Sun 23 Dec 23:41:38 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 2glz-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-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/2glz-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-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 23:41:42 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-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 277 and 0 Target number of residues in the AU: 277 Target solvent content: 0.6218 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-3.6-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: 19 Cell parameters: 46.427 84.786 100.702 90.000 90.000 90.000 Input sequence file: 2glz-3.6-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 3.600 Wilson plot Bfac: 61.87 4925 reflections ( 99.72 % complete ) and 0 restraints for refining 2723 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3352 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3357 (Rfree = 0.000) for 2723 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.03 Search for helices and strands: 0 residues in 0 chains, 2782 seeds are put forward NCS extension: 0 residues added, 2782 seeds are put forward Round 1: 159 peptides, 30 chains. Longest chain 10 peptides. Score 0.346 Round 2: 192 peptides, 31 chains. Longest chain 11 peptides. Score 0.461 Round 3: 210 peptides, 32 chains. Longest chain 12 peptides. Score 0.510 Round 4: 193 peptides, 24 chains. Longest chain 24 peptides. Score 0.572 Round 5: 195 peptides, 26 chains. Longest chain 15 peptides. Score 0.549 Taking the results from Round 4 Chains 25, Residues 169, Estimated correctness of the model 3.4 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4526 restraints for refining 2218 atoms. 3756 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2781 (Rfree = 0.000) for 2218 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 2: After refmac, R = 0.2853 (Rfree = 0.000) for 2184 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 3: After refmac, R = 0.2753 (Rfree = 0.000) for 2166 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 4: After refmac, R = 0.2757 (Rfree = 0.000) for 2147 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 5: After refmac, R = 0.2255 (Rfree = 0.000) for 2123 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 2.97 Search for helices and strands: 0 residues in 0 chains, 2201 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 2220 seeds are put forward Round 1: 178 peptides, 29 chains. Longest chain 13 peptides. Score 0.441 Round 2: 196 peptides, 29 chains. Longest chain 18 peptides. Score 0.507 Round 3: 197 peptides, 27 chains. Longest chain 17 peptides. Score 0.541 Round 4: 199 peptides, 26 chains. Longest chain 20 peptides. Score 0.562 Round 5: 207 peptides, 25 chains. Longest chain 25 peptides. Score 0.601 Taking the results from Round 5 Chains 25, Residues 182, Estimated correctness of the model 15.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4882 restraints for refining 2219 atoms. 4179 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2845 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 7: After refmac, R = 0.2527 (Rfree = 0.000) for 2193 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 8: After refmac, R = 0.2458 (Rfree = 0.000) for 2178 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 9: After refmac, R = 0.2265 (Rfree = 0.000) for 2166 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 10: After refmac, R = 0.2266 (Rfree = 0.000) for 2163 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 2.93 Search for helices and strands: 0 residues in 0 chains, 2277 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2294 seeds are put forward Round 1: 163 peptides, 32 chains. Longest chain 15 peptides. Score 0.327 Round 2: 191 peptides, 29 chains. Longest chain 24 peptides. Score 0.489 Round 3: 189 peptides, 27 chains. Longest chain 26 peptides. Score 0.513 Round 4: 200 peptides, 30 chains. Longest chain 14 peptides. Score 0.506 Round 5: 189 peptides, 27 chains. Longest chain 16 peptides. Score 0.513 Taking the results from Round 5 Chains 27, Residues 162, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4855 restraints for refining 2219 atoms. 4181 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2588 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 12: After refmac, R = 0.2327 (Rfree = 0.000) for 2209 atoms. Found 11 (14 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.2101 (Rfree = 0.000) for 2206 atoms. Found 7 (14 requested) and removed 14 (7 requested) atoms. Cycle 14: After refmac, R = 0.2024 (Rfree = 0.000) for 2195 atoms. Found 8 (14 requested) and removed 9 (7 requested) atoms. Cycle 15: After refmac, R = 0.2020 (Rfree = 0.000) for 2188 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 2.95 Search for helices and strands: 0 residues in 0 chains, 2266 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2280 seeds are put forward Round 1: 155 peptides, 27 chains. Longest chain 13 peptides. Score 0.383 Round 2: 176 peptides, 25 chains. Longest chain 15 peptides. Score 0.499 Round 3: 194 peptides, 27 chains. Longest chain 16 peptides. Score 0.531 Round 4: 182 peptides, 28 chains. Longest chain 15 peptides. Score 0.472 Round 5: 182 peptides, 25 chains. Longest chain 22 peptides. Score 0.520 Taking the results from Round 3 Chains 27, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4835 restraints for refining 2218 atoms. 4194 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2576 (Rfree = 0.000) for 2218 atoms. Found 11 (14 requested) and removed 15 (7 requested) atoms. Cycle 17: After refmac, R = 0.2284 (Rfree = 0.000) for 2191 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 18: After refmac, R = 0.2148 (Rfree = 0.000) for 2188 atoms. Found 11 (14 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.2126 (Rfree = 0.000) for 2186 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.2018 (Rfree = 0.000) for 2186 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 2.95 Search for helices and strands: 0 residues in 0 chains, 2298 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2315 seeds are put forward Round 1: 163 peptides, 31 chains. Longest chain 13 peptides. Score 0.345 Round 2: 189 peptides, 28 chains. Longest chain 17 peptides. Score 0.498 Round 3: 198 peptides, 30 chains. Longest chain 14 peptides. Score 0.499 Round 4: 193 peptides, 29 chains. Longest chain 15 peptides. Score 0.496 Round 5: 199 peptides, 31 chains. Longest chain 13 peptides. Score 0.486 Taking the results from Round 3 Chains 30, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4977 restraints for refining 2219 atoms. 4335 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2480 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 22: After refmac, R = 0.2499 (Rfree = 0.000) for 2206 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 23: After refmac, R = 0.2428 (Rfree = 0.000) for 2191 atoms. Found 12 (14 requested) and removed 12 (7 requested) atoms. Cycle 24: After refmac, R = 0.2471 (Rfree = 0.000) for 2184 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 25: After refmac, R = 0.2421 (Rfree = 0.000) for 2177 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 2.98 Search for helices and strands: 0 residues in 0 chains, 2264 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2284 seeds are put forward Round 1: 152 peptides, 27 chains. Longest chain 12 peptides. Score 0.371 Round 2: 171 peptides, 25 chains. Longest chain 22 peptides. Score 0.480 Round 3: 163 peptides, 22 chains. Longest chain 19 peptides. Score 0.500 Round 4: 177 peptides, 24 chains. Longest chain 18 peptides. Score 0.518 Round 5: 189 peptides, 25 chains. Longest chain 22 peptides. Score 0.544 Taking the results from Round 5 Chains 25, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4867 restraints for refining 2219 atoms. 4236 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2733 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 27: After refmac, R = 0.2690 (Rfree = 0.000) for 2206 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.2573 (Rfree = 0.000) for 2193 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 29: After refmac, R = 0.2102 (Rfree = 0.000) for 2188 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 30: After refmac, R = 0.2289 (Rfree = 0.000) for 2181 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 2.97 Search for helices and strands: 0 residues in 0 chains, 2269 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2283 seeds are put forward Round 1: 155 peptides, 28 chains. Longest chain 14 peptides. Score 0.365 Round 2: 171 peptides, 23 chains. Longest chain 19 peptides. Score 0.513 Round 3: 159 peptides, 23 chains. Longest chain 12 peptides. Score 0.469 Round 4: 156 peptides, 23 chains. Longest chain 18 peptides. Score 0.457 Round 5: 166 peptides, 23 chains. Longest chain 18 peptides. Score 0.495 Taking the results from Round 2 Chains 25, Residues 148, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4631 restraints for refining 2218 atoms. 3979 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2595 (Rfree = 0.000) for 2218 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 32: After refmac, R = 0.2262 (Rfree = 0.000) for 2191 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 33: After refmac, R = 0.2184 (Rfree = 0.000) for 2175 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 34: After refmac, R = 0.2040 (Rfree = 0.000) for 2171 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 35: After refmac, R = 0.1957 (Rfree = 0.000) for 2167 atoms. Found 12 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 2.96 Search for helices and strands: 0 residues in 0 chains, 2242 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2257 seeds are put forward Round 1: 161 peptides, 29 chains. Longest chain 12 peptides. Score 0.373 Round 2: 171 peptides, 25 chains. Longest chain 13 peptides. Score 0.480 Round 3: 152 peptides, 23 chains. Longest chain 21 peptides. Score 0.442 Round 4: 162 peptides, 27 chains. Longest chain 12 peptides. Score 0.412 Round 5: 175 peptides, 24 chains. Longest chain 18 peptides. Score 0.511 Taking the results from Round 5 Chains 24, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4837 restraints for refining 2219 atoms. 4257 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2481 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 37: After refmac, R = 0.2414 (Rfree = 0.000) for 2207 atoms. Found 13 (14 requested) and removed 11 (7 requested) atoms. Cycle 38: After refmac, R = 0.2339 (Rfree = 0.000) for 2201 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2399 (Rfree = 0.000) for 2194 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2309 (Rfree = 0.000) for 2193 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 2.96 Search for helices and strands: 0 residues in 0 chains, 2284 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2302 seeds are put forward Round 1: 143 peptides, 29 chains. Longest chain 12 peptides. Score 0.295 Round 2: 148 peptides, 25 chains. Longest chain 9 peptides. Score 0.390 Round 3: 155 peptides, 25 chains. Longest chain 12 peptides. Score 0.419 Round 4: 154 peptides, 26 chains. Longest chain 13 peptides. Score 0.397 Round 5: 155 peptides, 22 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 5 Chains 22, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4944 restraints for refining 2219 atoms. 4434 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2658 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 42: After refmac, R = 0.2603 (Rfree = 0.000) for 2210 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 43: After refmac, R = 0.2459 (Rfree = 0.000) for 2200 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 44: After refmac, R = 0.2460 (Rfree = 0.000) for 2192 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 45: After refmac, R = 0.2445 (Rfree = 0.000) for 2184 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 2.89 Search for helices and strands: 0 residues in 0 chains, 2274 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2292 seeds are put forward Round 1: 125 peptides, 24 chains. Longest chain 11 peptides. Score 0.309 Round 2: 148 peptides, 24 chains. Longest chain 11 peptides. Score 0.408 Round 3: 160 peptides, 21 chains. Longest chain 19 peptides. Score 0.506 Round 4: 161 peptides, 22 chains. Longest chain 16 peptides. Score 0.493 Round 5: 154 peptides, 21 chains. Longest chain 15 peptides. Score 0.484 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 139, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2glz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4925 reflections ( 99.72 % complete ) and 4747 restraints for refining 2218 atoms. 4181 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2574 (Rfree = 0.000) for 2218 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2536 (Rfree = 0.000) for 2203 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2361 (Rfree = 0.000) for 2189 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2517 (Rfree = 0.000) for 2179 atoms. TimeTaking 30