Sun 23 Dec 22:23:05 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2otm-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2otm-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-4.0-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 22:23:14 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-4.0-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 359 and 0 Target number of residues in the AU: 359 Target solvent content: 0.6489 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3696 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: 78.536 4.001 Wilson plot Bfac: 77.35 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4718 reflections ( 99.68 % complete ) and 0 restraints for refining 4082 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3175 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2709 (Rfree = 0.000) for 4082 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 4135 seeds are put forward NCS extension: 0 residues added, 4135 seeds are put forward Round 1: 226 peptides, 37 chains. Longest chain 13 peptides. Score 0.420 Round 2: 266 peptides, 38 chains. Longest chain 15 peptides. Score 0.515 Round 3: 271 peptides, 35 chains. Longest chain 19 peptides. Score 0.560 Round 4: 274 peptides, 32 chains. Longest chain 30 peptides. Score 0.598 Round 5: 284 peptides, 31 chains. Longest chain 32 peptides. Score 0.629 Taking the results from Round 5 Chains 31, Residues 253, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7290 restraints for refining 3337 atoms. 6213 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2594 (Rfree = 0.000) for 3337 atoms. Found 8 (15 requested) and removed 28 (7 requested) atoms. Cycle 2: After refmac, R = 0.2252 (Rfree = 0.000) for 3278 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. Cycle 3: After refmac, R = 0.2138 (Rfree = 0.000) for 3261 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2124 (Rfree = 0.000) for 3238 atoms. Found 4 (15 requested) and removed 15 (7 requested) atoms. Cycle 5: After refmac, R = 0.2020 (Rfree = 0.000) for 3222 atoms. Found 2 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 3282 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3305 seeds are put forward Round 1: 249 peptides, 42 chains. Longest chain 19 peptides. Score 0.424 Round 2: 270 peptides, 34 chains. Longest chain 18 peptides. Score 0.568 Round 3: 277 peptides, 37 chains. Longest chain 20 peptides. Score 0.553 Round 4: 278 peptides, 35 chains. Longest chain 19 peptides. Score 0.576 Round 5: 284 peptides, 36 chains. Longest chain 23 peptides. Score 0.579 Taking the results from Round 5 Chains 38, Residues 248, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7435 restraints for refining 3338 atoms. 6440 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2323 (Rfree = 0.000) for 3338 atoms. Found 12 (15 requested) and removed 17 (7 requested) atoms. Cycle 7: After refmac, R = 0.2083 (Rfree = 0.000) for 3309 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.2027 (Rfree = 0.000) for 3283 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 9: After refmac, R = 0.1980 (Rfree = 0.000) for 3275 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 10: After refmac, R = 0.1940 (Rfree = 0.000) for 3268 atoms. Found 0 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.36 Search for helices and strands: 0 residues in 0 chains, 3340 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 3350 seeds are put forward Round 1: 245 peptides, 42 chains. Longest chain 11 peptides. Score 0.413 Round 2: 257 peptides, 34 chains. Longest chain 23 peptides. Score 0.537 Round 3: 261 peptides, 39 chains. Longest chain 20 peptides. Score 0.491 Round 4: 265 peptides, 35 chains. Longest chain 24 peptides. Score 0.546 Round 5: 276 peptides, 39 chains. Longest chain 23 peptides. Score 0.529 Taking the results from Round 4 Chains 36, Residues 230, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4718 reflections ( 99.68 % complete ) and 7471 restraints for refining 3337 atoms. 6498 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2175 (Rfree = 0.000) for 3337 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. Cycle 12: After refmac, R = 0.1934 (Rfree = 0.000) for 3308 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.1908 (Rfree = 0.000) for 3291 atoms. Found 2 (15 requested) and removed 12 (7 requested) atoms. Cycle 14: After refmac, R = 0.1888 (Rfree = 0.000) for 3267 atoms. Found 8 (15 requested) and removed 14 (7 requested) atoms. Cycle 15: After refmac, R = 0.1846 (Rfree = 0.000) for 3248 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 3334 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3356 seeds are put forward Round 1: 236 peptides, 38 chains. Longest chain 16 peptides. Score 0.436 Round 2: 254 peptides, 35 chains. Longest chain 14 peptides. Score 0.519 Round 3: 259 peptides, 36 chains. Longest chain 18 peptides. Score 0.520 Round 4: 265 peptides, 33 chains. Longest chain 20 peptides. Score 0.567 Round 5: 262 peptides, 35 chains. Longest chain 16 peptides. Score 0.538 Taking the results from Round 4 Chains 33, Residues 232, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7456 restraints for refining 3338 atoms. 6522 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1983 (Rfree = 0.000) for 3338 atoms. Found 11 (15 requested) and removed 11 (7 requested) atoms. Cycle 17: After refmac, R = 0.1784 (Rfree = 0.000) for 3313 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. Cycle 18: After refmac, R = 0.1836 (Rfree = 0.000) for 3295 atoms. Found 8 (15 requested) and removed 13 (7 requested) atoms. Cycle 19: After refmac, R = 0.1705 (Rfree = 0.000) for 3269 atoms. Found 5 (15 requested) and removed 15 (7 requested) atoms. Cycle 20: After refmac, R = 0.1541 (Rfree = 0.000) for 3250 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 3332 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3347 seeds are put forward Round 1: 219 peptides, 40 chains. Longest chain 12 peptides. Score 0.362 Round 2: 231 peptides, 35 chains. Longest chain 17 peptides. Score 0.459 Round 3: 225 peptides, 32 chains. Longest chain 24 peptides. Score 0.478 Round 4: 233 peptides, 30 chains. Longest chain 22 peptides. Score 0.523 Round 5: 249 peptides, 30 chains. Longest chain 19 peptides. Score 0.562 Taking the results from Round 5 Chains 31, Residues 219, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7443 restraints for refining 3337 atoms. 6521 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2047 (Rfree = 0.000) for 3337 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. Cycle 22: After refmac, R = 0.1910 (Rfree = 0.000) for 3324 atoms. Found 8 (15 requested) and removed 17 (7 requested) atoms. Cycle 23: After refmac, R = 0.1793 (Rfree = 0.000) for 3301 atoms. Found 10 (15 requested) and removed 15 (7 requested) atoms. Cycle 24: After refmac, R = 0.1732 (Rfree = 0.000) for 3289 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. Cycle 25: After refmac, R = 0.1733 (Rfree = 0.000) for 3281 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.35 Search for helices and strands: 0 residues in 0 chains, 3370 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3387 seeds are put forward Round 1: 206 peptides, 40 chains. Longest chain 10 peptides. Score 0.322 Round 2: 205 peptides, 34 chains. Longest chain 16 peptides. Score 0.397 Round 3: 223 peptides, 38 chains. Longest chain 11 peptides. Score 0.399 Round 4: 233 peptides, 35 chains. Longest chain 16 peptides. Score 0.464 Round 5: 243 peptides, 38 chains. Longest chain 14 peptides. Score 0.455 Taking the results from Round 4 Chains 35, Residues 198, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7704 restraints for refining 3338 atoms. 6932 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1876 (Rfree = 0.000) for 3338 atoms. Found 9 (15 requested) and removed 16 (7 requested) atoms. Cycle 27: After refmac, R = 0.1660 (Rfree = 0.000) for 3318 atoms. Found 1 (15 requested) and removed 11 (7 requested) atoms. Cycle 28: After refmac, R = 0.1644 (Rfree = 0.000) for 3302 atoms. Found 1 (15 requested) and removed 12 (7 requested) atoms. Cycle 29: After refmac, R = 0.1628 (Rfree = 0.000) for 3288 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. Cycle 30: After refmac, R = 0.1606 (Rfree = 0.000) for 3280 atoms. Found 2 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.31 Search for helices and strands: 0 residues in 0 chains, 3363 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3379 seeds are put forward Round 1: 210 peptides, 39 chains. Longest chain 11 peptides. Score 0.347 Round 2: 226 peptides, 37 chains. Longest chain 16 peptides. Score 0.420 Round 3: 243 peptides, 38 chains. Longest chain 15 peptides. Score 0.455 Round 4: 245 peptides, 35 chains. Longest chain 26 peptides. Score 0.496 Round 5: 250 peptides, 34 chains. Longest chain 24 peptides. Score 0.520 Taking the results from Round 5 Chains 34, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7703 restraints for refining 3338 atoms. 6873 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1809 (Rfree = 0.000) for 3338 atoms. Found 7 (15 requested) and removed 14 (7 requested) atoms. Cycle 32: After refmac, R = 0.1636 (Rfree = 0.000) for 3318 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.1593 (Rfree = 0.000) for 3304 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1547 (Rfree = 0.000) for 3293 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1532 (Rfree = 0.000) for 3286 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 3366 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3387 seeds are put forward Round 1: 198 peptides, 39 chains. Longest chain 10 peptides. Score 0.310 Round 2: 202 peptides, 32 chains. Longest chain 11 peptides. Score 0.414 Round 3: 218 peptides, 35 chains. Longest chain 12 peptides. Score 0.422 Round 4: 233 peptides, 33 chains. Longest chain 18 peptides. Score 0.488 Round 5: 234 peptides, 33 chains. Longest chain 17 peptides. Score 0.490 Taking the results from Round 5 Chains 33, Residues 201, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7535 restraints for refining 3338 atoms. 6727 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2109 (Rfree = 0.000) for 3338 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. Cycle 37: After refmac, R = 0.1833 (Rfree = 0.000) for 3307 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. Cycle 38: After refmac, R = 0.1800 (Rfree = 0.000) for 3294 atoms. Found 7 (15 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.1695 (Rfree = 0.000) for 3282 atoms. Found 1 (15 requested) and removed 13 (7 requested) atoms. Cycle 40: After refmac, R = 0.1621 (Rfree = 0.000) for 3264 atoms. Found 1 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.34 Search for helices and strands: 0 residues in 0 chains, 3335 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3357 seeds are put forward Round 1: 188 peptides, 36 chains. Longest chain 15 peptides. Score 0.318 Round 2: 236 peptides, 40 chains. Longest chain 12 peptides. Score 0.412 Round 3: 232 peptides, 38 chains. Longest chain 14 peptides. Score 0.425 Round 4: 232 peptides, 37 chains. Longest chain 16 peptides. Score 0.437 Round 5: 233 peptides, 35 chains. Longest chain 15 peptides. Score 0.464 Taking the results from Round 5 Chains 35, Residues 198, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 4718 reflections ( 99.68 % complete ) and 7508 restraints for refining 3338 atoms. 6662 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1928 (Rfree = 0.000) for 3338 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. Cycle 42: After refmac, R = 0.1723 (Rfree = 0.000) for 3309 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. Cycle 43: After refmac, R = 0.1719 (Rfree = 0.000) for 3291 atoms. Found 1 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.1783 (Rfree = 0.000) for 3279 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1581 (Rfree = 0.000) for 3272 atoms. Found 0 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.36 Search for helices and strands: 0 residues in 0 chains, 3345 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3368 seeds are put forward Round 1: 166 peptides, 32 chains. Longest chain 9 peptides. Score 0.302 Round 2: 205 peptides, 36 chains. Longest chain 19 peptides. Score 0.371 Round 3: 219 peptides, 32 chains. Longest chain 26 peptides. Score 0.462 Round 4: 228 peptides, 35 chains. Longest chain 15 peptides. Score 0.450 Round 5: 234 peptides, 31 chains. Longest chain 19 peptides. Score 0.514 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 203, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2otm-4_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 116 A and 125 A 30 chains (207 residues) following loop building 3 chains (36 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4718 reflections ( 99.68 % complete ) and 7330 restraints for refining 3338 atoms. 6425 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2125 (Rfree = 0.000) for 3338 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1934 (Rfree = 0.000) for 3317 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1843 (Rfree = 0.000) for 3299 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1777 (Rfree = 0.000) for 3289 atoms. TimeTaking 55.62