Mon 24 Dec 00:15:38 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gnr-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gnr-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-3.4-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 ============================================================ Mon 24 Dec 00:15:43 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gnr-3.4-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 212 and 0 Target number of residues in the AU: 212 Target solvent content: 0.6479 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-3.4-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-3.4-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 3.401 Wilson plot Bfac: 76.15 4909 reflections ( 99.47 % complete ) and 0 restraints for refining 2577 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3294 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2800 (Rfree = 0.000) for 2577 atoms. Found 19 (19 requested) and removed 33 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 2583 seeds are put forward NCS extension: 0 residues added, 2583 seeds are put forward Round 1: 158 peptides, 29 chains. Longest chain 13 peptides. Score 0.391 Round 2: 192 peptides, 23 chains. Longest chain 23 peptides. Score 0.639 Round 3: 186 peptides, 20 chains. Longest chain 32 peptides. Score 0.664 Round 4: 189 peptides, 18 chains. Longest chain 40 peptides. Score 0.702 Round 5: 192 peptides, 18 chains. Longest chain 27 peptides. Score 0.711 Taking the results from Round 5 Chains 19, Residues 174, Estimated correctness of the model 60.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4909 reflections ( 99.47 % complete ) and 4465 restraints for refining 2108 atoms. 3755 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2374 (Rfree = 0.000) for 2108 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 2: After refmac, R = 0.2194 (Rfree = 0.000) for 2060 atoms. Found 5 (15 requested) and removed 13 (7 requested) atoms. Cycle 3: After refmac, R = 0.2136 (Rfree = 0.000) for 2043 atoms. Found 6 (14 requested) and removed 18 (7 requested) atoms. Cycle 4: After refmac, R = 0.2062 (Rfree = 0.000) for 2028 atoms. Found 4 (14 requested) and removed 16 (7 requested) atoms. Cycle 5: After refmac, R = 0.2042 (Rfree = 0.000) for 2010 atoms. Found 3 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 2064 seeds are put forward NCS extension: 38 residues added (3 deleted due to clashes), 2102 seeds are put forward Round 1: 182 peptides, 27 chains. Longest chain 20 peptides. Score 0.536 Round 2: 189 peptides, 22 chains. Longest chain 21 peptides. Score 0.644 Round 3: 194 peptides, 19 chains. Longest chain 42 peptides. Score 0.703 Round 4: 197 peptides, 20 chains. Longest chain 51 peptides. Score 0.698 Round 5: 196 peptides, 19 chains. Longest chain 27 peptides. Score 0.708 Taking the results from Round 5 Chains 19, Residues 177, Estimated correctness of the model 59.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4909 reflections ( 99.47 % complete ) and 4396 restraints for refining 2060 atoms. 3707 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2383 (Rfree = 0.000) for 2060 atoms. Found 4 (13 requested) and removed 9 (7 requested) atoms. Cycle 7: After refmac, R = 0.2409 (Rfree = 0.000) for 2044 atoms. Found 6 (13 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.2128 (Rfree = 0.000) for 2032 atoms. Found 3 (13 requested) and removed 24 (7 requested) atoms. Cycle 9: After refmac, R = 0.2414 (Rfree = 0.000) for 2008 atoms. Found 12 (13 requested) and removed 14 (7 requested) atoms. Cycle 10: After refmac, R = 0.2017 (Rfree = 0.000) for 2002 atoms. Found 4 (12 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 2032 seeds are put forward NCS extension: 46 residues added (7 deleted due to clashes), 2078 seeds are put forward Round 1: 164 peptides, 23 chains. Longest chain 16 peptides. Score 0.535 Round 2: 175 peptides, 20 chains. Longest chain 17 peptides. Score 0.628 Round 3: 177 peptides, 22 chains. Longest chain 14 peptides. Score 0.603 Round 4: 192 peptides, 21 chains. Longest chain 19 peptides. Score 0.669 Round 5: 200 peptides, 22 chains. Longest chain 34 peptides. Score 0.679 Taking the results from Round 5 Chains 24, Residues 178, Estimated correctness of the model 52.3 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 4909 reflections ( 99.47 % complete ) and 4301 restraints for refining 2109 atoms. 3508 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2407 (Rfree = 0.000) for 2109 atoms. Found 10 (12 requested) and removed 21 (7 requested) atoms. Cycle 12: After refmac, R = 0.2236 (Rfree = 0.000) for 2092 atoms. Found 7 (12 requested) and removed 12 (7 requested) atoms. Cycle 13: After refmac, R = 0.2162 (Rfree = 0.000) for 2083 atoms. Found 4 (12 requested) and removed 12 (7 requested) atoms. Cycle 14: After refmac, R = 0.2132 (Rfree = 0.000) for 2074 atoms. Found 6 (12 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.2509 (Rfree = 0.000) for 2070 atoms. Found 12 (12 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 2117 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2132 seeds are put forward Round 1: 166 peptides, 26 chains. Longest chain 30 peptides. Score 0.487 Round 2: 161 peptides, 19 chains. Longest chain 21 peptides. Score 0.594 Round 3: 171 peptides, 20 chains. Longest chain 27 peptides. Score 0.614 Round 4: 184 peptides, 20 chains. Longest chain 33 peptides. Score 0.658 Round 5: 184 peptides, 22 chains. Longest chain 28 peptides. Score 0.627 Taking the results from Round 4 Chains 20, Residues 164, Estimated correctness of the model 46.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4909 reflections ( 99.47 % complete ) and 4650 restraints for refining 2109 atoms. 4014 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2177 (Rfree = 0.000) for 2109 atoms. Found 3 (12 requested) and removed 14 (7 requested) atoms. Cycle 17: After refmac, R = 0.2088 (Rfree = 0.000) for 2092 atoms. Found 5 (12 requested) and removed 7 (7 requested) atoms. Cycle 18: After refmac, R = 0.1983 (Rfree = 0.000) for 2088 atoms. Found 5 (12 requested) and removed 9 (7 requested) atoms. Cycle 19: After refmac, R = 0.1926 (Rfree = 0.000) for 2082 atoms. Found 4 (12 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1897 (Rfree = 0.000) for 2079 atoms. Found 4 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 2144 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 2171 seeds are put forward Round 1: 154 peptides, 23 chains. Longest chain 18 peptides. Score 0.492 Round 2: 183 peptides, 22 chains. Longest chain 30 peptides. Score 0.624 Round 3: 173 peptides, 22 chains. Longest chain 27 peptides. Score 0.588 Round 4: 180 peptides, 18 chains. Longest chain 23 peptides. Score 0.675 Round 5: 186 peptides, 18 chains. Longest chain 33 peptides. Score 0.693 Taking the results from Round 5 Chains 20, Residues 168, Estimated correctness of the model 56.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4909 reflections ( 99.47 % complete ) and 4457 restraints for refining 2108 atoms. 3765 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2174 (Rfree = 0.000) for 2108 atoms. Found 6 (12 requested) and removed 9 (7 requested) atoms. Cycle 22: After refmac, R = 0.2064 (Rfree = 0.000) for 2101 atoms. Found 4 (12 requested) and removed 9 (7 requested) atoms. Cycle 23: After refmac, R = 0.1977 (Rfree = 0.000) for 2091 atoms. Found 3 (12 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.1907 (Rfree = 0.000) for 2086 atoms. Found 3 (12 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.1842 (Rfree = 0.000) for 2082 atoms. Found 1 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 2139 seeds are put forward NCS extension: 47 residues added (4 deleted due to clashes), 2186 seeds are put forward Round 1: 168 peptides, 28 chains. Longest chain 14 peptides. Score 0.458 Round 2: 189 peptides, 21 chains. Longest chain 31 peptides. Score 0.659 Round 3: 176 peptides, 19 chains. Longest chain 31 peptides. Score 0.647 Round 4: 190 peptides, 20 chains. Longest chain 31 peptides. Score 0.677 Round 5: 188 peptides, 21 chains. Longest chain 21 peptides. Score 0.656 Taking the results from Round 4 Chains 21, Residues 170, Estimated correctness of the model 51.7 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4909 reflections ( 99.47 % complete ) and 4491 restraints for refining 2109 atoms. 3784 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2240 (Rfree = 0.000) for 2109 atoms. Found 12 (12 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.2154 (Rfree = 0.000) for 2106 atoms. Found 9 (12 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.2098 (Rfree = 0.000) for 2104 atoms. Found 5 (12 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.2026 (Rfree = 0.000) for 2099 atoms. Found 4 (12 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1948 (Rfree = 0.000) for 2094 atoms. Found 1 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 2153 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2173 seeds are put forward Round 1: 159 peptides, 26 chains. Longest chain 13 peptides. Score 0.456 Round 2: 168 peptides, 21 chains. Longest chain 28 peptides. Score 0.586 Round 3: 170 peptides, 20 chains. Longest chain 18 peptides. Score 0.610 Round 4: 171 peptides, 20 chains. Longest chain 27 peptides. Score 0.614 Round 5: 174 peptides, 19 chains. Longest chain 28 peptides. Score 0.640 Taking the results from Round 5 Chains 19, Residues 155, Estimated correctness of the model 41.1 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 4909 reflections ( 99.47 % complete ) and 4390 restraints for refining 2109 atoms. 3643 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2415 (Rfree = 0.000) for 2109 atoms. Found 9 (12 requested) and removed 13 (7 requested) atoms. Cycle 32: After refmac, R = 0.2252 (Rfree = 0.000) for 2095 atoms. Found 5 (12 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.2089 (Rfree = 0.000) for 2088 atoms. Found 4 (12 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1996 (Rfree = 0.000) for 2081 atoms. Found 6 (12 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.2008 (Rfree = 0.000) for 2078 atoms. Found 1 (12 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 2120 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2140 seeds are put forward Round 1: 144 peptides, 21 chains. Longest chain 19 peptides. Score 0.487 Round 2: 160 peptides, 21 chains. Longest chain 16 peptides. Score 0.555 Round 3: 171 peptides, 20 chains. Longest chain 21 peptides. Score 0.614 Round 4: 171 peptides, 21 chains. Longest chain 19 peptides. Score 0.597 Round 5: 167 peptides, 21 chains. Longest chain 20 peptides. Score 0.582 Taking the results from Round 3 Chains 20, Residues 151, Estimated correctness of the model 33.1 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4909 reflections ( 99.47 % complete ) and 4686 restraints for refining 2097 atoms. 4086 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2162 (Rfree = 0.000) for 2097 atoms. Found 11 (12 requested) and removed 14 (7 requested) atoms. Cycle 37: After refmac, R = 0.2361 (Rfree = 0.000) for 2087 atoms. Found 6 (12 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.1977 (Rfree = 0.000) for 2078 atoms. Found 6 (12 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.1874 (Rfree = 0.000) for 2075 atoms. Found 4 (12 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1842 (Rfree = 0.000) for 2072 atoms. Found 6 (12 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 2123 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2144 seeds are put forward Round 1: 143 peptides, 23 chains. Longest chain 15 peptides. Score 0.442 Round 2: 161 peptides, 23 chains. Longest chain 18 peptides. Score 0.522 Round 3: 164 peptides, 22 chains. Longest chain 20 peptides. Score 0.553 Round 4: 165 peptides, 21 chains. Longest chain 20 peptides. Score 0.574 Round 5: 169 peptides, 21 chains. Longest chain 21 peptides. Score 0.590 Taking the results from Round 5 Chains 21, Residues 148, Estimated correctness of the model 25.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4909 reflections ( 99.47 % complete ) and 4666 restraints for refining 2109 atoms. 4095 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2124 (Rfree = 0.000) for 2109 atoms. Found 6 (12 requested) and removed 11 (7 requested) atoms. Cycle 42: After refmac, R = 0.1916 (Rfree = 0.000) for 2098 atoms. Found 9 (12 requested) and removed 9 (7 requested) atoms. Cycle 43: After refmac, R = 0.1909 (Rfree = 0.000) for 2097 atoms. Found 8 (12 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1823 (Rfree = 0.000) for 2094 atoms. Found 5 (12 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.1850 (Rfree = 0.000) for 2088 atoms. Found 8 (12 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 2153 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 2172 seeds are put forward Round 1: 121 peptides, 20 chains. Longest chain 16 peptides. Score 0.399 Round 2: 161 peptides, 24 chains. Longest chain 19 peptides. Score 0.504 Round 3: 169 peptides, 19 chains. Longest chain 26 peptides. Score 0.623 Round 4: 160 peptides, 20 chains. Longest chain 19 peptides. Score 0.573 Round 5: 167 peptides, 23 chains. Longest chain 26 peptides. Score 0.547 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 150, Estimated correctness of the model 35.9 % 3 chains (45 residues) have been docked in sequence Sequence coverage is 29 % Consider running further cycles of model building using 2gnr-3_warpNtrace.pdb as input Building loops using Loopy2018 22 chains (150 residues) following loop building 3 chains (45 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4909 reflections ( 99.47 % complete ) and 4223 restraints for refining 2109 atoms. 3469 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2178 (Rfree = 0.000) for 2109 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2117 (Rfree = 0.000) for 2093 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2229 (Rfree = 0.000) for 2082 atoms. Found 0 (12 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2030 (Rfree = 0.000) for 2072 atoms. TimeTaking 30.08