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 1vqz-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-3.6-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/1vqz-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-3.6-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 19:28:06 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/1vqz-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-3.6-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 251 and 0 Target number of residues in the AU: 251 Target solvent content: 0.6262 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.49 Input MTZ file: 1vqz-3.6-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: 45.503 70.280 113.629 90.000 90.000 90.000 Input sequence file: 1vqz-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 target number of atoms Had to go as low as 0.75 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: 59.771 3.600 Wilson plot Bfac: 64.10 4548 reflections ( 99.72 % complete ) and 0 restraints for refining 3026 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3329 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3301 (Rfree = 0.000) for 3026 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 3088 seeds are put forward Round 1: 134 peptides, 26 chains. Longest chain 9 peptides. Score 0.321 Round 2: 181 peptides, 31 chains. Longest chain 17 peptides. Score 0.436 Round 3: 195 peptides, 29 chains. Longest chain 17 peptides. Score 0.525 Round 4: 198 peptides, 28 chains. Longest chain 18 peptides. Score 0.552 Round 5: 197 peptides, 27 chains. Longest chain 18 peptides. Score 0.564 Taking the results from Round 5 Chains 27, Residues 170, Estimated correctness of the model 0.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4548 reflections ( 99.72 % complete ) and 5514 restraints for refining 2473 atoms. 4861 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3094 (Rfree = 0.000) for 2473 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 2: After refmac, R = 0.3059 (Rfree = 0.000) for 2421 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 3: After refmac, R = 0.2970 (Rfree = 0.000) for 2394 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 4: After refmac, R = 0.2697 (Rfree = 0.000) for 2359 atoms. Found 14 (15 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.3091 (Rfree = 0.000) for 2343 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.38 Search for helices and strands: 0 residues in 0 chains, 2452 seeds are put forward Round 1: 146 peptides, 27 chains. Longest chain 9 peptides. Score 0.357 Round 2: 164 peptides, 25 chains. Longest chain 17 peptides. Score 0.473 Round 3: 163 peptides, 25 chains. Longest chain 11 peptides. Score 0.469 Round 4: 168 peptides, 24 chains. Longest chain 15 peptides. Score 0.506 Round 5: 162 peptides, 20 chains. Longest chain 15 peptides. Score 0.551 Taking the results from Round 5 Chains 20, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4548 reflections ( 99.72 % complete ) and 5599 restraints for refining 2433 atoms. 5051 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3116 (Rfree = 0.000) for 2433 atoms. Found 15 (15 requested) and removed 29 (7 requested) atoms. Cycle 7: After refmac, R = 0.2972 (Rfree = 0.000) for 2385 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 8: After refmac, R = 0.2694 (Rfree = 0.000) for 2359 atoms. Found 12 (15 requested) and removed 16 (7 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.3010 (Rfree = 0.000) for 2335 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2898 (Rfree = 0.000) for 2325 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 2416 seeds are put forward Round 1: 128 peptides, 25 chains. Longest chain 11 peptides. Score 0.313 Round 2: 171 peptides, 28 chains. Longest chain 12 peptides. Score 0.448 Round 3: 174 peptides, 27 chains. Longest chain 12 peptides. Score 0.478 Round 4: 164 peptides, 27 chains. Longest chain 12 peptides. Score 0.437 Round 5: 171 peptides, 28 chains. Longest chain 14 peptides. Score 0.448 Taking the results from Round 3 Chains 27, Residues 147, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4548 reflections ( 99.72 % complete ) and 5013 restraints for refining 2303 atoms. 4452 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2927 (Rfree = 0.000) for 2303 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2864 (Rfree = 0.000) for 2278 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.2631 (Rfree = 0.000) for 2269 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 14: After refmac, R = 0.2795 (Rfree = 0.000) for 2263 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 15: After refmac, R = 0.2353 (Rfree = 0.000) for 2262 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.38 Search for helices and strands: 0 residues in 0 chains, 2328 seeds are put forward Round 1: 138 peptides, 26 chains. Longest chain 11 peptides. Score 0.340 Round 2: 165 peptides, 28 chains. Longest chain 12 peptides. Score 0.423 Round 3: 161 peptides, 27 chains. Longest chain 13 peptides. Score 0.424 Round 4: 161 peptides, 24 chains. Longest chain 16 peptides. Score 0.478 Round 5: 177 peptides, 23 chains. Longest chain 16 peptides. Score 0.556 Taking the results from Round 5 Chains 23, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4548 reflections ( 99.72 % complete ) and 5541 restraints for refining 2436 atoms. 4948 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3098 (Rfree = 0.000) for 2436 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 17: After refmac, R = 0.2937 (Rfree = 0.000) for 2408 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2894 (Rfree = 0.000) for 2386 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.2808 (Rfree = 0.000) for 2375 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 20: After refmac, R = 0.2786 (Rfree = 0.000) for 2356 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 2429 seeds are put forward Round 1: 130 peptides, 26 chains. Longest chain 9 peptides. Score 0.302 Round 2: 152 peptides, 23 chains. Longest chain 11 peptides. Score 0.460 Round 3: 155 peptides, 26 chains. Longest chain 12 peptides. Score 0.417 Round 4: 154 peptides, 24 chains. Longest chain 12 peptides. Score 0.450 Round 5: 143 peptides, 21 chains. Longest chain 11 peptides. Score 0.459 Taking the results from Round 2 Chains 23, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4548 reflections ( 99.72 % complete ) and 5356 restraints for refining 2376 atoms. 4863 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3037 (Rfree = 0.000) for 2376 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.3033 (Rfree = 0.000) for 2346 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 23: After refmac, R = 0.2970 (Rfree = 0.000) for 2342 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2557 (Rfree = 0.000) for 2330 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 25: After refmac, R = 0.3026 (Rfree = 0.000) for 2323 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 2398 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 9 peptides. Score 0.261 Round 2: 155 peptides, 28 chains. Longest chain 14 peptides. Score 0.379 Round 3: 148 peptides, 26 chains. Longest chain 13 peptides. Score 0.386 Round 4: 148 peptides, 25 chains. Longest chain 13 peptides. Score 0.405 Round 5: 158 peptides, 24 chains. Longest chain 17 peptides. Score 0.466 Taking the results from Round 5 Chains 24, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4548 reflections ( 99.72 % complete ) and 5636 restraints for refining 2418 atoms. 5124 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3201 (Rfree = 0.000) for 2418 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 27: After refmac, R = 0.3085 (Rfree = 0.000) for 2391 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2953 (Rfree = 0.000) for 2370 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 29: After refmac, R = 0.2927 (Rfree = 0.000) for 2357 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 30: After refmac, R = 0.2894 (Rfree = 0.000) for 2343 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 2414 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 8 peptides. Score 0.283 Round 2: 142 peptides, 26 chains. Longest chain 10 peptides. Score 0.359 Round 3: 151 peptides, 26 chains. Longest chain 11 peptides. Score 0.399 Round 4: 146 peptides, 24 chains. Longest chain 14 peptides. Score 0.415 Round 5: 159 peptides, 25 chains. Longest chain 13 peptides. Score 0.452 Taking the results from Round 5 Chains 25, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4548 reflections ( 99.72 % complete ) and 5507 restraints for refining 2437 atoms. 4996 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3000 (Rfree = 0.000) for 2437 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2940 (Rfree = 0.000) for 2422 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2922 (Rfree = 0.000) for 2415 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2812 (Rfree = 0.000) for 2404 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2728 (Rfree = 0.000) for 2398 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 2477 seeds are put forward Round 1: 119 peptides, 23 chains. Longest chain 8 peptides. Score 0.310 Round 2: 140 peptides, 25 chains. Longest chain 13 peptides. Score 0.369 Round 3: 133 peptides, 24 chains. Longest chain 9 peptides. Score 0.357 Round 4: 128 peptides, 22 chains. Longest chain 13 peptides. Score 0.374 Round 5: 134 peptides, 23 chains. Longest chain 14 peptides. Score 0.381 Taking the results from Round 5 Chains 23, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4548 reflections ( 99.72 % complete ) and 5760 restraints for refining 2473 atoms. 5339 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2938 (Rfree = 0.000) for 2473 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 37: After refmac, R = 0.2441 (Rfree = 0.000) for 2449 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 38: After refmac, R = 0.2804 (Rfree = 0.000) for 2439 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.3009 (Rfree = 0.000) for 2428 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2894 (Rfree = 0.000) for 2415 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 2460 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 6 peptides. Score 0.217 Round 2: 109 peptides, 22 chains. Longest chain 8 peptides. Score 0.281 Round 3: 114 peptides, 22 chains. Longest chain 8 peptides. Score 0.306 Round 4: 113 peptides, 20 chains. Longest chain 9 peptides. Score 0.344 Round 5: 109 peptides, 19 chains. Longest chain 10 peptides. Score 0.346 Taking the results from Round 5 Chains 19, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4548 reflections ( 99.72 % complete ) and 5583 restraints for refining 2378 atoms. 5242 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3156 (Rfree = 0.000) for 2378 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2448 (Rfree = 0.000) for 2355 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.3080 (Rfree = 0.000) for 2351 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.3039 (Rfree = 0.000) for 2344 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2990 (Rfree = 0.000) for 2334 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 2395 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 7 peptides. Score 0.231 Round 2: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.297 Round 3: 77 peptides, 14 chains. Longest chain 11 peptides. Score 0.295 Round 4: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.327 Round 5: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.290 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 76, 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 1vqz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4548 reflections ( 99.72 % complete ) and 4818 restraints for refining 2175 atoms. 4530 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3090 (Rfree = 0.000) for 2175 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2858 (Rfree = 0.000) for 2161 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2443 (Rfree = 0.000) for 2145 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2995 (Rfree = 0.000) for 2132 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:14:26 GMT 2018 Job finished. TimeTaking 46.48