null Sun 23 Dec 22:22:41 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 1z85-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z85-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z85-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-4.0-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/1z85-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-4.0-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 22:22:50 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/1z85-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-4.0-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 356 and 0 Target number of residues in the AU: 356 Target solvent content: 0.6657 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 468 Adjusted target solvent content: 0.56 Input MTZ file: 1z85-4.0-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: 19 Cell parameters: 65.676 82.546 106.310 90.000 90.000 90.000 Input sequence file: 1z85-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3744 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: 65.199 4.000 Wilson plot Bfac: 88.57 5207 reflections ( 99.64 % complete ) and 0 restraints for refining 4138 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3398 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3256 (Rfree = 0.000) for 4138 atoms. Found 19 (19 requested) and removed 52 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.47 Search for helices and strands: 0 residues in 0 chains, 4171 seeds are put forward NCS extension: 0 residues added, 4171 seeds are put forward Round 1: 194 peptides, 36 chains. Longest chain 9 peptides. Score 0.333 Round 2: 243 peptides, 39 chains. Longest chain 11 peptides. Score 0.435 Round 3: 249 peptides, 32 chains. Longest chain 17 peptides. Score 0.530 Round 4: 249 peptides, 35 chains. Longest chain 16 peptides. Score 0.497 Round 5: 247 peptides, 29 chains. Longest chain 17 peptides. Score 0.557 Taking the results from Round 5 Chains 29, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 8065 restraints for refining 3380 atoms. 7222 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2727 (Rfree = 0.000) for 3380 atoms. Found 15 (16 requested) and removed 23 (8 requested) atoms. Cycle 2: After refmac, R = 0.2695 (Rfree = 0.000) for 3266 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 3: After refmac, R = 0.2504 (Rfree = 0.000) for 3208 atoms. Found 14 (15 requested) and removed 19 (7 requested) atoms. Cycle 4: After refmac, R = 0.2413 (Rfree = 0.000) for 3163 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 5: After refmac, R = 0.2298 (Rfree = 0.000) for 3120 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.80 3.51 Search for helices and strands: 0 residues in 0 chains, 3211 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3231 seeds are put forward Round 1: 227 peptides, 39 chains. Longest chain 11 peptides. Score 0.391 Round 2: 237 peptides, 30 chains. Longest chain 17 peptides. Score 0.523 Round 3: 243 peptides, 31 chains. Longest chain 20 peptides. Score 0.526 Round 4: 246 peptides, 34 chains. Longest chain 13 peptides. Score 0.500 Round 5: 259 peptides, 31 chains. Longest chain 22 peptides. Score 0.564 Taking the results from Round 5 Chains 31, Residues 228, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7515 restraints for refining 3301 atoms. 6634 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2430 (Rfree = 0.000) for 3301 atoms. Found 9 (15 requested) and removed 63 (7 requested) atoms. Cycle 7: After refmac, R = 0.2240 (Rfree = 0.000) for 3205 atoms. Found 3 (15 requested) and removed 38 (7 requested) atoms. Cycle 8: After refmac, R = 0.2228 (Rfree = 0.000) for 3147 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 9: After refmac, R = 0.2201 (Rfree = 0.000) for 3135 atoms. Found 2 (14 requested) and removed 14 (7 requested) atoms. Cycle 10: After refmac, R = 0.2205 (Rfree = 0.000) for 3112 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.49 Search for helices and strands: 0 residues in 0 chains, 3192 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3210 seeds are put forward Round 1: 210 peptides, 36 chains. Longest chain 12 peptides. Score 0.380 Round 2: 230 peptides, 31 chains. Longest chain 13 peptides. Score 0.494 Round 3: 247 peptides, 32 chains. Longest chain 18 peptides. Score 0.525 Round 4: 230 peptides, 28 chains. Longest chain 23 peptides. Score 0.528 Round 5: 244 peptides, 35 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 4 Chains 29, Residues 202, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7296 restraints for refining 3267 atoms. 6442 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2398 (Rfree = 0.000) for 3267 atoms. Found 11 (15 requested) and removed 46 (7 requested) atoms. Cycle 12: After refmac, R = 0.2275 (Rfree = 0.000) for 3196 atoms. Found 8 (15 requested) and removed 28 (7 requested) atoms. Cycle 13: After refmac, R = 0.2240 (Rfree = 0.000) for 3154 atoms. Found 11 (15 requested) and removed 27 (7 requested) atoms. Cycle 14: After refmac, R = 0.2204 (Rfree = 0.000) for 3122 atoms. Found 7 (14 requested) and removed 25 (7 requested) atoms. Cycle 15: After refmac, R = 0.2161 (Rfree = 0.000) for 3095 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.48 Search for helices and strands: 0 residues in 0 chains, 3171 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3194 seeds are put forward Round 1: 200 peptides, 38 chains. Longest chain 10 peptides. Score 0.325 Round 2: 231 peptides, 37 chains. Longest chain 10 peptides. Score 0.427 Round 3: 232 peptides, 35 chains. Longest chain 13 peptides. Score 0.453 Round 4: 233 peptides, 37 chains. Longest chain 12 peptides. Score 0.432 Round 5: 228 peptides, 32 chains. Longest chain 16 peptides. Score 0.478 Taking the results from Round 5 Chains 32, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7522 restraints for refining 3293 atoms. 6770 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2378 (Rfree = 0.000) for 3293 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Cycle 17: After refmac, R = 0.2299 (Rfree = 0.000) for 3256 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Cycle 18: After refmac, R = 0.2263 (Rfree = 0.000) for 3230 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 19: After refmac, R = 0.2158 (Rfree = 0.000) for 3205 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 20: After refmac, R = 0.2035 (Rfree = 0.000) for 3193 atoms. Found 11 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.47 Search for helices and strands: 0 residues in 0 chains, 3313 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3330 seeds are put forward Round 1: 207 peptides, 37 chains. Longest chain 13 peptides. Score 0.359 Round 2: 232 peptides, 37 chains. Longest chain 20 peptides. Score 0.429 Round 3: 252 peptides, 35 chains. Longest chain 24 peptides. Score 0.504 Round 4: 234 peptides, 30 chains. Longest chain 19 peptides. Score 0.515 Round 5: 243 peptides, 35 chains. Longest chain 21 peptides. Score 0.482 Taking the results from Round 4 Chains 30, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7929 restraints for refining 3381 atoms. 7143 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2311 (Rfree = 0.000) for 3381 atoms. Found 7 (16 requested) and removed 23 (8 requested) atoms. Cycle 22: After refmac, R = 0.2097 (Rfree = 0.000) for 3347 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Cycle 23: After refmac, R = 0.1923 (Rfree = 0.000) for 3332 atoms. Found 2 (15 requested) and removed 14 (7 requested) atoms. Cycle 24: After refmac, R = 0.1867 (Rfree = 0.000) for 3309 atoms. Found 1 (15 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.1813 (Rfree = 0.000) for 3293 atoms. Found 1 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.47 Search for helices and strands: 0 residues in 0 chains, 3408 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3435 seeds are put forward Round 1: 172 peptides, 34 chains. Longest chain 9 peptides. Score 0.291 Round 2: 216 peptides, 37 chains. Longest chain 17 peptides. Score 0.385 Round 3: 225 peptides, 37 chains. Longest chain 14 peptides. Score 0.410 Round 4: 226 peptides, 35 chains. Longest chain 16 peptides. Score 0.437 Round 5: 231 peptides, 35 chains. Longest chain 13 peptides. Score 0.450 Taking the results from Round 5 Chains 35, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7974 restraints for refining 3381 atoms. 7225 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2124 (Rfree = 0.000) for 3381 atoms. Found 11 (16 requested) and removed 76 (8 requested) atoms. Cycle 27: After refmac, R = 0.2055 (Rfree = 0.000) for 3289 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.1956 (Rfree = 0.000) for 3270 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. Cycle 29: After refmac, R = 0.2071 (Rfree = 0.000) for 3255 atoms. Found 12 (15 requested) and removed 13 (7 requested) atoms. Cycle 30: After refmac, R = 0.1863 (Rfree = 0.000) for 3248 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 3331 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3345 seeds are put forward Round 1: 181 peptides, 34 chains. Longest chain 14 peptides. Score 0.319 Round 2: 196 peptides, 33 chains. Longest chain 14 peptides. Score 0.377 Round 3: 201 peptides, 34 chains. Longest chain 15 peptides. Score 0.379 Round 4: 207 peptides, 29 chains. Longest chain 24 peptides. Score 0.458 Round 5: 189 peptides, 30 chains. Longest chain 18 peptides. Score 0.395 Taking the results from Round 4 Chains 29, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 8065 restraints for refining 3380 atoms. 7382 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2093 (Rfree = 0.000) for 3380 atoms. Found 8 (16 requested) and removed 19 (8 requested) atoms. Cycle 32: After refmac, R = 0.1989 (Rfree = 0.000) for 3346 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 33: After refmac, R = 0.1979 (Rfree = 0.000) for 3337 atoms. Found 9 (15 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.1788 (Rfree = 0.000) for 3330 atoms. Found 1 (15 requested) and removed 11 (7 requested) atoms. Cycle 35: After refmac, R = 0.1813 (Rfree = 0.000) for 3315 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 3.49 Search for helices and strands: 0 residues in 0 chains, 3406 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 3435 seeds are put forward Round 1: 167 peptides, 37 chains. Longest chain 7 peptides. Score 0.233 Round 2: 182 peptides, 32 chains. Longest chain 12 peptides. Score 0.349 Round 3: 199 peptides, 34 chains. Longest chain 15 peptides. Score 0.373 Round 4: 208 peptides, 34 chains. Longest chain 12 peptides. Score 0.399 Round 5: 203 peptides, 33 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 4 Chains 34, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7968 restraints for refining 3379 atoms. 7306 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2286 (Rfree = 0.000) for 3379 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 37: After refmac, R = 0.2142 (Rfree = 0.000) for 3365 atoms. Found 13 (16 requested) and removed 15 (8 requested) atoms. Cycle 38: After refmac, R = 0.2066 (Rfree = 0.000) for 3345 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 39: After refmac, R = 0.1677 (Rfree = 0.000) for 3335 atoms. Found 4 (15 requested) and removed 12 (7 requested) atoms. Cycle 40: After refmac, R = 0.1572 (Rfree = 0.000) for 3320 atoms. Found 2 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.45 Search for helices and strands: 0 residues in 0 chains, 3405 seeds are put forward NCS extension: 0 residues added, 3405 seeds are put forward Round 1: 145 peptides, 31 chains. Longest chain 10 peptides. Score 0.243 Round 2: 189 peptides, 34 chains. Longest chain 12 peptides. Score 0.344 Round 3: 189 peptides, 34 chains. Longest chain 10 peptides. Score 0.344 Round 4: 205 peptides, 35 chains. Longest chain 11 peptides. Score 0.378 Round 5: 195 peptides, 35 chains. Longest chain 9 peptides. Score 0.349 Taking the results from Round 4 Chains 35, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5207 reflections ( 99.64 % complete ) and 7869 restraints for refining 3381 atoms. 7224 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1899 (Rfree = 0.000) for 3381 atoms. Found 9 (16 requested) and removed 13 (8 requested) atoms. Cycle 42: After refmac, R = 0.1895 (Rfree = 0.000) for 3360 atoms. Found 13 (16 requested) and removed 15 (8 requested) atoms. Cycle 43: After refmac, R = 0.1867 (Rfree = 0.000) for 3339 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 44: After refmac, R = 0.1581 (Rfree = 0.000) for 3329 atoms. Found 5 (15 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.1506 (Rfree = 0.000) for 3314 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.44 Search for helices and strands: 0 residues in 0 chains, 3411 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3424 seeds are put forward Round 1: 167 peptides, 34 chains. Longest chain 10 peptides. Score 0.274 Round 2: 193 peptides, 30 chains. Longest chain 16 peptides. Score 0.407 Round 3: 184 peptides, 33 chains. Longest chain 11 peptides. Score 0.341 Round 4: 198 peptides, 31 chains. Longest chain 15 peptides. Score 0.408 Round 5: 180 peptides, 30 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 167, 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 1z85-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5207 reflections ( 99.64 % complete ) and 7797 restraints for refining 3381 atoms. 7160 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1879 (Rfree = 0.000) for 3381 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1821 (Rfree = 0.000) for 3355 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1955 (Rfree = 0.000) for 3341 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1874 (Rfree = 0.000) for 3326 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:17:34 GMT 2018 Job finished. TimeTaking 54.88 Used memory is bytes: 7597456