Longest chain 15 peptides. Score 0.525 Taking the results from Round 4 Chains 19, Residues 129, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3862 restraints for refining 1777 atoms. 3320 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2923 (Rfree = 0.000) for 1777 atoms. Found 7 (8 requested) and removed 23 (4 requested) atoms. Cycle 2: After refmac, R = 0.2709 (Rfree = 0.000) for 1720 atoms. Found 5 (8 requested) and removed 20 (4 requested) atoms. Cycle 3: After refmac, R = 0.2529 (Rfree = 0.000) for 1683 atoms. Found 4 (8 requested) and removed 11 (4 requested) atoms. Cycle 4: After refmac, R = 0.2481 (Rfree = 0.000) for 1663 atoms. Found 5 (7 requested) and removed 9 (3 requested) atoms. Cycle 5: After refmac, R = 0.2430 (Rfree = 0.000) for 1645 atoms. Found 4 (7 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.34 Search for helices and strands: 0 residues in 0 chains, 1721 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 1744 seeds are put forward Round 1: 121 peptides, 18 chains. Longest chain 18 peptides. Score 0.458 Round 2: 145 peptides, 17 chains. Longest chain 20 peptides. Score 0.588 Round 3: 147 peptides, 16 chains. Longest chain 20 peptides. Score 0.614 Round 4: 148 peptides, 16 chains. Longest chain 39 peptides. Score 0.618 Round 5: 140 peptides, 16 chains. Longest chain 18 peptides. Score 0.586 Taking the results from Round 4 Chains 16, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3575 restraints for refining 1696 atoms. 3063 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2346 (Rfree = 0.000) for 1696 atoms. Found 3 (8 requested) and removed 9 (4 requested) atoms. Cycle 7: After refmac, R = 0.2149 (Rfree = 0.000) for 1685 atoms. Found 3 (8 requested) and removed 10 (4 requested) atoms. Cycle 8: After refmac, R = 0.2053 (Rfree = 0.000) for 1677 atoms. Found 1 (7 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.2006 (Rfree = 0.000) for 1669 atoms. Found 1 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.1966 (Rfree = 0.000) for 1664 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.37 Search for helices and strands: 0 residues in 0 chains, 1735 seeds are put forward NCS extension: 45 residues added (2 deleted due to clashes), 1780 seeds are put forward Round 1: 136 peptides, 21 chains. Longest chain 18 peptides. Score 0.466 Round 2: 147 peptides, 18 chains. Longest chain 17 peptides. Score 0.577 Round 3: 157 peptides, 19 chains. Longest chain 33 peptides. Score 0.599 Round 4: 152 peptides, 17 chains. Longest chain 20 peptides. Score 0.616 Round 5: 155 peptides, 16 chains. Longest chain 37 peptides. Score 0.645 Taking the results from Round 5 Chains 16, Residues 139, Estimated correctness of the model 4.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3843 restraints for refining 1777 atoms. 3303 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2739 (Rfree = 0.000) for 1777 atoms. Found 6 (8 requested) and removed 13 (4 requested) atoms. Cycle 12: After refmac, R = 0.2524 (Rfree = 0.000) for 1757 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 13: After refmac, R = 0.2526 (Rfree = 0.000) for 1744 atoms. Found 5 (8 requested) and removed 17 (4 requested) atoms. Cycle 14: After refmac, R = 0.2289 (Rfree = 0.000) for 1729 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.2398 (Rfree = 0.000) for 1723 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.41 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 1836 seeds are put forward Round 1: 114 peptides, 16 chains. Longest chain 28 peptides. Score 0.468 Round 2: 126 peptides, 17 chains. Longest chain 18 peptides. Score 0.504 Round 3: 131 peptides, 15 chains. Longest chain 24 peptides. Score 0.568 Round 4: 130 peptides, 14 chains. Longest chain 26 peptides. Score 0.583 Round 5: 140 peptides, 15 chains. Longest chain 39 peptides. Score 0.605 Taking the results from Round 5 Chains 17, Residues 125, Estimated correctness of the model 0.0 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3633 restraints for refining 1777 atoms. 3021 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2656 (Rfree = 0.000) for 1777 atoms. Found 4 (8 requested) and removed 27 (4 requested) atoms. Cycle 17: After refmac, R = 0.2467 (Rfree = 0.000) for 1735 atoms. Found 7 (8 requested) and removed 13 (4 requested) atoms. Cycle 18: After refmac, R = 0.2221 (Rfree = 0.000) for 1721 atoms. Found 2 (8 requested) and removed 13 (4 requested) atoms. Cycle 19: After refmac, R = 0.2312 (Rfree = 0.000) for 1705 atoms. Found 2 (8 requested) and removed 13 (4 requested) atoms. Cycle 20: After refmac, R = 0.2086 (Rfree = 0.000) for 1691 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.41 Search for helices and strands: 0 residues in 0 chains, 1752 seeds are put forward NCS extension: 49 residues added (2 deleted due to clashes), 1801 seeds are put forward Round 1: 114 peptides, 23 chains. Longest chain 10 peptides. Score 0.302 Round 2: 117 peptides, 18 chains. Longest chain 14 peptides. Score 0.437 Round 3: 125 peptides, 19 chains. Longest chain 13 peptides. Score 0.456 Round 4: 121 peptides, 21 chains. Longest chain 15 peptides. Score 0.389 Round 5: 125 peptides, 20 chains. Longest chain 16 peptides. Score 0.433 Taking the results from Round 3 Chains 19, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 4011 restraints for refining 1777 atoms. 3606 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2968 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 22: After refmac, R = 0.2441 (Rfree = 0.000) for 1753 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 23: After refmac, R = 0.2371 (Rfree = 0.000) for 1734 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 24: After refmac, R = 0.2425 (Rfree = 0.000) for 1719 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 25: After refmac, R = 0.2357 (Rfree = 0.000) for 1717 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.38 Search for helices and strands: 0 residues in 0 chains, 1789 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1807 seeds are put forward Round 1: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.294 Round 2: 118 peptides, 18 chains. Longest chain 13 peptides. Score 0.442 Round 3: 110 peptides, 17 chains. Longest chain 14 peptides. Score 0.424 Round 4: 127 peptides, 18 chains. Longest chain 15 peptides. Score 0.487 Round 5: 131 peptides, 19 chains. Longest chain 15 peptides. Score 0.485 Taking the results from Round 4 Chains 19, Residues 109, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3851 restraints for refining 1775 atoms. 3404 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2992 (Rfree = 0.000) for 1775 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 27: After refmac, R = 0.2575 (Rfree = 0.000) for 1751 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 28: After refmac, R = 0.2415 (Rfree = 0.000) for 1733 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 29: After refmac, R = 0.1984 (Rfree = 0.000) for 1722 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 30: After refmac, R = 0.2203 (Rfree = 0.000) for 1720 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.67 3.39 Search for helices and strands: 0 residues in 0 chains, 1778 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1787 seeds are put forward Round 1: 116 peptides, 24 chains. Longest chain 7 peptides. Score 0.290 Round 2: 118 peptides, 19 chains. Longest chain 13 peptides. Score 0.420 Round 3: 129 peptides, 21 chains. Longest chain 13 peptides. Score 0.431 Round 4: 118 peptides, 18 chains. Longest chain 13 peptides. Score 0.442 Round 5: 122 peptides, 17 chains. Longest chain 16 peptides. Score 0.485 Taking the results from Round 5 Chains 17, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3955 restraints for refining 1777 atoms. 3552 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2666 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 32: After refmac, R = 0.2582 (Rfree = 0.000) for 1755 atoms. Found 4 (8 requested) and removed 36 (4 requested) atoms. Cycle 33: After refmac, R = 0.2136 (Rfree = 0.000) for 1711 atoms. Found 2 (8 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.2101 (Rfree = 0.000) for 1700 atoms. Found 4 (8 requested) and removed 45 (4 requested) atoms. Cycle 35: After refmac, R = 0.2357 (Rfree = 0.000) for 1654 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.28 Search for helices and strands: 0 residues in 0 chains, 1710 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1723 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 13 peptides. Score 0.319 Round 2: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.364 Round 3: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.362 Round 4: 120 peptides, 18 chains. Longest chain 13 peptides. Score 0.453 Round 5: 132 peptides, 18 chains. Longest chain 19 peptides. Score 0.511 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 ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3949 restraints for refining 1777 atoms. 3511 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2909 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 37: After refmac, R = 0.2671 (Rfree = 0.000) for 1760 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 38: After refmac, R = 0.2270 (Rfree = 0.000) for 1750 atoms. Found 5 (8 requested) and removed 14 (4 requested) atoms. Cycle 39: After refmac, R = 0.2276 (Rfree = 0.000) for 1738 atoms. Found 2 (8 requested) and removed 14 (4 requested) atoms. Cycle 40: After refmac, R = 0.2219 (Rfree = 0.000) for 1718 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.30 Search for helices and strands: 0 residues in 0 chains, 1781 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1797 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.274 Round 2: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.349 Round 3: 101 peptides, 17 chains. Longest chain 12 peptides. Score 0.375 Round 4: 100 peptides, 15 chains. Longest chain 12 peptides. Score 0.418 Round 5: 102 peptides, 17 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 4 Chains 16, Residues 85, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2744 reflections ( 98.21 % complete ) and 3888 restraints for refining 1777 atoms. 3524 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2947 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 42: After refmac, R = 0.2496 (Rfree = 0.000) for 1766 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 43: After refmac, R = 0.2627 (Rfree = 0.000) for 1752 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.2290 (Rfree = 0.000) for 1745 atoms. Found 4 (8 requested) and removed 13 (4 requested) atoms. Cycle 45: After refmac, R = 0.2075 (Rfree = 0.000) for 1730 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.37 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1820 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 6 peptides. Score 0.222 Round 2: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.329 Round 3: 96 peptides, 19 chains. Longest chain 7 peptides. Score 0.296 Round 4: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.327 Round 5: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 76, 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 2i8d-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2744 reflections ( 98.21 % complete ) and 4001 restraints for refining 1746 atoms. 3714 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2430 (Rfree = 0.000) for 1746 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2251 (Rfree = 0.000) for 1735 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2314 (Rfree = 0.000) for 1725 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2291 (Rfree = 0.000) for 1717 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:16:08 GMT 2018 Job finished. TimeTaking 24.42 Used memory is bytes: 2369816