null Mon 24 Dec 00:49:50 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.6-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 00:49:54 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/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.6-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 205 and 0 Target number of residues in the AU: 205 Target solvent content: 0.6332 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 68.10 3754 reflections ( 98.69 % complete ) and 0 restraints for refining 2198 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3367 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2762 (Rfree = 0.000) for 2198 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.12 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 0 residues added, 2248 seeds are put forward Round 1: 149 peptides, 24 chains. Longest chain 14 peptides. Score 0.466 Round 2: 157 peptides, 20 chains. Longest chain 14 peptides. Score 0.581 Round 3: 174 peptides, 20 chains. Longest chain 23 peptides. Score 0.646 Round 4: 176 peptides, 18 chains. Longest chain 37 peptides. Score 0.685 Round 5: 170 peptides, 19 chains. Longest chain 28 peptides. Score 0.648 Taking the results from Round 4 Chains 18, Residues 158, Estimated correctness of the model 44.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3769 restraints for refining 1784 atoms. 3155 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2645 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 2: After refmac, R = 0.2401 (Rfree = 0.000) for 1779 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 3: After refmac, R = 0.2317 (Rfree = 0.000) for 1776 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 4: After refmac, R = 0.2270 (Rfree = 0.000) for 1770 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2353 (Rfree = 0.000) for 1769 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.19 Search for helices and strands: 0 residues in 0 chains, 1847 seeds are put forward NCS extension: 30 residues added (12 deleted due to clashes), 1877 seeds are put forward Round 1: 147 peptides, 21 chains. Longest chain 18 peptides. Score 0.518 Round 2: 157 peptides, 21 chains. Longest chain 17 peptides. Score 0.562 Round 3: 165 peptides, 20 chains. Longest chain 21 peptides. Score 0.613 Round 4: 161 peptides, 19 chains. Longest chain 17 peptides. Score 0.615 Round 5: 162 peptides, 16 chains. Longest chain 21 peptides. Score 0.669 Taking the results from Round 5 Chains 16, Residues 146, Estimated correctness of the model 39.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3941 restraints for refining 1784 atoms. 3373 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2780 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 7: After refmac, R = 0.2453 (Rfree = 0.000) for 1787 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.2356 (Rfree = 0.000) for 1781 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 9: After refmac, R = 0.2291 (Rfree = 0.000) for 1777 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2253 (Rfree = 0.000) for 1770 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.12 Search for helices and strands: 0 residues in 0 chains, 1827 seeds are put forward NCS extension: 0 residues added, 1827 seeds are put forward Round 1: 168 peptides, 22 chains. Longest chain 20 peptides. Score 0.589 Round 2: 174 peptides, 19 chains. Longest chain 21 peptides. Score 0.662 Round 3: 169 peptides, 20 chains. Longest chain 18 peptides. Score 0.628 Round 4: 174 peptides, 18 chains. Longest chain 27 peptides. Score 0.678 Round 5: 171 peptides, 19 chains. Longest chain 35 peptides. Score 0.652 Taking the results from Round 4 Chains 19, Residues 156, Estimated correctness of the model 42.6 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3658 restraints for refining 1784 atoms. 2982 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2584 (Rfree = 0.000) for 1784 atoms. Found 8 (11 requested) and removed 12 (5 requested) atoms. Cycle 12: After refmac, R = 0.2426 (Rfree = 0.000) for 1773 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. Cycle 13: After refmac, R = 0.2333 (Rfree = 0.000) for 1766 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2526 (Rfree = 0.000) for 1757 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2451 (Rfree = 0.000) for 1751 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1830 seeds are put forward Round 1: 139 peptides, 20 chains. Longest chain 22 peptides. Score 0.502 Round 2: 158 peptides, 18 chains. Longest chain 28 peptides. Score 0.621 Round 3: 156 peptides, 22 chains. Longest chain 22 peptides. Score 0.539 Round 4: 160 peptides, 18 chains. Longest chain 24 peptides. Score 0.629 Round 5: 156 peptides, 16 chains. Longest chain 20 peptides. Score 0.648 Taking the results from Round 5 Chains 16, Residues 140, Estimated correctness of the model 32.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3963 restraints for refining 1784 atoms. 3419 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2628 (Rfree = 0.000) for 1784 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 17: After refmac, R = 0.2336 (Rfree = 0.000) for 1775 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2335 (Rfree = 0.000) for 1770 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.2260 (Rfree = 0.000) for 1758 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2220 (Rfree = 0.000) for 1757 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 1822 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1840 seeds are put forward Round 1: 139 peptides, 19 chains. Longest chain 18 peptides. Score 0.523 Round 2: 161 peptides, 20 chains. Longest chain 20 peptides. Score 0.597 Round 3: 162 peptides, 18 chains. Longest chain 26 peptides. Score 0.636 Round 4: 167 peptides, 16 chains. Longest chain 27 peptides. Score 0.686 Round 5: 152 peptides, 20 chains. Longest chain 23 peptides. Score 0.560 Taking the results from Round 4 Chains 16, Residues 151, Estimated correctness of the model 45.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3748 restraints for refining 1782 atoms. 3160 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2773 (Rfree = 0.000) for 1782 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 22: After refmac, R = 0.2546 (Rfree = 0.000) for 1774 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 23: After refmac, R = 0.2472 (Rfree = 0.000) for 1774 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 24: After refmac, R = 0.2504 (Rfree = 0.000) for 1768 atoms. Found 0 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2559 (Rfree = 0.000) for 1761 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 1826 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1853 seeds are put forward Round 1: 126 peptides, 20 chains. Longest chain 21 peptides. Score 0.438 Round 2: 135 peptides, 20 chains. Longest chain 17 peptides. Score 0.483 Round 3: 144 peptides, 21 chains. Longest chain 13 peptides. Score 0.505 Round 4: 144 peptides, 22 chains. Longest chain 10 peptides. Score 0.484 Round 5: 136 peptides, 20 chains. Longest chain 11 peptides. Score 0.488 Taking the results from Round 3 Chains 21, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 4054 restraints for refining 1784 atoms. 3583 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2767 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 27: After refmac, R = 0.2528 (Rfree = 0.000) for 1787 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2517 (Rfree = 0.000) for 1784 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2541 (Rfree = 0.000) for 1782 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2445 (Rfree = 0.000) for 1778 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.14 Search for helices and strands: 0 residues in 0 chains, 1833 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1851 seeds are put forward Round 1: 134 peptides, 22 chains. Longest chain 17 peptides. Score 0.435 Round 2: 142 peptides, 18 chains. Longest chain 17 peptides. Score 0.556 Round 3: 144 peptides, 16 chains. Longest chain 17 peptides. Score 0.603 Round 4: 150 peptides, 15 chains. Longest chain 19 peptides. Score 0.644 Round 5: 133 peptides, 17 chains. Longest chain 12 peptides. Score 0.536 Taking the results from Round 4 Chains 15, Residues 135, Estimated correctness of the model 31.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3851 restraints for refining 1784 atoms. 3326 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2716 (Rfree = 0.000) for 1784 atoms. Found 9 (11 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2571 (Rfree = 0.000) for 1785 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2487 (Rfree = 0.000) for 1779 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2447 (Rfree = 0.000) for 1777 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2385 (Rfree = 0.000) for 1776 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.17 Search for helices and strands: 0 residues in 0 chains, 1819 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 1841 seeds are put forward Round 1: 125 peptides, 20 chains. Longest chain 12 peptides. Score 0.433 Round 2: 157 peptides, 22 chains. Longest chain 13 peptides. Score 0.543 Round 3: 140 peptides, 21 chains. Longest chain 12 peptides. Score 0.486 Round 4: 137 peptides, 17 chains. Longest chain 15 peptides. Score 0.554 Round 5: 142 peptides, 19 chains. Longest chain 20 peptides. Score 0.536 Taking the results from Round 4 Chains 17, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 4046 restraints for refining 1784 atoms. 3583 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2618 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 37: After refmac, R = 0.2440 (Rfree = 0.000) for 1786 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2354 (Rfree = 0.000) for 1779 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 39: After refmac, R = 0.2255 (Rfree = 0.000) for 1775 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2271 (Rfree = 0.000) for 1770 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 1825 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1838 seeds are put forward Round 1: 115 peptides, 19 chains. Longest chain 13 peptides. Score 0.404 Round 2: 118 peptides, 18 chains. Longest chain 15 peptides. Score 0.442 Round 3: 120 peptides, 18 chains. Longest chain 16 peptides. Score 0.453 Round 4: 119 peptides, 16 chains. Longest chain 14 peptides. Score 0.492 Round 5: 133 peptides, 18 chains. Longest chain 16 peptides. Score 0.516 Taking the results from Round 5 Chains 18, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 4070 restraints for refining 1784 atoms. 3628 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2477 (Rfree = 0.000) for 1784 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 42: After refmac, R = 0.2314 (Rfree = 0.000) for 1774 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2240 (Rfree = 0.000) for 1766 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2191 (Rfree = 0.000) for 1763 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2163 (Rfree = 0.000) for 1757 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.15 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward NCS extension: 0 residues added, 1816 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 10 peptides. Score 0.262 Round 2: 119 peptides, 21 chains. Longest chain 11 peptides. Score 0.378 Round 3: 123 peptides, 22 chains. Longest chain 9 peptides. Score 0.377 Round 4: 124 peptides, 20 chains. Longest chain 12 peptides. Score 0.428 Round 5: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 104, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3754 reflections ( 98.69 % complete ) and 4102 restraints for refining 1784 atoms. 3706 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2433 (Rfree = 0.000) for 1784 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2324 (Rfree = 0.000) for 1778 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2284 (Rfree = 0.000) for 1773 atoms. Found 0 (11 requested) and removed 1 (5 requested) atoms. Cycle 49: After refmac, R = 0.2260 (Rfree = 0.000) for 1771 atoms. Found 0 (11 requested) and removed 1 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:14:31 GMT 2018 Job finished. TimeTaking 24.68 Used memory is bytes: 1981072