Mon 24 Dec 00:32:43 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 2a6a-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-4.0-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/2a6a-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-4.0-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 00:32:47 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/2a6a-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-4.0-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 310 and 0 Target number of residues in the AU: 310 Target solvent content: 0.6814 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-4.0-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: 21 Cell parameters: 93.313 217.176 51.977 90.000 90.000 90.000 Input sequence file: 2a6a-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3488 target number of atoms Had to go as low as 0.75 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 4.000 Wilson plot Bfac: 102.25 4693 reflections ( 98.41 % complete ) and 0 restraints for refining 3875 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3619 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3566 (Rfree = 0.000) for 3875 atoms. Found 18 (18 requested) and removed 51 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.93 3.68 Search for helices and strands: 0 residues in 0 chains, 3900 seeds are put forward NCS extension: 0 residues added, 3900 seeds are put forward Round 1: 123 peptides, 24 chains. Longest chain 10 peptides. Score 0.276 Round 2: 177 peptides, 30 chains. Longest chain 12 peptides. Score 0.373 Round 3: 196 peptides, 31 chains. Longest chain 16 peptides. Score 0.418 Round 4: 196 peptides, 27 chains. Longest chain 16 peptides. Score 0.471 Round 5: 199 peptides, 25 chains. Longest chain 19 peptides. Score 0.505 Taking the results from Round 5 Chains 25, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 7583 restraints for refining 3144 atoms. 6912 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2673 (Rfree = 0.000) for 3144 atoms. Found 14 (14 requested) and removed 48 (7 requested) atoms. Cycle 2: After refmac, R = 0.2790 (Rfree = 0.000) for 3046 atoms. Found 14 (14 requested) and removed 63 (7 requested) atoms. Cycle 3: After refmac, R = 0.2902 (Rfree = 0.000) for 2962 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 4: After refmac, R = 0.2444 (Rfree = 0.000) for 2929 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 5: After refmac, R = 0.2762 (Rfree = 0.000) for 2899 atoms. Found 13 (13 requested) and removed 32 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.90 3.65 Search for helices and strands: 0 residues in 0 chains, 3006 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 3035 seeds are put forward Round 1: 176 peptides, 34 chains. Longest chain 9 peptides. Score 0.312 Round 2: 191 peptides, 28 chains. Longest chain 16 peptides. Score 0.443 Round 3: 196 peptides, 26 chains. Longest chain 25 peptides. Score 0.484 Round 4: 203 peptides, 28 chains. Longest chain 16 peptides. Score 0.478 Round 5: 206 peptides, 26 chains. Longest chain 16 peptides. Score 0.512 Taking the results from Round 5 Chains 26, Residues 180, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6852 restraints for refining 2973 atoms. 6143 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2669 (Rfree = 0.000) for 2973 atoms. Found 14 (14 requested) and removed 42 (7 requested) atoms. Cycle 7: After refmac, R = 0.2514 (Rfree = 0.000) for 2910 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 8: After refmac, R = 0.2491 (Rfree = 0.000) for 2864 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 9: After refmac, R = 0.2333 (Rfree = 0.000) for 2830 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 10: After refmac, R = 0.2454 (Rfree = 0.000) for 2804 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.93 3.68 Search for helices and strands: 0 residues in 0 chains, 2924 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2938 seeds are put forward Round 1: 170 peptides, 31 chains. Longest chain 12 peptides. Score 0.335 Round 2: 195 peptides, 29 chains. Longest chain 13 peptides. Score 0.442 Round 3: 202 peptides, 29 chains. Longest chain 14 peptides. Score 0.462 Round 4: 201 peptides, 28 chains. Longest chain 15 peptides. Score 0.473 Round 5: 209 peptides, 27 chains. Longest chain 19 peptides. Score 0.507 Taking the results from Round 5 Chains 27, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6956 restraints for refining 3055 atoms. 6255 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2389 (Rfree = 0.000) for 3055 atoms. Found 14 (14 requested) and removed 36 (7 requested) atoms. Cycle 12: After refmac, R = 0.2288 (Rfree = 0.000) for 3006 atoms. Found 14 (14 requested) and removed 27 (7 requested) atoms. Cycle 13: After refmac, R = 0.2332 (Rfree = 0.000) for 2977 atoms. Found 14 (14 requested) and removed 31 (7 requested) atoms. Cycle 14: After refmac, R = 0.2307 (Rfree = 0.000) for 2947 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 15: After refmac, R = 0.2420 (Rfree = 0.000) for 2923 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.96 3.70 Search for helices and strands: 0 residues in 0 chains, 3050 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3069 seeds are put forward Round 1: 167 peptides, 32 chains. Longest chain 10 peptides. Score 0.311 Round 2: 191 peptides, 29 chains. Longest chain 16 peptides. Score 0.430 Round 3: 210 peptides, 30 chains. Longest chain 15 peptides. Score 0.473 Round 4: 210 peptides, 29 chains. Longest chain 18 peptides. Score 0.485 Round 5: 209 peptides, 29 chains. Longest chain 13 peptides. Score 0.482 Taking the results from Round 4 Chains 29, Residues 181, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6767 restraints for refining 3040 atoms. 6052 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2575 (Rfree = 0.000) for 3040 atoms. Found 14 (14 requested) and removed 50 (7 requested) atoms. Cycle 17: After refmac, R = 0.2484 (Rfree = 0.000) for 2960 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 18: After refmac, R = 0.2276 (Rfree = 0.000) for 2923 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 19: After refmac, R = 0.2458 (Rfree = 0.000) for 2900 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 20: After refmac, R = 0.2306 (Rfree = 0.000) for 2881 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.91 3.66 Search for helices and strands: 0 residues in 0 chains, 3024 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3041 seeds are put forward Round 1: 178 peptides, 34 chains. Longest chain 8 peptides. Score 0.319 Round 2: 188 peptides, 33 chains. Longest chain 13 peptides. Score 0.366 Round 3: 198 peptides, 32 chains. Longest chain 18 peptides. Score 0.411 Round 4: 194 peptides, 30 chains. Longest chain 12 peptides. Score 0.426 Round 5: 199 peptides, 28 chains. Longest chain 11 peptides. Score 0.467 Taking the results from Round 5 Chains 28, Residues 171, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6913 restraints for refining 3066 atoms. 6220 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2514 (Rfree = 0.000) for 3066 atoms. Found 14 (14 requested) and removed 43 (7 requested) atoms. Cycle 22: After refmac, R = 0.2274 (Rfree = 0.000) for 3019 atoms. Found 14 (14 requested) and removed 36 (7 requested) atoms. Cycle 23: After refmac, R = 0.2282 (Rfree = 0.000) for 2983 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 24: After refmac, R = 0.2442 (Rfree = 0.000) for 2957 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 25: After refmac, R = 0.2273 (Rfree = 0.000) for 2929 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.94 3.69 Search for helices and strands: 0 residues in 0 chains, 3063 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3074 seeds are put forward Round 1: 155 peptides, 26 chains. Longest chain 13 peptides. Score 0.358 Round 2: 186 peptides, 28 chains. Longest chain 13 peptides. Score 0.428 Round 3: 199 peptides, 29 chains. Longest chain 15 peptides. Score 0.454 Round 4: 195 peptides, 27 chains. Longest chain 11 peptides. Score 0.468 Round 5: 203 peptides, 27 chains. Longest chain 18 peptides. Score 0.491 Taking the results from Round 5 Chains 27, Residues 176, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6543 restraints for refining 2987 atoms. 5836 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2465 (Rfree = 0.000) for 2987 atoms. Found 14 (14 requested) and removed 75 (7 requested) atoms. Cycle 27: After refmac, R = 0.2354 (Rfree = 0.000) for 2905 atoms. Found 13 (13 requested) and removed 36 (6 requested) atoms. Cycle 28: After refmac, R = 0.2157 (Rfree = 0.000) for 2859 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 29: After refmac, R = 0.2237 (Rfree = 0.000) for 2835 atoms. Found 13 (13 requested) and removed 35 (6 requested) atoms. Cycle 30: After refmac, R = 0.2157 (Rfree = 0.000) for 2802 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.98 3.72 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2963 seeds are put forward Round 1: 179 peptides, 34 chains. Longest chain 10 peptides. Score 0.323 Round 2: 192 peptides, 31 chains. Longest chain 15 peptides. Score 0.406 Round 3: 180 peptides, 26 chains. Longest chain 13 peptides. Score 0.437 Round 4: 179 peptides, 26 chains. Longest chain 12 peptides. Score 0.434 Round 5: 184 peptides, 26 chains. Longest chain 13 peptides. Score 0.449 Taking the results from Round 5 Chains 26, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6773 restraints for refining 2948 atoms. 6167 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2355 (Rfree = 0.000) for 2948 atoms. Found 14 (14 requested) and removed 45 (7 requested) atoms. Cycle 32: After refmac, R = 0.2330 (Rfree = 0.000) for 2886 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 33: After refmac, R = 0.2397 (Rfree = 0.000) for 2870 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. Cycle 34: After refmac, R = 0.2234 (Rfree = 0.000) for 2834 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. Cycle 35: After refmac, R = 0.2323 (Rfree = 0.000) for 2811 atoms. Found 13 (13 requested) and removed 28 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.95 3.69 Search for helices and strands: 0 residues in 0 chains, 2935 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2951 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 9 peptides. Score 0.257 Round 2: 165 peptides, 28 chains. Longest chain 18 peptides. Score 0.362 Round 3: 163 peptides, 27 chains. Longest chain 11 peptides. Score 0.370 Round 4: 166 peptides, 27 chains. Longest chain 12 peptides. Score 0.380 Round 5: 167 peptides, 28 chains. Longest chain 13 peptides. Score 0.369 Taking the results from Round 4 Chains 27, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6281 restraints for refining 2817 atoms. 5752 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2043 (Rfree = 0.000) for 2817 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 37: After refmac, R = 0.2115 (Rfree = 0.000) for 2777 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 38: After refmac, R = 0.2267 (Rfree = 0.000) for 2753 atoms. Found 13 (13 requested) and removed 33 (6 requested) atoms. Cycle 39: After refmac, R = 0.2231 (Rfree = 0.000) for 2724 atoms. Found 12 (12 requested) and removed 32 (6 requested) atoms. Cycle 40: After refmac, R = 0.2541 (Rfree = 0.000) for 2692 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.93 3.68 Search for helices and strands: 0 residues in 0 chains, 2813 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2828 seeds are put forward Round 1: 145 peptides, 30 chains. Longest chain 11 peptides. Score 0.263 Round 2: 154 peptides, 27 chains. Longest chain 11 peptides. Score 0.340 Round 3: 168 peptides, 29 chains. Longest chain 12 peptides. Score 0.358 Round 4: 171 peptides, 28 chains. Longest chain 11 peptides. Score 0.382 Round 5: 171 peptides, 28 chains. Longest chain 10 peptides. Score 0.382 Taking the results from Round 5 Chains 28, Residues 143, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4693 reflections ( 98.41 % complete ) and 6032 restraints for refining 2704 atoms. 5476 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2358 (Rfree = 0.000) for 2704 atoms. Found 12 (12 requested) and removed 67 (6 requested) atoms. Cycle 42: After refmac, R = 0.2404 (Rfree = 0.000) for 2630 atoms. Found 12 (12 requested) and removed 31 (6 requested) atoms. Cycle 43: After refmac, R = 0.2272 (Rfree = 0.000) for 2602 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 44: After refmac, R = 0.2294 (Rfree = 0.000) for 2587 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 45: After refmac, R = 0.2202 (Rfree = 0.000) for 2578 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.99 3.73 Search for helices and strands: 0 residues in 0 chains, 2722 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 2731 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 8 peptides. Score 0.235 Round 2: 155 peptides, 26 chains. Longest chain 16 peptides. Score 0.358 Round 3: 155 peptides, 27 chains. Longest chain 11 peptides. Score 0.344 Round 4: 166 peptides, 25 chains. Longest chain 17 peptides. Score 0.408 Round 5: 159 peptides, 24 chains. Longest chain 11 peptides. Score 0.400 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 141, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2a6a-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4693 reflections ( 98.41 % complete ) and 5913 restraints for refining 2688 atoms. 5362 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2230 (Rfree = 0.000) for 2688 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2374 (Rfree = 0.000) for 2666 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2192 (Rfree = 0.000) for 2654 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2506 (Rfree = 0.000) for 2641 atoms. TimeTaking 42.23