null Sun 23 Dec 22:22:46 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 2a6a-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6a-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6a-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-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/2a6a-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-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 ============================================================ Sun 23 Dec 22:22:56 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/2a6a-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6a-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 323 and 0 Target number of residues in the AU: 323 Target solvent content: 0.6681 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 436 Adjusted target solvent content: 0.55 Input MTZ file: 2a6a-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: 21 Cell parameters: 93.313 217.176 51.977 90.000 90.000 90.000 Input sequence file: 2a6a-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3488 target number of atoms Had to go as low as 0.70 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 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: 108.588 3.600 Wilson plot Bfac: 90.78 6404 reflections ( 98.81 % complete ) and 0 restraints for refining 3863 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3445 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3247 (Rfree = 0.000) for 3863 atoms. Found 24 (24 requested) and removed 46 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.42 Search for helices and strands: 0 residues in 0 chains, 3918 seeds are put forward NCS extension: 0 residues added, 3918 seeds are put forward Round 1: 177 peptides, 35 chains. Longest chain 10 peptides. Score 0.301 Round 2: 219 peptides, 34 chains. Longest chain 18 peptides. Score 0.447 Round 3: 256 peptides, 32 chains. Longest chain 23 peptides. Score 0.570 Round 4: 258 peptides, 28 chains. Longest chain 21 peptides. Score 0.617 Round 5: 249 peptides, 29 chains. Longest chain 24 peptides. Score 0.586 Taking the results from Round 4 Chains 30, Residues 230, Estimated correctness of the model 21.2 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 7099 restraints for refining 3162 atoms. 6176 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2598 (Rfree = 0.000) for 3162 atoms. Found 13 (20 requested) and removed 44 (10 requested) atoms. Cycle 2: After refmac, R = 0.2416 (Rfree = 0.000) for 3057 atoms. Found 17 (20 requested) and removed 35 (10 requested) atoms. Cycle 3: After refmac, R = 0.2322 (Rfree = 0.000) for 3010 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. Cycle 4: After refmac, R = 0.2786 (Rfree = 0.000) for 2992 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 5: After refmac, R = 0.2446 (Rfree = 0.000) for 2962 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.39 Search for helices and strands: 0 residues in 0 chains, 3109 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3128 seeds are put forward Round 1: 209 peptides, 35 chains. Longest chain 13 peptides. Score 0.405 Round 2: 251 peptides, 32 chains. Longest chain 18 peptides. Score 0.557 Round 3: 251 peptides, 30 chains. Longest chain 19 peptides. Score 0.580 Round 4: 273 peptides, 34 chains. Longest chain 20 peptides. Score 0.589 Round 5: 254 peptides, 28 chains. Longest chain 23 peptides. Score 0.608 Taking the results from Round 5 Chains 29, Residues 226, Estimated correctness of the model 17.8 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6919 restraints for refining 3092 atoms. 6019 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2546 (Rfree = 0.000) for 3092 atoms. Found 18 (19 requested) and removed 37 (9 requested) atoms. Cycle 7: After refmac, R = 0.2666 (Rfree = 0.000) for 3035 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 8: After refmac, R = 0.2455 (Rfree = 0.000) for 3001 atoms. Found 14 (19 requested) and removed 25 (9 requested) atoms. Cycle 9: After refmac, R = 0.2761 (Rfree = 0.000) for 2972 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 10: After refmac, R = 0.2233 (Rfree = 0.000) for 2956 atoms. Found 12 (19 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.43 Search for helices and strands: 0 residues in 0 chains, 3039 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3060 seeds are put forward Round 1: 216 peptides, 33 chains. Longest chain 14 peptides. Score 0.451 Round 2: 229 peptides, 29 chains. Longest chain 17 peptides. Score 0.536 Round 3: 258 peptides, 31 chains. Longest chain 20 peptides. Score 0.585 Round 4: 244 peptides, 29 chains. Longest chain 20 peptides. Score 0.574 Round 5: 240 peptides, 28 chains. Longest chain 18 peptides. Score 0.575 Taking the results from Round 3 Chains 31, Residues 227, Estimated correctness of the model 8.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6702 restraints for refining 3038 atoms. 5825 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2929 (Rfree = 0.000) for 3038 atoms. Found 19 (19 requested) and removed 156 (9 requested) atoms. Cycle 12: After refmac, R = 0.2133 (Rfree = 0.000) for 2871 atoms. Found 11 (18 requested) and removed 53 (9 requested) atoms. Cycle 13: After refmac, R = 0.2221 (Rfree = 0.000) for 2818 atoms. Found 13 (18 requested) and removed 44 (9 requested) atoms. Cycle 14: After refmac, R = 0.2835 (Rfree = 0.000) for 2779 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 15: After refmac, R = 0.2385 (Rfree = 0.000) for 2756 atoms. Found 17 (17 requested) and removed 38 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.44 Search for helices and strands: 0 residues in 0 chains, 2875 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 2903 seeds are put forward Round 1: 197 peptides, 38 chains. Longest chain 11 peptides. Score 0.326 Round 2: 222 peptides, 35 chains. Longest chain 13 peptides. Score 0.443 Round 3: 239 peptides, 33 chains. Longest chain 20 peptides. Score 0.515 Round 4: 230 peptides, 33 chains. Longest chain 17 peptides. Score 0.491 Round 5: 228 peptides, 31 chains. Longest chain 18 peptides. Score 0.510 Taking the results from Round 3 Chains 33, Residues 206, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6362 restraints for refining 2875 atoms. 5571 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2331 (Rfree = 0.000) for 2875 atoms. Found 11 (18 requested) and removed 36 (9 requested) atoms. Cycle 17: After refmac, R = 0.2337 (Rfree = 0.000) for 2838 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 18: After refmac, R = 0.2718 (Rfree = 0.000) for 2824 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 19: After refmac, R = 0.2559 (Rfree = 0.000) for 2811 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 20: After refmac, R = 0.2540 (Rfree = 0.000) for 2795 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.33 Search for helices and strands: 0 residues in 0 chains, 2915 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2933 seeds are put forward Round 1: 196 peptides, 33 chains. Longest chain 11 peptides. Score 0.391 Round 2: 222 peptides, 32 chains. Longest chain 15 peptides. Score 0.481 Round 3: 225 peptides, 29 chains. Longest chain 24 peptides. Score 0.526 Round 4: 238 peptides, 31 chains. Longest chain 25 peptides. Score 0.536 Round 5: 229 peptides, 30 chains. Longest chain 17 peptides. Score 0.524 Taking the results from Round 4 Chains 32, Residues 207, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6394 restraints for refining 2975 atoms. 5555 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2376 (Rfree = 0.000) for 2975 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 22: After refmac, R = 0.2314 (Rfree = 0.000) for 2958 atoms. Found 17 (19 requested) and removed 16 (9 requested) atoms. Cycle 23: After refmac, R = 0.2344 (Rfree = 0.000) for 2951 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 24: After refmac, R = 0.2567 (Rfree = 0.000) for 2946 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 25: After refmac, R = 0.2329 (Rfree = 0.000) for 2925 atoms. Found 17 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.46 Search for helices and strands: 0 residues in 0 chains, 3042 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 3069 seeds are put forward Round 1: 186 peptides, 33 chains. Longest chain 17 peptides. Score 0.360 Round 2: 215 peptides, 30 chains. Longest chain 18 peptides. Score 0.487 Round 3: 232 peptides, 32 chains. Longest chain 20 peptides. Score 0.509 Round 4: 233 peptides, 30 chains. Longest chain 18 peptides. Score 0.535 Round 5: 229 peptides, 29 chains. Longest chain 21 peptides. Score 0.536 Taking the results from Round 5 Chains 29, Residues 200, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6561 restraints for refining 3006 atoms. 5779 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2425 (Rfree = 0.000) for 3006 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 27: After refmac, R = 0.2329 (Rfree = 0.000) for 2989 atoms. Found 10 (19 requested) and removed 21 (9 requested) atoms. Cycle 28: After refmac, R = 0.2758 (Rfree = 0.000) for 2952 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 29: After refmac, R = 0.2284 (Rfree = 0.000) for 2931 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 30: After refmac, R = 0.2481 (Rfree = 0.000) for 2918 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.40 Search for helices and strands: 0 residues in 0 chains, 3061 seeds are put forward NCS extension: 42 residues added (1 deleted due to clashes), 3103 seeds are put forward Round 1: 175 peptides, 30 chains. Longest chain 17 peptides. Score 0.366 Round 2: 202 peptides, 30 chains. Longest chain 19 peptides. Score 0.449 Round 3: 212 peptides, 28 chains. Longest chain 22 peptides. Score 0.503 Round 4: 217 peptides, 26 chains. Longest chain 19 peptides. Score 0.541 Round 5: 201 peptides, 25 chains. Longest chain 19 peptides. Score 0.511 Taking the results from Round 4 Chains 27, Residues 191, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6329 restraints for refining 2967 atoms. 5520 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2318 (Rfree = 0.000) for 2967 atoms. Found 14 (19 requested) and removed 25 (9 requested) atoms. Cycle 32: After refmac, R = 0.2208 (Rfree = 0.000) for 2942 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 33: After refmac, R = 0.2077 (Rfree = 0.000) for 2917 atoms. Found 14 (18 requested) and removed 14 (9 requested) atoms. Cycle 34: After refmac, R = 0.2150 (Rfree = 0.000) for 2909 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 35: After refmac, R = 0.2583 (Rfree = 0.000) for 2896 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.38 Search for helices and strands: 0 residues in 0 chains, 2975 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 3008 seeds are put forward Round 1: 160 peptides, 30 chains. Longest chain 9 peptides. Score 0.316 Round 2: 198 peptides, 28 chains. Longest chain 12 peptides. Score 0.464 Round 3: 207 peptides, 30 chains. Longest chain 17 peptides. Score 0.464 Round 4: 199 peptides, 24 chains. Longest chain 18 peptides. Score 0.518 Round 5: 196 peptides, 25 chains. Longest chain 19 peptides. Score 0.497 Taking the results from Round 4 Chains 24, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6504 restraints for refining 2939 atoms. 5828 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2545 (Rfree = 0.000) for 2939 atoms. Found 18 (18 requested) and removed 31 (9 requested) atoms. Cycle 37: After refmac, R = 0.2783 (Rfree = 0.000) for 2904 atoms. Found 18 (18 requested) and removed 35 (9 requested) atoms. Cycle 38: After refmac, R = 0.2506 (Rfree = 0.000) for 2867 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 39: After refmac, R = 0.2168 (Rfree = 0.000) for 2856 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 40: After refmac, R = 0.2081 (Rfree = 0.000) for 2851 atoms. Found 15 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.40 Search for helices and strands: 0 residues in 0 chains, 3003 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 3029 seeds are put forward Round 1: 163 peptides, 30 chains. Longest chain 12 peptides. Score 0.326 Round 2: 187 peptides, 28 chains. Longest chain 15 peptides. Score 0.431 Round 3: 196 peptides, 29 chains. Longest chain 26 peptides. Score 0.445 Round 4: 202 peptides, 30 chains. Longest chain 19 peptides. Score 0.449 Round 5: 198 peptides, 28 chains. Longest chain 25 peptides. Score 0.464 Taking the results from Round 5 Chains 28, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6404 reflections ( 98.81 % complete ) and 6498 restraints for refining 2904 atoms. 5846 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2168 (Rfree = 0.000) for 2904 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 42: After refmac, R = 0.2255 (Rfree = 0.000) for 2885 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 43: After refmac, R = 0.2917 (Rfree = 0.000) for 2861 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 44: After refmac, R = 0.2137 (Rfree = 0.000) for 2832 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 45: After refmac, R = 0.2057 (Rfree = 0.000) for 2820 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.46 Search for helices and strands: 0 residues in 0 chains, 2948 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 2987 seeds are put forward Round 1: 137 peptides, 26 chains. Longest chain 10 peptides. Score 0.296 Round 2: 173 peptides, 30 chains. Longest chain 12 peptides. Score 0.360 Round 3: 178 peptides, 29 chains. Longest chain 12 peptides. Score 0.390 Round 4: 163 peptides, 26 chains. Longest chain 13 peptides. Score 0.385 Round 5: 173 peptides, 28 chains. Longest chain 17 peptides. Score 0.388 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 149, 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 2a6a-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6404 reflections ( 98.81 % complete ) and 6269 restraints for refining 2842 atoms. 5702 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2661 (Rfree = 0.000) for 2842 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2615 (Rfree = 0.000) for 2817 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2212 (Rfree = 0.000) for 2786 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2042 (Rfree = 0.000) for 2760 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:18:57 GMT 2018 Job finished. TimeTaking 56.17 Used memory is bytes: 3754344