Mon 24 Dec 07:49:53 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 2i5i-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-4.0-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/2i5i-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-4.0-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 07:49:58 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/2i5i-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-4.0-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 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.6670 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-4.0-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 4208 target number of atoms Had to go as low as 0.80 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: 29.446 4.002 Wilson plot Bfac: 89.81 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4552 reflections ( 98.94 % complete ) and 0 restraints for refining 4658 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3561 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3130 (Rfree = 0.000) for 4658 atoms. Found 21 (22 requested) and removed 66 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.85 Search for helices and strands: 0 residues in 0 chains, 4657 seeds are put forward NCS extension: 0 residues added, 4657 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 7 peptides. Score 0.191 Round 2: 105 peptides, 24 chains. Longest chain 8 peptides. Score 0.204 Round 3: 112 peptides, 25 chains. Longest chain 8 peptides. Score 0.215 Round 4: 133 peptides, 30 chains. Longest chain 8 peptides. Score 0.216 Round 5: 143 peptides, 32 chains. Longest chain 8 peptides. Score 0.222 Taking the results from Round 5 Chains 32, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 9742 restraints for refining 3798 atoms. 9330 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2512 (Rfree = 0.000) for 3798 atoms. Found 16 (18 requested) and removed 24 (9 requested) atoms. Cycle 2: After refmac, R = 0.2410 (Rfree = 0.000) for 3731 atoms. Found 17 (17 requested) and removed 38 (8 requested) atoms. Cycle 3: After refmac, R = 0.2322 (Rfree = 0.000) for 3682 atoms. Found 13 (17 requested) and removed 31 (8 requested) atoms. Cycle 4: After refmac, R = 0.1861 (Rfree = 0.000) for 3650 atoms. Found 4 (17 requested) and removed 22 (8 requested) atoms. Cycle 5: After refmac, R = 0.1984 (Rfree = 0.000) for 3610 atoms. Found 14 (17 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 3668 seeds are put forward NCS extension: 0 residues added, 3668 seeds are put forward Round 1: 104 peptides, 23 chains. Longest chain 8 peptides. Score 0.216 Round 2: 151 peptides, 32 chains. Longest chain 8 peptides. Score 0.251 Round 3: 160 peptides, 34 chains. Longest chain 7 peptides. Score 0.253 Round 4: 172 peptides, 34 chains. Longest chain 9 peptides. Score 0.293 Round 5: 164 peptides, 33 chains. Longest chain 11 peptides. Score 0.280 Taking the results from Round 4 Chains 34, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7464 restraints for refining 3233 atoms. 6946 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1924 (Rfree = 0.000) for 3233 atoms. Found 13 (15 requested) and removed 19 (7 requested) atoms. Cycle 7: After refmac, R = 0.2023 (Rfree = 0.000) for 3189 atoms. Found 14 (15 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.1962 (Rfree = 0.000) for 3166 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 9: After refmac, R = 0.1830 (Rfree = 0.000) for 3151 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.1877 (Rfree = 0.000) for 3149 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.79 Search for helices and strands: 0 residues in 0 chains, 3233 seeds are put forward NCS extension: 0 residues added, 3233 seeds are put forward Round 1: 152 peptides, 32 chains. Longest chain 10 peptides. Score 0.254 Round 2: 177 peptides, 37 chains. Longest chain 10 peptides. Score 0.268 Round 3: 185 peptides, 34 chains. Longest chain 16 peptides. Score 0.334 Round 4: 169 peptides, 30 chains. Longest chain 13 peptides. Score 0.338 Round 5: 193 peptides, 34 chains. Longest chain 15 peptides. Score 0.359 Taking the results from Round 5 Chains 34, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7133 restraints for refining 3246 atoms. 6531 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2205 (Rfree = 0.000) for 3246 atoms. Found 8 (15 requested) and removed 29 (7 requested) atoms. Cycle 12: After refmac, R = 0.1597 (Rfree = 0.000) for 3193 atoms. Found 9 (15 requested) and removed 18 (7 requested) atoms. Cycle 13: After refmac, R = 0.1496 (Rfree = 0.000) for 3175 atoms. Found 9 (15 requested) and removed 10 (7 requested) atoms. Cycle 14: After refmac, R = 0.1466 (Rfree = 0.000) for 3165 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.1530 (Rfree = 0.000) for 3158 atoms. Found 8 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 3240 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3258 seeds are put forward Round 1: 191 peptides, 42 chains. Longest chain 8 peptides. Score 0.245 Round 2: 206 peptides, 40 chains. Longest chain 10 peptides. Score 0.320 Round 3: 198 peptides, 36 chains. Longest chain 12 peptides. Score 0.348 Round 4: 194 peptides, 34 chains. Longest chain 15 peptides. Score 0.362 Round 5: 200 peptides, 35 chains. Longest chain 13 peptides. Score 0.367 Taking the results from Round 5 Chains 35, Residues 165, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7397 restraints for refining 3360 atoms. 6740 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1853 (Rfree = 0.000) for 3360 atoms. Found 14 (15 requested) and removed 32 (7 requested) atoms. Cycle 17: After refmac, R = 0.1610 (Rfree = 0.000) for 3314 atoms. Found 6 (15 requested) and removed 23 (7 requested) atoms. Cycle 18: After refmac, R = 0.1534 (Rfree = 0.000) for 3290 atoms. Found 4 (15 requested) and removed 12 (7 requested) atoms. Cycle 19: After refmac, R = 0.1556 (Rfree = 0.000) for 3273 atoms. Found 7 (15 requested) and removed 11 (7 requested) atoms. Cycle 20: After refmac, R = 0.1535 (Rfree = 0.000) for 3263 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.77 Search for helices and strands: 0 residues in 0 chains, 3337 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3356 seeds are put forward Round 1: 163 peptides, 35 chains. Longest chain 7 peptides. Score 0.249 Round 2: 204 peptides, 37 chains. Longest chain 11 peptides. Score 0.353 Round 3: 206 peptides, 34 chains. Longest chain 14 peptides. Score 0.398 Round 4: 203 peptides, 36 chains. Longest chain 11 peptides. Score 0.363 Round 5: 195 peptides, 34 chains. Longest chain 17 peptides. Score 0.365 Taking the results from Round 3 Chains 34, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7569 restraints for refining 3361 atoms. 6915 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1884 (Rfree = 0.000) for 3361 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 22: After refmac, R = 0.1721 (Rfree = 0.000) for 3317 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 23: After refmac, R = 0.1855 (Rfree = 0.000) for 3301 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 24: After refmac, R = 0.1728 (Rfree = 0.000) for 3286 atoms. Found 10 (15 requested) and removed 14 (7 requested) atoms. Cycle 25: After refmac, R = 0.1781 (Rfree = 0.000) for 3270 atoms. Found 11 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 3342 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3362 seeds are put forward Round 1: 175 peptides, 38 chains. Longest chain 7 peptides. Score 0.247 Round 2: 194 peptides, 37 chains. Longest chain 9 peptides. Score 0.322 Round 3: 177 peptides, 34 chains. Longest chain 12 peptides. Score 0.309 Round 4: 181 peptides, 37 chains. Longest chain 10 peptides. Score 0.281 Round 5: 189 peptides, 36 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 2 Chains 37, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7354 restraints for refining 3289 atoms. 6763 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1781 (Rfree = 0.000) for 3289 atoms. Found 13 (15 requested) and removed 23 (7 requested) atoms. Cycle 27: After refmac, R = 0.1570 (Rfree = 0.000) for 3260 atoms. Found 0 (15 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.1519 (Rfree = 0.000) for 3247 atoms. Found 2 (15 requested) and removed 10 (7 requested) atoms. Cycle 29: After refmac, R = 0.1493 (Rfree = 0.000) for 3238 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. Cycle 30: After refmac, R = 0.1473 (Rfree = 0.000) for 3228 atoms. Found 0 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.78 Search for helices and strands: 0 residues in 0 chains, 3261 seeds are put forward NCS extension: 0 residues added, 3261 seeds are put forward Round 1: 151 peptides, 33 chains. Longest chain 7 peptides. Score 0.236 Round 2: 174 peptides, 33 chains. Longest chain 11 peptides. Score 0.313 Round 3: 171 peptides, 30 chains. Longest chain 9 peptides. Score 0.345 Round 4: 170 peptides, 28 chains. Longest chain 14 peptides. Score 0.369 Round 5: 174 peptides, 30 chains. Longest chain 13 peptides. Score 0.354 Taking the results from Round 4 Chains 28, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7464 restraints for refining 3304 atoms. 6924 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1727 (Rfree = 0.000) for 3304 atoms. Found 11 (15 requested) and removed 20 (7 requested) atoms. Cycle 32: After refmac, R = 0.1567 (Rfree = 0.000) for 3287 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.1621 (Rfree = 0.000) for 3278 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.1476 (Rfree = 0.000) for 3275 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1561 (Rfree = 0.000) for 3267 atoms. Found 3 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 3334 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3352 seeds are put forward Round 1: 154 peptides, 33 chains. Longest chain 10 peptides. Score 0.246 Round 2: 175 peptides, 33 chains. Longest chain 13 peptides. Score 0.316 Round 3: 171 peptides, 29 chains. Longest chain 13 peptides. Score 0.358 Round 4: 174 peptides, 27 chains. Longest chain 15 peptides. Score 0.395 Round 5: 177 peptides, 31 chains. Longest chain 11 peptides. Score 0.350 Taking the results from Round 4 Chains 27, Residues 147, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7570 restraints for refining 3411 atoms. 6971 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1652 (Rfree = 0.000) for 3411 atoms. Found 5 (16 requested) and removed 17 (8 requested) atoms. Cycle 37: After refmac, R = 0.1657 (Rfree = 0.000) for 3384 atoms. Found 9 (16 requested) and removed 17 (8 requested) atoms. Cycle 38: After refmac, R = 0.1470 (Rfree = 0.000) for 3372 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. Cycle 39: After refmac, R = 0.1425 (Rfree = 0.000) for 3360 atoms. Found 1 (15 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.1424 (Rfree = 0.000) for 3351 atoms. Found 1 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.82 Search for helices and strands: 0 residues in 0 chains, 3409 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3433 seeds are put forward Round 1: 126 peptides, 28 chains. Longest chain 8 peptides. Score 0.221 Round 2: 135 peptides, 27 chains. Longest chain 11 peptides. Score 0.269 Round 3: 134 peptides, 26 chains. Longest chain 8 peptides. Score 0.280 Round 4: 129 peptides, 23 chains. Longest chain 11 peptides. Score 0.308 Round 5: 146 peptides, 27 chains. Longest chain 11 peptides. Score 0.306 Taking the results from Round 4 Chains 23, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8037 restraints for refining 3412 atoms. 7636 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2219 (Rfree = 0.000) for 3412 atoms. Found 16 (16 requested) and removed 35 (8 requested) atoms. Cycle 42: After refmac, R = 0.1957 (Rfree = 0.000) for 3381 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.2004 (Rfree = 0.000) for 3374 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 44: After refmac, R = 0.1663 (Rfree = 0.000) for 3361 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.1381 (Rfree = 0.000) for 3362 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 3.84 Search for helices and strands: 0 residues in 0 chains, 3407 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 3416 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 7 peptides. Score 0.218 Round 2: 135 peptides, 28 chains. Longest chain 8 peptides. Score 0.254 Round 3: 129 peptides, 26 chains. Longest chain 7 peptides. Score 0.263 Round 4: 141 peptides, 29 chains. Longest chain 8 peptides. Score 0.260 Round 5: 139 peptides, 27 chains. Longest chain 11 peptides. Score 0.283 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 112, 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 2i5i-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4552 reflections ( 98.94 % complete ) and 7825 restraints for refining 3381 atoms. 7404 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1952 (Rfree = 0.000) for 3381 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1893 (Rfree = 0.000) for 3360 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1803 (Rfree = 0.000) for 3341 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1463 (Rfree = 0.000) for 3327 atoms. TimeTaking 42.27