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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-4.0-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/1vqz-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-4.0-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 232 and 0 Target number of residues in the AU: 232 Target solvent content: 0.6545 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 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 Loops will be built when appropriate and at the last cycle Resolution range: 59.771 4.000 Wilson plot Bfac: 80.49 3353 reflections ( 99.61 % complete ) and 0 restraints for refining 3029 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3371 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3193 (Rfree = 0.000) for 3029 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.68 Search for helices and strands: 0 residues in 0 chains, 3090 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 8 peptides. Score 0.238 Round 2: 140 peptides, 27 chains. Longest chain 9 peptides. Score 0.329 Round 3: 150 peptides, 26 chains. Longest chain 12 peptides. Score 0.395 Round 4: 161 peptides, 27 chains. Longest chain 10 peptides. Score 0.424 Round 5: 172 peptides, 26 chains. Longest chain 15 peptides. Score 0.487 Taking the results from Round 5 Chains 26, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3353 reflections ( 99.61 % complete ) and 5763 restraints for refining 2464 atoms. 5205 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2825 (Rfree = 0.000) for 2464 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 2: After refmac, R = 0.2766 (Rfree = 0.000) for 2414 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 3: After refmac, R = 0.2624 (Rfree = 0.000) for 2382 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 4: After refmac, R = 0.2500 (Rfree = 0.000) for 2358 atoms. Found 9 (11 requested) and removed 17 (5 requested) atoms. Cycle 5: After refmac, R = 0.2372 (Rfree = 0.000) for 2337 atoms. Found 9 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.67 Search for helices and strands: 0 residues in 0 chains, 2434 seeds are put forward Round 1: 140 peptides, 28 chains. Longest chain 9 peptides. Score 0.309 Round 2: 156 peptides, 27 chains. Longest chain 12 peptides. Score 0.402 Round 3: 169 peptides, 24 chains. Longest chain 13 peptides. Score 0.510 Round 4: 175 peptides, 25 chains. Longest chain 16 peptides. Score 0.516 Round 5: 180 peptides, 28 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 4 Chains 26, Residues 150, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3353 reflections ( 99.61 % complete ) and 5405 restraints for refining 2420 atoms. 4802 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1976 (Rfree = 0.000) for 2420 atoms. Found 6 (11 requested) and removed 15 (5 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1888 (Rfree = 0.000) for 2390 atoms. Found 8 (11 requested) and removed 11 (5 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2045 (Rfree = 0.000) for 2378 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1952 (Rfree = 0.000) for 2369 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2127 (Rfree = 0.000) for 2362 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 2459 seeds are put forward Round 1: 147 peptides, 30 chains. Longest chain 12 peptides. Score 0.303 Round 2: 168 peptides, 28 chains. Longest chain 15 peptides. Score 0.435 Round 3: 166 peptides, 28 chains. Longest chain 15 peptides. Score 0.427 Round 4: 169 peptides, 25 chains. Longest chain 17 peptides. Score 0.493 Round 5: 160 peptides, 25 chains. Longest chain 16 peptides. Score 0.456 Taking the results from Round 4 Chains 25, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3353 reflections ( 99.61 % complete ) and 5645 restraints for refining 2463 atoms. 5094 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1960 (Rfree = 0.000) for 2463 atoms. Found 10 (11 requested) and removed 13 (5 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2174 (Rfree = 0.000) for 2444 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2098 (Rfree = 0.000) for 2431 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2047 (Rfree = 0.000) for 2404 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1934 (Rfree = 0.000) for 2400 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.68 Search for helices and strands: 0 residues in 0 chains, 2493 seeds are put forward Round 1: 153 peptides, 33 chains. Longest chain 8 peptides. Score 0.272 Round 2: 158 peptides, 27 chains. Longest chain 12 peptides. Score 0.411 Round 3: 165 peptides, 24 chains. Longest chain 15 peptides. Score 0.494 Round 4: 169 peptides, 25 chains. Longest chain 15 peptides. Score 0.493 Round 5: 173 peptides, 26 chains. Longest chain 15 peptides. Score 0.491 Taking the results from Round 3 Chains 24, Residues 141, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3353 reflections ( 99.61 % complete ) and 5472 restraints for refining 2464 atoms. 4889 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1933 (Rfree = 0.000) for 2464 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 17: After refmac, R = 0.1866 (Rfree = 0.000) for 2450 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.1839 (Rfree = 0.000) for 2443 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.1767 (Rfree = 0.000) for 2439 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1433 (Rfree = 0.000) for 2433 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.67 Search for helices and strands: 0 residues in 0 chains, 2500 seeds are put forward Round 1: 129 peptides, 24 chains. Longest chain 10 peptides. Score 0.338 Round 2: 151 peptides, 23 chains. Longest chain 17 peptides. Score 0.456 Round 3: 152 peptides, 19 chains. Longest chain 16 peptides. Score 0.531 Round 4: 138 peptides, 20 chains. Longest chain 14 peptides. Score 0.457 Round 5: 146 peptides, 24 chains. Longest chain 12 peptides. Score 0.415 Taking the results from Round 3 Chains 20, Residues 133, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3353 reflections ( 99.61 % complete ) and 5609 restraints for refining 2464 atoms. 5058 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2153 (Rfree = 0.000) for 2464 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. Cycle 22: After refmac, R = 0.2094 (Rfree = 0.000) for 2442 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 23: After refmac, R = 0.1592 (Rfree = 0.000) for 2434 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.1596 (Rfree = 0.000) for 2423 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.1621 (Rfree = 0.000) for 2412 atoms. Found 9 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 2473 seeds are put forward Round 1: 127 peptides, 24 chains. Longest chain 11 peptides. Score 0.328 Round 2: 161 peptides, 27 chains. Longest chain 10 peptides. Score 0.424 Round 3: 160 peptides, 26 chains. Longest chain 12 peptides. Score 0.438 Round 4: 166 peptides, 25 chains. Longest chain 14 peptides. Score 0.481 Round 5: 167 peptides, 26 chains. Longest chain 14 peptides. Score 0.467 Taking the results from Round 4 Chains 25, Residues 141, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3353 reflections ( 99.61 % complete ) and 5566 restraints for refining 2464 atoms. 4995 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2240 (Rfree = 0.000) for 2464 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.2353 (Rfree = 0.000) for 2447 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 28: After refmac, R = 0.2144 (Rfree = 0.000) for 2429 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2188 (Rfree = 0.000) for 2409 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 30: After refmac, R = 0.2485 (Rfree = 0.000) for 2393 atoms. Found 11 (11 requested) and removed 21 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 2477 seeds are put forward Round 1: 111 peptides, 23 chains. Longest chain 8 peptides. Score 0.270 Round 2: 128 peptides, 25 chains. Longest chain 7 peptides. Score 0.313 Round 3: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.352 Round 4: 137 peptides, 22 chains. Longest chain 16 peptides. Score 0.414 Round 5: 135 peptides, 23 chains. Longest chain 12 peptides. Score 0.386 Taking the results from Round 4 Chains 22, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3353 reflections ( 99.61 % complete ) and 5733 restraints for refining 2463 atoms. 5295 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2336 (Rfree = 0.000) for 2463 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2144 (Rfree = 0.000) for 2437 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.2096 (Rfree = 0.000) for 2430 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.1560 (Rfree = 0.000) for 2423 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.1529 (Rfree = 0.000) for 2413 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 2487 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 7 peptides. Score 0.249 Round 2: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.326 Round 3: 121 peptides, 23 chains. Longest chain 8 peptides. Score 0.320 Round 4: 123 peptides, 20 chains. Longest chain 11 peptides. Score 0.391 Round 5: 131 peptides, 21 chains. Longest chain 12 peptides. Score 0.407 Taking the results from Round 5 Chains 21, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3353 reflections ( 99.61 % complete ) and 5778 restraints for refining 2463 atoms. 5359 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2082 (Rfree = 0.000) for 2463 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2129 (Rfree = 0.000) for 2448 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 38: After refmac, R = 0.2090 (Rfree = 0.000) for 2439 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 39: After refmac, R = 0.2002 (Rfree = 0.000) for 2429 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 40: After refmac, R = 0.2034 (Rfree = 0.000) for 2424 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 2511 seeds are put forward Round 1: 97 peptides, 23 chains. Longest chain 5 peptides. Score 0.195 Round 2: 122 peptides, 23 chains. Longest chain 13 peptides. Score 0.325 Round 3: 116 peptides, 22 chains. Longest chain 9 peptides. Score 0.316 Round 4: 126 peptides, 24 chains. Longest chain 9 peptides. Score 0.323 Round 5: 117 peptides, 21 chains. Longest chain 12 peptides. Score 0.342 Taking the results from Round 5 Chains 21, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3353 reflections ( 99.61 % complete ) and 5844 restraints for refining 2464 atoms. 5481 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1808 (Rfree = 0.000) for 2464 atoms. Found 3 (11 requested) and removed 16 (5 requested) atoms. Cycle 42: After refmac, R = 0.2169 (Rfree = 0.000) for 2442 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2086 (Rfree = 0.000) for 2435 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.2123 (Rfree = 0.000) for 2425 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.2138 (Rfree = 0.000) for 2414 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 2491 seeds are put forward Round 1: 81 peptides, 18 chains. Longest chain 7 peptides. Score 0.221 Round 2: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.285 Round 3: 90 peptides, 17 chains. Longest chain 7 peptides. Score 0.294 Round 4: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.278 Round 5: 96 peptides, 17 chains. Longest chain 8 peptides. Score 0.325 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 79, 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-4_warpNtrace.pdb as input ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 3353 reflections ( 99.61 % complete ) and 5615 restraints for refining 2361 atoms. 5316 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2214 (Rfree = 0.000) for 2361 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2168 (Rfree = 0.000) for 2344 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2259 (Rfree = 0.000) for 2334 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2189 (Rfree = 0.000) for 2326 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:15:14 GMT 2018 Job finished. TimeTaking 47.28