Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i8d-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-parrot-hancs ############### 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 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.8-parrot-hancs/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 199 and 0 Target number of residues in the AU: 199 Target solvent content: 0.6440 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-3.8-parrot-hancs.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-3.8-parrot-hancs.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 3.801 Wilson plot Bfac: 74.39 3202 reflections ( 98.46 % complete ) and 0 restraints for refining 2177 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3475 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3444 (Rfree = 0.000) for 2177 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 2222 seeds are put forward NCS extension: 0 residues added, 2222 seeds are put forward Round 1: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.352 Round 2: 145 peptides, 19 chains. Longest chain 19 peptides. Score 0.549 Round 3: 145 peptides, 20 chains. Longest chain 24 peptides. Score 0.529 Round 4: 160 peptides, 16 chains. Longest chain 24 peptides. Score 0.662 Round 5: 163 peptides, 17 chains. Longest chain 25 peptides. Score 0.656 Taking the results from Round 4 Chains 17, Residues 144, Estimated correctness of the model 25.6 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3661 restraints for refining 1778 atoms. 3031 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2835 (Rfree = 0.000) for 1778 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2645 (Rfree = 0.000) for 1757 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.2743 (Rfree = 0.000) for 1746 atoms. Found 1 (9 requested) and removed 10 (4 requested) atoms. Cycle 4: After refmac, R = 0.2781 (Rfree = 0.000) for 1737 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 5: After refmac, R = 0.2721 (Rfree = 0.000) for 1734 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.36 Search for helices and strands: 0 residues in 0 chains, 1802 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 1825 seeds are put forward Round 1: 123 peptides, 18 chains. Longest chain 10 peptides. Score 0.468 Round 2: 139 peptides, 17 chains. Longest chain 24 peptides. Score 0.563 Round 3: 140 peptides, 16 chains. Longest chain 22 peptides. Score 0.586 Round 4: 147 peptides, 15 chains. Longest chain 21 peptides. Score 0.632 Round 5: 136 peptides, 15 chains. Longest chain 21 peptides. Score 0.589 Taking the results from Round 4 Chains 15, Residues 132, Estimated correctness of the model 13.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4106 restraints for refining 1780 atoms. 3593 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3097 (Rfree = 0.000) for 1780 atoms. Found 7 (9 requested) and removed 7 (4 requested) atoms. Cycle 7: After refmac, R = 0.2674 (Rfree = 0.000) for 1771 atoms. Found 4 (9 requested) and removed 13 (4 requested) atoms. Cycle 8: After refmac, R = 0.2511 (Rfree = 0.000) for 1753 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 9: After refmac, R = 0.2427 (Rfree = 0.000) for 1739 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 10: After refmac, R = 0.2422 (Rfree = 0.000) for 1736 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.24 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward NCS extension: 0 residues added, 1805 seeds are put forward Round 1: 124 peptides, 20 chains. Longest chain 10 peptides. Score 0.428 Round 2: 135 peptides, 18 chains. Longest chain 19 peptides. Score 0.525 Round 3: 143 peptides, 17 chains. Longest chain 28 peptides. Score 0.580 Round 4: 140 peptides, 16 chains. Longest chain 26 peptides. Score 0.586 Round 5: 142 peptides, 20 chains. Longest chain 14 peptides. Score 0.516 Taking the results from Round 4 Chains 18, Residues 124, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3865 restraints for refining 1780 atoms. 3342 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2267 (Rfree = 0.000) for 1780 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.2368 (Rfree = 0.000) for 1770 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 13: After refmac, R = 0.2229 (Rfree = 0.000) for 1756 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2179 (Rfree = 0.000) for 1752 atoms. Found 8 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.1797 (Rfree = 0.000) for 1748 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.29 Search for helices and strands: 0 residues in 0 chains, 1797 seeds are put forward NCS extension: 0 residues added, 1797 seeds are put forward Round 1: 116 peptides, 19 chains. Longest chain 13 peptides. Score 0.409 Round 2: 131 peptides, 19 chains. Longest chain 16 peptides. Score 0.485 Round 3: 132 peptides, 18 chains. Longest chain 23 peptides. Score 0.511 Round 4: 121 peptides, 18 chains. Longest chain 17 peptides. Score 0.458 Round 5: 133 peptides, 19 chains. Longest chain 16 peptides. Score 0.495 Taking the results from Round 3 Chains 18, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4075 restraints for refining 1780 atoms. 3637 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2876 (Rfree = 0.000) for 1780 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 17: After refmac, R = 0.2691 (Rfree = 0.000) for 1776 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 18: After refmac, R = 0.2496 (Rfree = 0.000) for 1761 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 19: After refmac, R = 0.2686 (Rfree = 0.000) for 1755 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.2325 (Rfree = 0.000) for 1754 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.35 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward NCS extension: 52 residues added (1 deleted due to clashes), 1870 seeds are put forward Round 1: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.378 Round 2: 129 peptides, 20 chains. Longest chain 18 peptides. Score 0.454 Round 3: 128 peptides, 20 chains. Longest chain 16 peptides. Score 0.448 Round 4: 137 peptides, 19 chains. Longest chain 17 peptides. Score 0.513 Round 5: 137 peptides, 20 chains. Longest chain 17 peptides. Score 0.493 Taking the results from Round 4 Chains 19, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4091 restraints for refining 1780 atoms. 3638 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2553 (Rfree = 0.000) for 1780 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.2366 (Rfree = 0.000) for 1768 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.2261 (Rfree = 0.000) for 1760 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2245 (Rfree = 0.000) for 1756 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2237 (Rfree = 0.000) for 1753 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 1800 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 1822 seeds are put forward Round 1: 111 peptides, 20 chains. Longest chain 11 peptides. Score 0.358 Round 2: 127 peptides, 19 chains. Longest chain 13 peptides. Score 0.465 Round 3: 121 peptides, 19 chains. Longest chain 12 peptides. Score 0.435 Round 4: 130 peptides, 19 chains. Longest chain 16 peptides. Score 0.480 Round 5: 125 peptides, 17 chains. Longest chain 16 peptides. Score 0.499 Taking the results from Round 5 Chains 17, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4146 restraints for refining 1780 atoms. 3731 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2573 (Rfree = 0.000) for 1780 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 27: After refmac, R = 0.2255 (Rfree = 0.000) for 1764 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Cycle 28: After refmac, R = 0.2020 (Rfree = 0.000) for 1760 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.2002 (Rfree = 0.000) for 1756 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.2144 (Rfree = 0.000) for 1747 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 1808 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1823 seeds are put forward Round 1: 99 peptides, 18 chains. Longest chain 12 peptides. Score 0.339 Round 2: 113 peptides, 18 chains. Longest chain 13 peptides. Score 0.416 Round 3: 116 peptides, 17 chains. Longest chain 16 peptides. Score 0.455 Round 4: 127 peptides, 18 chains. Longest chain 23 peptides. Score 0.487 Round 5: 124 peptides, 19 chains. Longest chain 14 peptides. Score 0.450 Taking the results from Round 4 Chains 19, Residues 109, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 3904 restraints for refining 1780 atoms. 3427 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2436 (Rfree = 0.000) for 1780 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 32: After refmac, R = 0.2193 (Rfree = 0.000) for 1772 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2109 (Rfree = 0.000) for 1760 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2048 (Rfree = 0.000) for 1753 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1989 (Rfree = 0.000) for 1751 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.27 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 1839 seeds are put forward Round 1: 106 peptides, 20 chains. Longest chain 9 peptides. Score 0.330 Round 2: 121 peptides, 20 chains. Longest chain 12 peptides. Score 0.412 Round 3: 125 peptides, 20 chains. Longest chain 17 peptides. Score 0.433 Round 4: 117 peptides, 19 chains. Longest chain 13 peptides. Score 0.414 Round 5: 115 peptides, 19 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 3 Chains 20, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4098 restraints for refining 1780 atoms. 3698 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2316 (Rfree = 0.000) for 1780 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 37: After refmac, R = 0.1999 (Rfree = 0.000) for 1779 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.1940 (Rfree = 0.000) for 1775 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.1914 (Rfree = 0.000) for 1770 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1903 (Rfree = 0.000) for 1768 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.27 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1835 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 11 peptides. Score 0.309 Round 2: 118 peptides, 20 chains. Longest chain 12 peptides. Score 0.396 Round 3: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.405 Round 4: 118 peptides, 19 chains. Longest chain 15 peptides. Score 0.420 Round 5: 118 peptides, 16 chains. Longest chain 15 peptides. Score 0.487 Taking the results from Round 5 Chains 16, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3202 reflections ( 98.46 % complete ) and 4107 restraints for refining 1780 atoms. 3715 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2345 (Rfree = 0.000) for 1780 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2230 (Rfree = 0.000) for 1764 atoms. Found 8 (9 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.2187 (Rfree = 0.000) for 1764 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.2492 (Rfree = 0.000) for 1756 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.2224 (Rfree = 0.000) for 1755 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.31 Search for helices and strands: 0 residues in 0 chains, 1815 seeds are put forward NCS extension: 0 residues added, 1815 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.297 Round 2: 109 peptides, 20 chains. Longest chain 10 peptides. Score 0.347 Round 3: 115 peptides, 18 chains. Longest chain 11 peptides. Score 0.427 Round 4: 119 peptides, 16 chains. Longest chain 12 peptides. Score 0.492 Round 5: 124 peptides, 19 chains. Longest chain 11 peptides. Score 0.450 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 103, 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. 3202 reflections ( 98.46 % complete ) and 4004 restraints for refining 1780 atoms. 3608 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2820 (Rfree = 0.000) for 1780 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2624 (Rfree = 0.000) for 1762 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2535 (Rfree = 0.000) for 1753 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2015 (Rfree = 0.000) for 1744 atoms. TimeTaking 31.4