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 2gno-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gno-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gno-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-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/2gno-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-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/2gno-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-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 210 and 0 Target number of residues in the AU: 210 Target solvent content: 0.6522 Checking the provided sequence file Detected sequence length: 305 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 305 Adjusted target solvent content: 0.49 Input MTZ file: 2gno-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: 79 Cell parameters: 135.560 135.560 35.560 90.000 90.000 90.000 Input sequence file: 2gno-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2440 target number of atoms Had to go as low as 0.70 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 Loops will be built when appropriate and at the last cycle Resolution range: 95.855 3.200 Wilson plot Bfac: 79.20 5527 reflections ( 99.25 % complete ) and 0 restraints for refining 2724 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3415 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2905 (Rfree = 0.000) for 2724 atoms. Found 10 (24 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 2787 seeds are put forward Round 1: 130 peptides, 25 chains. Longest chain 11 peptides. Score 0.335 Round 2: 139 peptides, 21 chains. Longest chain 16 peptides. Score 0.464 Round 3: 157 peptides, 23 chains. Longest chain 13 peptides. Score 0.505 Round 4: 170 peptides, 23 chains. Longest chain 20 peptides. Score 0.558 Round 5: 160 peptides, 21 chains. Longest chain 27 peptides. Score 0.554 Taking the results from Round 4 Chains 23, Residues 147, Estimated correctness of the model 29.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5527 reflections ( 99.25 % complete ) and 5093 restraints for refining 2228 atoms. 4528 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2833 (Rfree = 0.000) for 2228 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. Cycle 2: After refmac, R = 0.3038 (Rfree = 0.000) for 2194 atoms. Found 11 (19 requested) and removed 13 (9 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2784 (Rfree = 0.000) for 2165 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. Cycle 4: After refmac, R = 0.2765 (Rfree = 0.000) for 2140 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 5: After refmac, R = 0.2787 (Rfree = 0.000) for 2118 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 2222 seeds are put forward Round 1: 162 peptides, 25 chains. Longest chain 21 peptides. Score 0.488 Round 2: 173 peptides, 21 chains. Longest chain 22 peptides. Score 0.604 Round 3: 160 peptides, 21 chains. Longest chain 19 peptides. Score 0.554 Round 4: 167 peptides, 23 chains. Longest chain 15 peptides. Score 0.546 Round 5: 162 peptides, 23 chains. Longest chain 20 peptides. Score 0.526 Taking the results from Round 2 Chains 21, Residues 152, Estimated correctness of the model 42.1 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5527 reflections ( 99.25 % complete ) and 4520 restraints for refining 2151 atoms. 3831 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2858 (Rfree = 0.000) for 2151 atoms. Found 12 (19 requested) and removed 18 (9 requested) atoms. Cycle 7: After refmac, R = 0.2531 (Rfree = 0.000) for 2133 atoms. Found 1 (19 requested) and removed 10 (9 requested) atoms. Cycle 8: After refmac, R = 0.2561 (Rfree = 0.000) for 2114 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2773 (Rfree = 0.000) for 2101 atoms. Found 5 (18 requested) and removed 13 (9 requested) atoms. Cycle 10: After refmac, R = 0.2521 (Rfree = 0.000) for 2086 atoms. Found 12 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.36 Search for helices and strands: 0 residues in 0 chains, 2177 seeds are put forward Round 1: 146 peptides, 24 chains. Longest chain 14 peptides. Score 0.435 Round 2: 171 peptides, 23 chains. Longest chain 22 peptides. Score 0.562 Round 3: 159 peptides, 23 chains. Longest chain 14 peptides. Score 0.513 Round 4: 160 peptides, 22 chains. Longest chain 16 peptides. Score 0.536 Round 5: 164 peptides, 25 chains. Longest chain 12 peptides. Score 0.497 Taking the results from Round 2 Chains 23, Residues 148, Estimated correctness of the model 30.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5527 reflections ( 99.25 % complete ) and 4853 restraints for refining 2185 atoms. 4284 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2749 (Rfree = 0.000) for 2185 atoms. Found 8 (19 requested) and removed 13 (9 requested) atoms. Cycle 12: After refmac, R = 0.2418 (Rfree = 0.000) for 2175 atoms. Found 2 (19 requested) and removed 14 (9 requested) atoms. Cycle 13: After refmac, R = 0.2365 (Rfree = 0.000) for 2162 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. Cycle 14: After refmac, R = 0.2332 (Rfree = 0.000) for 2155 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2873 (Rfree = 0.000) for 2149 atoms. Found 13 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 2214 seeds are put forward Round 1: 139 peptides, 25 chains. Longest chain 13 peptides. Score 0.381 Round 2: 145 peptides, 23 chains. Longest chain 13 peptides. Score 0.451 Round 3: 150 peptides, 22 chains. Longest chain 16 peptides. Score 0.493 Round 4: 142 peptides, 18 chains. Longest chain 21 peptides. Score 0.536 Round 5: 140 peptides, 21 chains. Longest chain 16 peptides. Score 0.468 Taking the results from Round 4 Chains 18, Residues 124, Estimated correctness of the model 22.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5527 reflections ( 99.25 % complete ) and 5053 restraints for refining 2227 atoms. 4575 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2532 (Rfree = 0.000) for 2227 atoms. Found 4 (19 requested) and removed 12 (9 requested) atoms. Cycle 17: After refmac, R = 0.2383 (Rfree = 0.000) for 2209 atoms. Found 11 (19 requested) and removed 12 (9 requested) atoms. Cycle 18: After refmac, R = 0.2534 (Rfree = 0.000) for 2193 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2310 (Rfree = 0.000) for 2183 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2828 (Rfree = 0.000) for 2179 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 2287 seeds are put forward Round 1: 112 peptides, 21 chains. Longest chain 9 peptides. Score 0.330 Round 2: 135 peptides, 24 chains. Longest chain 11 peptides. Score 0.382 Round 3: 124 peptides, 20 chains. Longest chain 12 peptides. Score 0.414 Round 4: 125 peptides, 22 chains. Longest chain 9 peptides. Score 0.375 Round 5: 133 peptides, 21 chains. Longest chain 12 peptides. Score 0.436 Taking the results from Round 5 Chains 21, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5527 reflections ( 99.25 % complete ) and 5136 restraints for refining 2228 atoms. 4709 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2519 (Rfree = 0.000) for 2228 atoms. Found 8 (19 requested) and removed 11 (9 requested) atoms. Cycle 22: After refmac, R = 0.2472 (Rfree = 0.000) for 2218 atoms. Found 11 (19 requested) and removed 13 (9 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2538 (Rfree = 0.000) for 2209 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.2544 (Rfree = 0.000) for 2194 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 25: After refmac, R = 0.2184 (Rfree = 0.000) for 2184 atoms. Found 12 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.35 Search for helices and strands: 0 residues in 0 chains, 2274 seeds are put forward Round 1: 104 peptides, 20 chains. Longest chain 11 peptides. Score 0.310 Round 2: 133 peptides, 21 chains. Longest chain 16 peptides. Score 0.436 Round 3: 136 peptides, 22 chains. Longest chain 13 peptides. Score 0.429 Round 4: 148 peptides, 26 chains. Longest chain 12 peptides. Score 0.404 Round 5: 141 peptides, 22 chains. Longest chain 12 peptides. Score 0.453 Taking the results from Round 5 Chains 22, Residues 119, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5527 reflections ( 99.25 % complete ) and 4912 restraints for refining 2228 atoms. 4415 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2517 (Rfree = 0.000) for 2228 atoms. Found 18 (19 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2350 (Rfree = 0.000) for 2227 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 28: After refmac, R = 0.2335 (Rfree = 0.000) for 2223 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.2338 (Rfree = 0.000) for 2225 atoms. Found 16 (20 requested) and removed 13 (10 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.3098 (Rfree = 0.000) for 2221 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 2314 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 8 peptides. Score 0.262 Round 2: 134 peptides, 24 chains. Longest chain 10 peptides. Score 0.377 Round 3: 132 peptides, 24 chains. Longest chain 12 peptides. Score 0.367 Round 4: 126 peptides, 22 chains. Longest chain 12 peptides. Score 0.380 Round 5: 134 peptides, 24 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 4 Chains 22, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5527 reflections ( 99.25 % complete ) and 5169 restraints for refining 2228 atoms. 4775 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2738 (Rfree = 0.000) for 2228 atoms. Found 14 (19 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2655 (Rfree = 0.000) for 2230 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.2332 (Rfree = 0.000) for 2223 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.2367 (Rfree = 0.000) for 2217 atoms. Found 1 (19 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2467 (Rfree = 0.000) for 2209 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.41 Search for helices and strands: 0 residues in 0 chains, 2273 seeds are put forward Round 1: 111 peptides, 21 chains. Longest chain 13 peptides. Score 0.324 Round 2: 130 peptides, 22 chains. Longest chain 14 peptides. Score 0.400 Round 3: 134 peptides, 22 chains. Longest chain 14 peptides. Score 0.420 Round 4: 146 peptides, 24 chains. Longest chain 14 peptides. Score 0.435 Round 5: 142 peptides, 24 chains. Longest chain 13 peptides. Score 0.416 Taking the results from Round 4 Chains 24, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5527 reflections ( 99.25 % complete ) and 5068 restraints for refining 2227 atoms. 4604 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2531 (Rfree = 0.000) for 2227 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. Cycle 37: After refmac, R = 0.2548 (Rfree = 0.000) for 2223 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. Cycle 38: After refmac, R = 0.2619 (Rfree = 0.000) for 2222 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 39: After refmac, R = 0.2535 (Rfree = 0.000) for 2221 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.2354 (Rfree = 0.000) for 2221 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 2283 seeds are put forward Round 1: 110 peptides, 22 chains. Longest chain 9 peptides. Score 0.296 Round 2: 135 peptides, 23 chains. Longest chain 16 peptides. Score 0.404 Round 3: 125 peptides, 21 chains. Longest chain 16 peptides. Score 0.397 Round 4: 130 peptides, 20 chains. Longest chain 16 peptides. Score 0.443 Round 5: 130 peptides, 22 chains. Longest chain 11 peptides. Score 0.400 Taking the results from Round 4 Chains 20, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5527 reflections ( 99.25 % complete ) and 5138 restraints for refining 2227 atoms. 4718 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2662 (Rfree = 0.000) for 2227 atoms. Found 11 (19 requested) and removed 9 (9 requested) atoms. Cycle 42: After refmac, R = 0.2893 (Rfree = 0.000) for 2224 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.2640 (Rfree = 0.000) for 2216 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2485 (Rfree = 0.000) for 2223 atoms. Found 15 (19 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2336 (Rfree = 0.000) for 2225 atoms. Found 12 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 2309 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 9 peptides. Score 0.254 Round 2: 110 peptides, 21 chains. Longest chain 17 peptides. Score 0.319 Round 3: 102 peptides, 18 chains. Longest chain 14 peptides. Score 0.346 Round 4: 105 peptides, 21 chains. Longest chain 12 peptides. Score 0.292 Round 5: 104 peptides, 18 chains. Longest chain 13 peptides. Score 0.356 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 86, 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 2gno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5527 reflections ( 99.25 % complete ) and 5236 restraints for refining 2228 atoms. 4910 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2553 (Rfree = 0.000) for 2228 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2637 (Rfree = 0.000) for 2215 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2316 (Rfree = 0.000) for 2201 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2529 (Rfree = 0.000) for 2186 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... TimeTaking 49.41