Sun 23 Dec 23:46:38 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ffj-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ffj-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ffj-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.8-parrot-mrncs ############### 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 23:46:49 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.8-parrot-mrncs/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 417 and 0 Target number of residues in the AU: 417 Target solvent content: 0.6636 Checking the provided sequence file Detected sequence length: 300 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 600 Adjusted target solvent content: 0.52 Input MTZ file: 2ffj-3.8-parrot-mrncs.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: 68.806 80.677 120.868 90.000 90.000 90.000 Input sequence file: 2ffj-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4800 target number of atoms Had to go as low as 0.55 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: 29.898 3.800 Wilson plot Bfac: 87.62 6939 reflections ( 98.80 % complete ) and 0 restraints for refining 5295 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3397 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3598 (Rfree = 0.000) for 5295 atoms. Found 29 (29 requested) and removed 36 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 5416 seeds are put forward NCS extension: 0 residues added, 5416 seeds are put forward Round 1: 241 peptides, 48 chains. Longest chain 11 peptides. Score 0.304 Round 2: 312 peptides, 47 chains. Longest chain 16 peptides. Score 0.485 Round 3: 316 peptides, 39 chains. Longest chain 24 peptides. Score 0.566 Round 4: 327 peptides, 44 chains. Longest chain 22 peptides. Score 0.543 Round 5: 339 peptides, 43 chains. Longest chain 22 peptides. Score 0.575 Taking the results from Round 5 Chains 43, Residues 296, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9993 restraints for refining 4257 atoms. 8852 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2952 (Rfree = 0.000) for 4257 atoms. Found 22 (23 requested) and removed 58 (11 requested) atoms. Cycle 2: After refmac, R = 0.2753 (Rfree = 0.000) for 4166 atoms. Found 15 (23 requested) and removed 34 (11 requested) atoms. Cycle 3: After refmac, R = 0.2527 (Rfree = 0.000) for 4114 atoms. Found 12 (22 requested) and removed 34 (11 requested) atoms. Cycle 4: After refmac, R = 0.2391 (Rfree = 0.000) for 4053 atoms. Found 18 (22 requested) and removed 22 (11 requested) atoms. Cycle 5: After refmac, R = 0.2319 (Rfree = 0.000) for 4026 atoms. Found 15 (22 requested) and removed 26 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 4253 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 4281 seeds are put forward Round 1: 275 peptides, 46 chains. Longest chain 11 peptides. Score 0.411 Round 2: 319 peptides, 46 chains. Longest chain 22 peptides. Score 0.509 Round 3: 320 peptides, 44 chains. Longest chain 15 peptides. Score 0.529 Round 4: 323 peptides, 43 chains. Longest chain 31 peptides. Score 0.544 Round 5: 325 peptides, 42 chains. Longest chain 24 peptides. Score 0.557 Taking the results from Round 5 Chains 45, Residues 283, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9482 restraints for refining 4270 atoms. 8296 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2876 (Rfree = 0.000) for 4270 atoms. Found 23 (23 requested) and removed 68 (11 requested) atoms. Cycle 7: After refmac, R = 0.2615 (Rfree = 0.000) for 4154 atoms. Found 23 (23 requested) and removed 56 (11 requested) atoms. Cycle 8: After refmac, R = 0.2168 (Rfree = 0.000) for 4077 atoms. Found 8 (22 requested) and removed 23 (11 requested) atoms. Cycle 9: After refmac, R = 0.2333 (Rfree = 0.000) for 4044 atoms. Found 12 (22 requested) and removed 33 (11 requested) atoms. Cycle 10: After refmac, R = 0.2280 (Rfree = 0.000) for 4013 atoms. Found 13 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 4207 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4225 seeds are put forward Round 1: 261 peptides, 48 chains. Longest chain 17 peptides. Score 0.356 Round 2: 289 peptides, 43 chains. Longest chain 16 peptides. Score 0.473 Round 3: 299 peptides, 44 chains. Longest chain 16 peptides. Score 0.485 Round 4: 298 peptides, 41 chains. Longest chain 21 peptides. Score 0.512 Round 5: 323 peptides, 46 chains. Longest chain 19 peptides. Score 0.517 Taking the results from Round 5 Chains 46, Residues 277, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9953 restraints for refining 4301 atoms. 8881 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2740 (Rfree = 0.000) for 4301 atoms. Found 20 (23 requested) and removed 69 (11 requested) atoms. Cycle 12: After refmac, R = 0.2509 (Rfree = 0.000) for 4215 atoms. Found 15 (23 requested) and removed 43 (11 requested) atoms. Cycle 13: After refmac, R = 0.2541 (Rfree = 0.000) for 4147 atoms. Found 23 (23 requested) and removed 39 (11 requested) atoms. Cycle 14: After refmac, R = 0.2472 (Rfree = 0.000) for 4112 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 15: After refmac, R = 0.2433 (Rfree = 0.000) for 4082 atoms. Found 15 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 4289 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4309 seeds are put forward Round 1: 251 peptides, 51 chains. Longest chain 10 peptides. Score 0.298 Round 2: 298 peptides, 46 chains. Longest chain 11 peptides. Score 0.464 Round 3: 303 peptides, 45 chains. Longest chain 13 peptides. Score 0.484 Round 4: 300 peptides, 43 chains. Longest chain 16 peptides. Score 0.497 Round 5: 309 peptides, 42 chains. Longest chain 15 peptides. Score 0.525 Taking the results from Round 5 Chains 42, Residues 267, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9677 restraints for refining 4238 atoms. 8651 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2703 (Rfree = 0.000) for 4238 atoms. Found 21 (23 requested) and removed 48 (11 requested) atoms. Cycle 17: After refmac, R = 0.2554 (Rfree = 0.000) for 4175 atoms. Found 19 (23 requested) and removed 32 (11 requested) atoms. Cycle 18: After refmac, R = 0.2430 (Rfree = 0.000) for 4141 atoms. Found 21 (22 requested) and removed 28 (11 requested) atoms. Cycle 19: After refmac, R = 0.2136 (Rfree = 0.000) for 4112 atoms. Found 4 (22 requested) and removed 23 (11 requested) atoms. Cycle 20: After refmac, R = 0.2003 (Rfree = 0.000) for 4085 atoms. Found 3 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 4255 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4274 seeds are put forward Round 1: 263 peptides, 48 chains. Longest chain 14 peptides. Score 0.361 Round 2: 281 peptides, 42 chains. Longest chain 17 peptides. Score 0.465 Round 3: 288 peptides, 40 chains. Longest chain 19 peptides. Score 0.500 Round 4: 289 peptides, 45 chains. Longest chain 17 peptides. Score 0.453 Round 5: 289 peptides, 41 chains. Longest chain 18 peptides. Score 0.492 Taking the results from Round 3 Chains 41, Residues 248, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9649 restraints for refining 4290 atoms. 8618 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2524 (Rfree = 0.000) for 4290 atoms. Found 23 (23 requested) and removed 43 (11 requested) atoms. Cycle 22: After refmac, R = 0.2397 (Rfree = 0.000) for 4243 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 23: After refmac, R = 0.2022 (Rfree = 0.000) for 4209 atoms. Found 7 (23 requested) and removed 19 (11 requested) atoms. Cycle 24: After refmac, R = 0.2021 (Rfree = 0.000) for 4178 atoms. Found 6 (23 requested) and removed 20 (11 requested) atoms. Cycle 25: After refmac, R = 0.2027 (Rfree = 0.000) for 4157 atoms. Found 4 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 4332 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4354 seeds are put forward Round 1: 232 peptides, 47 chains. Longest chain 10 peptides. Score 0.292 Round 2: 270 peptides, 44 chains. Longest chain 17 peptides. Score 0.420 Round 3: 278 peptides, 44 chains. Longest chain 16 peptides. Score 0.438 Round 4: 292 peptides, 45 chains. Longest chain 15 peptides. Score 0.460 Round 5: 295 peptides, 43 chains. Longest chain 26 peptides. Score 0.486 Taking the results from Round 5 Chains 45, Residues 252, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9452 restraints for refining 4332 atoms. 8413 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2636 (Rfree = 0.000) for 4332 atoms. Found 21 (23 requested) and removed 58 (11 requested) atoms. Cycle 27: After refmac, R = 0.2347 (Rfree = 0.000) for 4256 atoms. Found 14 (23 requested) and removed 33 (11 requested) atoms. Cycle 28: After refmac, R = 0.2375 (Rfree = 0.000) for 4223 atoms. Found 16 (23 requested) and removed 24 (11 requested) atoms. Cycle 29: After refmac, R = 0.2275 (Rfree = 0.000) for 4202 atoms. Found 17 (23 requested) and removed 22 (11 requested) atoms. Cycle 30: After refmac, R = 0.2235 (Rfree = 0.000) for 4190 atoms. Found 7 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 4350 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 4387 seeds are put forward Round 1: 243 peptides, 46 chains. Longest chain 12 peptides. Score 0.332 Round 2: 274 peptides, 45 chains. Longest chain 13 peptides. Score 0.419 Round 3: 279 peptides, 47 chains. Longest chain 19 peptides. Score 0.410 Round 4: 293 peptides, 45 chains. Longest chain 17 peptides. Score 0.462 Round 5: 302 peptides, 47 chains. Longest chain 14 peptides. Score 0.463 Taking the results from Round 5 Chains 47, Residues 255, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 9971 restraints for refining 4341 atoms. 8984 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2546 (Rfree = 0.000) for 4341 atoms. Found 22 (23 requested) and removed 51 (11 requested) atoms. Cycle 32: After refmac, R = 0.2397 (Rfree = 0.000) for 4292 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2303 (Rfree = 0.000) for 4266 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 34: After refmac, R = 0.2279 (Rfree = 0.000) for 4238 atoms. Found 20 (23 requested) and removed 32 (11 requested) atoms. Cycle 35: After refmac, R = 0.2199 (Rfree = 0.000) for 4216 atoms. Found 17 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 4391 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4405 seeds are put forward Round 1: 222 peptides, 49 chains. Longest chain 10 peptides. Score 0.242 Round 2: 257 peptides, 47 chains. Longest chain 12 peptides. Score 0.356 Round 3: 233 peptides, 43 chains. Longest chain 10 peptides. Score 0.339 Round 4: 248 peptides, 44 chains. Longest chain 11 peptides. Score 0.366 Round 5: 230 peptides, 40 chains. Longest chain 14 peptides. Score 0.365 Taking the results from Round 4 Chains 44, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 10366 restraints for refining 4342 atoms. 9594 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2323 (Rfree = 0.000) for 4342 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 37: After refmac, R = 0.2282 (Rfree = 0.000) for 4311 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 38: After refmac, R = 0.2198 (Rfree = 0.000) for 4294 atoms. Found 22 (23 requested) and removed 27 (11 requested) atoms. Cycle 39: After refmac, R = 0.2163 (Rfree = 0.000) for 4275 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 40: After refmac, R = 0.2144 (Rfree = 0.000) for 4271 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 4439 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4451 seeds are put forward Round 1: 195 peptides, 42 chains. Longest chain 9 peptides. Score 0.247 Round 2: 223 peptides, 42 chains. Longest chain 10 peptides. Score 0.324 Round 3: 229 peptides, 42 chains. Longest chain 11 peptides. Score 0.340 Round 4: 246 peptides, 44 chains. Longest chain 10 peptides. Score 0.361 Round 5: 253 peptides, 41 chains. Longest chain 12 peptides. Score 0.411 Taking the results from Round 5 Chains 41, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6939 reflections ( 98.80 % complete ) and 10345 restraints for refining 4334 atoms. 9538 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2548 (Rfree = 0.000) for 4334 atoms. Found 17 (23 requested) and removed 43 (11 requested) atoms. Cycle 42: After refmac, R = 0.2380 (Rfree = 0.000) for 4285 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1955 (Rfree = 0.000) for 4266 atoms. Found 3 (23 requested) and removed 16 (11 requested) atoms. Cycle 44: After refmac, R = 0.1892 (Rfree = 0.000) for 4242 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. Cycle 45: After refmac, R = 0.1944 (Rfree = 0.000) for 4228 atoms. Found 3 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 4376 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4391 seeds are put forward Round 1: 168 peptides, 36 chains. Longest chain 10 peptides. Score 0.242 Round 2: 204 peptides, 40 chains. Longest chain 9 peptides. Score 0.296 Round 3: 200 peptides, 37 chains. Longest chain 12 peptides. Score 0.320 Round 4: 212 peptides, 39 chains. Longest chain 10 peptides. Score 0.329 Round 5: 225 peptides, 39 chains. Longest chain 15 peptides. Score 0.363 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 186, 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 2ffj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6939 reflections ( 98.80 % complete ) and 10396 restraints for refining 4324 atoms. 9691 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2587 (Rfree = 0.000) for 4324 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2451 (Rfree = 0.000) for 4303 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2460 (Rfree = 0.000) for 4278 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2380 (Rfree = 0.000) for 4253 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... TimeTaking 55.48