Mon 24 Dec 07:27:07 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2od6-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2od6-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2od6-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.2-parrot-noncs ############### 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 07:27:11 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/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-3.2-parrot-noncs/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 333 and 0 Target number of residues in the AU: 333 Target solvent content: 0.6318 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-3.2-parrot-noncs.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: 19 Cell parameters: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3520 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: 29.066 3.200 Wilson plot Bfac: 67.36 8570 reflections ( 99.12 % complete ) and 0 restraints for refining 3917 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3384 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3257 (Rfree = 0.000) for 3917 atoms. Found 25 (35 requested) and removed 109 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 3913 seeds are put forward NCS extension: 0 residues added, 3913 seeds are put forward Round 1: 178 peptides, 33 chains. Longest chain 11 peptides. Score 0.343 Round 2: 212 peptides, 33 chains. Longest chain 15 peptides. Score 0.455 Round 3: 239 peptides, 42 chains. Longest chain 16 peptides. Score 0.418 Round 4: 245 peptides, 35 chains. Longest chain 16 peptides. Score 0.526 Round 5: 272 peptides, 39 chains. Longest chain 18 peptides. Score 0.551 Taking the results from Round 5 Chains 39, Residues 233, Estimated correctness of the model 27.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6968 restraints for refining 3212 atoms. 6075 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2838 (Rfree = 0.000) for 3212 atoms. Found 17 (28 requested) and removed 27 (14 requested) atoms. Cycle 2: After refmac, R = 0.2794 (Rfree = 0.000) for 3179 atoms. Found 17 (28 requested) and removed 24 (14 requested) atoms. Cycle 3: After refmac, R = 0.2597 (Rfree = 0.000) for 3161 atoms. Found 11 (28 requested) and removed 18 (14 requested) atoms. Cycle 4: After refmac, R = 0.3074 (Rfree = 0.000) for 3148 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. Cycle 5: After refmac, R = 0.2649 (Rfree = 0.000) for 3145 atoms. Found 17 (28 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 3279 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3293 seeds are put forward Round 1: 250 peptides, 43 chains. Longest chain 15 peptides. Score 0.439 Round 2: 270 peptides, 36 chains. Longest chain 20 peptides. Score 0.580 Round 3: 259 peptides, 33 chains. Longest chain 18 peptides. Score 0.586 Round 4: 260 peptides, 35 chains. Longest chain 16 peptides. Score 0.566 Round 5: 272 peptides, 33 chains. Longest chain 18 peptides. Score 0.618 Taking the results from Round 5 Chains 33, Residues 239, Estimated correctness of the model 45.8 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6888 restraints for refining 3213 atoms. 5902 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2720 (Rfree = 0.000) for 3213 atoms. Found 13 (28 requested) and removed 20 (14 requested) atoms. Cycle 7: After refmac, R = 0.2586 (Rfree = 0.000) for 3187 atoms. Found 10 (28 requested) and removed 20 (14 requested) atoms. Cycle 8: After refmac, R = 0.2534 (Rfree = 0.000) for 3165 atoms. Found 13 (28 requested) and removed 15 (14 requested) atoms. Cycle 9: After refmac, R = 0.2486 (Rfree = 0.000) for 3159 atoms. Found 12 (28 requested) and removed 15 (14 requested) atoms. Cycle 10: After refmac, R = 0.2828 (Rfree = 0.000) for 3150 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 3282 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3304 seeds are put forward Round 1: 235 peptides, 35 chains. Longest chain 14 peptides. Score 0.497 Round 2: 257 peptides, 33 chains. Longest chain 17 peptides. Score 0.581 Round 3: 286 peptides, 31 chains. Longest chain 39 peptides. Score 0.669 Round 4: 285 peptides, 33 chains. Longest chain 19 peptides. Score 0.647 Round 5: 280 peptides, 30 chains. Longest chain 41 peptides. Score 0.666 Taking the results from Round 3 Chains 31, Residues 255, Estimated correctness of the model 58.3 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6677 restraints for refining 3213 atoms. 5621 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2678 (Rfree = 0.000) for 3213 atoms. Found 13 (28 requested) and removed 25 (14 requested) atoms. Cycle 12: After refmac, R = 0.2651 (Rfree = 0.000) for 3194 atoms. Found 10 (28 requested) and removed 21 (14 requested) atoms. Cycle 13: After refmac, R = 0.2906 (Rfree = 0.000) for 3171 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. Cycle 14: After refmac, R = 0.2588 (Rfree = 0.000) for 3168 atoms. Found 12 (28 requested) and removed 18 (14 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2936 (Rfree = 0.000) for 3158 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 3269 seeds are put forward NCS extension: 58 residues added (2 deleted due to clashes), 3327 seeds are put forward Round 1: 237 peptides, 32 chains. Longest chain 18 peptides. Score 0.540 Round 2: 246 peptides, 30 chains. Longest chain 23 peptides. Score 0.588 Round 3: 261 peptides, 31 chains. Longest chain 21 peptides. Score 0.613 Round 4: 266 peptides, 33 chains. Longest chain 25 peptides. Score 0.603 Round 5: 257 peptides, 30 chains. Longest chain 23 peptides. Score 0.615 Taking the results from Round 5 Chains 30, Residues 227, Estimated correctness of the model 45.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6969 restraints for refining 3213 atoms. 6091 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2579 (Rfree = 0.000) for 3213 atoms. Found 13 (28 requested) and removed 18 (14 requested) atoms. Cycle 17: After refmac, R = 0.2521 (Rfree = 0.000) for 3201 atoms. Found 13 (28 requested) and removed 18 (14 requested) atoms. Cycle 18: After refmac, R = 0.2546 (Rfree = 0.000) for 3191 atoms. Found 12 (28 requested) and removed 16 (14 requested) atoms. Cycle 19: After refmac, R = 0.2397 (Rfree = 0.000) for 3185 atoms. Found 9 (28 requested) and removed 15 (14 requested) atoms. Cycle 20: After refmac, R = 0.2989 (Rfree = 0.000) for 3175 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 3283 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 3313 seeds are put forward Round 1: 241 peptides, 32 chains. Longest chain 26 peptides. Score 0.551 Round 2: 254 peptides, 33 chains. Longest chain 22 peptides. Score 0.574 Round 3: 242 peptides, 31 chains. Longest chain 24 peptides. Score 0.566 Round 4: 269 peptides, 33 chains. Longest chain 26 peptides. Score 0.611 Round 5: 269 peptides, 38 chains. Longest chain 20 peptides. Score 0.555 Taking the results from Round 4 Chains 33, Residues 236, Estimated correctness of the model 44.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6724 restraints for refining 3213 atoms. 5728 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2664 (Rfree = 0.000) for 3213 atoms. Found 14 (28 requested) and removed 19 (14 requested) atoms. Cycle 22: After refmac, R = 0.2605 (Rfree = 0.000) for 3196 atoms. Found 10 (28 requested) and removed 19 (14 requested) atoms. Cycle 23: After refmac, R = 0.2531 (Rfree = 0.000) for 3181 atoms. Found 12 (28 requested) and removed 16 (14 requested) atoms. Cycle 24: After refmac, R = 0.2480 (Rfree = 0.000) for 3174 atoms. Found 5 (28 requested) and removed 15 (14 requested) atoms. Cycle 25: After refmac, R = 0.2477 (Rfree = 0.000) for 3164 atoms. Found 6 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 3253 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3282 seeds are put forward Round 1: 250 peptides, 37 chains. Longest chain 17 peptides. Score 0.515 Round 2: 247 peptides, 30 chains. Longest chain 23 peptides. Score 0.590 Round 3: 270 peptides, 33 chains. Longest chain 18 peptides. Score 0.613 Round 4: 255 peptides, 30 chains. Longest chain 25 peptides. Score 0.610 Round 5: 267 peptides, 31 chains. Longest chain 27 peptides. Score 0.627 Taking the results from Round 5 Chains 32, Residues 236, Estimated correctness of the model 48.1 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6846 restraints for refining 3213 atoms. 5879 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2635 (Rfree = 0.000) for 3213 atoms. Found 16 (28 requested) and removed 27 (14 requested) atoms. Cycle 27: After refmac, R = 0.2474 (Rfree = 0.000) for 3196 atoms. Found 8 (28 requested) and removed 16 (14 requested) atoms. Cycle 28: After refmac, R = 0.2355 (Rfree = 0.000) for 3180 atoms. Found 9 (28 requested) and removed 14 (14 requested) atoms. Cycle 29: After refmac, R = 0.2324 (Rfree = 0.000) for 3166 atoms. Found 12 (28 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.2393 (Rfree = 0.000) for 3161 atoms. Found 10 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 3239 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 3274 seeds are put forward Round 1: 223 peptides, 32 chains. Longest chain 15 peptides. Score 0.501 Round 2: 246 peptides, 34 chains. Longest chain 19 peptides. Score 0.541 Round 3: 239 peptides, 32 chains. Longest chain 22 peptides. Score 0.546 Round 4: 238 peptides, 33 chains. Longest chain 18 peptides. Score 0.531 Round 5: 253 peptides, 37 chains. Longest chain 20 peptides. Score 0.523 Taking the results from Round 3 Chains 32, Residues 207, Estimated correctness of the model 25.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 7158 restraints for refining 3212 atoms. 6362 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2472 (Rfree = 0.000) for 3212 atoms. Found 12 (28 requested) and removed 14 (14 requested) atoms. Cycle 32: After refmac, R = 0.2494 (Rfree = 0.000) for 3205 atoms. Found 18 (28 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.2339 (Rfree = 0.000) for 3204 atoms. Found 2 (28 requested) and removed 14 (14 requested) atoms. Cycle 34: After refmac, R = 0.2340 (Rfree = 0.000) for 3192 atoms. Found 8 (28 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.2420 (Rfree = 0.000) for 3186 atoms. Found 9 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 3268 seeds are put forward NCS extension: 28 residues added (7 deleted due to clashes), 3296 seeds are put forward Round 1: 207 peptides, 31 chains. Longest chain 19 peptides. Score 0.466 Round 2: 214 peptides, 32 chains. Longest chain 21 peptides. Score 0.474 Round 3: 219 peptides, 30 chains. Longest chain 20 peptides. Score 0.515 Round 4: 234 peptides, 27 chains. Longest chain 21 peptides. Score 0.592 Round 5: 235 peptides, 38 chains. Longest chain 17 peptides. Score 0.459 Taking the results from Round 4 Chains 27, Residues 207, Estimated correctness of the model 38.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 6967 restraints for refining 3213 atoms. 6166 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2743 (Rfree = 0.000) for 3213 atoms. Found 15 (28 requested) and removed 16 (14 requested) atoms. Cycle 37: After refmac, R = 0.2645 (Rfree = 0.000) for 3207 atoms. Found 25 (28 requested) and removed 15 (14 requested) atoms. Cycle 38: After refmac, R = 0.2573 (Rfree = 0.000) for 3211 atoms. Found 23 (28 requested) and removed 14 (14 requested) atoms. Cycle 39: After refmac, R = 0.2280 (Rfree = 0.000) for 3211 atoms. Found 6 (28 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.2402 (Rfree = 0.000) for 3200 atoms. Found 22 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.22 Search for helices and strands: 0 residues in 0 chains, 3310 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 3334 seeds are put forward Round 1: 172 peptides, 29 chains. Longest chain 16 peptides. Score 0.382 Round 2: 203 peptides, 28 chains. Longest chain 19 peptides. Score 0.495 Round 3: 214 peptides, 30 chains. Longest chain 16 peptides. Score 0.501 Round 4: 209 peptides, 29 chains. Longest chain 21 peptides. Score 0.499 Round 5: 212 peptides, 30 chains. Longest chain 17 peptides. Score 0.495 Taking the results from Round 3 Chains 30, Residues 184, Estimated correctness of the model 11.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8570 reflections ( 99.12 % complete ) and 7135 restraints for refining 3212 atoms. 6429 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2393 (Rfree = 0.000) for 3212 atoms. Found 10 (28 requested) and removed 15 (14 requested) atoms. Cycle 42: After refmac, R = 0.2429 (Rfree = 0.000) for 3206 atoms. Found 13 (28 requested) and removed 17 (14 requested) atoms. Cycle 43: After refmac, R = 0.2388 (Rfree = 0.000) for 3201 atoms. Found 9 (28 requested) and removed 15 (14 requested) atoms. Cycle 44: After refmac, R = 0.2447 (Rfree = 0.000) for 3191 atoms. Found 15 (28 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.2390 (Rfree = 0.000) for 3189 atoms. Found 8 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 3262 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3282 seeds are put forward Round 1: 196 peptides, 33 chains. Longest chain 16 peptides. Score 0.404 Round 2: 216 peptides, 34 chains. Longest chain 17 peptides. Score 0.454 Round 3: 223 peptides, 30 chains. Longest chain 22 peptides. Score 0.526 Round 4: 222 peptides, 30 chains. Longest chain 21 peptides. Score 0.524 Round 5: 227 peptides, 34 chains. Longest chain 18 peptides. Score 0.487 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 193, Estimated correctness of the model 19.6 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2od6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8570 reflections ( 99.12 % complete ) and 6997 restraints for refining 3213 atoms. 6255 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2401 (Rfree = 0.000) for 3213 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2356 (Rfree = 0.000) for 3193 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2362 (Rfree = 0.000) for 3179 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2423 (Rfree = 0.000) for 3162 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... TimeTaking 41.15