Mon 24 Dec 00:53:12 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 2a6a-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-3.8-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/2a6a-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-3.8-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 00:53:17 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/2a6a-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-3.8-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 317 and 0 Target number of residues in the AU: 317 Target solvent content: 0.6743 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 436 Adjusted target solvent content: 0.55 Input MTZ file: 2a6a-3.8-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: 21 Cell parameters: 93.313 217.176 51.977 90.000 90.000 90.000 Input sequence file: 2a6a-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3488 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: 108.588 3.800 Wilson plot Bfac: 95.98 5455 reflections ( 98.61 % complete ) and 0 restraints for refining 3854 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3517 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3242 (Rfree = 0.000) for 3854 atoms. Found 21 (21 requested) and removed 65 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.55 Search for helices and strands: 0 residues in 0 chains, 3875 seeds are put forward NCS extension: 0 residues added, 3875 seeds are put forward Round 1: 164 peptides, 32 chains. Longest chain 9 peptides. Score 0.301 Round 2: 202 peptides, 31 chains. Longest chain 12 peptides. Score 0.436 Round 3: 205 peptides, 29 chains. Longest chain 18 peptides. Score 0.471 Round 4: 201 peptides, 28 chains. Longest chain 17 peptides. Score 0.473 Round 5: 205 peptides, 24 chains. Longest chain 17 peptides. Score 0.534 Taking the results from Round 5 Chains 24, Residues 181, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 7492 restraints for refining 3154 atoms. 6781 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2476 (Rfree = 0.000) for 3154 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 2: After refmac, R = 0.2238 (Rfree = 0.000) for 3093 atoms. Found 11 (17 requested) and removed 16 (8 requested) atoms. Cycle 3: After refmac, R = 0.2007 (Rfree = 0.000) for 3067 atoms. Found 5 (16 requested) and removed 13 (8 requested) atoms. Cycle 4: After refmac, R = 0.1978 (Rfree = 0.000) for 3054 atoms. Found 4 (16 requested) and removed 16 (8 requested) atoms. Cycle 5: After refmac, R = 0.1909 (Rfree = 0.000) for 3041 atoms. Found 3 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.50 Search for helices and strands: 0 residues in 0 chains, 3173 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3198 seeds are put forward Round 1: 180 peptides, 31 chains. Longest chain 12 peptides. Score 0.368 Round 2: 212 peptides, 29 chains. Longest chain 14 peptides. Score 0.491 Round 3: 213 peptides, 25 chains. Longest chain 24 peptides. Score 0.542 Round 4: 216 peptides, 27 chains. Longest chain 14 peptides. Score 0.526 Round 5: 229 peptides, 26 chains. Longest chain 19 peptides. Score 0.571 Taking the results from Round 5 Chains 26, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 7371 restraints for refining 3155 atoms. 6585 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2482 (Rfree = 0.000) for 3155 atoms. Found 17 (17 requested) and removed 64 (8 requested) atoms. Cycle 7: After refmac, R = 0.2198 (Rfree = 0.000) for 3070 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 8: After refmac, R = 0.2178 (Rfree = 0.000) for 3040 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 9: After refmac, R = 0.2112 (Rfree = 0.000) for 3014 atoms. Found 15 (16 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.2128 (Rfree = 0.000) for 3004 atoms. Found 14 (16 requested) and removed 24 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.53 Search for helices and strands: 0 residues in 0 chains, 3137 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3157 seeds are put forward Round 1: 174 peptides, 29 chains. Longest chain 13 peptides. Score 0.377 Round 2: 206 peptides, 30 chains. Longest chain 15 peptides. Score 0.461 Round 3: 220 peptides, 31 chains. Longest chain 16 peptides. Score 0.488 Round 4: 235 peptides, 32 chains. Longest chain 14 peptides. Score 0.517 Round 5: 240 peptides, 28 chains. Longest chain 18 peptides. Score 0.575 Taking the results from Round 5 Chains 29, Residues 212, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 6897 restraints for refining 3114 atoms. 6056 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2409 (Rfree = 0.000) for 3114 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. Cycle 12: After refmac, R = 0.2238 (Rfree = 0.000) for 3061 atoms. Found 11 (16 requested) and removed 22 (8 requested) atoms. Cycle 13: After refmac, R = 0.2233 (Rfree = 0.000) for 3011 atoms. Found 11 (16 requested) and removed 25 (8 requested) atoms. Cycle 14: After refmac, R = 0.2028 (Rfree = 0.000) for 2975 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.2767 (Rfree = 0.000) for 2954 atoms. Found 16 (16 requested) and removed 32 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.49 Search for helices and strands: 0 residues in 0 chains, 3125 seeds are put forward NCS extension: 0 residues added, 3125 seeds are put forward Round 1: 183 peptides, 34 chains. Longest chain 14 peptides. Score 0.336 Round 2: 217 peptides, 32 chains. Longest chain 13 peptides. Score 0.467 Round 3: 219 peptides, 31 chains. Longest chain 17 peptides. Score 0.485 Round 4: 228 peptides, 30 chains. Longest chain 14 peptides. Score 0.522 Round 5: 224 peptides, 30 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 4 Chains 30, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 6973 restraints for refining 3132 atoms. 6211 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2176 (Rfree = 0.000) for 3132 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 17: After refmac, R = 0.1987 (Rfree = 0.000) for 3084 atoms. Found 5 (17 requested) and removed 24 (8 requested) atoms. Cycle 18: After refmac, R = 0.2025 (Rfree = 0.000) for 3046 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 19: After refmac, R = 0.2115 (Rfree = 0.000) for 3017 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 20: After refmac, R = 0.2158 (Rfree = 0.000) for 2978 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.56 Search for helices and strands: 0 residues in 0 chains, 3128 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3144 seeds are put forward Round 1: 183 peptides, 33 chains. Longest chain 11 peptides. Score 0.350 Round 2: 223 peptides, 32 chains. Longest chain 18 peptides. Score 0.484 Round 3: 210 peptides, 30 chains. Longest chain 16 peptides. Score 0.473 Round 4: 223 peptides, 30 chains. Longest chain 21 peptides. Score 0.509 Round 5: 228 peptides, 29 chains. Longest chain 19 peptides. Score 0.534 Taking the results from Round 5 Chains 32, Residues 199, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 6382 restraints for refining 3073 atoms. 5494 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2160 (Rfree = 0.000) for 3073 atoms. Found 12 (16 requested) and removed 35 (8 requested) atoms. Cycle 22: After refmac, R = 0.1986 (Rfree = 0.000) for 3038 atoms. Found 3 (16 requested) and removed 18 (8 requested) atoms. Cycle 23: After refmac, R = 0.2421 (Rfree = 0.000) for 3018 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 24: After refmac, R = 0.2045 (Rfree = 0.000) for 3001 atoms. Found 14 (16 requested) and removed 23 (8 requested) atoms. Cycle 25: After refmac, R = 0.2090 (Rfree = 0.000) for 2975 atoms. Found 15 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.53 Search for helices and strands: 0 residues in 0 chains, 3092 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3105 seeds are put forward Round 1: 191 peptides, 33 chains. Longest chain 11 peptides. Score 0.376 Round 2: 214 peptides, 28 chains. Longest chain 17 peptides. Score 0.509 Round 3: 217 peptides, 28 chains. Longest chain 15 peptides. Score 0.517 Round 4: 218 peptides, 29 chains. Longest chain 24 peptides. Score 0.507 Round 5: 219 peptides, 28 chains. Longest chain 19 peptides. Score 0.522 Taking the results from Round 5 Chains 28, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 7172 restraints for refining 3154 atoms. 6436 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2054 (Rfree = 0.000) for 3154 atoms. Found 12 (17 requested) and removed 30 (8 requested) atoms. Cycle 27: After refmac, R = 0.1931 (Rfree = 0.000) for 3122 atoms. Found 9 (17 requested) and removed 21 (8 requested) atoms. Cycle 28: After refmac, R = 0.1711 (Rfree = 0.000) for 3101 atoms. Found 5 (17 requested) and removed 16 (8 requested) atoms. Cycle 29: After refmac, R = 0.1736 (Rfree = 0.000) for 3086 atoms. Found 3 (16 requested) and removed 18 (8 requested) atoms. Cycle 30: After refmac, R = 0.2117 (Rfree = 0.000) for 3064 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.53 Search for helices and strands: 0 residues in 0 chains, 3192 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3215 seeds are put forward Round 1: 171 peptides, 33 chains. Longest chain 9 peptides. Score 0.310 Round 2: 193 peptides, 29 chains. Longest chain 13 peptides. Score 0.436 Round 3: 187 peptides, 25 chains. Longest chain 14 peptides. Score 0.471 Round 4: 205 peptides, 24 chains. Longest chain 17 peptides. Score 0.534 Round 5: 193 peptides, 25 chains. Longest chain 20 peptides. Score 0.489 Taking the results from Round 4 Chains 24, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 7130 restraints for refining 3155 atoms. 6430 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2009 (Rfree = 0.000) for 3155 atoms. Found 14 (17 requested) and removed 30 (8 requested) atoms. Cycle 32: After refmac, R = 0.1961 (Rfree = 0.000) for 3115 atoms. Found 9 (17 requested) and removed 26 (8 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1946 (Rfree = 0.000) for 3082 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 34: After refmac, R = 0.2027 (Rfree = 0.000) for 3065 atoms. Found 3 (16 requested) and removed 21 (8 requested) atoms. Cycle 35: After refmac, R = 0.2060 (Rfree = 0.000) for 3028 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.51 Search for helices and strands: 0 residues in 0 chains, 3148 seeds are put forward NCS extension: 0 residues added, 3148 seeds are put forward Round 1: 162 peptides, 31 chains. Longest chain 10 peptides. Score 0.308 Round 2: 177 peptides, 27 chains. Longest chain 13 peptides. Score 0.415 Round 3: 199 peptides, 31 chains. Longest chain 12 peptides. Score 0.427 Round 4: 199 peptides, 31 chains. Longest chain 17 peptides. Score 0.427 Round 5: 204 peptides, 27 chains. Longest chain 17 peptides. Score 0.494 Taking the results from Round 5 Chains 27, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 6714 restraints for refining 3064 atoms. 6033 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1962 (Rfree = 0.000) for 3064 atoms. Found 11 (16 requested) and removed 36 (8 requested) atoms. Cycle 37: After refmac, R = 0.2146 (Rfree = 0.000) for 3027 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 38: After refmac, R = 0.1945 (Rfree = 0.000) for 2989 atoms. Found 12 (16 requested) and removed 16 (8 requested) atoms. Cycle 39: After refmac, R = 0.2462 (Rfree = 0.000) for 2958 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 40: After refmac, R = 0.2540 (Rfree = 0.000) for 2934 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.53 Search for helices and strands: 0 residues in 0 chains, 3066 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3082 seeds are put forward Round 1: 136 peptides, 28 chains. Longest chain 11 peptides. Score 0.261 Round 2: 156 peptides, 28 chains. Longest chain 12 peptides. Score 0.332 Round 3: 163 peptides, 28 chains. Longest chain 12 peptides. Score 0.356 Round 4: 161 peptides, 26 chains. Longest chain 14 peptides. Score 0.378 Round 5: 166 peptides, 25 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 5 Chains 25, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5455 reflections ( 98.61 % complete ) and 6695 restraints for refining 2956 atoms. 6156 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2404 (Rfree = 0.000) for 2956 atoms. Found 16 (16 requested) and removed 39 (8 requested) atoms. Cycle 42: After refmac, R = 0.2029 (Rfree = 0.000) for 2917 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 43: After refmac, R = 0.2850 (Rfree = 0.000) for 2891 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Cycle 44: After refmac, R = 0.1893 (Rfree = 0.000) for 2871 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.1658 (Rfree = 0.000) for 2868 atoms. Found 9 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.53 Search for helices and strands: 0 residues in 0 chains, 2977 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2997 seeds are put forward Round 1: 129 peptides, 26 chains. Longest chain 9 peptides. Score 0.267 Round 2: 154 peptides, 29 chains. Longest chain 10 peptides. Score 0.310 Round 3: 167 peptides, 30 chains. Longest chain 12 peptides. Score 0.340 Round 4: 164 peptides, 28 chains. Longest chain 14 peptides. Score 0.359 Round 5: 176 peptides, 26 chains. Longest chain 19 peptides. Score 0.425 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 150, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2a6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5455 reflections ( 98.61 % complete ) and 6365 restraints for refining 2957 atoms. 5741 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1805 (Rfree = 0.000) for 2957 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1817 (Rfree = 0.000) for 2932 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2504 (Rfree = 0.000) for 2909 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1694 (Rfree = 0.000) for 2891 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 41.25