Sun 23 Dec 22:23:05 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i8d-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.6-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 22:23:13 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i8d-3.6-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 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-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-3.6-parrot-hancs.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 3.600 Wilson plot Bfac: 68.10 3754 reflections ( 98.69 % complete ) and 0 restraints for refining 2183 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3360 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2613 (Rfree = 0.000) for 2183 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 2241 seeds are put forward NCS extension: 0 residues added, 2241 seeds are put forward Round 1: 132 peptides, 21 chains. Longest chain 14 peptides. Score 0.447 Round 2: 158 peptides, 21 chains. Longest chain 15 peptides. Score 0.567 Round 3: 169 peptides, 21 chains. Longest chain 19 peptides. Score 0.611 Round 4: 161 peptides, 19 chains. Longest chain 16 peptides. Score 0.615 Round 5: 162 peptides, 18 chains. Longest chain 24 peptides. Score 0.636 Taking the results from Round 5 Chains 18, Residues 144, Estimated correctness of the model 28.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3850 restraints for refining 1784 atoms. 3292 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2404 (Rfree = 0.000) for 1784 atoms. Found 7 (11 requested) and removed 10 (5 requested) atoms. Cycle 2: After refmac, R = 0.2223 (Rfree = 0.000) for 1775 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.2134 (Rfree = 0.000) for 1765 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 4: After refmac, R = 0.2088 (Rfree = 0.000) for 1757 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2042 (Rfree = 0.000) for 1754 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 1871 seeds are put forward Round 1: 146 peptides, 23 chains. Longest chain 15 peptides. Score 0.473 Round 2: 157 peptides, 20 chains. Longest chain 16 peptides. Score 0.581 Round 3: 157 peptides, 19 chains. Longest chain 20 peptides. Score 0.599 Round 4: 164 peptides, 19 chains. Longest chain 20 peptides. Score 0.626 Round 5: 159 peptides, 17 chains. Longest chain 21 peptides. Score 0.642 Taking the results from Round 5 Chains 18, Residues 142, Estimated correctness of the model 30.3 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3651 restraints for refining 1784 atoms. 3030 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2457 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 7: After refmac, R = 0.2257 (Rfree = 0.000) for 1775 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2147 (Rfree = 0.000) for 1770 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2111 (Rfree = 0.000) for 1762 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.2046 (Rfree = 0.000) for 1760 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 1839 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1861 seeds are put forward Round 1: 134 peptides, 18 chains. Longest chain 32 peptides. Score 0.520 Round 2: 150 peptides, 19 chains. Longest chain 33 peptides. Score 0.571 Round 3: 155 peptides, 20 chains. Longest chain 22 peptides. Score 0.573 Round 4: 155 peptides, 18 chains. Longest chain 27 peptides. Score 0.610 Round 5: 159 peptides, 20 chains. Longest chain 18 peptides. Score 0.589 Taking the results from Round 4 Chains 18, Residues 137, Estimated correctness of the model 18.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3852 restraints for refining 1784 atoms. 3322 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2442 (Rfree = 0.000) for 1784 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. Cycle 12: After refmac, R = 0.2263 (Rfree = 0.000) for 1780 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. Cycle 13: After refmac, R = 0.2179 (Rfree = 0.000) for 1773 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.2120 (Rfree = 0.000) for 1767 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2102 (Rfree = 0.000) for 1760 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.09 Search for helices and strands: 0 residues in 0 chains, 1841 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 1868 seeds are put forward Round 1: 127 peptides, 21 chains. Longest chain 10 peptides. Score 0.421 Round 2: 148 peptides, 20 chains. Longest chain 20 peptides. Score 0.543 Round 3: 157 peptides, 22 chains. Longest chain 21 peptides. Score 0.543 Round 4: 148 peptides, 20 chains. Longest chain 16 peptides. Score 0.543 Round 5: 163 peptides, 20 chains. Longest chain 30 peptides. Score 0.605 Taking the results from Round 5 Chains 20, Residues 143, Estimated correctness of the model 16.6 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3552 restraints for refining 1784 atoms. 2859 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2572 (Rfree = 0.000) for 1784 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 17: After refmac, R = 0.2266 (Rfree = 0.000) for 1779 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.2157 (Rfree = 0.000) for 1771 atoms. Found 2 (11 requested) and removed 10 (5 requested) atoms. Cycle 19: After refmac, R = 0.2069 (Rfree = 0.000) for 1763 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2026 (Rfree = 0.000) for 1762 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 1844 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 1884 seeds are put forward Round 1: 140 peptides, 18 chains. Longest chain 15 peptides. Score 0.547 Round 2: 145 peptides, 17 chains. Longest chain 19 peptides. Score 0.588 Round 3: 149 peptides, 18 chains. Longest chain 21 peptides. Score 0.586 Round 4: 151 peptides, 17 chains. Longest chain 16 peptides. Score 0.612 Round 5: 160 peptides, 21 chains. Longest chain 24 peptides. Score 0.575 Taking the results from Round 4 Chains 17, Residues 134, Estimated correctness of the model 19.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3896 restraints for refining 1784 atoms. 3377 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2223 (Rfree = 0.000) for 1784 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. Cycle 22: After refmac, R = 0.2114 (Rfree = 0.000) for 1780 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.2039 (Rfree = 0.000) for 1771 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2008 (Rfree = 0.000) for 1767 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.1973 (Rfree = 0.000) for 1765 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 1840 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1859 seeds are put forward Round 1: 132 peptides, 21 chains. Longest chain 14 peptides. Score 0.447 Round 2: 141 peptides, 17 chains. Longest chain 18 peptides. Score 0.571 Round 3: 140 peptides, 19 chains. Longest chain 15 peptides. Score 0.527 Round 4: 140 peptides, 18 chains. Longest chain 19 peptides. Score 0.547 Round 5: 133 peptides, 16 chains. Longest chain 20 peptides. Score 0.557 Taking the results from Round 2 Chains 17, Residues 124, Estimated correctness of the model 3.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3982 restraints for refining 1784 atoms. 3503 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2164 (Rfree = 0.000) for 1784 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2072 (Rfree = 0.000) for 1781 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.1962 (Rfree = 0.000) for 1779 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2022 (Rfree = 0.000) for 1773 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2055 (Rfree = 0.000) for 1768 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.05 Search for helices and strands: 0 residues in 0 chains, 1841 seeds are put forward NCS extension: 0 residues added, 1841 seeds are put forward Round 1: 124 peptides, 23 chains. Longest chain 11 peptides. Score 0.359 Round 2: 138 peptides, 20 chains. Longest chain 15 peptides. Score 0.497 Round 3: 136 peptides, 18 chains. Longest chain 14 peptides. Score 0.529 Round 4: 137 peptides, 18 chains. Longest chain 17 peptides. Score 0.534 Round 5: 145 peptides, 15 chains. Longest chain 22 peptides. Score 0.625 Taking the results from Round 5 Chains 15, Residues 130, Estimated correctness of the model 24.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3972 restraints for refining 1784 atoms. 3467 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2222 (Rfree = 0.000) for 1784 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Cycle 32: After refmac, R = 0.2048 (Rfree = 0.000) for 1783 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.1987 (Rfree = 0.000) for 1783 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.1950 (Rfree = 0.000) for 1777 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1927 (Rfree = 0.000) for 1773 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.14 Search for helices and strands: 0 residues in 0 chains, 1841 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 1872 seeds are put forward Round 1: 106 peptides, 18 chains. Longest chain 10 peptides. Score 0.378 Round 2: 129 peptides, 18 chains. Longest chain 16 peptides. Score 0.497 Round 3: 127 peptides, 20 chains. Longest chain 13 peptides. Score 0.443 Round 4: 130 peptides, 19 chains. Longest chain 13 peptides. Score 0.480 Round 5: 127 peptides, 16 chains. Longest chain 18 peptides. Score 0.530 Taking the results from Round 5 Chains 16, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 4027 restraints for refining 1784 atoms. 3599 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2373 (Rfree = 0.000) for 1784 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. Cycle 37: After refmac, R = 0.2214 (Rfree = 0.000) for 1784 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 38: After refmac, R = 0.2037 (Rfree = 0.000) for 1784 atoms. Found 2 (11 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.1978 (Rfree = 0.000) for 1773 atoms. Found 3 (11 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.1885 (Rfree = 0.000) for 1767 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 1840 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 1870 seeds are put forward Round 1: 116 peptides, 21 chains. Longest chain 10 peptides. Score 0.362 Round 2: 141 peptides, 19 chains. Longest chain 25 peptides. Score 0.532 Round 3: 135 peptides, 18 chains. Longest chain 20 peptides. Score 0.525 Round 4: 135 peptides, 15 chains. Longest chain 26 peptides. Score 0.585 Round 5: 139 peptides, 19 chains. Longest chain 17 peptides. Score 0.523 Taking the results from Round 4 Chains 15, Residues 120, Estimated correctness of the model 8.7 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3754 reflections ( 98.69 % complete ) and 3693 restraints for refining 1783 atoms. 3106 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2498 (Rfree = 0.000) for 1783 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. Cycle 42: After refmac, R = 0.2325 (Rfree = 0.000) for 1782 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 43: After refmac, R = 0.2215 (Rfree = 0.000) for 1776 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.2155 (Rfree = 0.000) for 1770 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2114 (Rfree = 0.000) for 1766 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 43 residues added (0 deleted due to clashes), 1864 seeds are put forward Round 1: 110 peptides, 20 chains. Longest chain 14 peptides. Score 0.352 Round 2: 128 peptides, 18 chains. Longest chain 24 peptides. Score 0.492 Round 3: 136 peptides, 19 chains. Longest chain 25 peptides. Score 0.509 Round 4: 140 peptides, 19 chains. Longest chain 27 peptides. Score 0.527 Round 5: 132 peptides, 17 chains. Longest chain 25 peptides. Score 0.532 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 115, 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 4053 restraints for refining 1784 atoms. 3610 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2363 (Rfree = 0.000) for 1784 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2143 (Rfree = 0.000) for 1776 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2023 (Rfree = 0.000) for 1768 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2035 (Rfree = 0.000) for 1763 atoms. TimeTaking 31.85