null Sun 23 Dec 22:22:56 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fea-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fea-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-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 22:23:06 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-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 377 and 0 Target number of residues in the AU: 377 Target solvent content: 0.6295 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 66.13 7649 reflections ( 98.32 % complete ) and 0 restraints for refining 4184 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3201 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3213 (Rfree = 0.000) for 4184 atoms. Found 31 (31 requested) and removed 127 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 4159 seeds are put forward NCS extension: 0 residues added, 4159 seeds are put forward Round 1: 212 peptides, 40 chains. Longest chain 10 peptides. Score 0.341 Round 2: 234 peptides, 37 chains. Longest chain 13 peptides. Score 0.444 Round 3: 254 peptides, 35 chains. Longest chain 21 peptides. Score 0.520 Round 4: 245 peptides, 37 chains. Longest chain 12 peptides. Score 0.474 Round 5: 260 peptides, 39 chains. Longest chain 14 peptides. Score 0.490 Taking the results from Round 3 Chains 35, Residues 219, Estimated correctness of the model 0.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7737 restraints for refining 3431 atoms. 6896 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2849 (Rfree = 0.000) for 3431 atoms. Found 25 (25 requested) and removed 48 (12 requested) atoms. Cycle 2: After refmac, R = 0.2777 (Rfree = 0.000) for 3367 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 3: After refmac, R = 0.2360 (Rfree = 0.000) for 3346 atoms. Found 22 (25 requested) and removed 24 (12 requested) atoms. Cycle 4: After refmac, R = 0.2197 (Rfree = 0.000) for 3330 atoms. Found 14 (25 requested) and removed 17 (12 requested) atoms. Cycle 5: After refmac, R = 0.2060 (Rfree = 0.000) for 3319 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 3499 seeds are put forward NCS extension: 46 residues added (0 deleted due to clashes), 3545 seeds are put forward Round 1: 247 peptides, 46 chains. Longest chain 12 peptides. Score 0.370 Round 2: 287 peptides, 42 chains. Longest chain 22 peptides. Score 0.525 Round 3: 275 peptides, 39 chains. Longest chain 17 peptides. Score 0.528 Round 4: 283 peptides, 37 chains. Longest chain 20 peptides. Score 0.568 Round 5: 291 peptides, 36 chains. Longest chain 28 peptides. Score 0.597 Taking the results from Round 5 Chains 37, Residues 255, Estimated correctness of the model 27.7 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7285 restraints for refining 3432 atoms. 6163 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2391 (Rfree = 0.000) for 3432 atoms. Found 24 (25 requested) and removed 25 (12 requested) atoms. Cycle 7: After refmac, R = 0.2161 (Rfree = 0.000) for 3402 atoms. Found 14 (25 requested) and removed 19 (12 requested) atoms. Cycle 8: After refmac, R = 0.2107 (Rfree = 0.000) for 3379 atoms. Found 14 (25 requested) and removed 15 (12 requested) atoms. Cycle 9: After refmac, R = 0.2022 (Rfree = 0.000) for 3374 atoms. Found 10 (25 requested) and removed 18 (12 requested) atoms. Cycle 10: After refmac, R = 0.1966 (Rfree = 0.000) for 3362 atoms. Found 5 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 3475 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 3510 seeds are put forward Round 1: 274 peptides, 43 chains. Longest chain 14 peptides. Score 0.481 Round 2: 299 peptides, 41 chains. Longest chain 14 peptides. Score 0.564 Round 3: 292 peptides, 39 chains. Longest chain 23 peptides. Score 0.569 Round 4: 307 peptides, 38 chains. Longest chain 23 peptides. Score 0.611 Round 5: 297 peptides, 37 chains. Longest chain 26 peptides. Score 0.600 Taking the results from Round 4 Chains 39, Residues 269, Estimated correctness of the model 32.2 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7286 restraints for refining 3433 atoms. 6174 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2269 (Rfree = 0.000) for 3433 atoms. Found 23 (25 requested) and removed 21 (12 requested) atoms. Cycle 12: After refmac, R = 0.2124 (Rfree = 0.000) for 3422 atoms. Found 9 (25 requested) and removed 18 (12 requested) atoms. Cycle 13: After refmac, R = 0.2008 (Rfree = 0.000) for 3396 atoms. Found 8 (25 requested) and removed 17 (12 requested) atoms. Cycle 14: After refmac, R = 0.1914 (Rfree = 0.000) for 3377 atoms. Found 9 (25 requested) and removed 17 (12 requested) atoms. Cycle 15: After refmac, R = 0.1864 (Rfree = 0.000) for 3364 atoms. Found 7 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 3486 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3508 seeds are put forward Round 1: 245 peptides, 39 chains. Longest chain 17 peptides. Score 0.450 Round 2: 271 peptides, 36 chains. Longest chain 17 peptides. Score 0.551 Round 3: 276 peptides, 36 chains. Longest chain 17 peptides. Score 0.563 Round 4: 289 peptides, 38 chains. Longest chain 18 peptides. Score 0.572 Round 5: 276 peptides, 36 chains. Longest chain 17 peptides. Score 0.563 Taking the results from Round 4 Chains 38, Residues 251, Estimated correctness of the model 19.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7633 restraints for refining 3433 atoms. 6667 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2154 (Rfree = 0.000) for 3433 atoms. Found 24 (25 requested) and removed 14 (12 requested) atoms. Cycle 17: After refmac, R = 0.2002 (Rfree = 0.000) for 3432 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. Cycle 18: After refmac, R = 0.1963 (Rfree = 0.000) for 3424 atoms. Found 4 (25 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.1936 (Rfree = 0.000) for 3413 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.1901 (Rfree = 0.000) for 3402 atoms. Found 0 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3516 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 3535 seeds are put forward Round 1: 237 peptides, 41 chains. Longest chain 12 peptides. Score 0.403 Round 2: 261 peptides, 38 chains. Longest chain 21 peptides. Score 0.504 Round 3: 270 peptides, 34 chains. Longest chain 21 peptides. Score 0.570 Round 4: 273 peptides, 38 chains. Longest chain 15 peptides. Score 0.534 Round 5: 277 peptides, 38 chains. Longest chain 14 peptides. Score 0.544 Taking the results from Round 3 Chains 34, Residues 236, Estimated correctness of the model 18.6 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7632 restraints for refining 3432 atoms. 6700 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2294 (Rfree = 0.000) for 3432 atoms. Found 16 (25 requested) and removed 17 (12 requested) atoms. Cycle 22: After refmac, R = 0.2206 (Rfree = 0.000) for 3421 atoms. Found 11 (25 requested) and removed 17 (12 requested) atoms. Cycle 23: After refmac, R = 0.2125 (Rfree = 0.000) for 3410 atoms. Found 9 (25 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.2091 (Rfree = 0.000) for 3402 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.2058 (Rfree = 0.000) for 3394 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 3516 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 3541 seeds are put forward Round 1: 224 peptides, 38 chains. Longest chain 12 peptides. Score 0.403 Round 2: 255 peptides, 34 chains. Longest chain 15 peptides. Score 0.534 Round 3: 252 peptides, 37 chains. Longest chain 21 peptides. Score 0.492 Round 4: 254 peptides, 32 chains. Longest chain 16 peptides. Score 0.553 Round 5: 261 peptides, 38 chains. Longest chain 25 peptides. Score 0.504 Taking the results from Round 4 Chains 32, Residues 222, Estimated correctness of the model 12.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7772 restraints for refining 3433 atoms. 6916 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2171 (Rfree = 0.000) for 3433 atoms. Found 14 (25 requested) and removed 13 (12 requested) atoms. Cycle 27: After refmac, R = 0.2143 (Rfree = 0.000) for 3427 atoms. Found 23 (25 requested) and removed 16 (12 requested) atoms. Cycle 28: After refmac, R = 0.2049 (Rfree = 0.000) for 3429 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. Cycle 29: After refmac, R = 0.1982 (Rfree = 0.000) for 3417 atoms. Found 10 (25 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.1914 (Rfree = 0.000) for 3409 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 3521 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 3530 seeds are put forward Round 1: 222 peptides, 40 chains. Longest chain 11 peptides. Score 0.372 Round 2: 246 peptides, 40 chains. Longest chain 11 peptides. Score 0.441 Round 3: 228 peptides, 37 chains. Longest chain 17 peptides. Score 0.427 Round 4: 251 peptides, 40 chains. Longest chain 16 peptides. Score 0.455 Round 5: 247 peptides, 41 chains. Longest chain 16 peptides. Score 0.432 Taking the results from Round 4 Chains 40, Residues 211, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7857 restraints for refining 3432 atoms. 7053 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2058 (Rfree = 0.000) for 3432 atoms. Found 20 (25 requested) and removed 13 (12 requested) atoms. Cycle 32: After refmac, R = 0.1985 (Rfree = 0.000) for 3433 atoms. Found 6 (25 requested) and removed 15 (12 requested) atoms. Cycle 33: After refmac, R = 0.1989 (Rfree = 0.000) for 3422 atoms. Found 11 (25 requested) and removed 15 (12 requested) atoms. Cycle 34: After refmac, R = 0.2027 (Rfree = 0.000) for 3413 atoms. Found 12 (25 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.1918 (Rfree = 0.000) for 3406 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 3524 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3537 seeds are put forward Round 1: 216 peptides, 39 chains. Longest chain 22 peptides. Score 0.366 Round 2: 238 peptides, 35 chains. Longest chain 27 peptides. Score 0.479 Round 3: 239 peptides, 37 chains. Longest chain 27 peptides. Score 0.458 Round 4: 238 peptides, 35 chains. Longest chain 16 peptides. Score 0.479 Round 5: 252 peptides, 39 chains. Longest chain 22 peptides. Score 0.469 Taking the results from Round 4 Chains 35, Residues 203, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7831 restraints for refining 3433 atoms. 7037 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2158 (Rfree = 0.000) for 3433 atoms. Found 19 (25 requested) and removed 13 (12 requested) atoms. Cycle 37: After refmac, R = 0.2040 (Rfree = 0.000) for 3431 atoms. Found 13 (25 requested) and removed 14 (12 requested) atoms. Cycle 38: After refmac, R = 0.1987 (Rfree = 0.000) for 3420 atoms. Found 18 (25 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.1948 (Rfree = 0.000) for 3419 atoms. Found 10 (25 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.1879 (Rfree = 0.000) for 3411 atoms. Found 11 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3536 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 3559 seeds are put forward Round 1: 216 peptides, 39 chains. Longest chain 21 peptides. Score 0.366 Round 2: 233 peptides, 41 chains. Longest chain 12 peptides. Score 0.392 Round 3: 227 peptides, 33 chains. Longest chain 20 peptides. Score 0.473 Round 4: 231 peptides, 39 chains. Longest chain 14 peptides. Score 0.411 Round 5: 241 peptides, 37 chains. Longest chain 19 peptides. Score 0.463 Taking the results from Round 3 Chains 33, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7806 restraints for refining 3433 atoms. 7063 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2038 (Rfree = 0.000) for 3433 atoms. Found 14 (25 requested) and removed 13 (12 requested) atoms. Cycle 42: After refmac, R = 0.1925 (Rfree = 0.000) for 3425 atoms. Found 11 (25 requested) and removed 14 (12 requested) atoms. Cycle 43: After refmac, R = 0.1870 (Rfree = 0.000) for 3417 atoms. Found 7 (25 requested) and removed 15 (12 requested) atoms. Cycle 44: After refmac, R = 0.1889 (Rfree = 0.000) for 3406 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.1848 (Rfree = 0.000) for 3398 atoms. Found 5 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 3492 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 3524 seeds are put forward Round 1: 183 peptides, 38 chains. Longest chain 11 peptides. Score 0.275 Round 2: 187 peptides, 29 chains. Longest chain 14 peptides. Score 0.410 Round 3: 205 peptides, 32 chains. Longest chain 19 peptides. Score 0.424 Round 4: 200 peptides, 31 chains. Longest chain 14 peptides. Score 0.422 Round 5: 219 peptides, 33 chains. Longest chain 23 peptides. Score 0.451 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 186, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2fea-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7649 reflections ( 98.32 % complete ) and 7770 restraints for refining 3433 atoms. 7023 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2045 (Rfree = 0.000) for 3433 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2028 (Rfree = 0.000) for 3410 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1966 (Rfree = 0.000) for 3391 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1934 (Rfree = 0.000) for 3372 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:18:18 GMT 2018 Job finished. TimeTaking 55.37 Used memory is bytes: 15032752