Sun 23 Dec 22:23:08 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 2fea-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fea-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fea-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-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/2fea-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-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 22:23:18 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/2fea-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-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 353 and 0 Target number of residues in the AU: 353 Target solvent content: 0.6531 Checking the provided sequence file Detected sequence length: 236 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 472 Adjusted target solvent content: 0.54 Input MTZ file: 2fea-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: 4 Cell parameters: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3776 target number of atoms Had to go as low as 0.65 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: 22.949 3.800 Wilson plot Bfac: 80.04 5507 reflections ( 98.22 % complete ) and 0 restraints for refining 4185 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3325 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3207 (Rfree = 0.000) for 4185 atoms. Found 23 (23 requested) and removed 104 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 4160 seeds are put forward NCS extension: 0 residues added, 4160 seeds are put forward Round 1: 167 peptides, 35 chains. Longest chain 7 peptides. Score 0.264 Round 2: 225 peptides, 35 chains. Longest chain 18 peptides. Score 0.443 Round 3: 234 peptides, 37 chains. Longest chain 13 peptides. Score 0.444 Round 4: 250 peptides, 40 chains. Longest chain 17 peptides. Score 0.452 Round 5: 239 peptides, 38 chains. Longest chain 11 peptides. Score 0.446 Taking the results from Round 4 Chains 40, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7861 restraints for refining 3413 atoms. 7061 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2826 (Rfree = 0.000) for 3413 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 2: After refmac, R = 0.2449 (Rfree = 0.000) for 3361 atoms. Found 16 (18 requested) and removed 22 (9 requested) atoms. Cycle 3: After refmac, R = 0.2245 (Rfree = 0.000) for 3331 atoms. Found 12 (18 requested) and removed 22 (9 requested) atoms. Cycle 4: After refmac, R = 0.2244 (Rfree = 0.000) for 3297 atoms. Found 14 (18 requested) and removed 28 (9 requested) atoms. Cycle 5: After refmac, R = 0.1960 (Rfree = 0.000) for 3272 atoms. Found 4 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 3407 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3430 seeds are put forward Round 1: 203 peptides, 38 chains. Longest chain 9 peptides. Score 0.340 Round 2: 238 peptides, 40 chains. Longest chain 12 peptides. Score 0.418 Round 3: 235 peptides, 37 chains. Longest chain 14 peptides. Score 0.447 Round 4: 258 peptides, 42 chains. Longest chain 21 peptides. Score 0.450 Round 5: 260 peptides, 39 chains. Longest chain 14 peptides. Score 0.490 Taking the results from Round 5 Chains 39, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7940 restraints for refining 3415 atoms. 7095 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2390 (Rfree = 0.000) for 3415 atoms. Found 12 (18 requested) and removed 25 (9 requested) atoms. Cycle 7: After refmac, R = 0.2261 (Rfree = 0.000) for 3370 atoms. Found 17 (18 requested) and removed 28 (9 requested) atoms. Cycle 8: After refmac, R = 0.2152 (Rfree = 0.000) for 3341 atoms. Found 12 (18 requested) and removed 20 (9 requested) atoms. Cycle 9: After refmac, R = 0.1952 (Rfree = 0.000) for 3320 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 10: After refmac, R = 0.1761 (Rfree = 0.000) for 3305 atoms. Found 2 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3438 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3455 seeds are put forward Round 1: 216 peptides, 41 chains. Longest chain 11 peptides. Score 0.340 Round 2: 245 peptides, 38 chains. Longest chain 13 peptides. Score 0.462 Round 3: 246 peptides, 38 chains. Longest chain 14 peptides. Score 0.465 Round 4: 248 peptides, 36 chains. Longest chain 12 peptides. Score 0.493 Round 5: 258 peptides, 37 chains. Longest chain 14 peptides. Score 0.508 Taking the results from Round 5 Chains 37, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7825 restraints for refining 3415 atoms. 6978 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2398 (Rfree = 0.000) for 3415 atoms. Found 15 (18 requested) and removed 22 (9 requested) atoms. Cycle 12: After refmac, R = 0.2171 (Rfree = 0.000) for 3378 atoms. Found 11 (18 requested) and removed 15 (9 requested) atoms. Cycle 13: After refmac, R = 0.2045 (Rfree = 0.000) for 3358 atoms. Found 14 (18 requested) and removed 20 (9 requested) atoms. Cycle 14: After refmac, R = 0.2173 (Rfree = 0.000) for 3337 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 15: After refmac, R = 0.2039 (Rfree = 0.000) for 3331 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 3480 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3500 seeds are put forward Round 1: 193 peptides, 39 chains. Longest chain 11 peptides. Score 0.294 Round 2: 229 peptides, 36 chains. Longest chain 13 peptides. Score 0.442 Round 3: 232 peptides, 37 chains. Longest chain 11 peptides. Score 0.438 Round 4: 250 peptides, 38 chains. Longest chain 14 peptides. Score 0.475 Round 5: 239 peptides, 35 chains. Longest chain 14 peptides. Score 0.481 Taking the results from Round 5 Chains 35, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7905 restraints for refining 3414 atoms. 7124 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2205 (Rfree = 0.000) for 3414 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 17: After refmac, R = 0.2246 (Rfree = 0.000) for 3395 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 18: After refmac, R = 0.2140 (Rfree = 0.000) for 3380 atoms. Found 18 (18 requested) and removed 24 (9 requested) atoms. Cycle 19: After refmac, R = 0.2064 (Rfree = 0.000) for 3364 atoms. Found 17 (18 requested) and removed 15 (9 requested) atoms. Cycle 20: After refmac, R = 0.2019 (Rfree = 0.000) for 3359 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 3499 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3515 seeds are put forward Round 1: 177 peptides, 37 chains. Longest chain 10 peptides. Score 0.269 Round 2: 206 peptides, 34 chains. Longest chain 12 peptides. Score 0.401 Round 3: 214 peptides, 35 chains. Longest chain 12 peptides. Score 0.412 Round 4: 211 peptides, 33 chains. Longest chain 13 peptides. Score 0.429 Round 5: 212 peptides, 36 chains. Longest chain 12 peptides. Score 0.393 Taking the results from Round 4 Chains 33, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8096 restraints for refining 3414 atoms. 7417 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2178 (Rfree = 0.000) for 3414 atoms. Found 17 (18 requested) and removed 18 (9 requested) atoms. Cycle 22: After refmac, R = 0.2077 (Rfree = 0.000) for 3394 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.2029 (Rfree = 0.000) for 3384 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 24: After refmac, R = 0.1964 (Rfree = 0.000) for 3380 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 25: After refmac, R = 0.1847 (Rfree = 0.000) for 3375 atoms. Found 14 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 3516 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3530 seeds are put forward Round 1: 185 peptides, 37 chains. Longest chain 12 peptides. Score 0.296 Round 2: 215 peptides, 35 chains. Longest chain 14 peptides. Score 0.415 Round 3: 228 peptides, 38 chains. Longest chain 15 peptides. Score 0.415 Round 4: 230 peptides, 36 chains. Longest chain 18 peptides. Score 0.445 Round 5: 212 peptides, 35 chains. Longest chain 14 peptides. Score 0.406 Taking the results from Round 4 Chains 36, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7926 restraints for refining 3414 atoms. 7186 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1974 (Rfree = 0.000) for 3414 atoms. Found 13 (18 requested) and removed 11 (9 requested) atoms. Cycle 27: After refmac, R = 0.1948 (Rfree = 0.000) for 3394 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 28: After refmac, R = 0.2024 (Rfree = 0.000) for 3390 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 29: After refmac, R = 0.1911 (Rfree = 0.000) for 3389 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 30: After refmac, R = 0.1862 (Rfree = 0.000) for 3374 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 3503 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3521 seeds are put forward Round 1: 187 peptides, 40 chains. Longest chain 7 peptides. Score 0.261 Round 2: 227 peptides, 41 chains. Longest chain 15 peptides. Score 0.374 Round 3: 225 peptides, 41 chains. Longest chain 11 peptides. Score 0.368 Round 4: 244 peptides, 43 chains. Longest chain 10 peptides. Score 0.399 Round 5: 237 peptides, 41 chains. Longest chain 11 peptides. Score 0.403 Taking the results from Round 5 Chains 41, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7980 restraints for refining 3414 atoms. 7237 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2312 (Rfree = 0.000) for 3414 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 32: After refmac, R = 0.2075 (Rfree = 0.000) for 3402 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 33: After refmac, R = 0.2057 (Rfree = 0.000) for 3398 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 34: After refmac, R = 0.2015 (Rfree = 0.000) for 3391 atoms. Found 16 (18 requested) and removed 16 (9 requested) atoms. Cycle 35: After refmac, R = 0.1598 (Rfree = 0.000) for 3385 atoms. Found 5 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 3490 seeds are put forward NCS extension: 0 residues added, 3490 seeds are put forward Round 1: 199 peptides, 39 chains. Longest chain 17 peptides. Score 0.314 Round 2: 208 peptides, 36 chains. Longest chain 16 peptides. Score 0.381 Round 3: 217 peptides, 37 chains. Longest chain 14 peptides. Score 0.395 Round 4: 194 peptides, 32 chains. Longest chain 16 peptides. Score 0.392 Round 5: 202 peptides, 32 chains. Longest chain 16 peptides. Score 0.415 Taking the results from Round 5 Chains 32, Residues 170, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 7867 restraints for refining 3415 atoms. 7202 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2064 (Rfree = 0.000) for 3415 atoms. Found 16 (18 requested) and removed 15 (9 requested) atoms. Cycle 37: After refmac, R = 0.2018 (Rfree = 0.000) for 3400 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 38: After refmac, R = 0.1929 (Rfree = 0.000) for 3386 atoms. Found 15 (18 requested) and removed 12 (9 requested) atoms. Cycle 39: After refmac, R = 0.1941 (Rfree = 0.000) for 3385 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 40: After refmac, R = 0.1878 (Rfree = 0.000) for 3381 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 3475 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3504 seeds are put forward Round 1: 175 peptides, 36 chains. Longest chain 10 peptides. Score 0.277 Round 2: 209 peptides, 37 chains. Longest chain 14 peptides. Score 0.371 Round 3: 204 peptides, 34 chains. Longest chain 11 peptides. Score 0.395 Round 4: 209 peptides, 34 chains. Longest chain 13 peptides. Score 0.410 Round 5: 207 peptides, 31 chains. Longest chain 17 peptides. Score 0.442 Taking the results from Round 5 Chains 31, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5507 reflections ( 98.22 % complete ) and 8046 restraints for refining 3415 atoms. 7373 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2105 (Rfree = 0.000) for 3415 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 42: After refmac, R = 0.1981 (Rfree = 0.000) for 3409 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.2026 (Rfree = 0.000) for 3405 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 44: After refmac, R = 0.1971 (Rfree = 0.000) for 3405 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 45: After refmac, R = 0.1877 (Rfree = 0.000) for 3408 atoms. Found 17 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3521 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3551 seeds are put forward Round 1: 149 peptides, 32 chains. Longest chain 11 peptides. Score 0.245 Round 2: 168 peptides, 29 chains. Longest chain 11 peptides. Score 0.352 Round 3: 181 peptides, 32 chains. Longest chain 13 peptides. Score 0.352 Round 4: 193 peptides, 32 chains. Longest chain 12 peptides. Score 0.389 Round 5: 182 peptides, 31 chains. Longest chain 13 peptides. Score 0.368 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 161, 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 2fea-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5507 reflections ( 98.22 % complete ) and 8136 restraints for refining 3415 atoms. 7524 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2290 (Rfree = 0.000) for 3415 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2068 (Rfree = 0.000) for 3395 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1963 (Rfree = 0.000) for 3382 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1914 (Rfree = 0.000) for 3370 atoms. TimeTaking 54.37