Mon 24 Dec 00:40:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2aj7-2.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-2.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-2.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:40:06 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/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-mrncs/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 512 and 0 Target number of residues in the AU: 512 Target solvent content: 0.5104 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 326 Adjusted target solvent content: 0.69 Input MTZ file: 2aj7-2.2-parrot-mrncs.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: 173 Cell parameters: 108.801 108.801 82.811 90.000 90.000 120.000 Input sequence file: 2aj7-2.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 1.00 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 1 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 94.224 2.240 Wilson plot Bfac: 25.68 26900 reflections ( 99.98 % complete ) and 0 restraints for refining 2924 atoms. Observations/parameters ratio is 2.30 ------------------------------------------------------ Starting model: R = 0.3477 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3044 (Rfree = 0.000) for 2924 atoms. Found 72 (72 requested) and removed 38 (36 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.30 1.76 NCS extension: 0 residues added, 2958 seeds are put forward Round 1: 252 peptides, 22 chains. Longest chain 29 peptides. Score 0.644 Round 2: 257 peptides, 16 chains. Longest chain 41 peptides. Score 0.709 Round 3: 273 peptides, 12 chains. Longest chain 60 peptides. Score 0.767 Round 4: 280 peptides, 12 chains. Longest chain 54 peptides. Score 0.776 Round 5: 279 peptides, 11 chains. Longest chain 63 peptides. Score 0.782 Taking the results from Round 5 Chains 12, Residues 268, Estimated correctness of the model 93.7 % 6 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 B and 42 B Built loop between residues 134 B and 145 B 9 chains (275 residues) following loop building 4 chains (213 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 3229 restraints for refining 2791 atoms. 1270 conditional restraints added. Observations/parameters ratio is 2.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3005 (Rfree = 0.000) for 2791 atoms. Found 69 (69 requested) and removed 35 (34 requested) atoms. Cycle 2: After refmac, R = 0.2731 (Rfree = 0.000) for 2803 atoms. Found 69 (69 requested) and removed 36 (35 requested) atoms. Cycle 3: After refmac, R = 0.2551 (Rfree = 0.000) for 2812 atoms. Found 67 (67 requested) and removed 34 (35 requested) atoms. Cycle 4: After refmac, R = 0.2415 (Rfree = 0.000) for 2831 atoms. Found 66 (66 requested) and removed 29 (35 requested) atoms. Cycle 5: After refmac, R = 0.2316 (Rfree = 0.000) for 2856 atoms. Found 67 (67 requested) and removed 26 (35 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.22 1.70 NCS extension: 16 residues added (23 deleted due to clashes), 2920 seeds are put forward Round 1: 283 peptides, 8 chains. Longest chain 101 peptides. Score 0.809 Round 2: 286 peptides, 8 chains. Longest chain 102 peptides. Score 0.813 Round 3: 286 peptides, 8 chains. Longest chain 87 peptides. Score 0.813 Round 4: 283 peptides, 7 chains. Longest chain 102 peptides. Score 0.816 Round 5: 287 peptides, 7 chains. Longest chain 102 peptides. Score 0.820 Taking the results from Round 5 Chains 9, Residues 280, Estimated correctness of the model 95.6 % 6 chains (262 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 96 A and 102 A Built loop between residues 113 A and 116 A Built loop between residues 111 B and 116 B Built loop between residues 140 B and 144 B 3 chains (291 residues) following loop building 2 chains (276 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2856 restraints for refining 2863 atoms. 553 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2411 (Rfree = 0.000) for 2863 atoms. Found 67 (67 requested) and removed 39 (35 requested) atoms. Cycle 7: After refmac, R = 0.2237 (Rfree = 0.000) for 2883 atoms. Found 65 (65 requested) and removed 18 (35 requested) atoms. Cycle 8: After refmac, R = 0.2111 (Rfree = 0.000) for 2925 atoms. Found 66 (66 requested) and removed 25 (36 requested) atoms. Cycle 9: After refmac, R = 0.2033 (Rfree = 0.000) for 2956 atoms. Found 67 (67 requested) and removed 30 (36 requested) atoms. Cycle 10: After refmac, R = 0.1957 (Rfree = 0.000) for 2989 atoms. Found 66 (68 requested) and removed 31 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.19 1.68 NCS extension: 10 residues added (8 deleted due to clashes), 3037 seeds are put forward Round 1: 286 peptides, 7 chains. Longest chain 101 peptides. Score 0.819 Round 2: 291 peptides, 5 chains. Longest chain 102 peptides. Score 0.838 Round 3: 287 peptides, 6 chains. Longest chain 104 peptides. Score 0.827 Round 4: 288 peptides, 6 chains. Longest chain 86 peptides. Score 0.828 Round 5: 292 peptides, 5 chains. Longest chain 104 peptides. Score 0.839 Taking the results from Round 5 Chains 6, Residues 287, Estimated correctness of the model 96.4 % 5 chains (283 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 109 A and 116 A Built loop between residues 140 A and 143 A Built loop between residues 97 B and 102 B 2 chains (295 residues) following loop building 2 chains (295 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2724 restraints for refining 2906 atoms. 314 conditional restraints added. Observations/parameters ratio is 2.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2187 (Rfree = 0.000) for 2906 atoms. Found 66 (66 requested) and removed 37 (36 requested) atoms. Cycle 12: After refmac, R = 0.2047 (Rfree = 0.000) for 2932 atoms. Found 65 (65 requested) and removed 18 (36 requested) atoms. Cycle 13: After refmac, R = 0.1950 (Rfree = 0.000) for 2972 atoms. Found 66 (66 requested) and removed 23 (36 requested) atoms. Cycle 14: After refmac, R = 0.1899 (Rfree = 0.000) for 3010 atoms. Found 67 (67 requested) and removed 40 (37 requested) atoms. Cycle 15: After refmac, R = 0.1858 (Rfree = 0.000) for 3035 atoms. Found 66 (66 requested) and removed 40 (37 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.18 1.67 NCS extension: 0 residues added, 3063 seeds are put forward Round 1: 289 peptides, 7 chains. Longest chain 104 peptides. Score 0.823 Round 2: 290 peptides, 6 chains. Longest chain 105 peptides. Score 0.830 Round 3: 292 peptides, 4 chains. Longest chain 151 peptides. Score 0.845 Round 4: 294 peptides, 7 chains. Longest chain 88 peptides. Score 0.828 Round 5: 291 peptides, 6 chains. Longest chain 88 peptides. Score 0.832 Taking the results from Round 3 Chains 4, Residues 288, Estimated correctness of the model 96.6 % 3 chains (280 residues) have been docked in sequence Building loops using Loopy2018 4 chains (288 residues) following loop building 3 chains (280 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2896 restraints for refining 2896 atoms. 574 conditional restraints added. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2068 (Rfree = 0.000) for 2896 atoms. Found 61 (61 requested) and removed 35 (35 requested) atoms. Cycle 17: After refmac, R = 0.1942 (Rfree = 0.000) for 2916 atoms. Found 60 (60 requested) and removed 28 (36 requested) atoms. Cycle 18: After refmac, R = 0.1874 (Rfree = 0.000) for 2946 atoms. Found 61 (61 requested) and removed 32 (36 requested) atoms. Cycle 19: After refmac, R = 0.1826 (Rfree = 0.000) for 2975 atoms. Found 60 (60 requested) and removed 37 (36 requested) atoms. Cycle 20: After refmac, R = 0.1818 (Rfree = 0.000) for 2997 atoms. Found 59 (59 requested) and removed 43 (37 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.19 1.68 NCS extension: 23 residues added (39 deleted due to clashes), 3036 seeds are put forward Round 1: 292 peptides, 6 chains. Longest chain 104 peptides. Score 0.833 Round 2: 293 peptides, 5 chains. Longest chain 105 peptides. Score 0.840 Round 3: 296 peptides, 6 chains. Longest chain 103 peptides. Score 0.837 Round 4: 290 peptides, 7 chains. Longest chain 88 peptides. Score 0.824 Round 5: 294 peptides, 5 chains. Longest chain 105 peptides. Score 0.841 Taking the results from Round 5 Chains 5, Residues 289, Estimated correctness of the model 96.5 % 4 chains (278 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 116 A 4 chains (291 residues) following loop building 3 chains (280 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2876 restraints for refining 2885 atoms. 542 conditional restraints added. Observations/parameters ratio is 2.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2047 (Rfree = 0.000) for 2885 atoms. Found 55 (55 requested) and removed 22 (35 requested) atoms. Cycle 22: After refmac, R = 0.1932 (Rfree = 0.000) for 2913 atoms. Found 56 (56 requested) and removed 24 (36 requested) atoms. Cycle 23: After refmac, R = 0.1877 (Rfree = 0.000) for 2944 atoms. Found 57 (57 requested) and removed 40 (36 requested) atoms. Cycle 24: After refmac, R = 0.1836 (Rfree = 0.000) for 2957 atoms. Found 55 (55 requested) and removed 36 (36 requested) atoms. Cycle 25: After refmac, R = 0.1826 (Rfree = 0.000) for 2974 atoms. Found 54 (54 requested) and removed 40 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.18 1.67 NCS extension: 23 residues added (39 deleted due to clashes), 3011 seeds are put forward Round 1: 294 peptides, 8 chains. Longest chain 88 peptides. Score 0.822 Round 2: 294 peptides, 6 chains. Longest chain 106 peptides. Score 0.835 Round 3: 295 peptides, 7 chains. Longest chain 86 peptides. Score 0.829 Round 4: 295 peptides, 7 chains. Longest chain 88 peptides. Score 0.829 Round 5: 291 peptides, 5 chains. Longest chain 106 peptides. Score 0.838 Taking the results from Round 5 Chains 6, Residues 286, Estimated correctness of the model 96.4 % 4 chains (278 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 115 A 4 chains (287 residues) following loop building 3 chains (280 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2914 restraints for refining 2871 atoms. 592 conditional restraints added. Observations/parameters ratio is 2.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2022 (Rfree = 0.000) for 2871 atoms. Found 51 (51 requested) and removed 29 (35 requested) atoms. Cycle 27: After refmac, R = 0.1895 (Rfree = 0.000) for 2891 atoms. Found 50 (50 requested) and removed 14 (35 requested) atoms. Cycle 28: After refmac, R = 0.1835 (Rfree = 0.000) for 2924 atoms. Found 50 (50 requested) and removed 32 (36 requested) atoms. Cycle 29: After refmac, R = 0.1803 (Rfree = 0.000) for 2941 atoms. Found 49 (49 requested) and removed 30 (36 requested) atoms. Cycle 30: After refmac, R = 0.1787 (Rfree = 0.000) for 2958 atoms. Found 48 (48 requested) and removed 39 (36 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.18 1.67 NCS extension: 23 residues added (39 deleted due to clashes), 2992 seeds are put forward Round 1: 293 peptides, 8 chains. Longest chain 88 peptides. Score 0.821 Round 2: 296 peptides, 5 chains. Longest chain 107 peptides. Score 0.843 Round 3: 299 peptides, 9 chains. Longest chain 87 peptides. Score 0.821 Round 4: 294 peptides, 6 chains. Longest chain 88 peptides. Score 0.835 Round 5: 290 peptides, 7 chains. Longest chain 88 peptides. Score 0.824 Taking the results from Round 2 Chains 6, Residues 291, Estimated correctness of the model 96.6 % 4 chains (279 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 A and 115 A 4 chains (292 residues) following loop building 3 chains (282 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2860 restraints for refining 2873 atoms. 507 conditional restraints added. Observations/parameters ratio is 2.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1994 (Rfree = 0.000) for 2873 atoms. Found 45 (45 requested) and removed 21 (35 requested) atoms. Cycle 32: After refmac, R = 0.1874 (Rfree = 0.000) for 2896 atoms. Found 45 (45 requested) and removed 17 (35 requested) atoms. Cycle 33: After refmac, R = 0.1813 (Rfree = 0.000) for 2922 atoms. Found 46 (46 requested) and removed 31 (36 requested) atoms. Cycle 34: After refmac, R = 0.1788 (Rfree = 0.000) for 2936 atoms. Found 45 (45 requested) and removed 34 (36 requested) atoms. Cycle 35: After refmac, R = 0.1755 (Rfree = 0.000) for 2946 atoms. Found 44 (44 requested) and removed 36 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.18 1.67 NCS extension: 26 residues added (39 deleted due to clashes), 2983 seeds are put forward Round 1: 291 peptides, 7 chains. Longest chain 88 peptides. Score 0.825 Round 2: 297 peptides, 5 chains. Longest chain 88 peptides. Score 0.844 Round 3: 296 peptides, 5 chains. Longest chain 104 peptides. Score 0.843 Round 4: 297 peptides, 5 chains. Longest chain 104 peptides. Score 0.844 Round 5: 296 peptides, 5 chains. Longest chain 104 peptides. Score 0.843 Taking the results from Round 4 Chains 6, Residues 292, Estimated correctness of the model 96.6 % 5 chains (290 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 118 A Built loop between residues 97 B and 99 B Built loop between residues 112 B and 115 B 2 chains (297 residues) following loop building 2 chains (297 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2717 restraints for refining 2876 atoms. 287 conditional restraints added. Observations/parameters ratio is 2.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2022 (Rfree = 0.000) for 2876 atoms. Found 41 (41 requested) and removed 29 (35 requested) atoms. Cycle 37: After refmac, R = 0.1893 (Rfree = 0.000) for 2887 atoms. Found 40 (40 requested) and removed 17 (35 requested) atoms. Cycle 38: After refmac, R = 0.1816 (Rfree = 0.000) for 2909 atoms. Found 40 (40 requested) and removed 25 (36 requested) atoms. Cycle 39: After refmac, R = 0.1775 (Rfree = 0.000) for 2921 atoms. Found 39 (39 requested) and removed 25 (36 requested) atoms. Cycle 40: After refmac, R = 0.1746 (Rfree = 0.000) for 2935 atoms. Found 37 (37 requested) and removed 30 (36 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.18 1.67 NCS extension: 3 residues added (0 deleted due to clashes), 2947 seeds are put forward Round 1: 291 peptides, 5 chains. Longest chain 105 peptides. Score 0.838 Round 2: 295 peptides, 3 chains. Longest chain 150 peptides. Score 0.854 Round 3: 294 peptides, 5 chains. Longest chain 105 peptides. Score 0.841 Round 4: 296 peptides, 3 chains. Longest chain 150 peptides. Score 0.855 Round 5: 294 peptides, 6 chains. Longest chain 104 peptides. Score 0.835 Taking the results from Round 4 Chains 4, Residues 293, Estimated correctness of the model 97.0 % 3 chains (291 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 B and 118 B 2 chains (295 residues) following loop building 2 chains (295 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2736 restraints for refining 2867 atoms. 319 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1985 (Rfree = 0.000) for 2867 atoms. Found 35 (35 requested) and removed 26 (35 requested) atoms. Cycle 42: After refmac, R = 0.1858 (Rfree = 0.000) for 2875 atoms. Found 35 (35 requested) and removed 13 (35 requested) atoms. Cycle 43: After refmac, R = 0.1792 (Rfree = 0.000) for 2897 atoms. Found 35 (35 requested) and removed 21 (35 requested) atoms. Cycle 44: After refmac, R = 0.1779 (Rfree = 0.000) for 2911 atoms. Found 36 (36 requested) and removed 29 (36 requested) atoms. Cycle 45: After refmac, R = 0.1751 (Rfree = 0.000) for 2918 atoms. Found 36 (36 requested) and removed 28 (36 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.18 1.67 NCS extension: 0 residues added, 2927 seeds are put forward Round 1: 293 peptides, 5 chains. Longest chain 101 peptides. Score 0.840 Round 2: 293 peptides, 4 chains. Longest chain 104 peptides. Score 0.846 Round 3: 296 peptides, 4 chains. Longest chain 105 peptides. Score 0.849 Round 4: 295 peptides, 5 chains. Longest chain 104 peptides. Score 0.842 Round 5: 296 peptides, 4 chains. Longest chain 105 peptides. Score 0.849 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 292, Estimated correctness of the model 96.8 % 4 chains (288 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 112 A and 115 A Built loop between residues 109 B and 116 B 2 chains (296 residues) following loop building 2 chains (296 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 26900 reflections ( 99.98 % complete ) and 2425 restraints for refining 2371 atoms. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2527 (Rfree = 0.000) for 2371 atoms. Found 29 (29 requested) and removed 0 (29 requested) atoms. Cycle 47: After refmac, R = 0.2372 (Rfree = 0.000) for 2371 atoms. Found 24 (29 requested) and removed 1 (29 requested) atoms. Cycle 48: After refmac, R = 0.2278 (Rfree = 0.000) for 2371 atoms. Found 22 (30 requested) and removed 1 (30 requested) atoms. Cycle 49: After refmac, R = 0.2203 (Rfree = 0.000) for 2371 atoms. Found 21 (30 requested) and removed 2 (30 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 48.13