null Mon 24 Dec 08:06:22 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2otm-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2otm-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2otm-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 08:06:27 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/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-noncs/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 388 and 0 Target number of residues in the AU: 388 Target solvent content: 0.6205 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-3.4-parrot-noncs.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-3.4-parrot-noncs.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 3.400 Wilson plot Bfac: 61.75 7660 reflections ( 99.80 % complete ) and 0 restraints for refining 4125 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3073 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2764 (Rfree = 0.000) for 4125 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.98 Search for helices and strands: 0 residues in 0 chains, 4192 seeds are put forward NCS extension: 0 residues added, 4192 seeds are put forward Round 1: 258 peptides, 42 chains. Longest chain 13 peptides. Score 0.449 Round 2: 297 peptides, 42 chains. Longest chain 19 peptides. Score 0.548 Round 3: 298 peptides, 41 chains. Longest chain 21 peptides. Score 0.560 Round 4: 313 peptides, 35 chains. Longest chain 24 peptides. Score 0.650 Round 5: 325 peptides, 38 chains. Longest chain 21 peptides. Score 0.646 Taking the results from Round 4 Chains 38, Residues 278, Estimated correctness of the model 44.1 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6822 restraints for refining 3361 atoms. 5615 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2478 (Rfree = 0.000) for 3361 atoms. Found 12 (25 requested) and removed 21 (12 requested) atoms. Cycle 2: After refmac, R = 0.2345 (Rfree = 0.000) for 3319 atoms. Found 7 (25 requested) and removed 18 (12 requested) atoms. Cycle 3: After refmac, R = 0.2285 (Rfree = 0.000) for 3294 atoms. Found 5 (24 requested) and removed 18 (12 requested) atoms. Cycle 4: After refmac, R = 0.2243 (Rfree = 0.000) for 3272 atoms. Found 4 (24 requested) and removed 15 (12 requested) atoms. Cycle 5: After refmac, R = 0.2200 (Rfree = 0.000) for 3256 atoms. Found 9 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.01 Search for helices and strands: 0 residues in 0 chains, 3339 seeds are put forward NCS extension: 18 residues added (12 deleted due to clashes), 3357 seeds are put forward Round 1: 302 peptides, 43 chains. Longest chain 16 peptides. Score 0.549 Round 2: 344 peptides, 36 chains. Longest chain 26 peptides. Score 0.697 Round 3: 329 peptides, 36 chains. Longest chain 25 peptides. Score 0.671 Round 4: 330 peptides, 35 chains. Longest chain 31 peptides. Score 0.681 Round 5: 327 peptides, 37 chains. Longest chain 17 peptides. Score 0.659 Taking the results from Round 2 Chains 36, Residues 308, Estimated correctness of the model 57.1 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6834 restraints for refining 3360 atoms. 5478 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2422 (Rfree = 0.000) for 3360 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 7: After refmac, R = 0.2177 (Rfree = 0.000) for 3337 atoms. Found 7 (25 requested) and removed 15 (12 requested) atoms. Cycle 8: After refmac, R = 0.2144 (Rfree = 0.000) for 3314 atoms. Found 10 (25 requested) and removed 17 (12 requested) atoms. Cycle 9: After refmac, R = 0.2112 (Rfree = 0.000) for 3301 atoms. Found 10 (24 requested) and removed 17 (12 requested) atoms. Cycle 10: After refmac, R = 0.2048 (Rfree = 0.000) for 3293 atoms. Found 6 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 2.98 Search for helices and strands: 0 residues in 0 chains, 3385 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 3401 seeds are put forward Round 1: 316 peptides, 40 chains. Longest chain 25 peptides. Score 0.610 Round 2: 335 peptides, 36 chains. Longest chain 26 peptides. Score 0.682 Round 3: 333 peptides, 33 chains. Longest chain 26 peptides. Score 0.703 Round 4: 334 peptides, 35 chains. Longest chain 26 peptides. Score 0.688 Round 5: 318 peptides, 33 chains. Longest chain 32 peptides. Score 0.676 Taking the results from Round 3 Chains 35, Residues 300, Estimated correctness of the model 58.6 % 3 chains (46 residues) have been docked in sequence Building loops using Loopy2018 35 chains (300 residues) following loop building 3 chains (46 residues) in sequence following loop building ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6733 restraints for refining 3361 atoms. 5381 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2322 (Rfree = 0.000) for 3361 atoms. Found 24 (25 requested) and removed 32 (12 requested) atoms. Cycle 12: After refmac, R = 0.2164 (Rfree = 0.000) for 3339 atoms. Found 13 (24 requested) and removed 20 (12 requested) atoms. Cycle 13: After refmac, R = 0.2110 (Rfree = 0.000) for 3322 atoms. Found 3 (24 requested) and removed 17 (12 requested) atoms. Cycle 14: After refmac, R = 0.2070 (Rfree = 0.000) for 3302 atoms. Found 5 (23 requested) and removed 13 (12 requested) atoms. Cycle 15: After refmac, R = 0.1997 (Rfree = 0.000) for 3289 atoms. Found 3 (22 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 2.98 Search for helices and strands: 0 residues in 0 chains, 3361 seeds are put forward NCS extension: 17 residues added (13 deleted due to clashes), 3378 seeds are put forward Round 1: 298 peptides, 41 chains. Longest chain 18 peptides. Score 0.560 Round 2: 306 peptides, 37 chains. Longest chain 22 peptides. Score 0.617 Round 3: 320 peptides, 38 chains. Longest chain 27 peptides. Score 0.636 Round 4: 315 peptides, 34 chains. Longest chain 28 peptides. Score 0.662 Round 5: 327 peptides, 34 chains. Longest chain 21 peptides. Score 0.684 Taking the results from Round 5 Chains 35, Residues 293, Estimated correctness of the model 53.7 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6832 restraints for refining 3361 atoms. 5540 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2322 (Rfree = 0.000) for 3361 atoms. Found 18 (22 requested) and removed 20 (12 requested) atoms. Cycle 17: After refmac, R = 0.2156 (Rfree = 0.000) for 3339 atoms. Found 8 (22 requested) and removed 18 (12 requested) atoms. Cycle 18: After refmac, R = 0.2077 (Rfree = 0.000) for 3315 atoms. Found 5 (22 requested) and removed 14 (12 requested) atoms. Cycle 19: After refmac, R = 0.2038 (Rfree = 0.000) for 3302 atoms. Found 7 (22 requested) and removed 16 (12 requested) atoms. Cycle 20: After refmac, R = 0.2035 (Rfree = 0.000) for 3290 atoms. Found 5 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.97 Search for helices and strands: 0 residues in 0 chains, 3362 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3383 seeds are put forward Round 1: 288 peptides, 42 chains. Longest chain 15 peptides. Score 0.526 Round 2: 301 peptides, 41 chains. Longest chain 20 peptides. Score 0.567 Round 3: 295 peptides, 37 chains. Longest chain 23 peptides. Score 0.594 Round 4: 310 peptides, 42 chains. Longest chain 21 peptides. Score 0.577 Round 5: 293 peptides, 38 chains. Longest chain 26 peptides. Score 0.579 Taking the results from Round 3 Chains 39, Residues 258, Estimated correctness of the model 26.7 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 7050 restraints for refining 3361 atoms. 5944 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2263 (Rfree = 0.000) for 3361 atoms. Found 18 (22 requested) and removed 20 (12 requested) atoms. Cycle 22: After refmac, R = 0.2162 (Rfree = 0.000) for 3350 atoms. Found 6 (22 requested) and removed 16 (12 requested) atoms. Cycle 23: After refmac, R = 0.2124 (Rfree = 0.000) for 3334 atoms. Found 10 (22 requested) and removed 17 (12 requested) atoms. Cycle 24: After refmac, R = 0.2139 (Rfree = 0.000) for 3322 atoms. Found 7 (22 requested) and removed 20 (12 requested) atoms. Cycle 25: After refmac, R = 0.2095 (Rfree = 0.000) for 3302 atoms. Found 4 (22 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 2.97 Search for helices and strands: 0 residues in 0 chains, 3372 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3392 seeds are put forward Round 1: 286 peptides, 42 chains. Longest chain 22 peptides. Score 0.521 Round 2: 311 peptides, 40 chains. Longest chain 20 peptides. Score 0.599 Round 3: 307 peptides, 36 chains. Longest chain 23 peptides. Score 0.629 Round 4: 302 peptides, 38 chains. Longest chain 21 peptides. Score 0.599 Round 5: 307 peptides, 35 chains. Longest chain 22 peptides. Score 0.638 Taking the results from Round 5 Chains 39, Residues 272, Estimated correctness of the model 40.6 % 8 chains (81 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6379 restraints for refining 3361 atoms. 5029 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2282 (Rfree = 0.000) for 3361 atoms. Found 17 (22 requested) and removed 25 (12 requested) atoms. Cycle 27: After refmac, R = 0.2118 (Rfree = 0.000) for 3333 atoms. Found 13 (22 requested) and removed 16 (12 requested) atoms. Cycle 28: After refmac, R = 0.2038 (Rfree = 0.000) for 3322 atoms. Found 5 (22 requested) and removed 13 (12 requested) atoms. Cycle 29: After refmac, R = 0.2047 (Rfree = 0.000) for 3314 atoms. Found 7 (22 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.2000 (Rfree = 0.000) for 3305 atoms. Found 2 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.01 Search for helices and strands: 0 residues in 0 chains, 3392 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3408 seeds are put forward Round 1: 249 peptides, 37 chains. Longest chain 11 peptides. Score 0.483 Round 2: 268 peptides, 32 chains. Longest chain 18 peptides. Score 0.584 Round 3: 268 peptides, 32 chains. Longest chain 18 peptides. Score 0.584 Round 4: 286 peptides, 35 chains. Longest chain 21 peptides. Score 0.594 Round 5: 276 peptides, 33 chains. Longest chain 23 peptides. Score 0.592 Taking the results from Round 4 Chains 35, Residues 251, Estimated correctness of the model 26.7 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6966 restraints for refining 3361 atoms. 5853 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2216 (Rfree = 0.000) for 3361 atoms. Found 20 (22 requested) and removed 21 (12 requested) atoms. Cycle 32: After refmac, R = 0.2120 (Rfree = 0.000) for 3352 atoms. Found 6 (22 requested) and removed 15 (12 requested) atoms. Cycle 33: After refmac, R = 0.2098 (Rfree = 0.000) for 3341 atoms. Found 6 (22 requested) and removed 13 (12 requested) atoms. Cycle 34: After refmac, R = 0.2041 (Rfree = 0.000) for 3331 atoms. Found 7 (22 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1983 (Rfree = 0.000) for 3321 atoms. Found 1 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.02 Search for helices and strands: 0 residues in 0 chains, 3388 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 3403 seeds are put forward Round 1: 255 peptides, 38 chains. Longest chain 17 peptides. Score 0.487 Round 2: 264 peptides, 32 chains. Longest chain 23 peptides. Score 0.575 Round 3: 271 peptides, 30 chains. Longest chain 23 peptides. Score 0.611 Round 4: 277 peptides, 31 chains. Longest chain 26 peptides. Score 0.614 Round 5: 277 peptides, 32 chains. Longest chain 17 peptides. Score 0.604 Taking the results from Round 4 Chains 32, Residues 246, Estimated correctness of the model 33.2 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6999 restraints for refining 3361 atoms. 5925 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2179 (Rfree = 0.000) for 3361 atoms. Found 18 (22 requested) and removed 23 (12 requested) atoms. Cycle 37: After refmac, R = 0.2080 (Rfree = 0.000) for 3348 atoms. Found 10 (22 requested) and removed 16 (12 requested) atoms. Cycle 38: After refmac, R = 0.2024 (Rfree = 0.000) for 3337 atoms. Found 3 (22 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.2032 (Rfree = 0.000) for 3320 atoms. Found 6 (22 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2016 (Rfree = 0.000) for 3309 atoms. Found 7 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.05 Search for helices and strands: 0 residues in 0 chains, 3380 seeds are put forward NCS extension: 10 residues added (7 deleted due to clashes), 3390 seeds are put forward Round 1: 242 peptides, 37 chains. Longest chain 17 peptides. Score 0.465 Round 2: 246 peptides, 34 chains. Longest chain 21 peptides. Score 0.510 Round 3: 267 peptides, 33 chains. Longest chain 22 peptides. Score 0.572 Round 4: 261 peptides, 34 chains. Longest chain 22 peptides. Score 0.547 Round 5: 275 peptides, 33 chains. Longest chain 22 peptides. Score 0.590 Taking the results from Round 5 Chains 34, Residues 242, Estimated correctness of the model 25.4 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6867 restraints for refining 3361 atoms. 5749 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2335 (Rfree = 0.000) for 3361 atoms. Found 22 (22 requested) and removed 36 (12 requested) atoms. Cycle 42: After refmac, R = 0.2144 (Rfree = 0.000) for 3332 atoms. Found 10 (22 requested) and removed 23 (12 requested) atoms. Cycle 43: After refmac, R = 0.2031 (Rfree = 0.000) for 3313 atoms. Found 7 (22 requested) and removed 15 (12 requested) atoms. Cycle 44: After refmac, R = 0.2004 (Rfree = 0.000) for 3300 atoms. Found 9 (22 requested) and removed 23 (12 requested) atoms. Cycle 45: After refmac, R = 0.1943 (Rfree = 0.000) for 3284 atoms. Found 8 (22 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.03 Search for helices and strands: 0 residues in 0 chains, 3356 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3372 seeds are put forward Round 1: 235 peptides, 40 chains. Longest chain 13 peptides. Score 0.409 Round 2: 251 peptides, 35 chains. Longest chain 16 peptides. Score 0.511 Round 3: 262 peptides, 38 chains. Longest chain 16 peptides. Score 0.505 Round 4: 242 peptides, 30 chains. Longest chain 15 peptides. Score 0.545 Round 5: 245 peptides, 35 chains. Longest chain 16 peptides. Score 0.496 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 212, Estimated correctness of the model 9.7 % 5 chains (43 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 2otm-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (212 residues) following loop building 5 chains (43 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7660 reflections ( 99.80 % complete ) and 7020 restraints for refining 3361 atoms. 6060 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2291 (Rfree = 0.000) for 3361 atoms. Found 0 (22 requested) and removed 9 (12 requested) atoms. Cycle 47: After refmac, R = 0.2125 (Rfree = 0.000) for 3346 atoms. Found 0 (22 requested) and removed 8 (12 requested) atoms. Cycle 48: After refmac, R = 0.2010 (Rfree = 0.000) for 3335 atoms. Found 0 (22 requested) and removed 8 (12 requested) atoms. Cycle 49: After refmac, R = 0.1984 (Rfree = 0.000) for 3320 atoms. Found 0 (22 requested) and removed 3 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:44:49 GMT 2018 Job finished. TimeTaking 38.44 Used memory is bytes: 4033856