Tue 25 Dec 19:27:57 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 2o1q-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o1q-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o1q-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-3.4-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/2o1q-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-3.4-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 ============================================================ Tue 25 Dec 19:28:07 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/2o1q-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-3.4-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 178 and 0 Target number of residues in the AU: 178 Target solvent content: 0.6231 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.39 Input MTZ file: 2o1q-3.4-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.65 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: 56.142 3.400 Wilson plot Bfac: 62.14 3929 reflections ( 99.75 % complete ) and 0 restraints for refining 2584 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3301 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2668 (Rfree = 0.000) for 2584 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.75 Search for helices and strands: 0 residues in 0 chains, 2599 seeds are put forward NCS extension: 0 residues added, 2599 seeds are put forward Round 1: 142 peptides, 28 chains. Longest chain 11 peptides. Score 0.366 Round 2: 169 peptides, 25 chains. Longest chain 19 peptides. Score 0.583 Round 3: 196 peptides, 28 chains. Longest chain 17 peptides. Score 0.643 Round 4: 192 peptides, 22 chains. Longest chain 26 peptides. Score 0.726 Round 5: 204 peptides, 26 chains. Longest chain 21 peptides. Score 0.706 Taking the results from Round 4 Chains 25, Residues 170, Estimated correctness of the model 64.3 % 4 chains (41 residues) have been docked in sequence Building loops using Loopy2018 25 chains (170 residues) following loop building 4 chains (41 residues) in sequence following loop building ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4143 restraints for refining 2109 atoms. 3322 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2475 (Rfree = 0.000) for 2109 atoms. Found 11 (15 requested) and removed 24 (7 requested) atoms. Cycle 2: After refmac, R = 0.2251 (Rfree = 0.000) for 2072 atoms. Found 8 (15 requested) and removed 9 (7 requested) atoms. Cycle 3: After refmac, R = 0.2169 (Rfree = 0.000) for 2060 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2151 (Rfree = 0.000) for 2050 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2130 (Rfree = 0.000) for 2044 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2077 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2095 seeds are put forward Round 1: 136 peptides, 21 chains. Longest chain 16 peptides. Score 0.504 Round 2: 161 peptides, 21 chains. Longest chain 28 peptides. Score 0.626 Round 3: 158 peptides, 21 chains. Longest chain 33 peptides. Score 0.613 Round 4: 171 peptides, 22 chains. Longest chain 16 peptides. Score 0.649 Round 5: 170 peptides, 22 chains. Longest chain 19 peptides. Score 0.645 Taking the results from Round 4 Chains 22, Residues 149, Estimated correctness of the model 43.8 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3929 reflections ( 99.75 % complete ) and 4476 restraints for refining 2108 atoms. 3808 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2258 (Rfree = 0.000) for 2108 atoms. Found 12 (13 requested) and removed 10 (7 requested) atoms. Cycle 7: After refmac, R = 0.2040 (Rfree = 0.000) for 2103 atoms. Found 7 (13 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1968 (Rfree = 0.000) for 2098 atoms. Found 7 (13 requested) and removed 8 (7 requested) atoms. Cycle 9: After refmac, R = 0.1920 (Rfree = 0.000) for 2091 atoms. Found 6 (13 requested) and removed 7 (7 requested) atoms. Cycle 10: After refmac, R = 0.1869 (Rfree = 0.000) for 2089 atoms. Found 3 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.73 Search for helices and strands: 0 residues in 0 chains, 2118 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2134 seeds are put forward Round 1: 152 peptides, 25 chains. Longest chain 15 peptides. Score 0.498 Round 2: 181 peptides, 23 chains. Longest chain 19 peptides. Score 0.671 Round 3: 186 peptides, 25 chains. Longest chain 17 peptides. Score 0.656 Round 4: 179 peptides, 23 chains. Longest chain 19 peptides. Score 0.663 Round 5: 180 peptides, 23 chains. Longest chain 21 peptides. Score 0.667 Taking the results from Round 2 Chains 24, Residues 158, Estimated correctness of the model 50.1 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4359 restraints for refining 2109 atoms. 3615 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2121 (Rfree = 0.000) for 2109 atoms. Found 10 (13 requested) and removed 14 (7 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1995 (Rfree = 0.000) for 2100 atoms. Found 4 (13 requested) and removed 8 (7 requested) atoms. Cycle 13: After refmac, R = 0.1942 (Rfree = 0.000) for 2092 atoms. Found 5 (13 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.1949 (Rfree = 0.000) for 2086 atoms. Found 5 (13 requested) and removed 7 (7 requested) atoms. Cycle 15: After refmac, R = 0.1901 (Rfree = 0.000) for 2083 atoms. Found 5 (13 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2132 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2151 seeds are put forward Round 1: 165 peptides, 24 chains. Longest chain 17 peptides. Score 0.585 Round 2: 164 peptides, 23 chains. Longest chain 17 peptides. Score 0.600 Round 3: 177 peptides, 22 chains. Longest chain 21 peptides. Score 0.673 Round 4: 173 peptides, 25 chains. Longest chain 20 peptides. Score 0.601 Round 5: 174 peptides, 22 chains. Longest chain 21 peptides. Score 0.661 Taking the results from Round 3 Chains 25, Residues 155, Estimated correctness of the model 50.7 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4190 restraints for refining 2109 atoms. 3408 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2144 (Rfree = 0.000) for 2109 atoms. Found 13 (13 requested) and removed 14 (7 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2022 (Rfree = 0.000) for 2097 atoms. Found 10 (13 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1990 (Rfree = 0.000) for 2097 atoms. Found 5 (13 requested) and removed 8 (7 requested) atoms. Cycle 19: After refmac, R = 0.1949 (Rfree = 0.000) for 2092 atoms. Found 3 (13 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1959 (Rfree = 0.000) for 2087 atoms. Found 2 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2115 seeds are put forward NCS extension: 38 residues added (6 deleted due to clashes), 2153 seeds are put forward Round 1: 152 peptides, 24 chains. Longest chain 15 peptides. Score 0.521 Round 2: 174 peptides, 24 chains. Longest chain 20 peptides. Score 0.625 Round 3: 173 peptides, 22 chains. Longest chain 17 peptides. Score 0.657 Round 4: 176 peptides, 21 chains. Longest chain 18 peptides. Score 0.686 Round 5: 160 peptides, 21 chains. Longest chain 17 peptides. Score 0.622 Taking the results from Round 4 Chains 23, Residues 155, Estimated correctness of the model 54.2 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4617 restraints for refining 2108 atoms. 3966 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2031 (Rfree = 0.000) for 2108 atoms. Found 7 (13 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1884 (Rfree = 0.000) for 2098 atoms. Found 10 (13 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1795 (Rfree = 0.000) for 2100 atoms. Found 3 (13 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.1782 (Rfree = 0.000) for 2095 atoms. Found 4 (13 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1748 (Rfree = 0.000) for 2091 atoms. Found 1 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.80 Search for helices and strands: 0 residues in 0 chains, 2122 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2145 seeds are put forward Round 1: 141 peptides, 24 chains. Longest chain 14 peptides. Score 0.461 Round 2: 165 peptides, 25 chains. Longest chain 15 peptides. Score 0.564 Round 3: 153 peptides, 23 chains. Longest chain 21 peptides. Score 0.548 Round 4: 161 peptides, 22 chains. Longest chain 16 peptides. Score 0.607 Round 5: 148 peptides, 23 chains. Longest chain 18 peptides. Score 0.522 Taking the results from Round 4 Chains 22, Residues 139, Estimated correctness of the model 30.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4733 restraints for refining 2109 atoms. 4199 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1914 (Rfree = 0.000) for 2109 atoms. Found 13 (13 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.1749 (Rfree = 0.000) for 2112 atoms. Found 4 (13 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.1704 (Rfree = 0.000) for 2104 atoms. Found 2 (13 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.1699 (Rfree = 0.000) for 2098 atoms. Found 1 (13 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1688 (Rfree = 0.000) for 2091 atoms. Found 3 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.80 Search for helices and strands: 0 residues in 0 chains, 2118 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2134 seeds are put forward Round 1: 140 peptides, 21 chains. Longest chain 18 peptides. Score 0.526 Round 2: 152 peptides, 20 chains. Longest chain 19 peptides. Score 0.606 Round 3: 160 peptides, 21 chains. Longest chain 17 peptides. Score 0.622 Round 4: 157 peptides, 19 chains. Longest chain 20 peptides. Score 0.647 Round 5: 157 peptides, 21 chains. Longest chain 20 peptides. Score 0.608 Taking the results from Round 4 Chains 21, Residues 138, Estimated correctness of the model 43.3 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3929 reflections ( 99.75 % complete ) and 4549 restraints for refining 2108 atoms. 3929 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2121 (Rfree = 0.000) for 2108 atoms. Found 13 (13 requested) and removed 14 (7 requested) atoms. Cycle 32: After refmac, R = 0.2000 (Rfree = 0.000) for 2102 atoms. Found 9 (13 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.1946 (Rfree = 0.000) for 2103 atoms. Found 3 (13 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1913 (Rfree = 0.000) for 2099 atoms. Found 1 (13 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1872 (Rfree = 0.000) for 2092 atoms. Found 0 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.78 Search for helices and strands: 0 residues in 0 chains, 2117 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2131 seeds are put forward Round 1: 141 peptides, 21 chains. Longest chain 19 peptides. Score 0.531 Round 2: 150 peptides, 20 chains. Longest chain 21 peptides. Score 0.597 Round 3: 136 peptides, 19 chains. Longest chain 14 peptides. Score 0.550 Round 4: 144 peptides, 18 chains. Longest chain 21 peptides. Score 0.610 Round 5: 136 peptides, 19 chains. Longest chain 13 peptides. Score 0.550 Taking the results from Round 4 Chains 19, Residues 126, Estimated correctness of the model 31.9 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4710 restraints for refining 2109 atoms. 4125 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2017 (Rfree = 0.000) for 2109 atoms. Found 13 (13 requested) and removed 10 (7 requested) atoms. Cycle 37: After refmac, R = 0.1920 (Rfree = 0.000) for 2107 atoms. Found 13 (13 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.1841 (Rfree = 0.000) for 2112 atoms. Found 4 (13 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1808 (Rfree = 0.000) for 2107 atoms. Found 5 (13 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1767 (Rfree = 0.000) for 2105 atoms. Found 4 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.80 Search for helices and strands: 0 residues in 0 chains, 2139 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 2167 seeds are put forward Round 1: 102 peptides, 17 chains. Longest chain 11 peptides. Score 0.408 Round 2: 121 peptides, 17 chains. Longest chain 23 peptides. Score 0.518 Round 3: 120 peptides, 17 chains. Longest chain 14 peptides. Score 0.513 Round 4: 114 peptides, 15 chains. Longest chain 23 peptides. Score 0.529 Round 5: 125 peptides, 16 chains. Longest chain 24 peptides. Score 0.563 Taking the results from Round 5 Chains 17, Residues 109, Estimated correctness of the model 16.1 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 3929 reflections ( 99.75 % complete ) and 4727 restraints for refining 2109 atoms. 4239 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1896 (Rfree = 0.000) for 2109 atoms. Found 12 (13 requested) and removed 14 (7 requested) atoms. Cycle 42: After refmac, R = 0.1708 (Rfree = 0.000) for 2103 atoms. Found 4 (13 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.1687 (Rfree = 0.000) for 2099 atoms. Found 7 (13 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1645 (Rfree = 0.000) for 2099 atoms. Found 3 (13 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1658 (Rfree = 0.000) for 2094 atoms. Found 2 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.80 Search for helices and strands: 0 residues in 0 chains, 2141 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 2174 seeds are put forward Round 1: 111 peptides, 20 chains. Longest chain 10 peptides. Score 0.383 Round 2: 125 peptides, 18 chains. Longest chain 16 peptides. Score 0.516 Round 3: 119 peptides, 18 chains. Longest chain 18 peptides. Score 0.483 Round 4: 121 peptides, 17 chains. Longest chain 19 peptides. Score 0.518 Round 5: 124 peptides, 18 chains. Longest chain 12 peptides. Score 0.511 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 104, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2o1q-3_warpNtrace.pdb as input Building loops using Loopy2018 17 chains (104 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3929 reflections ( 99.75 % complete ) and 4938 restraints for refining 2109 atoms. 4530 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1877 (Rfree = 0.000) for 2109 atoms. Found 0 (13 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1824 (Rfree = 0.000) for 2100 atoms. Found 0 (13 requested) and removed 2 (7 requested) atoms. Cycle 48: After refmac, R = 0.1795 (Rfree = 0.000) for 2098 atoms. Found 0 (13 requested) and removed 1 (7 requested) atoms. Cycle 49: After refmac, R = 0.1782 (Rfree = 0.000) for 2097 atoms. Found 0 (13 requested) and removed 3 (7 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:12:55 GMT 2018 Job finished. TimeTaking 44.98