Mon 24 Dec 00:44:48 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 2glz-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-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/2glz-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-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 00:44:52 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/2glz-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-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 271 and 0 Target number of residues in the AU: 271 Target solvent content: 0.6300 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.58 Input MTZ file: 2glz-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: 19 Cell parameters: 46.427 84.786 100.702 90.000 90.000 90.000 Input sequence file: 2glz-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.90 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: 29.894 3.800 Wilson plot Bfac: 66.45 Failed to save intermediate PDB 4224 reflections ( 99.67 % complete ) and 0 restraints for refining 2706 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3477 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3336 (Rfree = 0.000) for 2706 atoms. Found 14 (14 requested) and removed 44 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.10 Search for helices and strands: 0 residues in 0 chains, 2753 seeds are put forward NCS extension: 0 residues added, 2753 seeds are put forward Round 1: 135 peptides, 24 chains. Longest chain 12 peptides. Score 0.354 Round 2: 162 peptides, 24 chains. Longest chain 12 peptides. Score 0.463 Round 3: 173 peptides, 26 chains. Longest chain 12 peptides. Score 0.471 Round 4: 186 peptides, 27 chains. Longest chain 15 peptides. Score 0.503 Round 5: 190 peptides, 28 chains. Longest chain 14 peptides. Score 0.501 Taking the results from Round 4 Chains 27, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4224 reflections ( 99.67 % complete ) and 4967 restraints for refining 2213 atoms. 4358 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2917 (Rfree = 0.000) for 2213 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 2: After refmac, R = 0.2688 (Rfree = 0.000) for 2174 atoms. Found 7 (12 requested) and removed 14 (6 requested) atoms. Cycle 3: After refmac, R = 0.2566 (Rfree = 0.000) for 2153 atoms. Found 9 (11 requested) and removed 15 (5 requested) atoms. Cycle 4: After refmac, R = 0.2852 (Rfree = 0.000) for 2135 atoms. Found 3 (11 requested) and removed 26 (5 requested) atoms. Cycle 5: After refmac, R = 0.2569 (Rfree = 0.000) for 2099 atoms. Found 9 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.10 Search for helices and strands: 0 residues in 0 chains, 2205 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 2222 seeds are put forward Round 1: 163 peptides, 28 chains. Longest chain 14 peptides. Score 0.399 Round 2: 185 peptides, 26 chains. Longest chain 20 peptides. Score 0.515 Round 3: 189 peptides, 25 chains. Longest chain 16 peptides. Score 0.544 Round 4: 192 peptides, 23 chains. Longest chain 19 peptides. Score 0.583 Round 5: 196 peptides, 27 chains. Longest chain 16 peptides. Score 0.537 Taking the results from Round 4 Chains 23, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4224 reflections ( 99.67 % complete ) and 4876 restraints for refining 2214 atoms. 4223 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2904 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 7: After refmac, R = 0.2513 (Rfree = 0.000) for 2170 atoms. Found 7 (12 requested) and removed 21 (6 requested) atoms. Cycle 8: After refmac, R = 0.2611 (Rfree = 0.000) for 2139 atoms. Found 9 (11 requested) and removed 15 (5 requested) atoms. Cycle 9: After refmac, R = 0.2361 (Rfree = 0.000) for 2120 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 10: After refmac, R = 0.2415 (Rfree = 0.000) for 2116 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.07 Search for helices and strands: 0 residues in 0 chains, 2198 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2222 seeds are put forward Round 1: 156 peptides, 29 chains. Longest chain 11 peptides. Score 0.352 Round 2: 173 peptides, 27 chains. Longest chain 15 peptides. Score 0.455 Round 3: 183 peptides, 30 chains. Longest chain 14 peptides. Score 0.443 Round 4: 166 peptides, 28 chains. Longest chain 13 peptides. Score 0.411 Round 5: 162 peptides, 22 chains. Longest chain 16 peptides. Score 0.497 Taking the results from Round 5 Chains 22, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4224 reflections ( 99.67 % complete ) and 5080 restraints for refining 2214 atoms. 4542 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2665 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 12: After refmac, R = 0.2557 (Rfree = 0.000) for 2188 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 13: After refmac, R = 0.2383 (Rfree = 0.000) for 2175 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 14: After refmac, R = 0.2752 (Rfree = 0.000) for 2159 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 15: After refmac, R = 0.2404 (Rfree = 0.000) for 2135 atoms. Found 9 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.05 Search for helices and strands: 0 residues in 0 chains, 2253 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 2271 seeds are put forward Round 1: 159 peptides, 32 chains. Longest chain 10 peptides. Score 0.310 Round 2: 164 peptides, 28 chains. Longest chain 14 peptides. Score 0.403 Round 3: 182 peptides, 28 chains. Longest chain 16 peptides. Score 0.472 Round 4: 162 peptides, 24 chains. Longest chain 18 peptides. Score 0.463 Round 5: 178 peptides, 21 chains. Longest chain 24 peptides. Score 0.568 Taking the results from Round 5 Chains 21, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4224 reflections ( 99.67 % complete ) and 5075 restraints for refining 2214 atoms. 4468 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2660 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 17: After refmac, R = 0.2818 (Rfree = 0.000) for 2188 atoms. Found 12 (12 requested) and removed 29 (6 requested) atoms. Cycle 18: After refmac, R = 0.2584 (Rfree = 0.000) for 2160 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 19: After refmac, R = 0.2477 (Rfree = 0.000) for 2149 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 20: After refmac, R = 0.2454 (Rfree = 0.000) for 2140 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.10 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 2262 seeds are put forward Round 1: 141 peptides, 27 chains. Longest chain 8 peptides. Score 0.324 Round 2: 170 peptides, 25 chains. Longest chain 23 peptides. Score 0.477 Round 3: 179 peptides, 25 chains. Longest chain 17 peptides. Score 0.509 Round 4: 175 peptides, 21 chains. Longest chain 18 peptides. Score 0.558 Round 5: 179 peptides, 25 chains. Longest chain 16 peptides. Score 0.509 Taking the results from Round 4 Chains 21, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4224 reflections ( 99.67 % complete ) and 4966 restraints for refining 2214 atoms. 4371 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2655 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 22: After refmac, R = 0.3070 (Rfree = 0.000) for 2192 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. Cycle 23: After refmac, R = 0.2412 (Rfree = 0.000) for 2159 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2434 (Rfree = 0.000) for 2157 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 25: After refmac, R = 0.2462 (Rfree = 0.000) for 2143 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.11 Search for helices and strands: 0 residues in 0 chains, 2266 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2294 seeds are put forward Round 1: 110 peptides, 22 chains. Longest chain 8 peptides. Score 0.279 Round 2: 140 peptides, 23 chains. Longest chain 12 peptides. Score 0.393 Round 3: 144 peptides, 23 chains. Longest chain 13 peptides. Score 0.410 Round 4: 159 peptides, 25 chains. Longest chain 15 peptides. Score 0.435 Round 5: 139 peptides, 21 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 4 Chains 25, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4224 reflections ( 99.67 % complete ) and 5115 restraints for refining 2214 atoms. 4604 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2666 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 27: After refmac, R = 0.2654 (Rfree = 0.000) for 2193 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 28: After refmac, R = 0.2552 (Rfree = 0.000) for 2177 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 29: After refmac, R = 0.2260 (Rfree = 0.000) for 2159 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 30: After refmac, R = 0.2033 (Rfree = 0.000) for 2152 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.05 Search for helices and strands: 0 residues in 0 chains, 2241 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2261 seeds are put forward Round 1: 143 peptides, 29 chains. Longest chain 8 peptides. Score 0.295 Round 2: 163 peptides, 30 chains. Longest chain 12 peptides. Score 0.363 Round 3: 160 peptides, 26 chains. Longest chain 16 peptides. Score 0.421 Round 4: 165 peptides, 27 chains. Longest chain 12 peptides. Score 0.424 Round 5: 154 peptides, 23 chains. Longest chain 13 peptides. Score 0.450 Taking the results from Round 5 Chains 23, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4224 reflections ( 99.67 % complete ) and 5029 restraints for refining 2214 atoms. 4528 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3121 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 32: After refmac, R = 0.2664 (Rfree = 0.000) for 2197 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 33: After refmac, R = 0.2497 (Rfree = 0.000) for 2184 atoms. Found 9 (12 requested) and removed 15 (6 requested) atoms. Cycle 34: After refmac, R = 0.2347 (Rfree = 0.000) for 2173 atoms. Found 9 (11 requested) and removed 14 (5 requested) atoms. Cycle 35: After refmac, R = 0.2173 (Rfree = 0.000) for 2167 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.07 Search for helices and strands: 0 residues in 0 chains, 2266 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2282 seeds are put forward Round 1: 140 peptides, 28 chains. Longest chain 11 peptides. Score 0.300 Round 2: 147 peptides, 24 chains. Longest chain 12 peptides. Score 0.404 Round 3: 144 peptides, 24 chains. Longest chain 12 peptides. Score 0.392 Round 4: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.416 Round 5: 160 peptides, 23 chains. Longest chain 15 peptides. Score 0.473 Taking the results from Round 5 Chains 23, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4224 reflections ( 99.67 % complete ) and 4970 restraints for refining 2214 atoms. 4445 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2775 (Rfree = 0.000) for 2214 atoms. Found 9 (12 requested) and removed 17 (6 requested) atoms. Cycle 37: After refmac, R = 0.2301 (Rfree = 0.000) for 2199 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.2324 (Rfree = 0.000) for 2185 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.2263 (Rfree = 0.000) for 2181 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 40: After refmac, R = 0.2311 (Rfree = 0.000) for 2180 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 2.99 Search for helices and strands: 0 residues in 0 chains, 2275 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2288 seeds are put forward Round 1: 119 peptides, 26 chains. Longest chain 7 peptides. Score 0.242 Round 2: 144 peptides, 25 chains. Longest chain 12 peptides. Score 0.374 Round 3: 142 peptides, 25 chains. Longest chain 11 peptides. Score 0.365 Round 4: 138 peptides, 24 chains. Longest chain 10 peptides. Score 0.367 Round 5: 146 peptides, 23 chains. Longest chain 13 peptides. Score 0.418 Taking the results from Round 5 Chains 23, Residues 123, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4224 reflections ( 99.67 % complete ) and 4813 restraints for refining 2214 atoms. 4312 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3621 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 42: After refmac, R = 0.2760 (Rfree = 0.000) for 2183 atoms. Found 10 (12 requested) and removed 16 (6 requested) atoms. Cycle 43: After refmac, R = 0.2836 (Rfree = 0.000) for 2172 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.2649 (Rfree = 0.000) for 2162 atoms. Found 6 (11 requested) and removed 13 (5 requested) atoms. Cycle 45: After refmac, R = 0.2349 (Rfree = 0.000) for 2149 atoms. Found 5 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.09 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2238 seeds are put forward Round 1: 109 peptides, 24 chains. Longest chain 8 peptides. Score 0.233 Round 2: 118 peptides, 23 chains. Longest chain 7 peptides. Score 0.297 Round 3: 124 peptides, 23 chains. Longest chain 11 peptides. Score 0.324 Round 4: 120 peptides, 22 chains. Longest chain 8 peptides. Score 0.326 Round 5: 112 peptides, 19 chains. Longest chain 11 peptides. Score 0.349 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 93, 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 2glz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4224 reflections ( 99.67 % complete ) and 5324 restraints for refining 2214 atoms. 4971 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2479 (Rfree = 0.000) for 2214 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2310 (Rfree = 0.000) for 2199 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2347 (Rfree = 0.000) for 2190 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2118 (Rfree = 0.000) for 2182 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 27.97