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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2glz-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2glz-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.4-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 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-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-3.4-parrot-hancs.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 2707 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3274 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2925 (Rfree = 0.000) for 2707 atoms. Found 20 (20 requested) and removed 78 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.07 2.76 Search for helices and strands: 0 residues in 0 chains, 2712 seeds are put forward NCS extension: 0 residues added, 2712 seeds are put forward Round 1: 150 peptides, 27 chains. Longest chain 15 peptides. Score 0.363 Round 2: 186 peptides, 27 chains. Longest chain 16 peptides. Score 0.503 Round 3: 190 peptides, 26 chains. Longest chain 15 peptides. Score 0.532 Round 4: 208 peptides, 27 chains. Longest chain 22 peptides. Score 0.576 Round 5: 210 peptides, 28 chains. Longest chain 20 peptides. Score 0.569 Taking the results from Round 4 Chains 28, Residues 181, Estimated correctness of the model 20.7 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4388 restraints for refining 2225 atoms. 3564 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2603 (Rfree = 0.000) for 2225 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 2: After refmac, R = 0.2360 (Rfree = 0.000) for 2196 atoms. Found 10 (16 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.2300 (Rfree = 0.000) for 2179 atoms. Found 9 (16 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2241 (Rfree = 0.000) for 2169 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2202 (Rfree = 0.000) for 2161 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 2.83 Search for helices and strands: 0 residues in 0 chains, 2251 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2272 seeds are put forward Round 1: 192 peptides, 27 chains. Longest chain 17 peptides. Score 0.524 Round 2: 196 peptides, 22 chains. Longest chain 20 peptides. Score 0.610 Round 3: 204 peptides, 22 chains. Longest chain 28 peptides. Score 0.633 Round 4: 204 peptides, 23 chains. Longest chain 19 peptides. Score 0.620 Round 5: 212 peptides, 26 chains. Longest chain 19 peptides. Score 0.603 Taking the results from Round 3 Chains 22, Residues 182, Estimated correctness of the model 39.1 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5830 reflections ( 99.76 % complete ) and 4643 restraints for refining 2226 atoms. 3840 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2458 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 7: After refmac, R = 0.2230 (Rfree = 0.000) for 2225 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2187 (Rfree = 0.000) for 2214 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 9: After refmac, R = 0.2138 (Rfree = 0.000) for 2209 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2131 (Rfree = 0.000) for 2199 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 2.81 Search for helices and strands: 0 residues in 0 chains, 2275 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 2312 seeds are put forward Round 1: 201 peptides, 27 chains. Longest chain 17 peptides. Score 0.554 Round 2: 213 peptides, 25 chains. Longest chain 18 peptides. Score 0.619 Round 3: 227 peptides, 24 chains. Longest chain 27 peptides. Score 0.670 Round 4: 224 peptides, 26 chains. Longest chain 26 peptides. Score 0.637 Round 5: 225 peptides, 27 chains. Longest chain 18 peptides. Score 0.627 Taking the results from Round 3 Chains 24, Residues 203, Estimated correctness of the model 49.8 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4405 restraints for refining 2226 atoms. 3520 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2415 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2194 (Rfree = 0.000) for 2222 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2248 (Rfree = 0.000) for 2218 atoms. Found 11 (16 requested) and removed 10 (8 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2041 (Rfree = 0.000) for 2213 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.1979 (Rfree = 0.000) for 2204 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 2290 seeds are put forward NCS extension: 48 residues added (2 deleted due to clashes), 2338 seeds are put forward Round 1: 208 peptides, 28 chains. Longest chain 22 peptides. Score 0.562 Round 2: 216 peptides, 25 chains. Longest chain 23 peptides. Score 0.628 Round 3: 225 peptides, 26 chains. Longest chain 23 peptides. Score 0.640 Round 4: 226 peptides, 23 chains. Longest chain 27 peptides. Score 0.679 Round 5: 233 peptides, 23 chains. Longest chain 34 peptides. Score 0.697 Taking the results from Round 5 Chains 25, Residues 210, Estimated correctness of the model 57.1 % 3 chains (57 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5830 reflections ( 99.76 % complete ) and 3953 restraints for refining 2226 atoms. 2890 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2596 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 17: After refmac, R = 0.2414 (Rfree = 0.000) for 2213 atoms. Found 8 (16 requested) and removed 15 (8 requested) atoms. Cycle 18: After refmac, R = 0.2313 (Rfree = 0.000) for 2201 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2233 (Rfree = 0.000) for 2197 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2183 (Rfree = 0.000) for 2187 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 2.79 Search for helices and strands: 0 residues in 0 chains, 2264 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 2299 seeds are put forward Round 1: 200 peptides, 27 chains. Longest chain 20 peptides. Score 0.551 Round 2: 214 peptides, 24 chains. Longest chain 27 peptides. Score 0.635 Round 3: 217 peptides, 26 chains. Longest chain 26 peptides. Score 0.617 Round 4: 217 peptides, 25 chains. Longest chain 28 peptides. Score 0.630 Round 5: 205 peptides, 26 chains. Longest chain 19 peptides. Score 0.581 Taking the results from Round 2 Chains 27, Residues 190, Estimated correctness of the model 39.7 % 3 chains (55 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4109 restraints for refining 2225 atoms. 3126 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2506 (Rfree = 0.000) for 2225 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 22: After refmac, R = 0.2380 (Rfree = 0.000) for 2212 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.2316 (Rfree = 0.000) for 2210 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2211 (Rfree = 0.000) for 2207 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.2198 (Rfree = 0.000) for 2196 atoms. Found 11 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 2.82 Search for helices and strands: 0 residues in 0 chains, 2277 seeds are put forward NCS extension: 34 residues added (6 deleted due to clashes), 2311 seeds are put forward Round 1: 203 peptides, 28 chains. Longest chain 23 peptides. Score 0.546 Round 2: 206 peptides, 24 chains. Longest chain 24 peptides. Score 0.612 Round 3: 197 peptides, 24 chains. Longest chain 30 peptides. Score 0.584 Round 4: 207 peptides, 23 chains. Longest chain 35 peptides. Score 0.628 Round 5: 209 peptides, 27 chains. Longest chain 19 peptides. Score 0.580 Taking the results from Round 4 Chains 23, Residues 184, Estimated correctness of the model 37.5 % 1 chains (34 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4331 restraints for refining 2226 atoms. 3456 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2415 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 27: After refmac, R = 0.2299 (Rfree = 0.000) for 2213 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.2236 (Rfree = 0.000) for 2211 atoms. Found 13 (16 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2141 (Rfree = 0.000) for 2209 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2079 (Rfree = 0.000) for 2197 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 2.83 Search for helices and strands: 0 residues in 0 chains, 2276 seeds are put forward NCS extension: 29 residues added (9 deleted due to clashes), 2305 seeds are put forward Round 1: 156 peptides, 25 chains. Longest chain 15 peptides. Score 0.423 Round 2: 180 peptides, 24 chains. Longest chain 23 peptides. Score 0.529 Round 3: 187 peptides, 23 chains. Longest chain 23 peptides. Score 0.567 Round 4: 184 peptides, 24 chains. Longest chain 25 peptides. Score 0.542 Round 5: 184 peptides, 23 chains. Longest chain 23 peptides. Score 0.557 Taking the results from Round 3 Chains 23, Residues 164, Estimated correctness of the model 17.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4860 restraints for refining 2226 atoms. 4227 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2347 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2207 (Rfree = 0.000) for 2229 atoms. Found 12 (16 requested) and removed 14 (8 requested) atoms. Cycle 33: After refmac, R = 0.2126 (Rfree = 0.000) for 2224 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2097 (Rfree = 0.000) for 2224 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2019 (Rfree = 0.000) for 2223 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 2.80 Search for helices and strands: 0 residues in 0 chains, 2316 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 2333 seeds are put forward Round 1: 160 peptides, 28 chains. Longest chain 14 peptides. Score 0.386 Round 2: 189 peptides, 25 chains. Longest chain 24 peptides. Score 0.544 Round 3: 191 peptides, 28 chains. Longest chain 23 peptides. Score 0.505 Round 4: 195 peptides, 27 chains. Longest chain 19 peptides. Score 0.534 Round 5: 189 peptides, 22 chains. Longest chain 21 peptides. Score 0.588 Taking the results from Round 5 Chains 22, Residues 167, Estimated correctness of the model 24.7 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5830 reflections ( 99.76 % complete ) and 4665 restraints for refining 2226 atoms. 3944 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2258 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2166 (Rfree = 0.000) for 2226 atoms. Found 12 (16 requested) and removed 12 (8 requested) atoms. Cycle 38: After refmac, R = 0.2093 (Rfree = 0.000) for 2226 atoms. Found 13 (16 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2046 (Rfree = 0.000) for 2230 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.2045 (Rfree = 0.000) for 2226 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 2.81 Search for helices and strands: 0 residues in 0 chains, 2293 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 2328 seeds are put forward Round 1: 174 peptides, 28 chains. Longest chain 21 peptides. Score 0.442 Round 2: 191 peptides, 23 chains. Longest chain 27 peptides. Score 0.580 Round 3: 195 peptides, 25 chains. Longest chain 25 peptides. Score 0.564 Round 4: 199 peptides, 29 chains. Longest chain 16 peptides. Score 0.517 Round 5: 190 peptides, 27 chains. Longest chain 21 peptides. Score 0.517 Taking the results from Round 2 Chains 24, Residues 168, Estimated correctness of the model 22.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5830 reflections ( 99.76 % complete ) and 4509 restraints for refining 2226 atoms. 3769 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2353 (Rfree = 0.000) for 2226 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 42: After refmac, R = 0.2219 (Rfree = 0.000) for 2229 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2155 (Rfree = 0.000) for 2227 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.2140 (Rfree = 0.000) for 2222 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.2102 (Rfree = 0.000) for 2217 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 2.78 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward NCS extension: 30 residues added (6 deleted due to clashes), 2312 seeds are put forward Round 1: 176 peptides, 32 chains. Longest chain 15 peptides. Score 0.382 Round 2: 176 peptides, 25 chains. Longest chain 15 peptides. Score 0.499 Round 3: 180 peptides, 28 chains. Longest chain 13 peptides. Score 0.465 Round 4: 188 peptides, 24 chains. Longest chain 24 peptides. Score 0.556 Round 5: 191 peptides, 27 chains. Longest chain 27 peptides. Score 0.520 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 164, Estimated correctness of the model 13.7 % 1 chains (23 residues) have been docked in sequence Sequence coverage is 13 % 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 4633 restraints for refining 2226 atoms. 3912 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2507 (Rfree = 0.000) for 2226 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2428 (Rfree = 0.000) for 2214 atoms. Found 0 (16 requested) and removed 2 (8 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2409 (Rfree = 0.000) for 2208 atoms. Found 0 (16 requested) and removed 2 (8 requested) atoms. Cycle 49: After refmac, R = 0.2354 (Rfree = 0.000) for 2206 atoms. Found 0 (16 requested) and removed 0 (8 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:16:29 GMT 2018 Job finished. TimeTaking 48.54