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 1vlc-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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/1vlc-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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/1vlc-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-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 357 and 0 Target number of residues in the AU: 357 Target solvent content: 0.5893 Checking the provided sequence file Detected sequence length: 366 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 366 Adjusted target solvent content: 0.58 Input MTZ file: 1vlc-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: 150 Cell parameters: 119.541 119.541 57.022 90.000 90.000 120.000 Input sequence file: 1vlc-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2928 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: 103.526 3.200 Wilson plot Bfac: 48.34 7977 reflections ( 99.80 % complete ) and 0 restraints for refining 3255 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3090 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2226 (Rfree = 0.000) for 3255 atoms. Found 22 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.90 2.60 Search for helices and strands: 0 residues in 0 chains, 3344 seeds are put forward Round 1: 235 peptides, 33 chains. Longest chain 20 peptides. Score 0.532 Round 2: 263 peptides, 29 chains. Longest chain 20 peptides. Score 0.650 Round 3: 282 peptides, 25 chains. Longest chain 37 peptides. Score 0.728 Round 4: 289 peptides, 29 chains. Longest chain 27 peptides. Score 0.705 Round 5: 297 peptides, 26 chains. Longest chain 34 peptides. Score 0.746 Taking the results from Round 5 Chains 27, Residues 271, Estimated correctness of the model 74.3 % 5 chains (87 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 266 A and 276 A Built loop between residues 288 A and 299 A 23 chains (278 residues) following loop building 3 chains (106 residues) in sequence following loop building ------------------------------------------------------ 7977 reflections ( 99.80 % complete ) and 4529 restraints for refining 2670 atoms. 3125 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2813 (Rfree = 0.000) for 2670 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 2: After refmac, R = 0.2652 (Rfree = 0.000) for 2606 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2546 (Rfree = 0.000) for 2586 atoms. Found 13 (22 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2433 (Rfree = 0.000) for 2570 atoms. Found 17 (22 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2320 (Rfree = 0.000) for 2567 atoms. Found 6 (21 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.96 2.66 Search for helices and strands: 0 residues in 0 chains, 2684 seeds are put forward Round 1: 278 peptides, 26 chains. Longest chain 31 peptides. Score 0.712 Round 2: 274 peptides, 24 chains. Longest chain 47 peptides. Score 0.722 Round 3: 298 peptides, 22 chains. Longest chain 45 peptides. Score 0.780 Round 4: 286 peptides, 24 chains. Longest chain 30 peptides. Score 0.744 Round 5: 295 peptides, 23 chains. Longest chain 35 peptides. Score 0.767 Taking the results from Round 3 Chains 22, Residues 276, Estimated correctness of the model 80.3 % 4 chains (115 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 240 A and 245 A 20 chains (278 residues) following loop building 3 chains (119 residues) in sequence following loop building ------------------------------------------------------ 7977 reflections ( 99.80 % complete ) and 4388 restraints for refining 2673 atoms. 2881 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2810 (Rfree = 0.000) for 2673 atoms. Found 21 (21 requested) and removed 25 (11 requested) atoms. Cycle 7: After refmac, R = 0.2572 (Rfree = 0.000) for 2647 atoms. Found 20 (20 requested) and removed 18 (11 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2423 (Rfree = 0.000) for 2631 atoms. Found 12 (20 requested) and removed 14 (11 requested) atoms. Cycle 9: After refmac, R = 0.2414 (Rfree = 0.000) for 2619 atoms. Found 8 (19 requested) and removed 15 (11 requested) atoms. Cycle 10: After refmac, R = 0.2342 (Rfree = 0.000) for 2604 atoms. Found 12 (19 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.93 2.63 Search for helices and strands: 0 residues in 0 chains, 2715 seeds are put forward Round 1: 284 peptides, 24 chains. Longest chain 43 peptides. Score 0.741 Round 2: 290 peptides, 23 chains. Longest chain 32 peptides. Score 0.759 Round 3: 289 peptides, 21 chains. Longest chain 40 peptides. Score 0.774 Round 4: 274 peptides, 26 chains. Longest chain 24 peptides. Score 0.704 Round 5: 274 peptides, 26 chains. Longest chain 32 peptides. Score 0.704 Taking the results from Round 3 Chains 24, Residues 268, Estimated correctness of the model 79.3 % 8 chains (155 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 229 A and 232 A Built loop between residues 276 A and 287 A Built loop between residues 298 A and 307 A 18 chains (281 residues) following loop building 5 chains (175 residues) in sequence following loop building ------------------------------------------------------ 7977 reflections ( 99.80 % complete ) and 3849 restraints for refining 2673 atoms. 2121 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2792 (Rfree = 0.000) for 2673 atoms. Found 18 (18 requested) and removed 33 (11 requested) atoms. Cycle 12: After refmac, R = 0.2600 (Rfree = 0.000) for 2637 atoms. Found 18 (18 requested) and removed 17 (11 requested) atoms. Cycle 13: After refmac, R = 0.2508 (Rfree = 0.000) for 2628 atoms. Found 12 (17 requested) and removed 12 (11 requested) atoms. Cycle 14: After refmac, R = 0.2473 (Rfree = 0.000) for 2625 atoms. Found 8 (17 requested) and removed 15 (11 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2331 (Rfree = 0.000) for 2612 atoms. Found 6 (17 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.93 2.63 Search for helices and strands: 0 residues in 0 chains, 2726 seeds are put forward Round 1: 266 peptides, 26 chains. Longest chain 37 peptides. Score 0.688 Round 2: 293 peptides, 25 chains. Longest chain 44 peptides. Score 0.748 Round 3: 297 peptides, 27 chains. Longest chain 37 peptides. Score 0.738 Round 4: 286 peptides, 25 chains. Longest chain 33 peptides. Score 0.736 Round 5: 290 peptides, 25 chains. Longest chain 43 peptides. Score 0.743 Taking the results from Round 2 Chains 28, Residues 268, Estimated correctness of the model 74.7 % 7 chains (152 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 209 A and 215 A 27 chains (271 residues) following loop building 6 chains (157 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 7977 reflections ( 99.80 % complete ) and 4042 restraints for refining 2673 atoms. 2331 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2709 (Rfree = 0.000) for 2673 atoms. Found 16 (16 requested) and removed 26 (11 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2501 (Rfree = 0.000) for 2648 atoms. Found 16 (16 requested) and removed 13 (11 requested) atoms. Cycle 18: After refmac, R = 0.2394 (Rfree = 0.000) for 2642 atoms. Found 15 (15 requested) and removed 15 (11 requested) atoms. Cycle 19: After refmac, R = 0.2281 (Rfree = 0.000) for 2640 atoms. Found 15 (15 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.2206 (Rfree = 0.000) for 2639 atoms. Found 8 (14 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.95 2.65 Search for helices and strands: 0 residues in 0 chains, 2718 seeds are put forward Round 1: 279 peptides, 29 chains. Longest chain 24 peptides. Score 0.685 Round 2: 292 peptides, 23 chains. Longest chain 47 peptides. Score 0.763 Round 3: 298 peptides, 26 chains. Longest chain 30 peptides. Score 0.748 Round 4: 303 peptides, 24 chains. Longest chain 32 peptides. Score 0.772 Round 5: 305 peptides, 16 chains. Longest chain 55 peptides. Score 0.832 Taking the results from Round 5 Chains 22, Residues 289, Estimated correctness of the model 88.0 % 7 chains (156 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 330 A and 336 A 19 chains (291 residues) following loop building 5 chains (161 residues) in sequence following loop building ------------------------------------------------------ 7977 reflections ( 99.80 % complete ) and 3935 restraints for refining 2673 atoms. 2145 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2712 (Rfree = 0.000) for 2673 atoms. Found 14 (14 requested) and removed 29 (11 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2428 (Rfree = 0.000) for 2649 atoms. Found 13 (13 requested) and removed 22 (11 requested) atoms. Cycle 23: After refmac, R = 0.2306 (Rfree = 0.000) for 2638 atoms. Found 13 (13 requested) and removed 15 (11 requested) atoms. Cycle 24: After refmac, R = 0.2253 (Rfree = 0.000) for 2636 atoms. Found 12 (12 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.2194 (Rfree = 0.000) for 2633 atoms. Found 12 (12 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.94 2.64 Search for helices and strands: 0 residues in 0 chains, 2737 seeds are put forward Round 1: 279 peptides, 28 chains. Longest chain 23 peptides. Score 0.695 Round 2: 287 peptides, 23 chains. Longest chain 35 peptides. Score 0.754 Round 3: 290 peptides, 25 chains. Longest chain 29 peptides. Score 0.743 Round 4: 285 peptides, 21 chains. Longest chain 54 peptides. Score 0.767 Round 5: 288 peptides, 17 chains. Longest chain 46 peptides. Score 0.803 Taking the results from Round 5 Chains 21, Residues 271, Estimated correctness of the model 83.9 % 6 chains (128 residues) have been docked in sequence Building loops using Loopy2018 21 chains (271 residues) following loop building 6 chains (128 residues) in sequence following loop building ------------------------------------------------------ 7977 reflections ( 99.80 % complete ) and 4283 restraints for refining 2673 atoms. 2702 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2757 (Rfree = 0.000) for 2673 atoms. Found 11 (11 requested) and removed 20 (11 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2561 (Rfree = 0.000) for 2648 atoms. Found 11 (11 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2490 (Rfree = 0.000) for 2644 atoms. Found 3 (11 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.2398 (Rfree = 0.000) for 2631 atoms. Found 7 (11 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2392 (Rfree = 0.000) for 2622 atoms. Found 10 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.97 2.67 Search for helices and strands: 0 residues in 0 chains, 2703 seeds are put forward Round 1: 269 peptides, 24 chains. Longest chain 26 peptides. Score 0.713 Round 2: 296 peptides, 25 chains. Longest chain 28 peptides. Score 0.753 Round 3: 302 peptides, 18 chains. Longest chain 66 peptides. Score 0.815 Round 4: 288 peptides, 24 chains. Longest chain 25 peptides. Score 0.748 Round 5: 300 peptides, 17 chains. Longest chain 34 peptides. Score 0.819 Taking the results from Round 5 Chains 22, Residues 283, Estimated correctness of the model 86.2 % 6 chains (137 residues) have been docked in sequence Building loops using Loopy2018 22 chains (283 residues) following loop building 6 chains (137 residues) in sequence following loop building ------------------------------------------------------ 7977 reflections ( 99.80 % complete ) and 4212 restraints for refining 2673 atoms. 2557 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2624 (Rfree = 0.000) for 2673 atoms. Found 11 (11 requested) and removed 17 (11 requested) atoms. Cycle 32: After refmac, R = 0.2435 (Rfree = 0.000) for 2659 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.2381 (Rfree = 0.000) for 2656 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 34: After refmac, R = 0.2224 (Rfree = 0.000) for 2652 atoms. Found 7 (11 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.2203 (Rfree = 0.000) for 2645 atoms. Found 3 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.95 2.65 Search for helices and strands: 0 residues in 0 chains, 2725 seeds are put forward Round 1: 265 peptides, 24 chains. Longest chain 27 peptides. Score 0.705 Round 2: 301 peptides, 21 chains. Longest chain 36 peptides. Score 0.792 Round 3: 279 peptides, 20 chains. Longest chain 41 peptides. Score 0.766 Round 4: 274 peptides, 22 chains. Longest chain 33 peptides. Score 0.740 Round 5: 273 peptides, 19 chains. Longest chain 27 peptides. Score 0.764 Taking the results from Round 2 Chains 27, Residues 280, Estimated correctness of the model 82.2 % 6 chains (91 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 202 A and 206 A 25 chains (282 residues) following loop building 4 chains (94 residues) in sequence following loop building ------------------------------------------------------ 7977 reflections ( 99.80 % complete ) and 4534 restraints for refining 2672 atoms. 3058 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2463 (Rfree = 0.000) for 2672 atoms. Found 11 (11 requested) and removed 18 (11 requested) atoms. Cycle 37: After refmac, R = 0.2306 (Rfree = 0.000) for 2661 atoms. Found 11 (11 requested) and removed 13 (11 requested) atoms. Cycle 38: After refmac, R = 0.2178 (Rfree = 0.000) for 2657 atoms. Found 8 (11 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2103 (Rfree = 0.000) for 2648 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.2048 (Rfree = 0.000) for 2645 atoms. Found 5 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.99 2.69 Search for helices and strands: 0 residues in 0 chains, 2742 seeds are put forward Round 1: 249 peptides, 25 chains. Longest chain 28 peptides. Score 0.661 Round 2: 278 peptides, 25 chains. Longest chain 31 peptides. Score 0.721 Round 3: 270 peptides, 22 chains. Longest chain 49 peptides. Score 0.733 Round 4: 277 peptides, 23 chains. Longest chain 32 peptides. Score 0.737 Round 5: 264 peptides, 27 chains. Longest chain 18 peptides. Score 0.673 Taking the results from Round 4 Chains 26, Residues 254, Estimated correctness of the model 72.6 % 5 chains (72 residues) have been docked in sequence Building loops using Loopy2018 26 chains (254 residues) following loop building 5 chains (72 residues) in sequence following loop building ------------------------------------------------------ 7977 reflections ( 99.80 % complete ) and 4867 restraints for refining 2673 atoms. 3598 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2506 (Rfree = 0.000) for 2673 atoms. Found 11 (11 requested) and removed 24 (11 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2408 (Rfree = 0.000) for 2652 atoms. Found 10 (11 requested) and removed 13 (11 requested) atoms. Cycle 43: After refmac, R = 0.2256 (Rfree = 0.000) for 2642 atoms. Found 5 (11 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.2293 (Rfree = 0.000) for 2634 atoms. Found 5 (11 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.2218 (Rfree = 0.000) for 2627 atoms. Found 6 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.96 2.66 Search for helices and strands: 0 residues in 0 chains, 2705 seeds are put forward Round 1: 245 peptides, 27 chains. Longest chain 25 peptides. Score 0.630 Round 2: 270 peptides, 24 chains. Longest chain 35 peptides. Score 0.715 Round 3: 285 peptides, 22 chains. Longest chain 49 peptides. Score 0.759 Round 4: 281 peptides, 21 chains. Longest chain 47 peptides. Score 0.761 Round 5: 281 peptides, 26 chains. Longest chain 34 peptides. Score 0.717 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 260, Estimated correctness of the model 77.0 % 3 chains (79 residues) have been docked in sequence Sequence coverage is 30 % Consider running further cycles of model building using 1vlc-3_warpNtrace.pdb as input Building loops using Loopy2018 23 chains (260 residues) following loop building 3 chains (79 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7977 reflections ( 99.80 % complete ) and 4763 restraints for refining 2673 atoms. 3433 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2448 (Rfree = 0.000) for 2673 atoms. Found 0 (11 requested) and removed 2 (11 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2364 (Rfree = 0.000) for 2664 atoms. Found 0 (11 requested) and removed 2 (11 requested) atoms. Cycle 48: After refmac, R = 0.2386 (Rfree = 0.000) for 2661 atoms. Found 0 (11 requested) and removed 3 (11 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2461 (Rfree = 0.000) for 2655 atoms. Found 0 (11 requested) and removed 8 (11 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:34:59 GMT 2018 Job finished. TimeTaking 67.04