Sun 23 Dec 22:22:53 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 2otm-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2otm-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2otm-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.8-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/2otm-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.8-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 22:23:03 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/2otm-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.8-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 369 and 0 Target number of residues in the AU: 369 Target solvent content: 0.6391 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-3.8-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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3696 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: 78.536 3.800 Wilson plot Bfac: 71.40 5499 reflections ( 99.73 % complete ) and 0 restraints for refining 4068 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3152 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2966 (Rfree = 0.000) for 4068 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 4131 seeds are put forward NCS extension: 0 residues added, 4131 seeds are put forward Round 1: 226 peptides, 41 chains. Longest chain 13 peptides. Score 0.370 Round 2: 256 peptides, 39 chains. Longest chain 13 peptides. Score 0.478 Round 3: 271 peptides, 39 chains. Longest chain 16 peptides. Score 0.517 Round 4: 283 peptides, 37 chains. Longest chain 15 peptides. Score 0.567 Round 5: 266 peptides, 32 chains. Longest chain 21 peptides. Score 0.580 Taking the results from Round 5 Chains 34, Residues 234, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7146 restraints for refining 3343 atoms. 6133 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2280 (Rfree = 0.000) for 3343 atoms. Found 12 (18 requested) and removed 26 (9 requested) atoms. Cycle 2: After refmac, R = 0.2097 (Rfree = 0.000) for 3273 atoms. Found 15 (18 requested) and removed 23 (9 requested) atoms. Cycle 3: After refmac, R = 0.1987 (Rfree = 0.000) for 3244 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. Cycle 4: After refmac, R = 0.2034 (Rfree = 0.000) for 3217 atoms. Found 4 (17 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.1950 (Rfree = 0.000) for 3196 atoms. Found 5 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.22 Search for helices and strands: 0 residues in 0 chains, 3318 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 3351 seeds are put forward Round 1: 245 peptides, 40 chains. Longest chain 14 peptides. Score 0.437 Round 2: 266 peptides, 39 chains. Longest chain 19 peptides. Score 0.504 Round 3: 291 peptides, 37 chains. Longest chain 30 peptides. Score 0.585 Round 4: 288 peptides, 36 chains. Longest chain 30 peptides. Score 0.588 Round 5: 295 peptides, 37 chains. Longest chain 26 peptides. Score 0.594 Taking the results from Round 5 Chains 37, Residues 258, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7060 restraints for refining 3343 atoms. 5981 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2382 (Rfree = 0.000) for 3343 atoms. Found 12 (18 requested) and removed 46 (9 requested) atoms. Cycle 7: After refmac, R = 0.2106 (Rfree = 0.000) for 3278 atoms. Found 12 (18 requested) and removed 21 (9 requested) atoms. Cycle 8: After refmac, R = 0.1987 (Rfree = 0.000) for 3240 atoms. Found 5 (17 requested) and removed 21 (8 requested) atoms. Cycle 9: After refmac, R = 0.1910 (Rfree = 0.000) for 3213 atoms. Found 7 (17 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.1963 (Rfree = 0.000) for 3202 atoms. Found 11 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 3289 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 3314 seeds are put forward Round 1: 241 peptides, 43 chains. Longest chain 17 peptides. Score 0.389 Round 2: 286 peptides, 33 chains. Longest chain 29 peptides. Score 0.614 Round 3: 279 peptides, 39 chains. Longest chain 21 peptides. Score 0.536 Round 4: 275 peptides, 35 chains. Longest chain 21 peptides. Score 0.569 Round 5: 274 peptides, 35 chains. Longest chain 21 peptides. Score 0.567 Taking the results from Round 2 Chains 34, Residues 253, Estimated correctness of the model 5.3 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 6886 restraints for refining 3343 atoms. 5759 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2211 (Rfree = 0.000) for 3343 atoms. Found 14 (18 requested) and removed 61 (9 requested) atoms. Cycle 12: After refmac, R = 0.1911 (Rfree = 0.000) for 3275 atoms. Found 12 (18 requested) and removed 23 (9 requested) atoms. Cycle 13: After refmac, R = 0.1827 (Rfree = 0.000) for 3252 atoms. Found 3 (17 requested) and removed 17 (8 requested) atoms. Cycle 14: After refmac, R = 0.1807 (Rfree = 0.000) for 3231 atoms. Found 8 (17 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.1774 (Rfree = 0.000) for 3225 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 3317 seeds are put forward NCS extension: 39 residues added (4 deleted due to clashes), 3356 seeds are put forward Round 1: 237 peptides, 34 chains. Longest chain 15 peptides. Score 0.487 Round 2: 272 peptides, 34 chains. Longest chain 21 peptides. Score 0.573 Round 3: 274 peptides, 32 chains. Longest chain 26 peptides. Score 0.598 Round 4: 280 peptides, 31 chains. Longest chain 26 peptides. Score 0.620 Round 5: 279 peptides, 29 chains. Longest chain 27 peptides. Score 0.637 Taking the results from Round 5 Chains 31, Residues 250, Estimated correctness of the model 15.3 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7103 restraints for refining 3343 atoms. 6040 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2340 (Rfree = 0.000) for 3343 atoms. Found 14 (18 requested) and removed 25 (9 requested) atoms. Cycle 17: After refmac, R = 0.1965 (Rfree = 0.000) for 3319 atoms. Found 9 (18 requested) and removed 24 (9 requested) atoms. Cycle 18: After refmac, R = 0.1955 (Rfree = 0.000) for 3303 atoms. Found 12 (18 requested) and removed 20 (9 requested) atoms. Cycle 19: After refmac, R = 0.1839 (Rfree = 0.000) for 3287 atoms. Found 7 (18 requested) and removed 18 (9 requested) atoms. Cycle 20: After refmac, R = 0.1857 (Rfree = 0.000) for 3269 atoms. Found 9 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 3352 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3375 seeds are put forward Round 1: 233 peptides, 39 chains. Longest chain 16 peptides. Score 0.415 Round 2: 248 peptides, 34 chains. Longest chain 15 peptides. Score 0.515 Round 3: 245 peptides, 32 chains. Longest chain 20 peptides. Score 0.530 Round 4: 277 peptides, 37 chains. Longest chain 15 peptides. Score 0.553 Round 5: 270 peptides, 38 chains. Longest chain 15 peptides. Score 0.525 Taking the results from Round 4 Chains 39, Residues 240, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7257 restraints for refining 3343 atoms. 6277 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2350 (Rfree = 0.000) for 3343 atoms. Found 9 (18 requested) and removed 25 (9 requested) atoms. Cycle 22: After refmac, R = 0.2067 (Rfree = 0.000) for 3307 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 23: After refmac, R = 0.1818 (Rfree = 0.000) for 3281 atoms. Found 11 (18 requested) and removed 23 (9 requested) atoms. Cycle 24: After refmac, R = 0.1803 (Rfree = 0.000) for 3260 atoms. Found 7 (17 requested) and removed 14 (8 requested) atoms. Cycle 25: After refmac, R = 0.1773 (Rfree = 0.000) for 3249 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 3354 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3370 seeds are put forward Round 1: 214 peptides, 36 chains. Longest chain 13 peptides. Score 0.398 Round 2: 223 peptides, 30 chains. Longest chain 16 peptides. Score 0.497 Round 3: 235 peptides, 32 chains. Longest chain 18 peptides. Score 0.505 Round 4: 251 peptides, 33 chains. Longest chain 18 peptides. Score 0.534 Round 5: 234 peptides, 32 chains. Longest chain 14 peptides. Score 0.502 Taking the results from Round 4 Chains 34, Residues 218, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7213 restraints for refining 3343 atoms. 6323 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2154 (Rfree = 0.000) for 3343 atoms. Found 12 (18 requested) and removed 30 (9 requested) atoms. Cycle 27: After refmac, R = 0.2044 (Rfree = 0.000) for 3308 atoms. Found 10 (18 requested) and removed 26 (9 requested) atoms. Cycle 28: After refmac, R = 0.1946 (Rfree = 0.000) for 3286 atoms. Found 8 (18 requested) and removed 16 (9 requested) atoms. Cycle 29: After refmac, R = 0.1859 (Rfree = 0.000) for 3275 atoms. Found 6 (18 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1815 (Rfree = 0.000) for 3265 atoms. Found 4 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 3336 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3348 seeds are put forward Round 1: 216 peptides, 40 chains. Longest chain 13 peptides. Score 0.353 Round 2: 226 peptides, 32 chains. Longest chain 19 peptides. Score 0.481 Round 3: 241 peptides, 35 chains. Longest chain 19 peptides. Score 0.485 Round 4: 238 peptides, 33 chains. Longest chain 17 peptides. Score 0.501 Round 5: 236 peptides, 33 chains. Longest chain 16 peptides. Score 0.496 Taking the results from Round 4 Chains 33, Residues 205, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7373 restraints for refining 3343 atoms. 6526 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2321 (Rfree = 0.000) for 3343 atoms. Found 18 (18 requested) and removed 39 (9 requested) atoms. Cycle 32: After refmac, R = 0.2019 (Rfree = 0.000) for 3305 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 33: After refmac, R = 0.1942 (Rfree = 0.000) for 3289 atoms. Found 17 (18 requested) and removed 21 (9 requested) atoms. Cycle 34: After refmac, R = 0.1945 (Rfree = 0.000) for 3282 atoms. Found 13 (18 requested) and removed 14 (9 requested) atoms. Cycle 35: After refmac, R = 0.1803 (Rfree = 0.000) for 3275 atoms. Found 8 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 3347 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3363 seeds are put forward Round 1: 201 peptides, 41 chains. Longest chain 10 peptides. Score 0.292 Round 2: 192 peptides, 34 chains. Longest chain 13 peptides. Score 0.358 Round 3: 207 peptides, 35 chains. Longest chain 11 peptides. Score 0.390 Round 4: 209 peptides, 36 chains. Longest chain 14 peptides. Score 0.383 Round 5: 209 peptides, 34 chains. Longest chain 18 peptides. Score 0.409 Taking the results from Round 5 Chains 34, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7777 restraints for refining 3342 atoms. 7111 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2277 (Rfree = 0.000) for 3342 atoms. Found 11 (18 requested) and removed 28 (9 requested) atoms. Cycle 37: After refmac, R = 0.2050 (Rfree = 0.000) for 3315 atoms. Found 14 (18 requested) and removed 15 (9 requested) atoms. Cycle 38: After refmac, R = 0.2077 (Rfree = 0.000) for 3304 atoms. Found 11 (18 requested) and removed 25 (9 requested) atoms. Cycle 39: After refmac, R = 0.2011 (Rfree = 0.000) for 3283 atoms. Found 14 (18 requested) and removed 17 (9 requested) atoms. Cycle 40: After refmac, R = 0.1912 (Rfree = 0.000) for 3278 atoms. Found 15 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 3386 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 3416 seeds are put forward Round 1: 160 peptides, 32 chains. Longest chain 14 peptides. Score 0.282 Round 2: 181 peptides, 30 chains. Longest chain 11 peptides. Score 0.378 Round 3: 190 peptides, 30 chains. Longest chain 14 peptides. Score 0.405 Round 4: 205 peptides, 33 chains. Longest chain 11 peptides. Score 0.410 Round 5: 206 peptides, 32 chains. Longest chain 18 peptides. Score 0.426 Taking the results from Round 5 Chains 32, Residues 174, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5499 reflections ( 99.73 % complete ) and 7681 restraints for refining 3342 atoms. 6986 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2062 (Rfree = 0.000) for 3342 atoms. Found 15 (18 requested) and removed 17 (9 requested) atoms. Cycle 42: After refmac, R = 0.2008 (Rfree = 0.000) for 3330 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 43: After refmac, R = 0.2201 (Rfree = 0.000) for 3320 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 44: After refmac, R = 0.1981 (Rfree = 0.000) for 3312 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 45: After refmac, R = 0.1953 (Rfree = 0.000) for 3309 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.25 Search for helices and strands: 0 residues in 0 chains, 3407 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3429 seeds are put forward Round 1: 169 peptides, 36 chains. Longest chain 7 peptides. Score 0.256 Round 2: 183 peptides, 32 chains. Longest chain 13 peptides. Score 0.357 Round 3: 192 peptides, 32 chains. Longest chain 11 peptides. Score 0.385 Round 4: 207 peptides, 33 chains. Longest chain 12 peptides. Score 0.416 Round 5: 198 peptides, 29 chains. Longest chain 13 peptides. Score 0.441 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 169, 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 2otm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5499 reflections ( 99.73 % complete ) and 7666 restraints for refining 3343 atoms. 7019 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2227 (Rfree = 0.000) for 3343 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2161 (Rfree = 0.000) for 3326 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1663 (Rfree = 0.000) for 3309 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1566 (Rfree = 0.000) for 3298 atoms. TimeTaking 54.93