null Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2glz-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2glz-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2glz-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:07 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/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-hancs/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 297 and 0 Target number of residues in the AU: 297 Target solvent content: 0.5945 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-3.2-parrot-hancs.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-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.80 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 3.200 Wilson plot Bfac: 50.12 6969 reflections ( 99.80 % complete ) and 0 restraints for refining 2732 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Starting model: R = 0.3292 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2997 (Rfree = 0.000) for 2732 atoms. Found 22 (24 requested) and removed 159 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.07 2.76 Search for helices and strands: 0 residues in 0 chains, 2620 seeds are put forward NCS extension: 0 residues added, 2620 seeds are put forward Round 1: 160 peptides, 32 chains. Longest chain 11 peptides. Score 0.314 Round 2: 207 peptides, 34 chains. Longest chain 20 peptides. Score 0.468 Round 3: 205 peptides, 32 chains. Longest chain 28 peptides. Score 0.492 Round 4: 208 peptides, 31 chains. Longest chain 25 peptides. Score 0.518 Round 5: 226 peptides, 33 chains. Longest chain 25 peptides. Score 0.549 Taking the results from Round 5 Chains 35, Residues 193, Estimated correctness of the model 26.6 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4462 restraints for refining 2235 atoms. 3668 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3015 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 39 (10 requested) atoms. Cycle 2: After refmac, R = 0.2798 (Rfree = 0.000) for 2195 atoms. Found 17 (19 requested) and removed 18 (9 requested) atoms. Cycle 3: After refmac, R = 0.2679 (Rfree = 0.000) for 2192 atoms. Found 9 (19 requested) and removed 14 (9 requested) atoms. Cycle 4: After refmac, R = 0.2640 (Rfree = 0.000) for 2182 atoms. Found 6 (19 requested) and removed 12 (9 requested) atoms. Cycle 5: After refmac, R = 0.2583 (Rfree = 0.000) for 2174 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 2.76 Search for helices and strands: 0 residues in 0 chains, 2256 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 2286 seeds are put forward Round 1: 203 peptides, 28 chains. Longest chain 24 peptides. Score 0.546 Round 2: 230 peptides, 30 chains. Longest chain 27 peptides. Score 0.603 Round 3: 228 peptides, 27 chains. Longest chain 30 peptides. Score 0.636 Round 4: 224 peptides, 25 chains. Longest chain 28 peptides. Score 0.650 Round 5: 222 peptides, 22 chains. Longest chain 25 peptides. Score 0.681 Taking the results from Round 5 Chains 24, Residues 200, Estimated correctness of the model 61.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4591 restraints for refining 2231 atoms. 3763 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2873 (Rfree = 0.000) for 2231 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 7: After refmac, R = 0.2619 (Rfree = 0.000) for 2221 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. Cycle 8: After refmac, R = 0.2541 (Rfree = 0.000) for 2218 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. Cycle 9: After refmac, R = 0.2530 (Rfree = 0.000) for 2206 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. Cycle 10: After refmac, R = 0.2510 (Rfree = 0.000) for 2198 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 2.74 Search for helices and strands: 0 residues in 0 chains, 2266 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2292 seeds are put forward Round 1: 183 peptides, 30 chains. Longest chain 22 peptides. Score 0.443 Round 2: 197 peptides, 28 chains. Longest chain 25 peptides. Score 0.526 Round 3: 215 peptides, 32 chains. Longest chain 24 peptides. Score 0.527 Round 4: 209 peptides, 29 chains. Longest chain 19 peptides. Score 0.551 Round 5: 213 peptides, 22 chains. Longest chain 42 peptides. Score 0.658 Taking the results from Round 5 Chains 22, Residues 191, Estimated correctness of the model 55.7 % 1 chains (41 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4243 restraints for refining 2235 atoms. 3305 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2982 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 33 (10 requested) atoms. Cycle 12: After refmac, R = 0.2745 (Rfree = 0.000) for 2216 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.2656 (Rfree = 0.000) for 2205 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 14: After refmac, R = 0.2624 (Rfree = 0.000) for 2197 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.2606 (Rfree = 0.000) for 2188 atoms. Found 7 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 2.75 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 53 residues added (3 deleted due to clashes), 2301 seeds are put forward Round 1: 208 peptides, 30 chains. Longest chain 21 peptides. Score 0.533 Round 2: 206 peptides, 22 chains. Longest chain 28 peptides. Score 0.639 Round 3: 208 peptides, 23 chains. Longest chain 24 peptides. Score 0.631 Round 4: 195 peptides, 23 chains. Longest chain 26 peptides. Score 0.593 Round 5: 212 peptides, 25 chains. Longest chain 19 peptides. Score 0.616 Taking the results from Round 2 Chains 22, Residues 184, Estimated correctness of the model 51.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4775 restraints for refining 2235 atoms. 4061 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2649 (Rfree = 0.000) for 2235 atoms. Found 17 (20 requested) and removed 11 (10 requested) atoms. Cycle 17: After refmac, R = 0.2517 (Rfree = 0.000) for 2239 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 18: After refmac, R = 0.2420 (Rfree = 0.000) for 2248 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.2378 (Rfree = 0.000) for 2243 atoms. Found 9 (20 requested) and removed 11 (10 requested) atoms. Cycle 20: After refmac, R = 0.2306 (Rfree = 0.000) for 2240 atoms. Found 5 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 2.76 Search for helices and strands: 0 residues in 0 chains, 2315 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2331 seeds are put forward Round 1: 187 peptides, 29 chains. Longest chain 17 peptides. Score 0.475 Round 2: 193 peptides, 24 chains. Longest chain 27 peptides. Score 0.572 Round 3: 196 peptides, 24 chains. Longest chain 29 peptides. Score 0.581 Round 4: 209 peptides, 23 chains. Longest chain 34 peptides. Score 0.634 Round 5: 212 peptides, 25 chains. Longest chain 44 peptides. Score 0.616 Taking the results from Round 4 Chains 23, Residues 186, Estimated correctness of the model 49.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4752 restraints for refining 2235 atoms. 4031 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2607 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 22: After refmac, R = 0.2414 (Rfree = 0.000) for 2242 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.2353 (Rfree = 0.000) for 2238 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.2311 (Rfree = 0.000) for 2231 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.2315 (Rfree = 0.000) for 2220 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.03 2.72 Search for helices and strands: 0 residues in 0 chains, 2289 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 2318 seeds are put forward Round 1: 191 peptides, 29 chains. Longest chain 16 peptides. Score 0.489 Round 2: 196 peptides, 24 chains. Longest chain 33 peptides. Score 0.581 Round 3: 195 peptides, 22 chains. Longest chain 32 peptides. Score 0.607 Round 4: 207 peptides, 25 chains. Longest chain 20 peptides. Score 0.601 Round 5: 210 peptides, 22 chains. Longest chain 35 peptides. Score 0.650 Taking the results from Round 5 Chains 23, Residues 188, Estimated correctness of the model 53.8 % 1 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4355 restraints for refining 2235 atoms. 3466 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2743 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 27: After refmac, R = 0.2581 (Rfree = 0.000) for 2227 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. Cycle 28: After refmac, R = 0.2480 (Rfree = 0.000) for 2224 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2458 (Rfree = 0.000) for 2219 atoms. Found 9 (19 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.2476 (Rfree = 0.000) for 2219 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.05 2.74 Search for helices and strands: 0 residues in 0 chains, 2280 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2295 seeds are put forward Round 1: 191 peptides, 28 chains. Longest chain 22 peptides. Score 0.505 Round 2: 197 peptides, 28 chains. Longest chain 22 peptides. Score 0.526 Round 3: 205 peptides, 26 chains. Longest chain 34 peptides. Score 0.581 Round 4: 193 peptides, 21 chains. Longest chain 25 peptides. Score 0.614 Round 5: 190 peptides, 23 chains. Longest chain 23 peptides. Score 0.577 Taking the results from Round 4 Chains 22, Residues 172, Estimated correctness of the model 44.8 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4516 restraints for refining 2235 atoms. 3735 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2695 (Rfree = 0.000) for 2235 atoms. Found 17 (20 requested) and removed 19 (10 requested) atoms. Cycle 32: After refmac, R = 0.2510 (Rfree = 0.000) for 2228 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.2458 (Rfree = 0.000) for 2223 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.2536 (Rfree = 0.000) for 2214 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2435 (Rfree = 0.000) for 2209 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.07 2.76 Search for helices and strands: 0 residues in 0 chains, 2276 seeds are put forward NCS extension: 40 residues added (4 deleted due to clashes), 2316 seeds are put forward Round 1: 189 peptides, 27 chains. Longest chain 18 peptides. Score 0.513 Round 2: 197 peptides, 26 chains. Longest chain 18 peptides. Score 0.556 Round 3: 200 peptides, 25 chains. Longest chain 22 peptides. Score 0.580 Round 4: 190 peptides, 23 chains. Longest chain 17 peptides. Score 0.577 Round 5: 197 peptides, 26 chains. Longest chain 19 peptides. Score 0.556 Taking the results from Round 3 Chains 27, Residues 175, Estimated correctness of the model 35.6 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4601 restraints for refining 2235 atoms. 3872 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2541 (Rfree = 0.000) for 2235 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. Cycle 37: After refmac, R = 0.2480 (Rfree = 0.000) for 2233 atoms. Found 17 (20 requested) and removed 12 (10 requested) atoms. Cycle 38: After refmac, R = 0.2396 (Rfree = 0.000) for 2238 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.2344 (Rfree = 0.000) for 2236 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.2326 (Rfree = 0.000) for 2233 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.96 2.66 Search for helices and strands: 0 residues in 0 chains, 2320 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2341 seeds are put forward Round 1: 162 peptides, 23 chains. Longest chain 15 peptides. Score 0.480 Round 2: 191 peptides, 23 chains. Longest chain 17 peptides. Score 0.580 Round 3: 211 peptides, 23 chains. Longest chain 32 peptides. Score 0.640 Round 4: 213 peptides, 20 chains. Longest chain 42 peptides. Score 0.682 Round 5: 207 peptides, 24 chains. Longest chain 21 peptides. Score 0.615 Taking the results from Round 4 Chains 20, Residues 193, Estimated correctness of the model 61.3 % 1 chains (41 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4161 restraints for refining 2235 atoms. 3229 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2644 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 42: After refmac, R = 0.2487 (Rfree = 0.000) for 2227 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. Cycle 43: After refmac, R = 0.2473 (Rfree = 0.000) for 2216 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. Cycle 44: After refmac, R = 0.2425 (Rfree = 0.000) for 2212 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2425 (Rfree = 0.000) for 2211 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 2.78 Search for helices and strands: 0 residues in 0 chains, 2264 seeds are put forward NCS extension: 52 residues added (7 deleted due to clashes), 2316 seeds are put forward Round 1: 185 peptides, 25 chains. Longest chain 30 peptides. Score 0.530 Round 2: 195 peptides, 26 chains. Longest chain 16 peptides. Score 0.549 Round 3: 204 peptides, 24 chains. Longest chain 18 peptides. Score 0.606 Round 4: 189 peptides, 24 chains. Longest chain 20 peptides. Score 0.559 Round 5: 201 peptides, 24 chains. Longest chain 20 peptides. Score 0.597 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 180, Estimated correctness of the model 42.7 % 1 chains (17 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2glz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6969 reflections ( 99.80 % complete ) and 4528 restraints for refining 2234 atoms. 3736 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2633 (Rfree = 0.000) for 2234 atoms. Found 0 (20 requested) and removed 7 (10 requested) atoms. Cycle 47: After refmac, R = 0.2558 (Rfree = 0.000) for 2222 atoms. Found 0 (19 requested) and removed 2 (9 requested) atoms. Cycle 48: After refmac, R = 0.2533 (Rfree = 0.000) for 2218 atoms. Found 0 (19 requested) and removed 5 (9 requested) atoms. Cycle 49: After refmac, R = 0.2508 (Rfree = 0.000) for 2212 atoms. Found 0 (19 requested) and removed 4 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:15:07 GMT 2018 Job finished. TimeTaking 47.18 Used memory is bytes: 14415624