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 2hoe-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-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/2hoe-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-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/2hoe-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-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 230 and 0 Target number of residues in the AU: 230 Target solvent content: 0.6837 Checking the provided sequence file Detected sequence length: 380 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 380 Adjusted target solvent content: 0.48 Input MTZ file: 2hoe-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: 151 Cell parameters: 62.599 62.599 173.950 90.000 90.000 120.000 Input sequence file: 2hoe-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3040 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 Loops will be built when appropriate and at the last cycle Resolution range: 57.983 4.001 Wilson plot Bfac: 104.46 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3470 reflections ( 99.71 % complete ) and 0 restraints for refining 3354 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3353 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3161 (Rfree = 0.000) for 3354 atoms. Found 10 (15 requested) and removed 127 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.93 Search for helices and strands: 0 residues in 0 chains, 3304 seeds are put forward Round 1: 97 peptides, 20 chains. Longest chain 12 peptides. Score 0.258 Round 2: 138 peptides, 27 chains. Longest chain 13 peptides. Score 0.311 Round 3: 146 peptides, 25 chains. Longest chain 14 peptides. Score 0.383 Round 4: 149 peptides, 26 chains. Longest chain 15 peptides. Score 0.378 Round 5: 154 peptides, 25 chains. Longest chain 16 peptides. Score 0.416 Taking the results from Round 5 Chains 25, Residues 129, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.71 % complete ) and 6606 restraints for refining 2745 atoms. 6092 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2750 (Rfree = 0.000) for 2745 atoms. Found 5 (13 requested) and removed 72 (6 requested) atoms. Cycle 2: After refmac, R = 0.2725 (Rfree = 0.000) for 2631 atoms. Found 7 (12 requested) and removed 30 (6 requested) atoms. Cycle 3: After refmac, R = 0.2433 (Rfree = 0.000) for 2577 atoms. Found 10 (12 requested) and removed 28 (6 requested) atoms. Cycle 4: After refmac, R = 0.2335 (Rfree = 0.000) for 2548 atoms. Found 5 (12 requested) and removed 15 (6 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2721 (Rfree = 0.000) for 2519 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.89 4.00 Search for helices and strands: 0 residues in 0 chains, 2626 seeds are put forward Round 1: 148 peptides, 30 chains. Longest chain 12 peptides. Score 0.299 Round 2: 178 peptides, 28 chains. Longest chain 15 peptides. Score 0.459 Round 3: 172 peptides, 27 chains. Longest chain 19 peptides. Score 0.453 Round 4: 169 peptides, 28 chains. Longest chain 14 peptides. Score 0.424 Round 5: 180 peptides, 26 chains. Longest chain 19 peptides. Score 0.499 Taking the results from Round 5 Chains 27, Residues 154, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3470 reflections ( 99.71 % complete ) and 5593 restraints for refining 2500 atoms. 4976 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2455 (Rfree = 0.000) for 2500 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 7: After refmac, R = 0.2367 (Rfree = 0.000) for 2455 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2249 (Rfree = 0.000) for 2421 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 9: After refmac, R = 0.2223 (Rfree = 0.000) for 2410 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 10: After refmac, R = 0.2259 (Rfree = 0.000) for 2388 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.97 4.08 Search for helices and strands: 0 residues in 0 chains, 2497 seeds are put forward Round 1: 132 peptides, 27 chains. Longest chain 10 peptides. Score 0.284 Round 2: 162 peptides, 27 chains. Longest chain 12 peptides. Score 0.413 Round 3: 159 peptides, 25 chains. Longest chain 12 peptides. Score 0.436 Round 4: 167 peptides, 27 chains. Longest chain 12 peptides. Score 0.433 Round 5: 179 peptides, 30 chains. Longest chain 10 peptides. Score 0.429 Taking the results from Round 3 Chains 25, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.71 % complete ) and 5420 restraints for refining 2395 atoms. 4909 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2289 (Rfree = 0.000) for 2395 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.2295 (Rfree = 0.000) for 2378 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 13: After refmac, R = 0.2006 (Rfree = 0.000) for 2349 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 14: After refmac, R = 0.2055 (Rfree = 0.000) for 2334 atoms. Found 10 (11 requested) and removed 30 (5 requested) atoms. Cycle 15: After refmac, R = 0.2048 (Rfree = 0.000) for 2304 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.94 4.05 Search for helices and strands: 0 residues in 0 chains, 2412 seeds are put forward Round 1: 134 peptides, 24 chains. Longest chain 10 peptides. Score 0.350 Round 2: 157 peptides, 27 chains. Longest chain 12 peptides. Score 0.393 Round 3: 173 peptides, 26 chains. Longest chain 12 peptides. Score 0.473 Round 4: 169 peptides, 27 chains. Longest chain 13 peptides. Score 0.441 Round 5: 180 peptides, 25 chains. Longest chain 16 peptides. Score 0.515 Taking the results from Round 5 Chains 26, Residues 155, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.71 % complete ) and 5515 restraints for refining 2517 atoms. 4873 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2535 (Rfree = 0.000) for 2517 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 17: After refmac, R = 0.2322 (Rfree = 0.000) for 2480 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2469 (Rfree = 0.000) for 2457 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 19: After refmac, R = 0.2317 (Rfree = 0.000) for 2446 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 20: After refmac, R = 0.1993 (Rfree = 0.000) for 2442 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.93 4.04 Search for helices and strands: 0 residues in 0 chains, 2544 seeds are put forward Round 1: 134 peptides, 26 chains. Longest chain 12 peptides. Score 0.312 Round 2: 163 peptides, 25 chains. Longest chain 15 peptides. Score 0.452 Round 3: 166 peptides, 25 chains. Longest chain 14 peptides. Score 0.463 Round 4: 157 peptides, 23 chains. Longest chain 13 peptides. Score 0.463 Round 5: 152 peptides, 24 chains. Longest chain 12 peptides. Score 0.426 Taking the results from Round 4 Chains 23, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.71 % complete ) and 5925 restraints for refining 2614 atoms. 5412 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2444 (Rfree = 0.000) for 2614 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2327 (Rfree = 0.000) for 2585 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 23: After refmac, R = 0.2133 (Rfree = 0.000) for 2559 atoms. Found 12 (12 requested) and removed 29 (6 requested) atoms. Cycle 24: After refmac, R = 0.2382 (Rfree = 0.000) for 2527 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.2093 (Rfree = 0.000) for 2514 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.94 4.05 Search for helices and strands: 0 residues in 0 chains, 2612 seeds are put forward Round 1: 121 peptides, 25 chains. Longest chain 7 peptides. Score 0.272 Round 2: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.372 Round 3: 129 peptides, 20 chains. Longest chain 21 peptides. Score 0.404 Round 4: 140 peptides, 23 chains. Longest chain 17 peptides. Score 0.395 Round 5: 135 peptides, 19 chains. Longest chain 18 peptides. Score 0.447 Taking the results from Round 5 Chains 19, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3470 reflections ( 99.71 % complete ) and 6037 restraints for refining 2586 atoms. 5592 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2272 (Rfree = 0.000) for 2586 atoms. Found 12 (12 requested) and removed 72 (6 requested) atoms. Cycle 27: After refmac, R = 0.2185 (Rfree = 0.000) for 2511 atoms. Found 8 (11 requested) and removed 14 (5 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1952 (Rfree = 0.000) for 2497 atoms. Found 7 (11 requested) and removed 14 (5 requested) atoms. Cycle 29: After refmac, R = 0.2211 (Rfree = 0.000) for 2480 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1885 (Rfree = 0.000) for 2471 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.91 4.02 Search for helices and strands: 0 residues in 0 chains, 2557 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.236 Round 2: 119 peptides, 22 chains. Longest chain 12 peptides. Score 0.322 Round 3: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.348 Round 4: 129 peptides, 22 chains. Longest chain 13 peptides. Score 0.367 Round 5: 138 peptides, 23 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 5 Chains 23, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3470 reflections ( 99.71 % complete ) and 5790 restraints for refining 2511 atoms. 5353 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2860 (Rfree = 0.000) for 2511 atoms. Found 10 (11 requested) and removed 25 (5 requested) atoms. Cycle 32: After refmac, R = 0.1994 (Rfree = 0.000) for 2471 atoms. Found 6 (11 requested) and removed 15 (5 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2004 (Rfree = 0.000) for 2451 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.2095 (Rfree = 0.000) for 2441 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 35: After refmac, R = 0.2133 (Rfree = 0.000) for 2435 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.93 4.04 Search for helices and strands: 0 residues in 0 chains, 2546 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 8 peptides. Score 0.230 Round 2: 119 peptides, 22 chains. Longest chain 14 peptides. Score 0.322 Round 3: 121 peptides, 21 chains. Longest chain 15 peptides. Score 0.351 Round 4: 119 peptides, 20 chains. Longest chain 18 peptides. Score 0.361 Round 5: 127 peptides, 22 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 4 Chains 21, Residues 99, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3470 reflections ( 99.71 % complete ) and 5450 restraints for refining 2469 atoms. 5041 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2422 (Rfree = 0.000) for 2469 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 37: After refmac, R = 0.2085 (Rfree = 0.000) for 2453 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2399 (Rfree = 0.000) for 2448 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 39: After refmac, R = 0.2128 (Rfree = 0.000) for 2435 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2109 (Rfree = 0.000) for 2433 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.99 4.10 Search for helices and strands: 0 residues in 0 chains, 2530 seeds are put forward Round 1: 90 peptides, 21 chains. Longest chain 7 peptides. Score 0.200 Round 2: 113 peptides, 23 chains. Longest chain 8 peptides. Score 0.274 Round 3: 120 peptides, 21 chains. Longest chain 10 peptides. Score 0.346 Round 4: 126 peptides, 23 chains. Longest chain 8 peptides. Score 0.334 Round 5: 116 peptides, 21 chains. Longest chain 9 peptides. Score 0.328 Taking the results from Round 3 Chains 21, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3470 reflections ( 99.71 % complete ) and 5370 restraints for refining 2385 atoms. 4995 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2298 (Rfree = 0.000) for 2385 atoms. Found 11 (11 requested) and removed 40 (5 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2470 (Rfree = 0.000) for 2349 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 43: After refmac, R = 0.2115 (Rfree = 0.000) for 2346 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2190 (Rfree = 0.000) for 2332 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.2097 (Rfree = 0.000) for 2325 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.85 3.95 Search for helices and strands: 0 residues in 0 chains, 2416 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 7 peptides. Score 0.197 Round 2: 87 peptides, 18 chains. Longest chain 8 peptides. Score 0.250 Round 3: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.312 Round 4: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.270 Round 5: 97 peptides, 16 chains. Longest chain 9 peptides. Score 0.342 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 81, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2hoe-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3470 reflections ( 99.71 % complete ) and 5272 restraints for refining 2370 atoms. 4935 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2274 (Rfree = 0.000) for 2370 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2218 (Rfree = 0.000) for 2358 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2000 (Rfree = 0.000) for 2345 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2166 (Rfree = 0.000) for 2335 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 50.1