null Sun 23 Dec 23:43:34 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i8d-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-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-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-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 23:43:38 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-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 218 and 0 Target number of residues in the AU: 218 Target solvent content: 0.6100 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-3.2-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-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1968 target number of atoms Had to go as low as 0.80 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 3.200 Wilson plot Bfac: 56.63 5298 reflections ( 99.07 % complete ) and 0 restraints for refining 2194 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3200 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3172 (Rfree = 0.000) for 2194 atoms. Found 15 (19 requested) and removed 30 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.99 2.76 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward NCS extension: 0 residues added, 2242 seeds are put forward Round 1: 140 peptides, 21 chains. Longest chain 13 peptides. Score 0.486 Round 2: 164 peptides, 23 chains. Longest chain 15 peptides. Score 0.554 Round 3: 189 peptides, 21 chains. Longest chain 25 peptides. Score 0.682 Round 4: 185 peptides, 22 chains. Longest chain 22 peptides. Score 0.653 Round 5: 187 peptides, 19 chains. Longest chain 25 peptides. Score 0.705 Taking the results from Round 5 Chains 21, Residues 168, Estimated correctness of the model 66.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3509 restraints for refining 1797 atoms. 2816 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2777 (Rfree = 0.000) for 1797 atoms. Found 9 (16 requested) and removed 16 (8 requested) atoms. Cycle 2: After refmac, R = 0.2744 (Rfree = 0.000) for 1770 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 3: After refmac, R = 0.2781 (Rfree = 0.000) for 1762 atoms. Found 13 (14 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2587 (Rfree = 0.000) for 1755 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 5: After refmac, R = 0.2389 (Rfree = 0.000) for 1750 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 2.81 Search for helices and strands: 0 residues in 0 chains, 1843 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 1871 seeds are put forward Round 1: 170 peptides, 25 chains. Longest chain 22 peptides. Score 0.542 Round 2: 183 peptides, 21 chains. Longest chain 20 peptides. Score 0.662 Round 3: 185 peptides, 21 chains. Longest chain 21 peptides. Score 0.668 Round 4: 186 peptides, 17 chains. Longest chain 27 peptides. Score 0.730 Round 5: 187 peptides, 18 chains. Longest chain 29 peptides. Score 0.719 Taking the results from Round 4 Chains 21, Residues 169, Estimated correctness of the model 71.3 % 4 chains (63 residues) have been docked in sequence Building loops using Loopy2018 21 chains (169 residues) following loop building 4 chains (63 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3093 restraints for refining 1797 atoms. 2143 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2850 (Rfree = 0.000) for 1797 atoms. Found 7 (14 requested) and removed 24 (8 requested) atoms. Cycle 7: After refmac, R = 0.2833 (Rfree = 0.000) for 1767 atoms. Found 13 (13 requested) and removed 11 (7 requested) atoms. Cycle 8: After refmac, R = 0.2992 (Rfree = 0.000) for 1766 atoms. Found 13 (13 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.2475 (Rfree = 0.000) for 1759 atoms. Found 10 (13 requested) and removed 10 (7 requested) atoms. Cycle 10: After refmac, R = 0.2425 (Rfree = 0.000) for 1757 atoms. Found 7 (12 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 2.87 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 1847 seeds are put forward Round 1: 164 peptides, 21 chains. Longest chain 18 peptides. Score 0.591 Round 2: 189 peptides, 18 chains. Longest chain 28 peptides. Score 0.724 Round 3: 182 peptides, 18 chains. Longest chain 34 peptides. Score 0.704 Round 4: 177 peptides, 20 chains. Longest chain 27 peptides. Score 0.657 Round 5: 177 peptides, 22 chains. Longest chain 20 peptides. Score 0.624 Taking the results from Round 2 Chains 18, Residues 171, Estimated correctness of the model 70.1 % 5 chains (90 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 83 A Built loop between residues 101 A and 106 A 15 chains (180 residues) following loop building 3 chains (104 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 2612 restraints for refining 1800 atoms. 1446 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2860 (Rfree = 0.000) for 1800 atoms. Found 13 (13 requested) and removed 22 (8 requested) atoms. Cycle 12: After refmac, R = 0.2487 (Rfree = 0.000) for 1785 atoms. Found 12 (12 requested) and removed 14 (8 requested) atoms. Cycle 13: After refmac, R = 0.2433 (Rfree = 0.000) for 1781 atoms. Found 12 (12 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2227 (Rfree = 0.000) for 1780 atoms. Found 7 (11 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.2173 (Rfree = 0.000) for 1776 atoms. Found 5 (11 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 2.76 Search for helices and strands: 0 residues in 0 chains, 1863 seeds are put forward NCS extension: 68 residues added (2 deleted due to clashes), 1931 seeds are put forward Round 1: 153 peptides, 18 chains. Longest chain 22 peptides. Score 0.602 Round 2: 168 peptides, 17 chains. Longest chain 24 peptides. Score 0.674 Round 3: 177 peptides, 18 chains. Longest chain 27 peptides. Score 0.688 Round 4: 184 peptides, 19 chains. Longest chain 25 peptides. Score 0.695 Round 5: 174 peptides, 14 chains. Longest chain 29 peptides. Score 0.737 Taking the results from Round 5 Chains 17, Residues 160, Estimated correctness of the model 72.6 % 4 chains (55 residues) have been docked in sequence Building loops using Loopy2018 17 chains (160 residues) following loop building 4 chains (55 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3160 restraints for refining 1797 atoms. 2283 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2861 (Rfree = 0.000) for 1797 atoms. Found 10 (11 requested) and removed 16 (8 requested) atoms. Cycle 17: After refmac, R = 0.2431 (Rfree = 0.000) for 1785 atoms. Found 11 (11 requested) and removed 12 (8 requested) atoms. Cycle 18: After refmac, R = 0.2452 (Rfree = 0.000) for 1781 atoms. Found 11 (11 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.2252 (Rfree = 0.000) for 1778 atoms. Found 5 (10 requested) and removed 12 (7 requested) atoms. Cycle 20: After refmac, R = 0.2189 (Rfree = 0.000) for 1766 atoms. Found 4 (9 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 2.80 Search for helices and strands: 0 residues in 0 chains, 1815 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 1846 seeds are put forward Round 1: 148 peptides, 18 chains. Longest chain 15 peptides. Score 0.581 Round 2: 172 peptides, 16 chains. Longest chain 29 peptides. Score 0.702 Round 3: 161 peptides, 18 chains. Longest chain 24 peptides. Score 0.632 Round 4: 167 peptides, 16 chains. Longest chain 27 peptides. Score 0.686 Round 5: 174 peptides, 17 chains. Longest chain 25 peptides. Score 0.693 Taking the results from Round 2 Chains 18, Residues 156, Estimated correctness of the model 65.6 % 3 chains (47 residues) have been docked in sequence Building loops using Loopy2018 18 chains (156 residues) following loop building 3 chains (47 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3181 restraints for refining 1797 atoms. 2354 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2459 (Rfree = 0.000) for 1797 atoms. Found 10 (10 requested) and removed 12 (8 requested) atoms. Cycle 22: After refmac, R = 0.2315 (Rfree = 0.000) for 1790 atoms. Found 2 (9 requested) and removed 9 (8 requested) atoms. Cycle 23: After refmac, R = 0.2215 (Rfree = 0.000) for 1779 atoms. Found 6 (9 requested) and removed 10 (8 requested) atoms. Cycle 24: After refmac, R = 0.2163 (Rfree = 0.000) for 1773 atoms. Found 3 (8 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.2155 (Rfree = 0.000) for 1769 atoms. Found 2 (8 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.04 2.81 Search for helices and strands: 0 residues in 0 chains, 1817 seeds are put forward NCS extension: 48 residues added (3 deleted due to clashes), 1865 seeds are put forward Round 1: 149 peptides, 19 chains. Longest chain 20 peptides. Score 0.567 Round 2: 162 peptides, 18 chains. Longest chain 26 peptides. Score 0.636 Round 3: 164 peptides, 17 chains. Longest chain 25 peptides. Score 0.660 Round 4: 171 peptides, 19 chains. Longest chain 24 peptides. Score 0.652 Round 5: 166 peptides, 18 chains. Longest chain 23 peptides. Score 0.651 Taking the results from Round 3 Chains 18, Residues 147, Estimated correctness of the model 56.2 % 3 chains (60 residues) have been docked in sequence ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3200 restraints for refining 1797 atoms. 2354 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2420 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.2333 (Rfree = 0.000) for 1789 atoms. Found 1 (8 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2296 (Rfree = 0.000) for 1779 atoms. Found 2 (7 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.2302 (Rfree = 0.000) for 1774 atoms. Found 3 (7 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.2275 (Rfree = 0.000) for 1768 atoms. Found 1 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 2.86 Search for helices and strands: 0 residues in 0 chains, 1824 seeds are put forward NCS extension: 47 residues added (0 deleted due to clashes), 1871 seeds are put forward Round 1: 162 peptides, 21 chains. Longest chain 21 peptides. Score 0.583 Round 2: 168 peptides, 15 chains. Longest chain 22 peptides. Score 0.705 Round 3: 167 peptides, 16 chains. Longest chain 24 peptides. Score 0.686 Round 4: 167 peptides, 19 chains. Longest chain 22 peptides. Score 0.638 Round 5: 166 peptides, 15 chains. Longest chain 24 peptides. Score 0.698 Taking the results from Round 2 Chains 16, Residues 153, Estimated correctness of the model 66.2 % 2 chains (39 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 A and 85 A 13 chains (156 residues) following loop building 1 chains (47 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3279 restraints for refining 1797 atoms. 2487 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2587 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 17 (8 requested) atoms. Cycle 32: After refmac, R = 0.2359 (Rfree = 0.000) for 1786 atoms. Found 6 (8 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.2256 (Rfree = 0.000) for 1784 atoms. Found 5 (8 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2173 (Rfree = 0.000) for 1781 atoms. Found 3 (7 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.2130 (Rfree = 0.000) for 1775 atoms. Found 2 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 2.79 Search for helices and strands: 0 residues in 0 chains, 1825 seeds are put forward NCS extension: 52 residues added (11 deleted due to clashes), 1877 seeds are put forward Round 1: 143 peptides, 17 chains. Longest chain 27 peptides. Score 0.580 Round 2: 159 peptides, 18 chains. Longest chain 28 peptides. Score 0.625 Round 3: 165 peptides, 20 chains. Longest chain 25 peptides. Score 0.613 Round 4: 164 peptides, 20 chains. Longest chain 18 peptides. Score 0.609 Round 5: 154 peptides, 19 chains. Longest chain 26 peptides. Score 0.587 Taking the results from Round 2 Chains 19, Residues 141, Estimated correctness of the model 47.6 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3624 restraints for refining 1797 atoms. 2952 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2315 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.2054 (Rfree = 0.000) for 1794 atoms. Found 5 (8 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1997 (Rfree = 0.000) for 1791 atoms. Found 5 (8 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1981 (Rfree = 0.000) for 1785 atoms. Found 2 (8 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.1971 (Rfree = 0.000) for 1776 atoms. Found 4 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 2.81 Search for helices and strands: 0 residues in 0 chains, 1827 seeds are put forward NCS extension: 39 residues added (7 deleted due to clashes), 1866 seeds are put forward Round 1: 152 peptides, 19 chains. Longest chain 20 peptides. Score 0.579 Round 2: 153 peptides, 15 chains. Longest chain 28 peptides. Score 0.654 Round 3: 158 peptides, 14 chains. Longest chain 29 peptides. Score 0.688 Round 4: 156 peptides, 18 chains. Longest chain 18 peptides. Score 0.613 Round 5: 157 peptides, 16 chains. Longest chain 26 peptides. Score 0.652 Taking the results from Round 3 Chains 14, Residues 144, Estimated correctness of the model 62.6 % 1 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3475 restraints for refining 1795 atoms. 2775 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2234 (Rfree = 0.000) for 1795 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. Cycle 42: After refmac, R = 0.2150 (Rfree = 0.000) for 1793 atoms. Found 6 (8 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2097 (Rfree = 0.000) for 1791 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.2082 (Rfree = 0.000) for 1786 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1904 (Rfree = 0.000) for 1784 atoms. Found 2 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 2.81 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward NCS extension: 19 residues added (6 deleted due to clashes), 1837 seeds are put forward Round 1: 133 peptides, 19 chains. Longest chain 15 peptides. Score 0.495 Round 2: 153 peptides, 18 chains. Longest chain 22 peptides. Score 0.602 Round 3: 155 peptides, 19 chains. Longest chain 18 peptides. Score 0.591 Round 4: 155 peptides, 16 chains. Longest chain 22 peptides. Score 0.645 Round 5: 154 peptides, 17 chains. Longest chain 25 peptides. Score 0.623 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 139, Estimated correctness of the model 52.6 % 1 chains (21 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2i8d-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5298 reflections ( 99.07 % complete ) and 3587 restraints for refining 1797 atoms. 2932 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2365 (Rfree = 0.000) for 1797 atoms. Found 0 (8 requested) and removed 2 (8 requested) atoms. Cycle 47: After refmac, R = 0.2238 (Rfree = 0.000) for 1793 atoms. Found 0 (8 requested) and removed 3 (8 requested) atoms. Cycle 48: After refmac, R = 0.2201 (Rfree = 0.000) for 1788 atoms. Found 0 (8 requested) and removed 3 (8 requested) atoms. Cycle 49: After refmac, R = 0.2353 (Rfree = 0.000) for 1784 atoms. Found 0 (8 requested) and removed 1 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:13:33 GMT 2018 Job finished. TimeTaking 29.99 Used memory is bytes: 18051888