Mon 24 Dec 07:27:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2glz-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2glz-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2glz-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-parrot-noncs ############### 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 07:27:58 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/noncs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-parrot-noncs/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 288 and 0 Target number of residues in the AU: 288 Target solvent content: 0.6068 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-3.4-parrot-noncs.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-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.85 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 3.400 Wilson plot Bfac: 55.20 5830 reflections ( 99.76 % complete ) and 0 restraints for refining 2723 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3388 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3071 (Rfree = 0.000) for 2723 atoms. Found 20 (20 requested) and removed 216 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 2.78 Search for helices and strands: 0 residues in 0 chains, 2550 seeds are put forward NCS extension: 0 residues added, 2550 seeds are put forward Round 1: 144 peptides, 28 chains. Longest chain 11 peptides. Score 0.318 Round 2: 171 peptides, 27 chains. Longest chain 13 peptides. Score 0.447 Round 3: 172 peptides, 25 chains. Longest chain 15 peptides. Score 0.484 Round 4: 167 peptides, 24 chains. Longest chain 17 peptides. Score 0.482 Round 5: 188 peptides, 27 chains. Longest chain 21 peptides. Score 0.510 Taking the results from Round 5 Chains 27, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4863 restraints for refining 2226 atoms. 4246 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2849 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 49 (8 requested) atoms. Cycle 2: After refmac, R = 0.2592 (Rfree = 0.000) for 2164 atoms. Found 12 (16 requested) and removed 29 (8 requested) atoms. Cycle 3: After refmac, R = 0.2433 (Rfree = 0.000) for 2138 atoms. Found 9 (16 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2340 (Rfree = 0.000) for 2126 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. Cycle 5: After refmac, R = 0.2315 (Rfree = 0.000) for 2113 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 2.81 Search for helices and strands: 0 residues in 0 chains, 2205 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 2231 seeds are put forward Round 1: 190 peptides, 30 chains. Longest chain 14 peptides. Score 0.470 Round 2: 206 peptides, 28 chains. Longest chain 29 peptides. Score 0.556 Round 3: 207 peptides, 25 chains. Longest chain 21 peptides. Score 0.601 Round 4: 227 peptides, 28 chains. Longest chain 31 peptides. Score 0.620 Round 5: 228 peptides, 32 chains. Longest chain 24 peptides. Score 0.569 Taking the results from Round 4 Chains 31, Residues 199, Estimated correctness of the model 35.1 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4457 restraints for refining 2226 atoms. 3590 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2708 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 7: After refmac, R = 0.2513 (Rfree = 0.000) for 2202 atoms. Found 15 (16 requested) and removed 16 (8 requested) atoms. Cycle 8: After refmac, R = 0.2395 (Rfree = 0.000) for 2193 atoms. Found 8 (16 requested) and removed 19 (8 requested) atoms. Cycle 9: After refmac, R = 0.2359 (Rfree = 0.000) for 2178 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2323 (Rfree = 0.000) for 2175 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 2.82 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2273 seeds are put forward Round 1: 194 peptides, 30 chains. Longest chain 18 peptides. Score 0.484 Round 2: 202 peptides, 26 chains. Longest chain 27 peptides. Score 0.572 Round 3: 211 peptides, 29 chains. Longest chain 20 peptides. Score 0.558 Round 4: 205 peptides, 26 chains. Longest chain 21 peptides. Score 0.581 Round 5: 202 peptides, 26 chains. Longest chain 30 peptides. Score 0.572 Taking the results from Round 4 Chains 26, Residues 179, Estimated correctness of the model 22.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4804 restraints for refining 2226 atoms. 4114 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2569 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 12: After refmac, R = 0.2377 (Rfree = 0.000) for 2218 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 13: After refmac, R = 0.2422 (Rfree = 0.000) for 2212 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.2397 (Rfree = 0.000) for 2205 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.2399 (Rfree = 0.000) for 2200 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.82 Search for helices and strands: 0 residues in 0 chains, 2276 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2297 seeds are put forward Round 1: 192 peptides, 28 chains. Longest chain 22 peptides. Score 0.508 Round 2: 209 peptides, 26 chains. Longest chain 23 peptides. Score 0.594 Round 3: 220 peptides, 25 chains. Longest chain 25 peptides. Score 0.639 Round 4: 213 peptides, 27 chains. Longest chain 22 peptides. Score 0.592 Round 5: 227 peptides, 26 chains. Longest chain 24 peptides. Score 0.646 Taking the results from Round 5 Chains 29, Residues 201, Estimated correctness of the model 43.0 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4147 restraints for refining 2226 atoms. 3230 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2668 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 17: After refmac, R = 0.2455 (Rfree = 0.000) for 2208 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. Cycle 18: After refmac, R = 0.2398 (Rfree = 0.000) for 2204 atoms. Found 13 (16 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.2308 (Rfree = 0.000) for 2206 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2231 (Rfree = 0.000) for 2203 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 2.80 Search for helices and strands: 0 residues in 0 chains, 2265 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 2292 seeds are put forward Round 1: 162 peptides, 20 chains. Longest chain 18 peptides. Score 0.529 Round 2: 187 peptides, 22 chains. Longest chain 20 peptides. Score 0.582 Round 3: 205 peptides, 26 chains. Longest chain 20 peptides. Score 0.581 Round 4: 199 peptides, 21 chains. Longest chain 22 peptides. Score 0.632 Round 5: 189 peptides, 23 chains. Longest chain 20 peptides. Score 0.574 Taking the results from Round 4 Chains 22, Residues 178, Estimated correctness of the model 38.8 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4614 restraints for refining 2226 atoms. 3868 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2672 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 22: After refmac, R = 0.2484 (Rfree = 0.000) for 2223 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.2434 (Rfree = 0.000) for 2212 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2394 (Rfree = 0.000) for 2207 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2416 (Rfree = 0.000) for 2200 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 2.86 Search for helices and strands: 0 residues in 0 chains, 2270 seeds are put forward NCS extension: 0 residues added, 2270 seeds are put forward Round 1: 176 peptides, 27 chains. Longest chain 19 peptides. Score 0.466 Round 2: 190 peptides, 24 chains. Longest chain 17 peptides. Score 0.562 Round 3: 202 peptides, 26 chains. Longest chain 15 peptides. Score 0.572 Round 4: 185 peptides, 24 chains. Longest chain 17 peptides. Score 0.546 Round 5: 190 peptides, 23 chains. Longest chain 16 peptides. Score 0.577 Taking the results from Round 5 Chains 23, Residues 167, Estimated correctness of the model 21.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4817 restraints for refining 2226 atoms. 4172 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2833 (Rfree = 0.000) for 2226 atoms. Found 9 (16 requested) and removed 14 (8 requested) atoms. Cycle 27: After refmac, R = 0.2608 (Rfree = 0.000) for 2218 atoms. Found 3 (16 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.2681 (Rfree = 0.000) for 2210 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2441 (Rfree = 0.000) for 2201 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.2642 (Rfree = 0.000) for 2193 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.82 Search for helices and strands: 0 residues in 0 chains, 2252 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 2265 seeds are put forward Round 1: 179 peptides, 30 chains. Longest chain 16 peptides. Score 0.428 Round 2: 190 peptides, 27 chains. Longest chain 18 peptides. Score 0.517 Round 3: 182 peptides, 27 chains. Longest chain 17 peptides. Score 0.488 Round 4: 177 peptides, 23 chains. Longest chain 17 peptides. Score 0.534 Round 5: 181 peptides, 24 chains. Longest chain 18 peptides. Score 0.532 Taking the results from Round 4 Chains 23, Residues 154, Estimated correctness of the model 5.7 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4794 restraints for refining 2226 atoms. 4144 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2629 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 32: After refmac, R = 0.2594 (Rfree = 0.000) for 2221 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2567 (Rfree = 0.000) for 2221 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2445 (Rfree = 0.000) for 2219 atoms. Found 3 (16 requested) and removed 12 (8 requested) atoms. Cycle 35: After refmac, R = 0.2458 (Rfree = 0.000) for 2210 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 2.85 Search for helices and strands: 0 residues in 0 chains, 2265 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2287 seeds are put forward Round 1: 157 peptides, 28 chains. Longest chain 13 peptides. Score 0.374 Round 2: 181 peptides, 27 chains. Longest chain 14 peptides. Score 0.485 Round 3: 178 peptides, 27 chains. Longest chain 14 peptides. Score 0.474 Round 4: 169 peptides, 25 chains. Longest chain 16 peptides. Score 0.473 Round 5: 171 peptides, 24 chains. Longest chain 18 peptides. Score 0.497 Taking the results from Round 5 Chains 24, Residues 147, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4896 restraints for refining 2226 atoms. 4332 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2592 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.2439 (Rfree = 0.000) for 2229 atoms. Found 5 (16 requested) and removed 13 (8 requested) atoms. Cycle 38: After refmac, R = 0.2347 (Rfree = 0.000) for 2220 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2341 (Rfree = 0.000) for 2213 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2260 (Rfree = 0.000) for 2211 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 2.83 Search for helices and strands: 0 residues in 0 chains, 2280 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2306 seeds are put forward Round 1: 152 peptides, 28 chains. Longest chain 13 peptides. Score 0.353 Round 2: 164 peptides, 27 chains. Longest chain 14 peptides. Score 0.420 Round 3: 173 peptides, 25 chains. Longest chain 18 peptides. Score 0.488 Round 4: 172 peptides, 23 chains. Longest chain 30 peptides. Score 0.516 Round 5: 173 peptides, 25 chains. Longest chain 17 peptides. Score 0.488 Taking the results from Round 4 Chains 24, Residues 149, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4741 restraints for refining 2226 atoms. 4122 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2573 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 42: After refmac, R = 0.2421 (Rfree = 0.000) for 2225 atoms. Found 7 (16 requested) and removed 16 (8 requested) atoms. Cycle 43: After refmac, R = 0.2366 (Rfree = 0.000) for 2212 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2337 (Rfree = 0.000) for 2207 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.2317 (Rfree = 0.000) for 2204 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 2.81 Search for helices and strands: 0 residues in 0 chains, 2270 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 2300 seeds are put forward Round 1: 147 peptides, 26 chains. Longest chain 10 peptides. Score 0.368 Round 2: 156 peptides, 22 chains. Longest chain 15 peptides. Score 0.474 Round 3: 168 peptides, 23 chains. Longest chain 15 peptides. Score 0.502 Round 4: 165 peptides, 20 chains. Longest chain 28 peptides. Score 0.540 Round 5: 165 peptides, 22 chains. Longest chain 26 peptides. Score 0.508 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 145, Estimated correctness of the model 7.9 % 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. 5830 reflections ( 99.76 % complete ) and 4963 restraints for refining 2226 atoms. 4403 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2609 (Rfree = 0.000) for 2226 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2525 (Rfree = 0.000) for 2214 atoms. Found 0 (16 requested) and removed 1 (8 requested) atoms. Cycle 48: After refmac, R = 0.2491 (Rfree = 0.000) for 2213 atoms. Found 0 (16 requested) and removed 0 (8 requested) atoms. Cycle 49: After refmac, R = 0.2469 (Rfree = 0.000) for 2213 atoms. Found 0 (16 requested) and removed 2 (8 requested) atoms. Writing output files ... TimeTaking 30.97