null 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2otm-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2otm-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.6-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 22:23:15 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.6-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 378 and 0 Target number of residues in the AU: 378 Target solvent content: 0.6303 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 66.47 6456 reflections ( 99.77 % complete ) and 0 restraints for refining 4132 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3069 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3008 (Rfree = 0.000) for 4132 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.15 Search for helices and strands: 0 residues in 0 chains, 4194 seeds are put forward NCS extension: 0 residues added, 4194 seeds are put forward Round 1: 241 peptides, 42 chains. Longest chain 13 peptides. Score 0.401 Round 2: 282 peptides, 38 chains. Longest chain 17 peptides. Score 0.554 Round 3: 291 peptides, 35 chains. Longest chain 22 peptides. Score 0.605 Round 4: 300 peptides, 34 chains. Longest chain 21 peptides. Score 0.633 Round 5: 314 peptides, 35 chains. Longest chain 31 peptides. Score 0.651 Taking the results from Round 5 Chains 37, Residues 279, Estimated correctness of the model 33.5 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7098 restraints for refining 3348 atoms. 5951 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2424 (Rfree = 0.000) for 3348 atoms. Found 11 (21 requested) and removed 26 (10 requested) atoms. Cycle 2: After refmac, R = 0.2239 (Rfree = 0.000) for 3302 atoms. Found 13 (21 requested) and removed 14 (10 requested) atoms. Cycle 3: After refmac, R = 0.2136 (Rfree = 0.000) for 3283 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. Cycle 4: After refmac, R = 0.2112 (Rfree = 0.000) for 3268 atoms. Found 2 (20 requested) and removed 14 (10 requested) atoms. Cycle 5: After refmac, R = 0.2070 (Rfree = 0.000) for 3255 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 3354 seeds are put forward NCS extension: 14 residues added (19 deleted due to clashes), 3368 seeds are put forward Round 1: 290 peptides, 42 chains. Longest chain 18 peptides. Score 0.531 Round 2: 303 peptides, 35 chains. Longest chain 23 peptides. Score 0.630 Round 3: 304 peptides, 38 chains. Longest chain 16 peptides. Score 0.603 Round 4: 297 peptides, 33 chains. Longest chain 22 peptides. Score 0.636 Round 5: 314 peptides, 34 chains. Longest chain 23 peptides. Score 0.660 Taking the results from Round 5 Chains 35, Residues 280, Estimated correctness of the model 36.6 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7067 restraints for refining 3349 atoms. 5901 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2439 (Rfree = 0.000) for 3349 atoms. Found 16 (21 requested) and removed 13 (10 requested) atoms. Cycle 7: After refmac, R = 0.2204 (Rfree = 0.000) for 3333 atoms. Found 4 (21 requested) and removed 13 (10 requested) atoms. Cycle 8: After refmac, R = 0.2133 (Rfree = 0.000) for 3313 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 9: After refmac, R = 0.2092 (Rfree = 0.000) for 3304 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Cycle 10: After refmac, R = 0.2055 (Rfree = 0.000) for 3295 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3375 seeds are put forward NCS extension: 39 residues added (7 deleted due to clashes), 3414 seeds are put forward Round 1: 254 peptides, 35 chains. Longest chain 14 peptides. Score 0.519 Round 2: 279 peptides, 34 chains. Longest chain 26 peptides. Score 0.588 Round 3: 280 peptides, 32 chains. Longest chain 18 peptides. Score 0.611 Round 4: 285 peptides, 34 chains. Longest chain 28 peptides. Score 0.602 Round 5: 268 peptides, 29 chains. Longest chain 28 peptides. Score 0.615 Taking the results from Round 5 Chains 29, Residues 239, Estimated correctness of the model 20.4 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7341 restraints for refining 3348 atoms. 6346 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2316 (Rfree = 0.000) for 3348 atoms. Found 9 (21 requested) and removed 17 (10 requested) atoms. Cycle 12: After refmac, R = 0.2127 (Rfree = 0.000) for 3332 atoms. Found 2 (21 requested) and removed 13 (10 requested) atoms. Cycle 13: After refmac, R = 0.2055 (Rfree = 0.000) for 3314 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. Cycle 14: After refmac, R = 0.2041 (Rfree = 0.000) for 3299 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. Cycle 15: After refmac, R = 0.2021 (Rfree = 0.000) for 3289 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.11 Search for helices and strands: 0 residues in 0 chains, 3365 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3386 seeds are put forward Round 1: 260 peptides, 40 chains. Longest chain 21 peptides. Score 0.477 Round 2: 274 peptides, 36 chains. Longest chain 21 peptides. Score 0.556 Round 3: 285 peptides, 32 chains. Longest chain 30 peptides. Score 0.621 Round 4: 273 peptides, 34 chains. Longest chain 24 peptides. Score 0.575 Round 5: 298 peptides, 34 chains. Longest chain 23 peptides. Score 0.629 Taking the results from Round 5 Chains 39, Residues 264, Estimated correctness of the model 25.6 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 6983 restraints for refining 3350 atoms. 5844 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2370 (Rfree = 0.000) for 3350 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 17: After refmac, R = 0.2104 (Rfree = 0.000) for 3337 atoms. Found 6 (21 requested) and removed 16 (10 requested) atoms. Cycle 18: After refmac, R = 0.2053 (Rfree = 0.000) for 3320 atoms. Found 6 (21 requested) and removed 20 (10 requested) atoms. Cycle 19: After refmac, R = 0.1983 (Rfree = 0.000) for 3304 atoms. Found 3 (21 requested) and removed 14 (10 requested) atoms. Cycle 20: After refmac, R = 0.1955 (Rfree = 0.000) for 3291 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.13 Search for helices and strands: 0 residues in 0 chains, 3373 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3397 seeds are put forward Round 1: 239 peptides, 42 chains. Longest chain 12 peptides. Score 0.395 Round 2: 273 peptides, 39 chains. Longest chain 14 peptides. Score 0.522 Round 3: 278 peptides, 33 chains. Longest chain 27 peptides. Score 0.596 Round 4: 267 peptides, 39 chains. Longest chain 17 peptides. Score 0.507 Round 5: 276 peptides, 35 chains. Longest chain 26 peptides. Score 0.571 Taking the results from Round 3 Chains 35, Residues 245, Estimated correctness of the model 13.1 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7156 restraints for refining 3349 atoms. 6107 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2352 (Rfree = 0.000) for 3349 atoms. Found 14 (21 requested) and removed 18 (10 requested) atoms. Cycle 22: After refmac, R = 0.2205 (Rfree = 0.000) for 3332 atoms. Found 3 (21 requested) and removed 14 (10 requested) atoms. Cycle 23: After refmac, R = 0.2170 (Rfree = 0.000) for 3318 atoms. Found 3 (21 requested) and removed 14 (10 requested) atoms. Cycle 24: After refmac, R = 0.2125 (Rfree = 0.000) for 3303 atoms. Found 1 (21 requested) and removed 16 (10 requested) atoms. Cycle 25: After refmac, R = 0.2073 (Rfree = 0.000) for 3281 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.11 Search for helices and strands: 0 residues in 0 chains, 3360 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3386 seeds are put forward Round 1: 245 peptides, 39 chains. Longest chain 15 peptides. Score 0.449 Round 2: 255 peptides, 33 chains. Longest chain 18 peptides. Score 0.543 Round 3: 263 peptides, 38 chains. Longest chain 15 peptides. Score 0.508 Round 4: 266 peptides, 37 chains. Longest chain 17 peptides. Score 0.526 Round 5: 265 peptides, 39 chains. Longest chain 14 peptides. Score 0.502 Taking the results from Round 2 Chains 34, Residues 222, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7512 restraints for refining 3350 atoms. 6617 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2115 (Rfree = 0.000) for 3350 atoms. Found 12 (21 requested) and removed 25 (10 requested) atoms. Cycle 27: After refmac, R = 0.2004 (Rfree = 0.000) for 3331 atoms. Found 1 (21 requested) and removed 23 (10 requested) atoms. Cycle 28: After refmac, R = 0.2018 (Rfree = 0.000) for 3298 atoms. Found 5 (21 requested) and removed 16 (10 requested) atoms. Cycle 29: After refmac, R = 0.1986 (Rfree = 0.000) for 3280 atoms. Found 2 (21 requested) and removed 14 (10 requested) atoms. Cycle 30: After refmac, R = 0.1985 (Rfree = 0.000) for 3264 atoms. Found 2 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.12 Search for helices and strands: 0 residues in 0 chains, 3337 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 3350 seeds are put forward Round 1: 225 peptides, 42 chains. Longest chain 12 peptides. Score 0.354 Round 2: 250 peptides, 36 chains. Longest chain 17 peptides. Score 0.497 Round 3: 254 peptides, 39 chains. Longest chain 17 peptides. Score 0.473 Round 4: 267 peptides, 32 chains. Longest chain 20 peptides. Score 0.582 Round 5: 271 peptides, 36 chains. Longest chain 15 peptides. Score 0.549 Taking the results from Round 4 Chains 33, Residues 235, Estimated correctness of the model 7.5 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7369 restraints for refining 3350 atoms. 6420 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2212 (Rfree = 0.000) for 3350 atoms. Found 19 (21 requested) and removed 31 (10 requested) atoms. Cycle 32: After refmac, R = 0.2010 (Rfree = 0.000) for 3327 atoms. Found 7 (21 requested) and removed 18 (10 requested) atoms. Cycle 33: After refmac, R = 0.1951 (Rfree = 0.000) for 3311 atoms. Found 5 (21 requested) and removed 14 (10 requested) atoms. Cycle 34: After refmac, R = 0.1935 (Rfree = 0.000) for 3299 atoms. Found 1 (21 requested) and removed 13 (10 requested) atoms. Cycle 35: After refmac, R = 0.1846 (Rfree = 0.000) for 3286 atoms. Found 2 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.16 Search for helices and strands: 0 residues in 0 chains, 3376 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3400 seeds are put forward Round 1: 193 peptides, 35 chains. Longest chain 9 peptides. Score 0.348 Round 2: 244 peptides, 36 chains. Longest chain 15 peptides. Score 0.482 Round 3: 233 peptides, 35 chains. Longest chain 13 peptides. Score 0.464 Round 4: 224 peptides, 31 chains. Longest chain 18 peptides. Score 0.488 Round 5: 246 peptides, 36 chains. Longest chain 12 peptides. Score 0.487 Taking the results from Round 4 Chains 31, Residues 193, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7599 restraints for refining 3350 atoms. 6823 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2164 (Rfree = 0.000) for 3350 atoms. Found 8 (21 requested) and removed 17 (10 requested) atoms. Cycle 37: After refmac, R = 0.2035 (Rfree = 0.000) for 3327 atoms. Found 4 (21 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.2003 (Rfree = 0.000) for 3312 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. Cycle 39: After refmac, R = 0.1933 (Rfree = 0.000) for 3300 atoms. Found 2 (21 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.1939 (Rfree = 0.000) for 3288 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.14 Search for helices and strands: 0 residues in 0 chains, 3353 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3370 seeds are put forward Round 1: 213 peptides, 40 chains. Longest chain 12 peptides. Score 0.343 Round 2: 232 peptides, 38 chains. Longest chain 15 peptides. Score 0.425 Round 3: 236 peptides, 35 chains. Longest chain 18 peptides. Score 0.472 Round 4: 248 peptides, 36 chains. Longest chain 17 peptides. Score 0.492 Round 5: 242 peptides, 38 chains. Longest chain 14 peptides. Score 0.453 Taking the results from Round 4 Chains 38, Residues 212, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6456 reflections ( 99.77 % complete ) and 7349 restraints for refining 3350 atoms. 6493 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2083 (Rfree = 0.000) for 3350 atoms. Found 13 (21 requested) and removed 16 (10 requested) atoms. Cycle 42: After refmac, R = 0.1888 (Rfree = 0.000) for 3336 atoms. Found 7 (21 requested) and removed 13 (10 requested) atoms. Cycle 43: After refmac, R = 0.1857 (Rfree = 0.000) for 3324 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.1813 (Rfree = 0.000) for 3309 atoms. Found 6 (21 requested) and removed 14 (10 requested) atoms. Cycle 45: After refmac, R = 0.1738 (Rfree = 0.000) for 3298 atoms. Found 0 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.09 Search for helices and strands: 0 residues in 0 chains, 3364 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3379 seeds are put forward Round 1: 187 peptides, 36 chains. Longest chain 11 peptides. Score 0.315 Round 2: 209 peptides, 31 chains. Longest chain 15 peptides. Score 0.447 Round 3: 230 peptides, 31 chains. Longest chain 14 peptides. Score 0.503 Round 4: 226 peptides, 34 chains. Longest chain 14 peptides. Score 0.457 Round 5: 225 peptides, 35 chains. Longest chain 13 peptides. Score 0.442 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 199, 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. 6456 reflections ( 99.77 % complete ) and 7602 restraints for refining 3328 atoms. 6837 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1991 (Rfree = 0.000) for 3328 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1943 (Rfree = 0.000) for 3312 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1935 (Rfree = 0.000) for 3295 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2070 (Rfree = 0.000) for 3281 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:19:18 GMT 2018 Job finished. TimeTaking 56.21 Used memory is bytes: 17478448