Sun 23 Dec 23:41:41 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 2gnr-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gnr-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gnr-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-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/2gnr-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-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 ============================================================ Sun 23 Dec 23:41:46 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/2gnr-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-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 208 and 0 Target number of residues in the AU: 208 Target solvent content: 0.6546 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: 0.52 Input MTZ file: 2gnr-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: 91 Cell parameters: 75.160 75.160 115.370 90.000 90.000 90.000 Input sequence file: 2gnr-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.70 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: 75.160 3.601 Wilson plot Bfac: 80.79 4162 reflections ( 99.38 % complete ) and 0 restraints for refining 2586 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3360 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2995 (Rfree = 0.000) for 2586 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 2625 seeds are put forward NCS extension: 0 residues added, 2625 seeds are put forward Round 1: 145 peptides, 27 chains. Longest chain 12 peptides. Score 0.369 Round 2: 160 peptides, 23 chains. Longest chain 14 peptides. Score 0.518 Round 3: 176 peptides, 22 chains. Longest chain 20 peptides. Score 0.599 Round 4: 167 peptides, 18 chains. Longest chain 25 peptides. Score 0.632 Round 5: 166 peptides, 20 chains. Longest chain 32 peptides. Score 0.595 Taking the results from Round 4 Chains 18, Residues 149, Estimated correctness of the model 26.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.38 % complete ) and 4715 restraints for refining 2102 atoms. 4137 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2435 (Rfree = 0.000) for 2102 atoms. Found 11 (13 requested) and removed 19 (6 requested) atoms. Cycle 2: After refmac, R = 0.2362 (Rfree = 0.000) for 2069 atoms. Found 9 (13 requested) and removed 26 (6 requested) atoms. Cycle 3: After refmac, R = 0.2226 (Rfree = 0.000) for 2043 atoms. Found 2 (13 requested) and removed 13 (6 requested) atoms. Cycle 4: After refmac, R = 0.2103 (Rfree = 0.000) for 2024 atoms. Found 4 (13 requested) and removed 13 (6 requested) atoms. Cycle 5: After refmac, R = 0.2232 (Rfree = 0.000) for 2012 atoms. Found 4 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.40 Search for helices and strands: 0 residues in 0 chains, 2053 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 2083 seeds are put forward Round 1: 147 peptides, 25 chains. Longest chain 14 peptides. Score 0.420 Round 2: 157 peptides, 25 chains. Longest chain 16 peptides. Score 0.467 Round 3: 171 peptides, 21 chains. Longest chain 20 peptides. Score 0.597 Round 4: 177 peptides, 26 chains. Longest chain 17 peptides. Score 0.534 Round 5: 183 peptides, 23 chains. Longest chain 16 peptides. Score 0.608 Taking the results from Round 5 Chains 23, Residues 160, Estimated correctness of the model 17.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.38 % complete ) and 4608 restraints for refining 2085 atoms. 3991 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2366 (Rfree = 0.000) for 2085 atoms. Found 5 (13 requested) and removed 30 (6 requested) atoms. Cycle 7: After refmac, R = 0.2201 (Rfree = 0.000) for 2047 atoms. Found 9 (13 requested) and removed 22 (6 requested) atoms. Cycle 8: After refmac, R = 0.2043 (Rfree = 0.000) for 2026 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.1901 (Rfree = 0.000) for 2023 atoms. Found 3 (12 requested) and removed 11 (6 requested) atoms. Cycle 10: After refmac, R = 0.1865 (Rfree = 0.000) for 2013 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 2079 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2104 seeds are put forward Round 1: 161 peptides, 25 chains. Longest chain 22 peptides. Score 0.485 Round 2: 169 peptides, 23 chains. Longest chain 21 peptides. Score 0.555 Round 3: 178 peptides, 25 chains. Longest chain 14 peptides. Score 0.555 Round 4: 173 peptides, 19 chains. Longest chain 24 peptides. Score 0.637 Round 5: 179 peptides, 20 chains. Longest chain 26 peptides. Score 0.641 Taking the results from Round 5 Chains 20, Residues 159, Estimated correctness of the model 29.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.38 % complete ) and 4609 restraints for refining 2103 atoms. 3993 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2292 (Rfree = 0.000) for 2103 atoms. Found 5 (13 requested) and removed 13 (6 requested) atoms. Cycle 12: After refmac, R = 0.2001 (Rfree = 0.000) for 2081 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2019 (Rfree = 0.000) for 2072 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.1845 (Rfree = 0.000) for 2067 atoms. Found 4 (13 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.1937 (Rfree = 0.000) for 2055 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 2113 seeds are put forward NCS extension: 40 residues added (1 deleted due to clashes), 2153 seeds are put forward Round 1: 137 peptides, 23 chains. Longest chain 16 peptides. Score 0.414 Round 2: 154 peptides, 21 chains. Longest chain 27 peptides. Score 0.530 Round 3: 159 peptides, 21 chains. Longest chain 19 peptides. Score 0.551 Round 4: 156 peptides, 19 chains. Longest chain 27 peptides. Score 0.575 Round 5: 156 peptides, 22 chains. Longest chain 15 peptides. Score 0.520 Taking the results from Round 4 Chains 20, Residues 137, Estimated correctness of the model 4.6 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.38 % complete ) and 4541 restraints for refining 2103 atoms. 3943 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2220 (Rfree = 0.000) for 2103 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 17: After refmac, R = 0.2133 (Rfree = 0.000) for 2092 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 18: After refmac, R = 0.1937 (Rfree = 0.000) for 2086 atoms. Found 10 (13 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1929 (Rfree = 0.000) for 2085 atoms. Found 7 (13 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.1909 (Rfree = 0.000) for 2078 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.41 Search for helices and strands: 0 residues in 0 chains, 2137 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2165 seeds are put forward Round 1: 134 peptides, 23 chains. Longest chain 12 peptides. Score 0.399 Round 2: 151 peptides, 23 chains. Longest chain 13 peptides. Score 0.479 Round 3: 139 peptides, 21 chains. Longest chain 13 peptides. Score 0.465 Round 4: 157 peptides, 21 chains. Longest chain 27 peptides. Score 0.543 Round 5: 163 peptides, 21 chains. Longest chain 29 peptides. Score 0.567 Taking the results from Round 5 Chains 21, Residues 142, Estimated correctness of the model 1.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.38 % complete ) and 4667 restraints for refining 2102 atoms. 4120 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2218 (Rfree = 0.000) for 2102 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 22: After refmac, R = 0.1976 (Rfree = 0.000) for 2089 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.2040 (Rfree = 0.000) for 2078 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.1912 (Rfree = 0.000) for 2077 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.1888 (Rfree = 0.000) for 2069 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 2137 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2150 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 12 peptides. Score 0.356 Round 2: 149 peptides, 22 chains. Longest chain 18 peptides. Score 0.490 Round 3: 150 peptides, 20 chains. Longest chain 20 peptides. Score 0.532 Round 4: 139 peptides, 20 chains. Longest chain 15 peptides. Score 0.485 Round 5: 145 peptides, 18 chains. Longest chain 16 peptides. Score 0.549 Taking the results from Round 5 Chains 18, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.38 % complete ) and 4726 restraints for refining 2103 atoms. 4236 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2100 (Rfree = 0.000) for 2103 atoms. Found 8 (13 requested) and removed 22 (6 requested) atoms. Cycle 27: After refmac, R = 0.1800 (Rfree = 0.000) for 2084 atoms. Found 7 (13 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.1790 (Rfree = 0.000) for 2083 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.1714 (Rfree = 0.000) for 2076 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1655 (Rfree = 0.000) for 2072 atoms. Found 6 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 2123 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2150 seeds are put forward Round 1: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.339 Round 2: 146 peptides, 20 chains. Longest chain 21 peptides. Score 0.515 Round 3: 152 peptides, 21 chains. Longest chain 18 peptides. Score 0.522 Round 4: 157 peptides, 21 chains. Longest chain 18 peptides. Score 0.543 Round 5: 153 peptides, 23 chains. Longest chain 14 peptides. Score 0.488 Taking the results from Round 4 Chains 22, Residues 136, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.38 % complete ) and 4633 restraints for refining 2103 atoms. 4071 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2121 (Rfree = 0.000) for 2103 atoms. Found 6 (13 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.1872 (Rfree = 0.000) for 2084 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.1843 (Rfree = 0.000) for 2074 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1759 (Rfree = 0.000) for 2066 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.1739 (Rfree = 0.000) for 2065 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 2120 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2145 seeds are put forward Round 1: 119 peptides, 24 chains. Longest chain 9 peptides. Score 0.299 Round 2: 148 peptides, 22 chains. Longest chain 17 peptides. Score 0.485 Round 3: 158 peptides, 21 chains. Longest chain 22 peptides. Score 0.547 Round 4: 158 peptides, 22 chains. Longest chain 16 peptides. Score 0.528 Round 5: 156 peptides, 19 chains. Longest chain 22 peptides. Score 0.575 Taking the results from Round 5 Chains 19, Residues 137, Estimated correctness of the model 4.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.38 % complete ) and 4607 restraints for refining 2103 atoms. 4078 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2140 (Rfree = 0.000) for 2103 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. Cycle 37: After refmac, R = 0.2055 (Rfree = 0.000) for 2094 atoms. Found 12 (13 requested) and removed 15 (6 requested) atoms. Cycle 38: After refmac, R = 0.1796 (Rfree = 0.000) for 2087 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.1667 (Rfree = 0.000) for 2082 atoms. Found 8 (13 requested) and removed 13 (6 requested) atoms. Cycle 40: After refmac, R = 0.1533 (Rfree = 0.000) for 2074 atoms. Found 4 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 2129 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 2165 seeds are put forward Round 1: 107 peptides, 21 chains. Longest chain 12 peptides. Score 0.303 Round 2: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.367 Round 3: 122 peptides, 17 chains. Longest chain 17 peptides. Score 0.468 Round 4: 129 peptides, 19 chains. Longest chain 16 peptides. Score 0.459 Round 5: 127 peptides, 19 chains. Longest chain 22 peptides. Score 0.450 Taking the results from Round 3 Chains 17, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4162 reflections ( 99.38 % complete ) and 4805 restraints for refining 2088 atoms. 4402 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1891 (Rfree = 0.000) for 2088 atoms. Found 7 (13 requested) and removed 12 (6 requested) atoms. Cycle 42: After refmac, R = 0.1817 (Rfree = 0.000) for 2083 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.1747 (Rfree = 0.000) for 2081 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 44: After refmac, R = 0.1793 (Rfree = 0.000) for 2077 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.1467 (Rfree = 0.000) for 2077 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.44 Search for helices and strands: 0 residues in 0 chains, 2140 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2165 seeds are put forward Round 1: 107 peptides, 20 chains. Longest chain 13 peptides. Score 0.326 Round 2: 113 peptides, 18 chains. Longest chain 14 peptides. Score 0.403 Round 3: 121 peptides, 22 chains. Longest chain 13 peptides. Score 0.355 Round 4: 123 peptides, 18 chains. Longest chain 14 peptides. Score 0.452 Round 5: 126 peptides, 20 chains. Longest chain 19 peptides. Score 0.424 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 105, 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 2gnr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4162 reflections ( 99.38 % complete ) and 4881 restraints for refining 2103 atoms. 4479 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2275 (Rfree = 0.000) for 2103 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2145 (Rfree = 0.000) for 2096 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1985 (Rfree = 0.000) for 2090 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1918 (Rfree = 0.000) for 2082 atoms. TimeTaking 29.63